Genome-Wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery During Germination in Rice

Abstract

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 p < 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 p < 0.001, a total of 20 QTLs were identified in the subset of japonica accessions, while 9 QTLs were identified in the subset of indica 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 japonica subset, and 7 distinct QTL regions in the indica subset. Among these QTL regions, three regions were common between the whole panel and japonica, three regions were common between the whole panel and indica, and one region was common between indica and japonica. A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the japonica subset, 4 from the indica 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 japonica subset, and 1 from the indica 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.

Can omics deliver temperature resilient ready-to-grow crops?

“…Recently, a GWAS experiment was conducted using 257 rice accessions worldwide to examine genetic behavior during germination under CS [127]. Interestingly, 51 QTLs were identified, and of these 17 QTLs were identified at different chilling points.…”

Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

“…Association analysis is time- and cost-effective, and can mine for genetic variations existed in the natural population, and more importantly, it takes advantage of the recombination information that has accumulated in the natural population over the long-term evolution process, thus achieving a higher mapping resolution, possibly identifying the causative genes [ 7 , 8 ]. Because of its effectiveness in QTL identification, association mapping has been widely used in crop species and plays an important role in molecular breeding [ 9 – 14 ].…”

Genome-Wide Association Study (GWAS) For Cold Tolerance at The Bud Burst Stage in Rice Using SNP Markers

“…26 QTLs were found related to cold tolerance in rice seedling stage by using a core collection of landraces of rice from 2,262 accessions of Ting's collection [25]. In addition, 31 distinct QTLs regions were identi ed in a panel of 257 rice accessions from all of the world for low temperature germination [26]. However, there are still few studies using GWAS to explore cold tolerance in rice at the bud burst stage.…”