Publishing type：Research paper (scientific journal)  

DOI： 10.1002/cche.10597

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Publisher：Cold Spring Harbor Laboratory  

Summary

Multiplexed inter-simple sequence repeats genotyping by sequencing (MIG-seq) is an next-generation sequencing library construction method developed for the analysis of DNA in ecology. Although MIG-seq can generate libraries from low-quality DNA, few polymorphisms can be obtained in species with small genomes. In this study, we developed degenerate oligonucleotide primer MIG-seq (dpMIG-seq) as an effective polymorphism discovery method that allows for variation in the number of polymorphisms while retaining the advantages of MIG-seq, including independence from DNA quality. In dpMIG-seq, a proportion of the simple sequence repeats in the primer sequence of the first PCR in MIG-seq was changed to degenerate oligonucleotides to enable annealing to a wider range of sequences. In tests of several crop species other than wheat, the number of loci that could be sequenced using dpMIG-seq with a data volume of 0.3 gigabases (Gb) was increased compared with that sequenced using MIG-seq. In wheat, the number of polymorphisms obtained via dpMIG-seq was higher than that obtained via MIG-seq when a data volume of about ≥2 Gb was obtained. In dpMIG-seq, different loci could be sequenced by changing the positions of the degenerate oligonucleotides. By applying dpMIG-seq, we constructed a linkage map consisting of 5,142 markers for the rice inter-subspecies F₂ population, and we detected quantitative trait loci for heading date in the regions where known heading-related genes were located. Overall, our results show that dpMIG-seq is a useful tool for the genetic analysis of crop species.

DOI： 10.1101/2022.08.25.504752

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

The major impact of both genotypic and environmental factors on grain-filling efficiency of rice (Oryza sativa L.) makes evaluating cultivar's grain-filling characteristics highly complicated. To assess grain-filling characteristics, the allocation index (Alli) was defined as a novel indicator representing the pattern of resource allocation in panicles. Alli was calculated as the ratio of source of yield utilized for producing well-filled grains to the total source consumed in a panicle, using estimated grain weight distribution data. We measured the Alli of 91 Japanese rice cultivars grown under nine environments involving multiple years, cropping seasons, three sites, and flag leaf clipping. Each cultivar's stability in Alli was evaluated using the data of various sink-source balance conditions. As a result of integrated analysis of multiple cultivars, we observed a trade-off relationship between the stability of Alli and the stability of mean weight of well-filled grains (mu2). The popular high-yielding cultivars Hokuriku 193 and Takanari showed high stability of Alli and mu2 under various sink-source balance conditions. Among the 91 cultivars, Hokuriku 193 showed stable characteristics with a high sink-filling ratio. Our results demonstrate that the grain weight distribution and Alli could be used as novel indicator of grain-filling characteristics, and that the trade-off relationship between the stability of Alli and mu2 should be considered when we select cultivars for multi-environmental cultivation.

DOI： 10.1080/1343943X.2021.2019593

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Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.253.0_84

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Language：English   Publishing type：Research paper (scientific journal)  

Phenotypic differences among breeding lines that introduce the same superior gene allele can be a barrier to effective development of cultivars with desirable traits in some crop species. For example, a deficient mutation of the Protein Disulfide Isomerase Like 1-1 (PDIL1-1) gene can cause accumulation of glutelin seed storage protein precursors in rice endosperm, and improves rice flour characteristics and food processing properties. However, the gene must be expressed to be useful. A deficient mutant allele of PDIL1-1 was introduced into two rice cultivars with different genetic backgrounds (Koshihikari and Oonari). The grain components, agronomic traits, and rice flour and food processing properties of the resulting lines were evaluated. The two breeding lines had similar seed storage protein accumulation, amylose content, and low-molecular-weight metabolites. However, only the Koshihikari breeding line had high flour quality and was highly suitable for rice bread, noodles, and sponge cake, evidence of the formation of high-molecular-weight protein complexes in the endosperm. Transcriptome analysis revealed that mRNA levels of fourteen PDI, Ero1, and BiP genes were increased in the Koshihikari breeding line, whereas this change was not observed in the Oonari breeding line. We elucidated part of the molecular basis of the phenotypic differences between two breeding lines possessing the same mutant allele in different genetic backgrounds. The results suggest that certain genetic backgrounds can negate the beneficial effect of the PDIL1-1 mutant allele. Better understanding of the molecular basis for such interactions may accelerate future breeding of novel rice cultivars to meet the strong demand for gluten-free foods.

DOI： 10.1186/s12284-022-00560-w

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Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Breeding  

DOI： 10.1270/jsbbs.22010

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Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study (GWAS). Ehd1 was detected in all the seven families and all the methods. On the other hand, Hd1 and Ghd7 were detected in some families, and joint QTL mapping and GWAS-based methods resulted in weaker and uncertain peaks. Overall, the high allelic variations in aus-NAM provide a valuable genetic resource for the rice community.

DOI： 10.3390/plants10061255

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Language：Japanese   Publishing type：Research paper (scientific journal)  

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Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.251.0_86

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Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.251.0_91

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media SA  

Accurate prediction of heading date under various environmental conditions is expected to facilitate the decision-making process in cultivation management and the breeding process of new cultivars adaptable to the environment. Days to heading (DTH) is a complex trait known to be controlled by multiple genes and genotype-by-environment interactions. Crop growth models (CGMs) have been widely used to predict the phenological development of a plant in an environment; however, they usually require substantial experimental data to calibrate the parameters of the model. The parameters are mostly genotype-specific and are thus usually estimated separately for each cultivar. We propose an integrated approach that links genotype marker data with the developmental genotype-specific parameters of CGMs with a machine learning model, and allows heading date prediction of a new genotype in a new environment. To estimate the parameters, we implemented a Bayesian approach with the advanced Markov chain Monte-Carlo algorithm called the differential evolution adaptive metropolis and conducted the estimation using a large amount of data on heading date and environmental variables. The data comprised sowing and heading dates of 112 cultivars/lines tested at 7 locations for 14 years and the corresponding environmental variables (day length and daily temperature). We compared the predictive accuracy of DTH between the proposed approach, a CGM, and a single machine learning model. The results showed that the extreme learning machine (one of the implemented machine learning models) was superior to the CGM for the prediction of a tested genotype in a tested location. The proposed approach outperformed the machine learning method in the prediction of an untested genotype in an untested location. We also evaluated the potential of the proposed approach in the prediction of the distribution of DTH in 103 F₂ segregation populations derived from crosses between a common parent, Koshihikari, and 103 cultivars/lines. The results showed a high correlation coefficient (ca. 0.8) of the 10, 50, and 90th percentiles of the observed and predicted distribution of DTH. In this study, the integration of a machine learning model and a CGM was better able to predict the heading date of a new rice cultivar in an untested potential environment.

