Table_1_High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing.xlsx

Rice is a major food crop that sustains approximately half of the world population. Recent worldwide improvements in the standard of living have increased the demand for high-quality rice. Accurate identification of quantitative trait loci (QTLs) for rice grain quality traits will facilitate rice quality breeding and improvement. In the present study, we performed high-resolution QTL mapping for rice grain quality traits using a genotyping-by-sequencing approach. An F2 population derived from a cross between an elite japonica variety, Koshihikari, and an indica variety, Nona Bokra, was used to construct a high-density genetic map. A total of 3,830 single nucleotide polymorphism markers were mapped to 12 linkage groups spanning a total length of 2,456.4 cM, with an average genetic distance of 0.82 cM. Seven grain quality traits—the percentage of whole grain, percentage of head rice, percentage of area of head rice, transparency, percentage of chalky rice, percentage of chalkiness area, and degree of chalkiness—of the F2 population were investigated. In total, 15 QTLs with logarithm of the odds (LOD) scores >4 were identified, which mapped to chromosomes 6, 7, and 9. These loci include four QTLs for transparency, four for percentage of chalky rice, four for percentage of chalkiness area, and three for degree of chalkiness, accounting for 0.01%–61.64% of the total phenotypic variation. Of these QTLs, only one overlapped with previously reported QTLs, and the others were novel. By comparing the major QTL regions in the rice genome, several key candidate genes reported to play crucial roles in grain quality traits were identified. These findings will expedite the fine mapping of these QTLs and QTL pyramiding, which will facilitate the genetic improvement of rice grain quality.

水稻是维系全球约半数人口口粮供给的主要粮食作物。近年来全球居民生活水平稳步提升，对优质稻米的需求日益增长。精准鉴定稻米品质性状的数量性状位点（quantitative trait loci, QTL），将为稻米品质育种与遗传改良提供重要支撑。本研究采用基于测序的基因分型（genotyping-by-sequencing）技术，针对稻米品质性状开展高分辨率QTL定位。
本研究以优良粳稻品种越光（Koshihikari）与籼稻品种诺娜博克拉（Nona Bokra）杂交获得的F₂群体为材料，构建了一张高密度遗传图谱。最终共将3830个单核苷酸多态性标记锚定至12个连锁群，图谱总长度达2456.4 cM，平均遗传距离为0.82 cM。
研究对该F₂群体的7项稻米品质性状进行了调查，分别为整粒米率、整精米率、整精米面积率、透明度、垩白米率、垩白面积率与垩白度。本研究共鉴定出15个对数似然比（logarithm of the odds, LOD）值大于4的QTL，这些位点均定位在第6、7、9号染色体上。其中包含调控透明度的4个QTL、调控垩白米率的4个QTL、调控垩白面积率的4个QTL以及调控垩白度的3个QTL，各位点解释的表型变异率范围为0.01%~61.64%。
在上述QTL中，仅1个与此前已报道的QTL存在重叠，其余均为新发现的位点。通过比对水稻基因组内的主要QTL区域，本研究鉴定出多个已被证实对稻米品质性状发挥关键调控作用的候选基因。上述研究结果将加速这些QTL的精细定位与QTL聚合，进而有效推动稻米品质的遗传改良。