Genome-wide association study of salt tolerance at the seed germination stage in rice.
Genome-wide association study of salt tolerance at the seed germination stage in rice.
复制标题
DOI：
10.1186/s12870-017-1044-0
复制
发表时间：
2017-05-30
影响因子：
5.3
通讯作者：
Li Z
中科院分区：
文献类型：
--
作者：
Shi Y;Gao L;Wu Z;Zhang X;Wang M;Zhang C;Zhang F;Zhou Y;Li Z
提高直播水稻种子发芽阶段的耐盐性是许多亚洲水稻种植国家的主要育种目标，这些国家的秧苗通常必须在含盐量高的土壤中生长。因此，了解水稻耐盐遗传机制，筛选种子萌发阶段耐盐种质具有重要意义。在这里，我们研究了控制和盐胁迫条件下的七种种子发芽相关性状，并基于 478 个不同水稻品种的重新测序进行了全基因组关联研究。该分析使用混合线性模型，基于 478 个水稻品种的 6,361,920 个单核苷酸多态性，这些品种分为整株、籼稻和非籼稻组。根据活力指数（VI）和平均发芽时间（MGT）的胁迫敏感性指数（SSIs）鉴定出11个含有22个显着耐盐相关单核苷酸多态性的位点。从 VI 的 SSI 中，鉴定出 6 个主要基因座，解释了 20.2% 的表型变异。从MGT的SSI中，检测到5个主要位点，解释了26.4%的表型变异。其中，1、5、6、11 和 12 号染色体上的 7 个位点接近先前确定的与盐度或其他非生物胁迫耐受性相关的 6 个定量基因位点/基因。 MGT SSI 的最强关联区域在 1 号染色体上约 13.3 kb 的区间 (15450039–15,463,330) 内被鉴定，靠近耐盐数量性状位点，控制 Na+: K+ 比例、总 Na+ 吸收和总 K+ 浓度。 VI 的 SSI 最强关联区域在 2 号染色体上约 164.2 kb 的区间 (526662–690,854) 中检测到，该区域包含两个硝酸盐转运蛋白家族基因（OsNRT2.1 和 OsNRT2.2），这些基因在盐胁迫下影响基因表达。单倍型分析表明OsNRT2.2与亚群分化相关，并检测到其次要/罕见的耐受单倍型。这些结果为耐盐相关基因克隆和了解种子萌发阶段耐盐遗传机制提供了有价值的信息。这些信息将有助于通过基因组选择或标记辅助选择来提高直播水稻品种的耐盐性。本文的在线版本 (doi:10.1186/s12870-017-1044-0) 包含补充材料，可供授权用户使用。
Improving the salt tolerance of direct-seeding rice at the seed germination stage is a major breeding goal in many Asian rice-growing countries, where seedlings must often establish in soils with a high salt content. Thus, it is important to understand the genetic mechanisms of salt tolerance in rice and to screen for germplasm with salt tolerance at the seed germination stage. Here, we investigated seven seed germination-related traits under control and salt-stress conditions and conducted a genome-wide association study based on the re-sequencing of 478 diverse rice accessions. The analysis used a mixed linear model and was based on 6,361,920 single nucleotide polymorphisms in 478 rice accessions grouped into whole, indica, and non-indica panels. Eleven loci containing 22 significant salt tolerance-associated single nucleotide polymorphisms were identified based on the stress-susceptibility indices (SSIs) of vigor index (VI) and mean germination time (MGT). From the SSI of VI, six major loci were identified, explaining 20.2% of the phenotypic variation. From the SSI of MGT, five major loci were detected, explaining 26.4% of the phenotypic variation. Of these, seven loci on chromosomes 1, 5, 6, 11, and 12 were close to six previously identified quantitative gene loci/genes related to tolerance to salinity or other abiotic stresses. The strongest association region for the SSI of MGT was identified in a ~ 13.3 kb interval (15450039–15,463,330) on chromosome 1, near salt-tolerance quantitative trait loci controlling the Na+: K+ ratio, total Na+ uptake, and total K+ concentration. The strongest association region for the SSI of VI was detected in a ~ 164.2 kb interval (526662–690,854) on chromosome 2 harboring two nitrate transporter family genes (OsNRT2.1 and OsNRT2.2), which affect gene expression under salt stress. The haplotype analysis indicated that OsNRT2.2 was associated with subpopulation differentiation and its minor/rare tolerant haplotype was detected. These results provide valuable information for salt tolerance-related gene cloning and for understanding the genetic mechanisms of salt tolerance at the seed germination stage. This information will be useful to improve the salt tolerance of direct-seeding rice varieties by genomic selection or marker-assisted selection. The online version of this article (doi:10.1186/s12870-017-1044-0) contains supplementary material, which is available to authorized users.