Integrating GWAS and transcriptomics to identify genes involved in seed dormancy in rice

Abstract

Seed dormancy is a key agricultural trait to prevent pre-harvest sprouting in crop plants such as rice (Oryza sativa L.), wheat (Triticum aestivum), and barley (Hordeum vulgare L.). However, our knowledge of seed dormancy is hampered by the complexities of studying a trait that changes over time after seed harvest, and is complicated by interactions between phytohormones, other regulators, and the environment. Here, we have conducted a genome-wide association study using a panel of 311 natural accessions of cultivated rice, examining a total of 519,158 single nucleotide polymorphisms (SNPs).Eight quantitative trait loci (QTLs) were found to associate with seed dormancy; expression of candidate genes within 100 kb of each QTL was examined in two published, germination-speci c transcriptomic datasets. Ten candidate genes, differentially expressed within the rst four days post-imbibition, were identi ed. Five of these genes had previously been associated with awn length, heading date, yield, and spikelet length phenotypes. In addition, previously identi ed genes involved in hormone signaling during germination were found to be differentially expressed between a japonica and an indica line; SNPs in the promoter of Os9BGlu33 were associated with germination index. Collectively, our results are useful for future characterization of seed dormancy mechanism and crop improvement, and suggest haplotypes for further analysis that may be of use to boost PHS resistance in rice. Key MessagesSeveral QTLs and genes responsible for seed dormancy were detected and SNP candidates were shown to cause changes in seed germination.

Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice

“…Similarly, PCA and the population structure base on the possible clusters (k) method also showed that these rice accessions could be divided into two subgroups as the phylogenetic tree classification ( Figures 2B, C ). Taken together, the category of population structure has a similar result compared to a previous study ( Shi et al., 2021 ; Li et al., 2022 ).…”

Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice

“…The parameters (traits) used to determine seed dormancy in rice are seed GR, GI, germination potential and germination uniformity, among which, seed GR is the most commonly used one [ 34 , 42 , 82 , 92 ]. In our study, QTLs for dormancy using GR as the criterion were distributed on all chromosomes, except chromosomes 7 and 12, with chromosomes 4 and 11 containing more QTLs ( Figure 4 and Figure 5 ), which is in agreement with the general distribution pattern of rice seed dormancy QTLs, especially those identified by GWAS [ 27 , 34 , 35 ]. Ten of the thirty QTLs identified in this study overlapped with QTLs previously identified by linkage mapping or GWAS ( Table 2 ).…”

“…Another GWAS using 453 indica rice accessions identified nine QTLs for panicle GR on 8 chromosomes [ 2 ]. A more recent study using 311 accessions identified eight QTLs for seed dormancy measured by the germination index (GI) [ 35 ].…”

Seed Dormancy and Pre-Harvest Sprouting in Rice—An Updated Overview

“…The mutation of this gene inhibited pre-harvest sprouting in rice. By mining GWASs and transcriptome data, Shi et al [ 122 ] found a significant effect of the variation in SNPs in the promoter region of the Os9BGlu33 gene regarding germination index. In the same vein, taking advantage of a worldwide rice subpopulation, including japonica and indica populations, Magwa et al [ 113 ] investigated candidate genes relative to seed dormancy by genome association analyses.…”