Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China.
Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China.
PLoS One. 2018 May 10;13(5):e0196690. doi: 10.1371/journal.pone.0196690. eCollection 2018.
Rice is an important cereal in the world. The study of the genetic basis of important agronomic traits in rice landraces and identification of genes will facilitate the breed improvement. Gelatinization temperature (GT), gel consistency (GC) and pericarp color (PC) are important indices of rice cooking and eating quality evaluation and potential nutritional importance, which attract wide attentions in the application of genetic and breeding. To dissect the genetic basis of GT, GC and PC, a total of 419 rice landraces core germplasm collections consisting of 330 indica lines, 78 japonica lines and 11 uncertain varieties were planted, collected, then GT, GC, PC were measured for two years, and sequenced using specific-locus amplified fragment sequencing (SLAF-seq) technology. In this study, 261,385,070 clean reads and 56,768 polymorphic SLAF tags were obtained, which a total of 211,818 single nucleotide polymorphisms (SNPs) were discovered. With 208,993 SNPs meeting the criterion of minor allele frequency (MAF) > 0.05 and integrity> 0.5, the phylogenetic tree and population structure analysis were performed for all 419 rice landraces, and the whole panel mainly separated into six subpopulations based on population structure analysis. Genome-wide association study (GWAS) was carried out for the whole panel, indica subpanel and japonica subpanel with subset SNPs respectively. One quantitative trait locus (QTL) on chromosome 6 for GT was detected in the whole panel and indica subpanel, and one QTL associated with GC was located on chromosome 6 in the whole panel and indica subpanel. For the PC trait, 8 QTLs were detected in the whole panel on chromosome 1, 3, 4, 7, 8, 10 and 11, and 7 QTLs in the indica subpanel on chromosome 3, 4, 7, 8, 10 and 11. For the three traits, no QTL was detected in japonica subpanel, probably because of the polymorphism repartition between the subpanel, or small population size of japonica subpanel. This paper provides new gene resources and insights into the molecular mechanisms of important agricultural trait of rice phenotypic variation and genetic improvement of rice quality variety breeding.
稻米是世界上重要的粮食作物之一。研究水稻地方品种重要农艺性状的遗传基础，鉴定相关基因，有助于品种改良。糊化温度（GT）、胶稠度（GC）和果皮颜色（PC）是稻米蒸煮和食用品质评价的重要指标，具有潜在的营养重要性，在遗传和育种应用中受到广泛关注。为了剖析 GT、GC 和 PC 的遗传基础，共种植和收集了由 330 份籼稻系、78 份粳稻系和 11 份不确定品种组成的 419 份水稻地方品种核心种质资源，两年后测量 GT、GC 和 PC，并利用特异位点扩增片段测序（SLAF-seq）技术进行测序。在这项研究中，共获得 26138.5 万条高质量的 SLAF 标签序列，发现了 56768 个多态性 SLAF 标签，总计 211818 个单核苷酸多态性（SNP）。在满足最小等位基因频率（MAF）>0.05 和完整性>0.5 的 208993 个 SNP 中，对 419 份水稻地方品种进行了系统发育树和群体结构分析，基于群体结构分析，整个群体主要分为六个亚群。利用全基因组关联研究（GWAS），分别对整个群体、籼稻亚群体和粳稻亚群体的 SNP 进行了分析。在整个群体和籼稻亚群体中，检测到 1 个与 GT 相关的 6 号染色体上的数量性状位点（QTL），在整个群体和籼稻亚群体中，检测到 1 个与 GC 相关的 6 号染色体上的 QTL。对于 PC 性状，在整个群体的 1、3、4、7、8、10 和 11 号染色体上检测到 8 个 QTL，在籼稻亚群体的 3、4、7、8、10 和 11 号染色体上检测到 7 个 QTL。在粳稻亚群体中，没有检测到三个性状的 QTL，可能是由于亚群体之间的多态性分布不同，或者是粳稻亚群体的种群规模较小。本研究为水稻表型变异的重要农艺性状和水稻品质品种遗传改良的分子机制提供了新的基因资源和见解。