DOI： 10.3389/fgene.2020.599510

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Language：English   Publishing type：Research paper (scientific journal)  

Lodging can reduce grain yield and quality in cereal crops including rice (Oryza sativa L.). To achieve both high biomass production and lodging resistance, the breeding of new cultivars with strong culms is a promising strategy. However, little is known about the diversity of culm strength in temperate japonica rice and underlying genetic factors. Here, we report a wide variation of culm strength among 135 temperate japonica cultivars, and some landraces having the strongest culms among these cultivars. The genome-wide association study (GWAS) identified 55 quantitative trait loci for culm strength and morphological traits, and revealed several candidate genes. The superior allele of candidate gene for culm thickness, OsRLCK191, was found in many landraces but had not inherited to the modern improved cultivars. Our results suggest that landraces of temperate japonica rice have unutilized superior alleles for contributing future improvements of culm strength and lodging resistance.

DOI： 10.1038/s41598-020-76949-8

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Language：English   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.250.0_8

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

Rice (Oryza sativaL.) in Japan is not only a food staple but also an important material for the Japanese alcoholic beverage,sake. The grain used insakebrewing has different characters from the cooking rice grain, including a large grain size and high white-core expression rate (WCE). Because large-sized grains often have a heavy grain weight and higher yield, this trait is also important for cooking rice. Chalky grains, such as white-core or white-belly grains, are not ideal as cooking rice. Here, we report that three grain-size quantitative trait loci (QTLs;qGL4-2,qGWh5,qGWh10), derived from the brewing cultivar, Yamadanishiki, affect grain shape, chalky grain rate, and yield, using near isogenic and pyramiding lines in the genetic background of the cooking cultivar, Koshihikari. First, these QTLs influenced multiple components of grain shape, where epistatic effects were detected betweenqGL4-2andqGWh5, for grain width and thickness, and betweenqGL4-2andqGWh10, for grain length. Therefore, these QTLs may coordinate to control grain shape. Second, lines harboringqGWh5orqGWh10at the Yamadanishiki allele exhibited increased WCE, whereas lines withqGL4-2andqGWh10exhibited decreased white-belly grain rate (WBR). Thus, grain shape is associated with the occurrence of chalky grain, where the chalky type depends on the QTL. Finally, we used total panicle weight of plants as a simplified rice yield index, and a promising line pyramidingqGL4-2andqGWh5emerged. In conclusion,qGL4-2would be useful for the breeding of cooking rice, to decrease WBR, whileqGWh5andqGWh10were definitely more beneficial for that of brewing rice, to increase grain weight and WCE.

DOI： 10.1007/s11032-020-01166-0

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Language：English   Publishing type：Research paper (scientific journal)  

Genomic selection (GS) has proven to be an efficient tool for predicting crop-rank performance of untested genotypes; however, when the traits have intermediate optima (phenology stages), this implementation might not be the most convenient. GS might deliver high-rank correlations but incurring in serious bias. Days to heading (DTH) is a crucial development stage in rice for regional adaptability with a significant impact on yield potential. The objective of this research consisted in develop a novel method that accurately predicts time-related traits such as DTH in unobserved environments. For this, we propose an implementation that incorporates day length information (DL) in the prediction process for two relevant scenarios: CV0, predicting tested genotypes in unobserved environments (C method); and CV00, predicting untested genotypes in unobserved environments (CB method). The use of DL has advantages over weather data since it can be determined in advance just by knowing the location and planting date. The proposed methods showed that DL information significantly helps to improve the predictive ability of DTH in unobserved environments. Under CV0, the C method returned a root-mean-square error (RMSE) of 3.9 days, a Pearson correlation (PC) of 0.98 and the differences between the predicted and observed environmental means (EMD) ranged between -4.95 and 4.67 days. For CV00, the CB method returned an RMSE of 7.3 days, a PC of 0.93 and the EMD ranged between -6.4 and 4.1 days while the conventional GS implementation produced an RMSE of 18.1 days, a PC of 0.41 and the EMD ranged between -31.5 and 28.7 days.

DOI： 10.1038/s41598-020-70267-9

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Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.249.0_160

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Language：English   Publishing type：Research paper (scientific journal)  

Genomic prediction (GP) is expected to become a powerful technology for accelerating the genetic improvement of complex crop traits. Several GP models have been proposed to enhance their applications in plant breeding, including environmental effects and genotype-by-environment interactions (G×E). In this study, we proposed a two-step model for plant biomass prediction wherein environmental information and growth-related traits were considered. First, the growth-related traits were predicted by GP. Second, the biomass was predicted from the GP-predicted values and environmental data using machine learning or crop growth modeling. We applied the model to a 2-year-old field trial dataset of recombinant inbred lines of japonica rice and evaluated the prediction accuracy with training and testing data by cross-validation performed over two years. Therefore, the proposed model achieved an equivalent or a higher correlation between the observed and predicted values (0.53 and 0.65 for each year, respectively) than the model in which biomass was directly predicted by GP (0.40 and 0.65 for each year, respectively). This result indicated that including growth-related traits enhanced accuracy of biomass prediction. Our findings are expected to contribute to the spread of the use of GP in crop breeding by enabling more precise prediction of environmental effects on crop traits.

DOI： 10.1371/journal.pone.0233951

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Language：English   Publishing type：Research paper (scientific journal)  

© 2020 The Authors. The Plant Genome published by Wiley Periodicals, Inc. on behalf of Crop Science Society of America A genome-wide association study (GWAS) needs to have a suitable population. The factors that affect a GWAS (e.g. population structure, sample size, and sequence analysis and field testing costs) need to be considered. Mixed populations containing subpopulations of different genetic backgrounds may be suitable populations. We conducted simulation experiments to see if a population with high genetic diversity, such as a diversity panel, should be added to a target population, especially when the target population harbors small genetic diversity. The target population was 112 accessions of Oryza sativa L. subsp. japonica, mainly developed in Japan. We combined the target population with three populations that had higher genetic diversity. These were 100 indica accessions, 100 japonica accessions, and 100 accessions with various genetic backgrounds. The results showed that the GWAS's power with a mixed population was generally higher than with a separate population. Also, the optimal GWAS populations varied depending on the fixation index (FST) of the quantitative trait nucleotides (QTNs) and the polymorphism of QTNs in each population. When a QTN was polymorphic in a target population, a target population combined with a higher diversity population improved the QTN's detection power. By investigating FST and the expected heterozygosity (He) as factors influencing the detection power, we showed that single nucleotide polymorphisms with high FST or low He are less likely to be detected by GWAS with mixed populations. Sequenced or genotyped germplasm collections can improve the GWAS's detection power by using a subset of the collections with a target population.

DOI： 10.1002/tpg2.20005

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Language：English   Publishing type：Research paper (scientific journal)  

Ralstonia solanacearum causes bacterial wilt, a soil-borne disease and one of the most important maladies of potato and other Solanaceae crops. We analyzed the resistance of a potato clone to bacterial wilt by quantitative trait locus (QTL) analysis. A resistant diploid potato clone 10-03-30 was crossed with a susceptible diploid clone F1-1 to generate a diploid, two-way pseudo-testcross F1 population comprised of 94 genotypes. Dense linkage maps, containing 4,139 single nucleotide polymorphism markers with an average distance of 0.6 and 0.3 cM between markers, were constructed for both parents. The resistance level was evaluated by in vitro inoculation test with R. solanacearum (phylotype I/biovar 4/race 1). Five QTLs (qBWR-1 to -5) were identified on potato chromosomes 1, 3, 7, 10, and 11, and they explained 9.3-18.4% of the phenotypic variance. The resistant parent had resistant alleles in qBWR-2, qBWR-3, and qBWR-4 and susceptible alleles in qBWR-1 and qBWR-5. Accumulation of the resistant alleles in all five QTLs increased the level of resistance compared with that of the resistant parent. This is the first study to identify novel QTLs for bacterial wilt resistance in potato by using genome-wide markers.

