Thapa Ranjita, Tabien Rodante E, Thomson Michael J, Septiningsih Endang M
Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States.
Texas A&M AgriLife Research Center, Beaumont, TX, United States.
Front Genet. 2020 Feb 21;11:22. doi: 10.3389/fgene.2020.00022. eCollection 2020.
Low temperature significantly affects rice growth and yield. Temperatures lower than 15°C are generally detrimental for germination and uniform seedling stand. To investigate the genetic architecture underlying cold tolerance during germination in rice, we conducted a genome-wide association study using a novel diversity panel of 257 rice accessions from around the world and the 7K SNP marker array. Phenotyping was conducted in controlled growth chambers under dark conditions at 13°C. The rice accessions were measured for low-temperature germinability, germination index, coleoptile length under cold stress, plumule length at 4-day recovery, and plumule length recovery rate. A total of 51 QTLs were identified at < 0.001 and 17 QTLs were identified using an FDR < 0.05 across the different chilling indices with the whole panel of accessions. At the threshold of < 0.001, a total of 20 QTLs were identified in the subset of accessions, while 9 QTLs were identified in the subset of accessions. Considering the recurring SNPs and linked SNPs across different chilling indices, we identified 31 distinct QTL regions in the whole panel, 13 QTL regions in the subset, and 7 distinct QTL regions in the subset. Among these QTL regions, three regions were common between the whole panel and , three regions were common between the whole panel and , and one region was common between and . A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the subset, 4 from the subset, and 6 from the whole panel. On the other hand, a total of 21 potentially novel QTL regions from the whole panel, 10 from the subset, and 1 from the subset were identified. The results of our study provide useful information on the genetic architecture underlying cold tolerance during germination in rice, which in turn can be used for further molecular study and crop improvement for low-temperature stressed environments.
低温显著影响水稻生长和产量。低于15°C的温度通常对发芽和整齐的秧苗生长不利。为了研究水稻发芽期耐冷性的遗传结构，我们使用了一个来自世界各地的由257份水稻种质组成的新型多样性群体以及7K SNP标记阵列进行了全基因组关联研究。表型分析在可控生长室中于13°C黑暗条件下进行。对水稻种质的低温发芽能力、发芽指数、冷胁迫下的胚芽鞘长度、4天恢复时的胚根长度以及胚根长度恢复率进行了测定。在全群体不同冷害指数下，共鉴定出51个LOD值<0.001的QTL以及17个FDR<0.05的QTL。在LOD值<0.001的阈值下，在种质亚群中鉴定出20个QTL，而在种质亚群中鉴定出9个QTL。考虑到不同冷害指数下重复出现的SNP和连锁SNP，我们在全群体中鉴定出31个不同的QTL区域，在种质亚群中鉴定出13个QTL区域，在种质亚群中鉴定出7个不同的QTL区域。在这些QTL区域中，有三个区域在全群体和之间是共同的，有三个区域在全群体和之间是共同的，有一个区域在和之间是共同的。一部分QTL区域可能与先前鉴定的基因和QTL共定位，包括来自种质亚群的10个、来自种质亚群的4个以及来自全群体的6个。另一方面，在全群体中鉴定出总共21个潜在的新QTL区域，在种质亚群中鉴定出10个，在种质亚群中鉴定出1个。我们的研究结果为水稻发芽期耐冷性的遗传结构提供了有用信息，进而可用于进一步的分子研究以及针对低温胁迫环境的作物改良。
