Cui Yanru, Zhang Fan, Zhou Yongli
Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
Front Plant Sci. 2018 Oct 4;9:1464. doi: 10.3389/fpls.2018.01464. eCollection 2018.
Improving the salt-tolerance of direct-seeding rice at the seed germination stage is a major goal of breeders. Efficiently identifying salt tolerance loci will help researchers develop effective rice breeding strategies. In this study, six multi-locus genome-wide association studies (GWAS) methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, and ISIS EM-BLASSO) were applied to identify quantitative trait nucleotides (QTNs) for the salt tolerance traits of 478 rice accessions with 162,529 SNPs at the seed germination stage. Among the 371 QTNs detected by the six methods, 56 were identified by at least three methods. Among these 56 QTNs, 12, 6, 7, 4, 13, 12, and 12 were found to be associated with SSI-GI, SSI-VI, SSI-MGT, SSI-IR-24h, SSI-IR-48h, SSI-GR-5d, and SSI-GR-10d, respectively. Additionally, 66 candidate genes were identified in the vicinity of the 56 QTNs, and two of these genes (LOC_Os01g45760 and LOC_Os10g04860) are involved in auxin biosynthesis according to the enriched GO terms and KEGG pathways. This information will be useful for identifying the genes responsible for rice salt tolerance. A comparison of the six methods revealed that ISIS EM-BLASSO identified the most co-detected QTNs and performed best, with the smallest residual errors and highest computing speed, followed by FASTmrMLM, pLARmEB, mrMLM, pKWmEB, and FASTmrEMMA. Although multi-locus GWAS methods are superior to single-locus GWAS methods, their utility for identifying QTNs may be enhanced by adding a bin analysis to the models or by developing a hybrid method that merges the results from different methods.
提高直播水稻种子萌发期的耐盐性是育种者的主要目标。有效鉴定耐盐位点将有助于研究人员制定有效的水稻育种策略。在本研究中，应用六种多位点全基因组关联研究（GWAS）方法（mrMLM、FASTmrMLM、FASTmrEMMA、pLARmEB、pKWmEB和ISIS EM-BLASSO），对478份水稻种质在种子萌发期的162,529个单核苷酸多态性（SNP）的耐盐性状进行数量性状核苷酸（QTN）鉴定。在六种方法检测到的371个QTN中，有56个被至少三种方法鉴定出来。在这56个QTN中，分别发现12、6、7、4、13、12和12个与种子萌发期耐盐指数（SSI-GI）、发芽期耐盐指数（SSI-VI）、平均发芽时间耐盐指数（SSI-MGT）、24小时相对盐害率耐盐指数（SSI-IR-24h）、48小时相对盐害率耐盐指数（SSI-IR-48h）、5天发芽率耐盐指数（SSI-GR-5d）和10天发芽率耐盐指数（SSI-GR-10d）相关。此外，在56个QTN附近鉴定出66个候选基因，根据富集的基因本体（GO）术语和京都基因与基因组百科全书（KEGG）通路，其中两个基因（LOC_Os01g45760和LOC_Os10g04860）参与生长素生物合成。这些信息将有助于鉴定水稻耐盐性相关基因。六种方法的比较表明，ISIS EM-BLASSO鉴定出的共检测QTN最多，表现最佳，剩余误差最小，计算速度最快，其次是FASTmrMLM、pLARmEB、mrMLM、pKWmEB和FASTmrEMMA。虽然多位点GWAS方法优于单位点GWAS方法，但通过在模型中添加箱式分析或开发一种融合不同方法结果的混合方法，可能会提高其鉴定QTN的效用。