DOI： 10.1270/jsbbs.19059

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Language：English   Publishing type：Research paper (scientific journal)  

Oryza sativa L. 'Takanari' is one of the most productive indica cultivars [1,2]. Reciprocal chromosome segment substitution lines (CSSLs) derived from a cross between 'Koshihikari' and 'Takanari' are useful tools for the detection and precise mapping of target quantitative trait loci (QTL) in 'Takanari'. Although the available Os-Nipponbare-Reference-IRGSP-1.0 reference genome is available and useful for evaluating genetic diversity among japonica cultivars, it is not always useful for evaluating genetic diversity harbored by indica cultivars such as 'Takanari'. To reveal sequence variants in 'Takanari' and to exploit these variants in rice breeding programs, the whole genome of 'Takanari' was sequenced using a combination of Illumina HiSeq X Ten (20,983,495 reads and %GC 43) and PacBio (2,847,220 high-quality subreads). NGS data obtained have been deposited in the DNA Data Bank of Japan (DDBJ) under accession number DRA007557.

DOI： 10.1016/j.dib.2019.104546

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

Sake-brewing cultivars among varieties of Japanese rice (Oryza sativa L.) have traits adapted to the sake-brewing process, such as a high white-core expression rate (WCE). Our previous study detected putative quantitative trait loci (QTLs) associated with a high WCE derived from Yamadanishiki, a popular brewing rice cultivar. Because the occurrence of white-core grains depends on air temperature and the position of the grain on the panicle, phenotyping of WCE must consider these variable conditions. In this study, qWCE6, a QTL for the WCE on chromosome 6, was validated for the first time, and the phenotyping method examined for its suitability in fine-mapping. A clear tendency towards high WCE was observed in late-heading substituted lines which headed under low daily mean temperature at the experimental location. White-core grains were often expressed by the primary spikelets on the upper panicle, producing a high percentage of superior grains. The segregating population for qWCE6 in late heading revealed a distinct difference in WCE between the Koshihikari and Yamadanishiki homozygous alleles at qWCE6 as determined from that locality. Further, two insertion/deletion markers were developed for the marker-assisted selection of qWCE6. Our results will be useful for informing the breeding of sake-brewing rice cultivars.

DOI： 10.1270/jsbbs.18166

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Genetic diversity of Japanese sugar beet elite inbred line diversity (JSBDIV) set consisting of 63 lines was investigated using 33 cleaved amplified polymorphic sequence and 38 simple sequence repeat analyses. JSBDIV set was significantly subdivided into six (pedigree information), seven (Neighbor-Joining method) or 12 (population structure analysis) groups. The highest value of a pairwise population differentiation estimate, ΦPT value, among groups was yielded from population structure analysis with explained variation 32%. Some of the groups defined in this study exhibited close association with ancestral open-pollinated varieties (OPVs), suggesting that inter-OPV cross was rare during the establishment of JSBDIV set. On the other hand, low ΦPT values between some groups suggest that genetic backgrounds of ancestral OPVs had historically overlapped to some extent. Phenotypic traits showed significant differences both among and within groups. A nearly identical group was identified as the highest sugar content group irrespective of the grouping methods. Groups with Aphanomyces root rot resistance are associated with an OPV 'Tmm-1', suggesting it as a source of this trait. 'Tmm-1' is also associated with Cercospora leaf spot resistance, but an exceptional resistant line with no association of 'Tmm-1' supports a notion that different genetic resources exist for this trait.

DOI： 10.1270/jsbbs.18121

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Public Library Science  

Grain-filling ability is one of the factors that controls grain yield in rice (Oryza sativa L.). We developed a method for describing grain weight distribution, which is the probability density function of single grain weight in a panicle, using 128 Japanese rice varieties. With this method, we quantitively analyzed genotypic differences in grain-filling ability and used the grain weight distribution parameters for genomic prediction subject to genetic improvement in grain yield in rice. The novel description method could represent the observed grain weight distribution with five genotype-specific parameters of a mixture of two gamma distributions. The estimated genotype-specific parameters representing the proportion of filled grains had applicability to explain the grain filling ability of genotypes comparable to that of sink-filling rate and the conventionally measured proportion of filled grains, which suggested the efficiency and flexibility of grain weight distribution parameters to handle several genotypes. We revealed that perfectly filled grains have to be prioritized over partially filled grains for the optimum allocation of the source of yield in a panicle, from the analysis for obtaining an ideal shape of grain weight distribution. We conducted genomic prediction of grain weight distribution considering five genotype-specific parameters of the distribution as phenotypes relating to grain filling ability. The proportion of filled grains, average weight of filled grains, and variance of filled grain weight, which were considered to control grain yield to a certain degree, were predicted with accuracies of 0.30, 0.28, and 0.53, respectively. The proposed description method of grain weight distribution facilitated not only the investigation of the optimum allocation of nutrients in a panicle for realizing high grain-filling ability, but also allowed genomic selection of grain weight distribution.

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

BACKGROUND: The improvement of rice yield is a crucial global issue, but evaluating yield requires substantial efforts. Rice yield comprises the following indices: panicle number (PN), grain number per panicle (GN), 1000-grain weight, and percentage of ripened grain. To simplify measurements, we analyzed one panicle weight (OPW) as a simplified yield index that integrates GN, grain weight, and percentage of ripened grain, and verified its suitability as a proxy for GN and grain weight in particular. RESULTS: Quantitative trait locus (QTL) analysis using 190 recombinant inbred lines derived from Koshihikari (large panicle and small grain) and Yamadanishiki (small panicle and large grain), japonica cultivars detected three QTLs on chromosomes 5 (qOPW5), 7 (qOPW7) and 11 (qOPW11). Of these, qOPW5 and qOPW11 were detected over two years. qOPW5 and qOPW7 increased OPW, and qOPW11 decreased it at Yamadanishiki alleles. A chromosome segment substitution line (CSSL) with a genomic segment from Yamadanishiki substituted in the Koshihikari genetic background harboring qOPW5 increased grain weight. qOPW11 had the largest genetic effect of QTLs, which was validated using a CSSL. Substitution mapping using four CSSLs revealed that qOPW11 was located in the range of 1.46 Mb on chromosome 11. The CSSL harboring qOPW11 decreased primary and secondary branch numbers, culm length, and panicle length, and increased PN. CONCLUSIONS: In this study, three QTLs associated with OPW were detected. The CSSL with the novel and largest QTL, qOPW11, differed in some traits associated with both panicle and plant architecture, indicating different functions for the meristem in the vegetative versus the reproductive stages. qOPW5 coincided with an identified QTL for grain width and grain weight, suggesting that qOPW5 was affected by rice grain size. OPW can be considered a useful trait for efficient detection of QTLs associated with rice yield.

