Genome-wide Association Study Of Rice Flooding Tolerance During Germination

Rice direct seeding is a low-cost cultivation technology which is characterized by saving labor source. Rice emergence rate is thought to be the crucial limiting factor of popularizing direct seeding technology. Thus improving the adaptation of direct seeding is the key to limitation. Oxygen deficiency caused by flooding during direct seeding is one of the essential environmental factors which lead to low emergence rate. Investigation on the genetic mechanism of flooding tolerance during rice germination will be contributed to breeding. The present study took use of local cultivars of indica rice to construct a natural population, and carried out genetic research on rice flooded germination by a genome-wide association study(GWAS). The main results are described as follows:1. We evaluated flooding tolerance during rice germination by measuring coleoptile length, and found abundant variation existed in indica population. Minority accessions were sensitive to oxygen deficiency and showed inability to germination. The board heritability which was calculated by data of several duplications was 70% while the analysis of variance indicated the trait was effect by environment.2. Via principal component analysis(PCA), we assessed the genetic structure of experimental population, the results demonstrated that structure had a significant influence on GWAS. The false positive error was reduced with the correction of the first ten PCs. Only 2.5% of the population had a pairwise relative kinship coefficients larger than 0.5 indicated the low kinship among individuals.3. Total 3971 SNP molecular markers were used to implement a GWAS on indica population, with a threshold of P=0.001 we detected 1359 significant SNPs in GLM, and 54, 9 SNPs in PCA, PCA+K model, respectively. Two SNPs(seq-rs2701 and seq-rs3087) were detected in both three models. The calculation of alleles’ effect found seq-rs2701, seq-rs3087 and seq-rs3121 had superior alleles which were tested as significant. The favorable alleles could be used directly in molecular assisted selection breeding. Analysis of combine effect showed the flooding tolerance increased along with the number of favorable alleles.4. With the application of expression profile chip data and quantitative PCR, we identified two genes LOC_Os08g39290 and LOC_Os06g03250 were induced by oxygen deficiency and highly expressed in flooding tolerant varieties. After sequenced the candidate genes, a single nucleotide variation, which was detected in LOC_Os06g03520, may be correlated with flooding tolerance of germination because of its changes in encoding amino acid. Thus, LOC_Os06g03520 was regarded as the optimal candidates.