DOI： 10.1186/s12284-018-0246-x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Association for the Advancement of Science (AAAS)  

DOI： 10.1126/science.aat1577

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Breeding  

Grain size is important for brewing-rice cultivars, but the genetic basis for this trait is still unclear. This paper aims to identify QTLs for grain size using novel chromosomal segment substitution lines (CSSLs) harboring chromosomal segments from Yamadanishiki, an excellent sake-brewing rice, in the genetic background of Koshihikari, a cooking cultivar. We developed a set of 49 CSSLs. Grain length (GL), grain width (GWh), grain thickness (GT), 100-grain weight (GWt) and days to heading (DTH) were evaluated, and a CSSL-QTL analysis was conducted. Eighteen QTLs for grain size and DTH were identified. Seven (qGL11, qGWh5, qGWh10, qGWt6-2, qGWt10-2, qDTH3, and qDTH6) that were detected in F2 and recombinant inbred lines (RILs) from Koshihikari/Yamadanishiki were validated, suggesting that they are important for large grain size and heading date in Yamadanishiki. Additionally, QTL reanalysis for GWt showed that qGWt10-2 was only detected in early-flowering RILs, while qGWt5 (in the same region as qGWh5) was only detected in late-flowering RILs, suggesting that these QTLs show different responses to the environment. Our study revealed that grain size in the Yamadanishiki cultivar is determined by a complex genetic mechanism. These findings could be useful for the breeding of both cooking and brewing rice.

DOI： 10.1270/jsbbs.17112

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

The grain traits of Yamadanishiki, an excellent sake-brewing rice cultivar in Japan, are governed by multiple QTLs, namely, a total of 42 QTLs including six major QTLs.
Japanese rice wine (sake) is produced using brewing rice (Oryza sativa L.) that carries traits desirable for sake-brewing, such as a larger grain size and higher white-core expression rate (WCE) compared to cooking rice cultivars. However, the genetic basis for these traits in brewing rice cultivars is still unclear. We performed analyses of quantitative trait locus (QTL) of grain and days to heading over 3 years on populations derived from crosses between Koshihikari, a cooking rice, and Yamadanishiki, an excellent sake-brewing rice. A total of 42 QTLs were detected for the grain traits, and the Yamadanishiki alleles at 16 QTLs contributed to larger grain size. Two major QTLs essential for regulating both 100-grain weight (GWt) and grain width (GWh) were harbored in the same regions on chromosomes 5 and 10. An interaction was noted between the environment and the QTL associated with WCE on chromosome 6, which was detected in two of 3 years. In addition, two QTLs for WCE on chromosomes 3 and 10 overlapped with the QTLs for GWt and GWh, suggesting that QTLs associated with grain size also play an important role in the formation of white-core. Despite differences in the rate of grain growth in both Koshihikari and Yamadanishiki across 2 years, the WCE in Yamadanishiki remained consistent, thus demonstrating that the formation of white-core does not depend on grain filling speed. These data can be informative for programs involved in breeding better cooking and brewing rice cultivars.

DOI： 10.1007/s00122-017-2977-2

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

Bio-refinery processes require use of the most suitable lignocellulosic biomass for enzymatic saccharification and microbial fermentation. Glucose yield from biomass solid fractions obtained after dilute sulfuric acid (1%) pretreatment (at 180 degrees C) was investigated using 14, 8, and 16 varieties of rice, wheat, and sorghum, respectively. Biomass solid fractions of each crop showed similar cellulose content. However, glucose yield after enzymatic hydrolysis (cellulase loading at 6.6 filter paper unit/g-biomass) was different among the varieties of each crop, indicating genotypic differences for rice, wheat, and sorghum. Nuclear magnetic resonance method revealed that the high residual level of lignin aromatic regions decreased glucose yield from solid fraction of sorghum.

DOI： 10.1080/09168451.2017.1336922

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media  

Jatropha curcas L. (Jatropha), a shrub species of the family Euphorbiaceae, has been recognized as a promising biofuel plant for reducing greenhouse gas emissions. However, recent attempts at commercial cultivation in Africa and Asia have failed because of low productivity. It is important to elucidate genetic diversity and relationship in worldwide Jatropha genetic resources for breeding of better commercial cultivars. Here, genetic diversity was analyzed by using 246 accessions from Mesoamerica, Africa and Asia, based on 59 simple sequence repeat markers and eight retrotransposon-based insertion polymorphism markers. We found that central Chiapas of Mexico possesses the most diverse genetic resources, and the Chiapas Central Depression could be the center of origin. We identified three genetic groups in Mesoamerica, whose distribution revealed a distinct geographic cline. One of them consists mainly of accessions from central Chiapas. This suggests that it represents the original genetic group. We found two Veracruz accessions in another group, whose ancestors might be shipped from Port of Veracruz to the Old World, to be the source of all African and Asian Jatropha. Our results suggest the human selection that caused low productivity in Africa and Asia, and also breeding strategies to improve African and Asian Jatropha. Cultivars improved in the productivity will contribute to expand mass commercial cultivation of Jatropha in Africa and Asia to increase biofuel production, and finally will support in the battle against the climate change.

DOI： 10.3389/fpls.2017.01539

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

A genome-wide association study ( GWAS) can be a powerful tool for the identification of genes associated with agronomic traits in crop species, but it is often hindered by population structure and the large extent of linkage disequilibrium. In this study, we identified agronomically important genes in rice using GWAS based on whole-genome sequencing, followed by the screening of candidate genes based on the estimated effect of nucleotide polymorphisms. Using this approach, we identified four new genes associated with agronomic traits. Some genes were undetectable by standard SNP analysis, but we detected them using gene-based association analysis. This study provides fundamental insights relevant to the rapid identification of genes associated with agronomic traits using GWAS and will accelerate future efforts aimed at crop improvement.

DOI： 10.1038/ng.3596

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

Rice straw is a promising resource for bioethanol production. Because the glucose content of pretreatment liquid hydrolysates is highly correlated with ethanol yield, the selection of appropriate rice cultivars is essential. The glucose content in liquid hydrolysates of pretreated rice straws of 208 diverse cultivars was evaluated in natural field in 2013 and 2014 using a novel high-throughput system. The glucose content of the rice straw samples varied across cultivars and was affected by environmental factors such as temperature and solar radiation. Several high-quality cultivars exhibiting high glucose content in both years were identified. The results of this study can aid in development of novel rice cultivars suitable as both feedstocks for bioethanol production and cooking.

DOI： 10.1080/09168451.2015.1136882

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PUBLIC LIBRARY SCIENCE  

Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of genomic selection in autogamous crops, especially bringing long-term improvement.

DOI： 10.1371/journal.pone.0153945

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PUBLIC LIBRARY SCIENCE  

Phenological traits of plants, such as flowering time, are linked to growth phase transition. Thus, phenological traits often influence other traits through the modification of the duration of growth period. This influence is a nuisance in plant breeding because it hampers genetic evaluation of the influenced traits. Genetic effects on the influenced traits have two components, one that directly affects the traits and one that indirectly affects the traits via the phenological trait. These cannot be distinguished by phenotypic evaluation and ordinary linear regression models. Consequently, if a phenological trait is modified by introgression or editing of the responsible genes, the phenotypes of the influenced traits can change unexpectedly. To uncover the influence of the phenological trait and evaluate the direct genetic effects on the influenced traits, we developed a nonlinear structural equation (NSE) incorporating a nonlinear influence of the phenological trait. We applied the NSE to real data for cultivated rice (Oryza sativa L.): days to heading (DH) as a phenological trait and culm length (CL) as the influenced trait. This showed that CL of the cultivars that showed extremely early heading was shortened by the strong influence of DH. In a simulation study, it was shown that the NSE was able to infer the nonlinear influence and direct genetic effects with reasonable accuracy. However, the NSE failed to infer the linear influence in this study. When no influence was simulated, an ordinary bi-trait linear model (OLM) tended to infer the genetic effects more accurately. In such cases, however, by comparing the NSE and OLM using an information criterion, we could assess whether the nonlinear assumption of the NSE was appropriate for the data analyzed. This study demonstrates the usefulness of the NSE in revealing the phenotypic influence of phenological traits.

DOI： 10.1371/journal.pone.0148609

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：GENETICS SOCIETY AMERICA  

We investigated the natural variations in the flag leaf morphology of rice. We conducted a principal component analysis based on nine flag leaf morphology traits using 103 accessions from the National Institute of Agrobiological Sciences Core Collection. The first component explained 39% of total variance, and the variable with highest loading was the width of the flag leaf (WFL). A genome-wide association analysis of 102 diverse Japanese accessions revealed that marker RM6992 on chromosome 4 was highly associated with WFL. In analyses of progenies derived from a cross between Takanari and Akenohoshi, the most significant quantitative trait locus (QTL) for WFL was in a 10.3-kb region containing the NARROW LEAF 1 (NAL1) gene, located 0.4 Mb downstream of RM6992. Analyses of chromosomal segment substitution lines indicated that a mutation (G1509A single-nucleotide mutation, causing an R233H amino acid substitution in NAL1) was present at the QTL. This explained 13 and 20% of total variability in WFL and the distance between small vascular bundles, respectively. The mutation apparently occurred during rice domestication and spread into japonica, tropical japonica, and indica subgroups. Notably, one accession, Phulba, had a NAL1 allele encoding only the N-terminal, or one-fourth, of the wild-type peptide. Given that the Phulba allele and the histidine-type allele showed essentially the same phenotype, the histidine-type allele was regarded as malfunctional. The phenotypes of transgenic plants varied depending on the ratio of histidine-type alleles to arginine-type alleles, raising the possibility that H-233-type products function differently from and compete with R-233-type products.

DOI： 10.1534/genetics.115.181040

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A renewable raw material, rice straw is pretreated for biorefinery usage. Solution-state two-dimensional (2D) H-1-(13) C hetero-nuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy, was used to analyze 13 cultivars of rice straw before and after dilute acid pretreatment, to characterize general changes in the lignin and polysaccharide components. Intensities of most (15 of 16) peaks related to lignin aromatic regions, such as p-coumarate, guaiacyl, syringyl, p-hydroxyphenyl, and cinnamyl alcohol, and methoxyl, increased or remained unchanged after pretreatment. In contrast, intensities of most (11 of 13) peaks related to lignin aliphatic linkages or ferulate decreased. Decreased heterogeneity in the intensities of three peaks related to cellulose components in acid-insoluble residues resulted in similar glucose yield (0.45-0.59 g/g-dry biomass). Starch-derived components showed positive correlations (r = 0.71 to 0.96) with glucose, 5-hydroxymethyl-furfural (5-HMF), and formate concentrations in the liquid hydrolysates, and negative correlations (r = -0.95 to -0.97) with xylose concentration and acid-insoluble residue yield. These results showed the fate of lignin and polysaccharide components by pretreatment, suggesting that lignin aromatic regions and cellulose components were retained in the acid insoluble residues and starch-derived components were transformed into glucose, 5-HMF, and formate in the liquid hydrolysate.

DOI： 10.1371/journal.pone.0128417

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

Grain weight is an important crop yield component; however, its underlying regulatory mechanisms are largely unknown. Here, we identify a grain-weight quantitative trait locus (QTL) encoding a new-type GNAT-like protein that harbors intrinsic histone acetyltransferase activity (OsglHAT1). Our genetic and molecular evidences pinpointed the QTL-OsglHAT1's allelic variations to a 1.2-kb region upstream of the gene body, which is consistent with its function as a positive regulator of the traits. Elevated OsglHAT1 expression enhances grain weight and yield by enlarging spikelet hulls via increasing cell number and accelerating grain filling, and increases global acetylation levels of histone H4. OsglHAT1 localizes to the nucleus, where it likely functions through the regulation of transcription. Despite its positive agronomical effects on grain weight, yield, and plant biomass, the rare allele elevating OsglHAT1 expression has so far escaped human selection. Our findings reveal the first example, to our knowledge, of a QTL for a yield component trait being due to a chromatin modifier that has the potential to improve crop high-yield breeding.

DOI： 10.1073/pnas.1421127112

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

Our simulation results clarify the areas of applicability of nine prediction methods and suggest the factors that affect their accuracy at predicting empirical traits.
Whole-genome prediction is used to predict genetic value from genome-wide markers. The choice of method is important for successful prediction. We compared nine methods using empirical data for eight phenological and morphological traits of Asian rice cultivars (Oryza sativa L.) and data simulated from real marker genotype data. The methods were genomic BLUP (GBLUP), reproducing kernel Hilbert spaces regression (RKHS), Lasso, elastic net, random forest (RForest), Bayesian lasso (Blasso), extended Bayesian lasso (EBlasso), weighted Bayesian shrinkage regression (wBSR), and the average of all methods (Ave). The objectives were to evaluate the predictive ability of these methods in a cultivar population, to characterize them by exploring the area of applicability of each method using simulation, and to investigate the causes of their different accuracies for empirical traits. GBLUP was the most accurate for one trait, RKHS and Ave for two, and RForest for three traits. In the simulation, Blasso, EBlasso, and Ave showed stable performance across the simulated scenarios, whereas the other methods, except wBSR, had specific areas of applicability; wBSR performed poorly in most scenarios. For each method, the accuracy ranking for the empirical traits was largely consistent with that in one of the simulated scenarios, suggesting that the simulation conditions reflected the factors that affected the method accuracy for the empirical results. This study will be useful for genomic prediction not only in Asian rice, but also in populations from other crops with relatively small training sets and strong linkage disequilibrium structures.

DOI： 10.1007/s00122-014-2411-y

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Authorship：Corresponding author   Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Breeding  

DOI： 10.1270/jsbbr.16.32

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Other Link： https://jlc.jst.go.jp/DN/JALC/10037456893?from=CiNii

Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCI LTD  

Lignocellulosic biomass, such as rice straw, is often utilized as a bioresource after being hydrolyzed using dilute acid and separated into liquid hydrolysate and acid-insoluble residue. However, the biomass component that determines the distribution between liquid hydrolysate and acid-insoluble residue has not yet been clarified. In this study, the glucose content in the liquid hydrolysate and weight of acid-insoluble residue of 13 rice cultivars were analyzed. Starch content was positively correlated with glucose content in the liquid hydrolysate, and negatively correlated with acid-insoluble residue weight. These results indicate that the glucose in the liquid hydrolysate is mainly liberated from starch rather than cellulose in the rice straw. These observations suggest that starch content is a good indicator of the glucose distribution between the liquid hydrolysate and insoluble residue. (C) 2013 Published by Elsevier Ltd.

DOI： 10.1016/j.biortech.2013.09.109

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC BREEDING  

The wild Oryza species are rich in genetic diversity and are good resources for modem breeding of rice varieties. The reliable ex situ conservation of various genetic resources supports both basic and applied rice research. For this purpose, we developed PCR-based and co-dominant insertion/deletion (INDEL) markers which enable the discrimination of the genome types or species in the genus Oryza. First, 12,107 INDEL candidate sequences were found in the BAC end sequences for 12 Oryza species available in public databases. Next, we designed PCR primers for INDEL-flanking sequences to match the characteristics of each INDEL, based on an assessment of their likelihood to give rise to a single or few PCR products in all 102 wild accessions, covering most Oryza genome types. Then, we selected 22 INDEL markers to discriminate all genome types in the genus Oryza. A phylogenetic tree of 102 wild accessions and two cultivars according to amplicon polymorphisms for the 22 INDEL markers corresponded well to those in previous studies, indicating that the INDEL markers developed in this study were a useful tool to improve the reliability of identification of wild Oryza species in the germplasm stocks.

DOI： 10.1270/jsbbs.63.246

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

Reduction in seed shattering was an important phenotypic change during cereal domestication(1,2). Here we show that a simple morphological change in rice panicle shape, controlled by the SPR3 locus, has a large impact on seed-shedding and pollinating behaviors. In the wild genetic background of rice, we found that plants with a cultivated-like type of closed panicle had significantly reduced seed shedding through seed retention. In addition, the long awns in closed panicles disturbed the free exposure of anthers and stigmas on the flowering spikelets, resulting in a significant reduction of the outcrossing rate. We localized the SPR3 locus to a 9.3-kb genomic region, and our complementation tests suggest that this region regulates the liguleless gene (OsLG1). Sequencing analysis identified reduced nucleotide diversity and a selective sweep at the SPR3 locus in cultivated rice. Our results suggest that a closed panicle was a selected trait during rice domestication.

DOI： 10.1038/ng.2567

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC BREEDING  

It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars.

DOI： 10.1270/jsbbs.63.49

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Authorship：Lead author,　Corresponding author   Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：The Society of Crop Science and Breeding in Kinki, Japan  

Accurate and complete phenotypic data are essential to fields in crop science, plant breeding, and genetic researches. Often phenotyping and management becomes complicated due to large population sizes and the measurements of multiple traits. The vast amount of data require much time and labor, simultaneously leading to human errors. Technology can be exploited to improve the phenotypic data collection process through better tools or information management systems. "FieldBook" is a system we have developed to collect phenotypic data quickly and accurately in maize and rice, with a little manual data entry using data capture tools.

DOI： 10.18964/jcr.57.0_55

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Language：Japanese   Publishing type：Research paper (scientific journal)  

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：GENETICS SOC JAPAN  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

Biomass properties of rice straws were compared among eight cultivars that formed a mini diverse set. The ethanol productivity from rice straws was evaluated employing a laboratory-scale method based on dilute acid-hydrolysis pretreatment. The results indicated significant variation in biomass properties among the cultivars.

DOI： 10.1271/bbb.1100821

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

The semidwarf phenotype has been extensively selected during modern crop breeding as an agronomically important trait. Introduction of the semidwarf gene, semi-dwarf1 (sd1), which encodes a gibberellin biosynthesis enzyme, made significant contributions to the "green revolution" in rice (Oryza sativa L.). Here we report that SD1 was involved not only in modern breeding including the green revolution, but also in early steps of rice domestication. We identified two SNPs in O. sativa subspecies (ssp.) japonica SD1 as functional nucleotide polymorphisms (FNPs) responsible for shorter culm length and low gibberellin biosynthetic activity. Genetic diversity analysis among O. sativa ssp. japonica and indica, along with their wild ancestor O. rufipogon Griff, revealed that these FNPs clearly differentiate the japonica landrace and O. rufipogon. We also found a dramatic reduction in nucleotide diversity around SD1 only in the japonica landrace, not in the indica landrace or O. rufipogon. These findings indicate that SD1 has been subjected to artificial selection in rice evolution and that the FNPs participated in japonica domestication, suggesting that ancient humans already used the green revolution gene.

DOI： 10.1073/pnas.1019490108

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC BREEDING  

Black soybean landraces that had been cultivated in Tanba region and the neighboring regions and conserved black soybean landraces, including those from other regions in Japan, were used in this study. The polymorphisms of 78 SSR markers in nuclear DNA and 6 SSRs in chloroplast DNA were analyzed in the black soybean landrace populations. The result of phylogenic analysis revealed that the black soybeans can be classified into six clades. The landraces originating from Tanba region were classed into first and second clades, and two chloroplast genotypes were found in the population of black soybeans from the Tanba region. Genotype A chloroplast was predominantly identified in major populations of the Tanba, while genotype B was widely distributed in the black soybean population. Population structure analysis in the Japanese black soybean accessions inferred there are six groups. The black soybean landrace from the Tanba region was classified into three groups, mainly corresponding to the distance-based phylogenic results. The two groups were probably derived from different ancestors with Type A and B chloroplast genomes, respectively, whereas the other group showed both types of chloroplast genome. The admixture situations suggested that the landraces in the main group have been widely cultivated in Tanba region, while the landraces that belong to other groups were cultivated in localized area. Several phenotypes were compared among genotype groups, dividing into two sub-groups: founder sub-group and admixed sub-group. Phenotypic differences were observed between founder landraces in group I and group 3. On the other hand, landraces in admixture landraces in group 1 and group 2 segregated for several traits, while founder landraces in group 1 were stabled for each trait. These observations suggest that gene flow events have occurred between different founder landraces.

DOI： 10.1270/jsbbs.61.593

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Publisher：The Japanese Society of Plant Physiologists  

It is known that the common cultivated rice, <I>Oryza sativa</I>, was domesticated from Asian wild rice, <I>O. rufipogon</I>. Loss of seed-shattering is one of the most important traits during rice domestication. In order to better understand the genetic control of seed shattering, chromosome segment substitution lines were prepared by introgressing non-shattering <I>qSH1</I> and <I>sh4</I> alleles from cultivated rice, <I>O. sativa</I> cv. Nipponbare, in the genetic background of wild rice. The degree of shattering was examined to evaluate the genetic interaction of two loci. The results showed that the backcross plants individually having Nipponbare homozygous alleles at either shattering locus (<I>qSH1</I> or <I>sh4</I>) shed all the seeds. These results indicated that two cultivated non-shattering alleles were not sufficient to express full non-shattering behavior in the genetic background of wild rice. Probably some other minor loci are still involved in the control of seed-shattering in wild rice.

DOI： 10.14841/jspp.2011.0.0037.0

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACADEMIC PRESS INC ELSEVIER SCIENCE  

We screened collagenolytic/gelatinolytic bacteria from rice leaves and soil which degraded the fungal extracellular matrix to establish a novel biological control measure inhibiting germling adhesion on the host plant surface against airborne fungal diseases such as rice blast disease Magnaporthe oryzae B. Coch. Two different screening methods, i.e., screening from the leaf-associated bacterial library and direct screening from leaf and soil with or without collagen incubation, were conducted. Screening from the collagen treated material resulted in a higher number of gelatinolytic isolates than without collagen treatment. The selected bacteria were identified as Acidovorax, Sphingomonas, Chryseobacterium, and Pseudomonas genera by 16S rDNA sequence. Based on treatment with EDTA and addition of divalent cations, four of the five screened isolates tested produced a metalloproteinase. Furthermore, the enzymes produced by Acidovorax and Sphingomonas sp. were categorized as calcium-dependent metalloproteinases, and the enzymes produced by Chryseobacterium sp. were categorized as calcium/zinc-dependent metalloproteinases. The screened bacterial culture showed inhibitory effects on spore adhesion on the plastic cover glass, and disease protective effects on rice. This study suggests that bacteria inhibiting germling adhesion by phytopathogenic fungi may have promise as a biological agent. (C) 2010 Elsevier Inc. All rights reserved.

DOI： 10.1016/j.biocontrol.2010.07.008

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：GENETICS SOC JAPAN  

It is known that the common cultivated rice (Oryza sativa) was domesticated from Asian wild rice, O. rufipogon. Among the morphological differences between them, loss of seed shattering is one of the striking characters specific for the cultivated forms. In order to understand the genetic control on shattering habit, QTL analysis was carried out using BC2F1 backcross population between O. sativa cv. Nipponbare (a recurrent parent) and O. rufipogon acc. W630 (a donor parent). As a result, two strong QTLs were detected on chromosomes 1 and 4, and they were found to be identical to the two major seed-shattering loci, qSH1 and sh4, respectively. The allelic interaction at these loci was further examined using two sets of backcross populations having reciprocal genetic backgrounds, cultivated and wild. In the genetic background of cultivated rice, the wild qSH1 allele has stronger effect on seed shattering than that of sh4. In addition, the wild alleles at both qSH1 and sh4 loci showed semi-dominant effects. On the other hand, in the genetic background of wild rice, non-shattering effects of Nipponbare alleles at both loci were examined to inspect rice domestication from a viewpoint of seed shattering. It was serendipitous that the backcross plants individually having Nipponbare homozygous alleles at either shattering locus (qSH1 or sh4) shed all the seeds. This fact strongly indicates that the non-shattering behavior was not obtained by a single mutation in the genetic background of wild rice. Probably, some other minor genes are still associated with the formation or activation of abscission layer, which enhance the seed shattering.

DOI： 10.1266/ggs.85.265

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL PUBLISHING, INC  

Aegilops tauschii Coss. is the D-genome progenitor of hexaploid wheat. Aegilops tauschii, a wild diploid species, has a wide natural species range in central Eurasia, spreading from Turkey to western China. Amplified fragment length polymorphism (AFLP) analysis using a total of 122 accessions of Ae. tauschii was conducted to clarify the population structure of this widespread wild wheat species. Phylogenetic and principal component analyses revealed two major lineages in Ae. tauschii. Bayesian population structure analyses based on the AFLP data showed that lineages one (L1) and two (L2) were respectively significantly divided into six and three sublineages. Only four out of the six L1 sublineages were diverged from those of western habitats in the Transcaucasia and northern Iran region to eastern habitats such as Pakistan and Afghanistan. Other sublineages including L2 were distributed to a limited extent in the western region. Subspecies strangulata seemed to be differentiated in one sublineage of L2. Among three major haplogroups (HG7, HG9 and HG16) previously identified in the Ae. tauschii population based on chloroplast variation, HG7 accessions were widely distributed to both L1 and L2, HG9 accessions were restricted to L2, and HG16 accessions belonged to L1, suggesting that HG9 and HG16 were formed from HG7 after divergence of the first two lineages of the nuclear genome. These results on the population structure of Ae. tauschii and the genealogical relationship among Ae. tauschii accessions should provide important agricultural and evolutionary knowledge on genetic resources and conservation of natural genetic diversity.

DOI： 10.1111/j.1365-294X.2010.04537.x

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：CROP SCIENCE SOC AMER  

Both domestication and crop improvement in maize (Zea mays ssp. mays) have involved selection of specific alleles at genes controlling key morphologic and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. This difference in genetic diversity has led to the development of genomic screens for artificial selection in maize that have identified similar to 50 candidate agronomic genes. One limitation of these initial genome screens is that the short length of the alignment (average length &lt; 300 bp) restricts the statistical power and may lead to false positives. The major objective of this research was to provide an empirical determination of the false positive rate of genomic screens for artificial selection in maize. Therefore, we performed extended sequencing throughout the available gene sequence of 27 previously identified selection candidates using maize inbred, maize landrace (for 12 genes), and teosinte (Zea mays ssp. parviglumis) accessions. The extended sequence alignments (average length &gt; 2000 bp) allowed clear separation of strong candidates for selection from those that cannot be distinguished from the tail of the diversity distribution of all maize genes. The extended alignments also allowed linkage disequilibrium to be considered in evaluating a candidate's selection status. This proved particularly useful in distinguishing selection at domestication versus subsequent crop improvement.

DOI： 10.3835/plantgenome2007.09.0530

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BIOMED CENTRAL LTD  

Background: With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naive programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor.
Results: We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected.
Conclusion: We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism.

DOI： 10.1186/1471-2105-9-154

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

As population structure can result in spurious associations, it has constrained the use of association studies in human and plant genetics. Association mapping, however, holds great promise if true signals of functional association can be separated from the vast number of false signals generated by population structure(1,2). We have developed a unified mixed-model approach to account for multiple levels of relatedness simultaneously as detected by random genetic markers. We applied this new approach to two samples: a family-based sample of 14 human families, for quantitative gene expression dissection, and a sample of 277 diverse maize inbred lines with complex familial relationships and population structure, for quantitative trait dissection. Our method demonstrates improved control of both type I and type II error rates over other methods. As this new method crosses the boundary between family-based and structured association samples, it provides a powerful complement to currently available methods for association mapping.

DOI： 10.1038/ng1702

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC PLANT BIOLOGISTS  

Maize (Zea mays subsp mays) was domesticated from teosinte (Z. mays subsp parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties, which were spread throughout the Americas by Native Americans and adapted to a wide range of environmental conditions. Starting with landraces, 20th century plant breeders selected inbred lines of maize for use in hybrid maize production. Both domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. Here, we sequenced 1095 maize genes from a sample of 14 inbred lines and chose 35 genes with zero sequence diversity as potential targets of selection. These 35 genes were then sequenced in a sample of diverse maize landraces and teosintes and tested for selection. Using two statistical tests, we identified eight candidate genes. Extended gene sequencing of these eight candidate loci confirmed that six were selected throughout the gene, and the remaining two exhibited evidence of selection in the 39 portion of each gene. The selected genes have functions consistent with agronomic selection for nutritional quality, maturity, and productivity. Our large-scale screen for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown.

DOI： 10.1105/tpc.105.037242

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER ASSOC ADVANCEMENT SCIENCE  

Domestication promotes rapid phenotypic evolution through artificial selection. We investigated the genetic history by which the wild grass teosinte (Zea mays ssp. parviglumis) was domesticated into modem maize (Z. mays ssp. mays). Analysis of single-nucleotide polymorphisms in 774 genes indicates that 2 to 4% of these genes experienced artificial selection. The remaining genes retain evidence of a population bottleneck associated with domestication. Candidate selected genes with putative function in plant growth are clustered near quantitative trait loci that contribute to phenotypic differences between maize and teosinte. If we assume that our sample of genes is representative, 1200 genes throughout the maize genome have been affected by artificial selection.

DOI： 10.1126/science.1107891

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：KLUWER ACADEMIC PUBL  

Rice (Oryza sativa L.) ovicidal response to the whitebacked planthopper (Sogatella furcifera Horvath) is characterized by formation of watery lesions and production of an ovicidal substance benzyl benzoate, which results in high egg mortality of whitebacked planthopper. A gene with ovicidal activity to whitebacked planthopper, designated Ovc, and four ovicidal quantitative trait loci (QTLs), qOVA-1-3, qOVA-4, qOVA-5-1 and qOVA-5-2 were identified using near isogenic lines with reciprocal genetic backgrounds of a non-ovicidal Indica variety IR24 and an ovicidal Japonica variety Asominori. Ovc and the four QTLs were mapped on chromosomes 6, 1, 4, 5 and 5, respectively. Ovc is the first gene identified that kills insect eggs in plants. The Asominori allele at Ovc was essential for increasing egg mortality and responsible for production of benzyl benzoate and formation of watery lesions. The Asominori alleles at qOVA-1-3, qOVA-5-1 and qOVA-5-2 increased egg mortality in the presence of Ovc. In contrast, the Asominori allele at qOVA-4 suppressed egg mortality, indicating that qOVA-4 caused transgressive segregation for egg mortality. It was concluded that Ovc and four ovicidal QTLs accounted for the majority of the phenotypic variance for the ovicidal response to whitebacked planthopper in Asominori.

DOI： 10.1023/A:1026018821472

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC BREEDING  

The brown planthopper (BPH), Nilaparvata lugens Stal, is a serious pest of rice (Oryza sativa L.) in Asia. The rice ovicidal response to BPH is characterized by the formation of watery lesions which result in the death of the eggs. It is one of the factors affecting the suppression of the multiplication of BPH. To detect quantitative trait loci (QTLs) for this ovicidal response, a set of 71 rice recombinant inbred lines (F-11) derived from a cross between a Japonica variety Asominori with ovicidal response and an Indica variety IR24 without ovicidal response were phenotyped for grade of watery lesions (GWL) and egg mortality (EM) of BPH, GWL and EM showed a significant positive correlation (P &lt; 0.001) and transgressive segregation was observed for EM. In composite interval mapping for GWL and EM with 293 RFLP marker loci, two QTLs each on the long arm of chromosome 1 (1L) and the short arm of chromosome 6 (6S) were detected for both GWL and EM. The 6S QTL explained 72.1% and 85.1% of the phenotypic variations for GWL and EM, respectively, The QTL on 1L explained 19.8% and 17.8% of the phenotypic variations for GWL and EM, respectively. Both alleles from Asominori increased GWL and EM. The Asominori allele at the 6S QTL was essential for the ovicidal response to BPH and the Asominori allele at the 1L QTL could increase the EM of BPH in the presence of the Asominori allele at the 6S QTL. It is concluded that the two RFLP loci, R1954 linked to 6S QTL and C112 linked to 1L QTL can be used for marker-assisted selection.

DOI： 10.1270/jsbbs.50.291

Web of Science

J-GLOBAL

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Crop Science Society of America  

The ovicidal response in rice (Oryza sativa L.) to whitebacked planthopper (WBPH), Sogatella furcifera Horvath, is characterized by the formation of watery lesions which result in the death of WBPH eggs. To determine the genetic mechanism of this ovicidal response, a set of 71 rice recombinant inbred (RI) lines (F8, F9, and F10) derived from a cross of japonica cultivar Asominori and indica cultivar IR24, the two parents, and the F1 were phenotyped for percentage of watery lesions (PWL) and WBPH egg mortality (EM). PWL and EM showed significant positive correlations (P &lt
0.001) and transgressive segregation was observed for both traits. A total of 10 quantitative trait loci (QTLs) for ovicidal response were detected with 292 RFLP markers in the F6 and F7 populations by composite interval mapping (LOD ≥ 1.5). Four of 10 QTLs coincided for PWL and EM and each three QTLs were only detected for PWL and EM. The QTL on chromosome 6 (R1954-L688) was most significantly associated with the ovicidal response and accounted for 69.9% of phenotypic variance for PWL (F8) and 46.0% of phenotypic variance for EM (F8). Positive alleles for ovicidal response came from Asominori on chromosomes 1, 3, 6S (short arm), 8, and 12 and from IR24 on chromosomes 2, 6L (long arm), and 10. QTL accumulation from both parents was the genetic basis of the transgressive segregation in the RI population. No epistatic interaction was detected. The Asominori allele on the chromosome 6S QTL was essential to the ovicidal response, and R1954 was found to be a target marker for marker assisted selection.

DOI： 10.2135/cropsci1999.0011183X003900040038x

Scopus

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Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.247.0_193

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Language：Japanese   Publisher：CROP SCIENCE SOCIETY OF JAPAN  

DOI： 10.14829/jcsproc.246.0_9

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DOI： 10.1270/jsbbr.16.23

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Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (scientific journal)  

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Language：English   Publishing type：Book review, literature introduction, etc.   Publisher：OXFORD UNIV PRESS  

Background Artificial selection results in phenotypic evolution. Maize ( Zea mays L. ssp. mays) was domesticated from its wild progenitor teosinte ( Zea mays subspecies parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties. The landraces provided the genetic material for modern plant breeders to select improved varieties and inbred lines by enhancing traits controlling agricultural productivity and performance. Artificial selection during domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes.
Scope This review is a summary of research on the identification and characterization by population genetics approaches of genes affected by artificial selection in maize.
Conclusions Analysis of DNA sequence diversity at a large number of genes in a sample of teosintes and maize inbred lines indicated that approx. 2 % of maize genes exhibit evidence of artificial selection. The remaining genes give evidence of a population bottleneck associated with domestication and crop improvement. In a second study to efficiently identify selected genes, the genes with zero sequence diversity in maize inbreds were chosen as potential targets of selection and sequenced in diverse maize landraces and teosintes, resulting in about half of candidate genes exhibiting evidence for artificial selection. Extended gene sequencing demonstrated a low false-positive rate in the approach. The selected genes have functions consistent with agronomic selection for plant growth, nutritional quality and maturity. Large-scale screening for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown. These approaches should also be applicable to other domesticated species if specific demographic conditions during domestication exist.

DOI： 10.1093/aob/mcm173

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Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (scientific journal)  

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Language：Japanese   Publisher：日本植物防疫協会  

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Language：Japanese   Publisher：日本育種学会  

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Event date： 2020.9

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Venue：St. Louis USA  

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Venue：Hohenheim, Germany  

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Venue：Ehime University  

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Venue：Tsukuba, Ibaraki  

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Venue：San Diego, California, USA  

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Award type：Award from Japanese society, conference, symposium, etc.  Country：Japan

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