Genome-wide Association Study Of Low Temperature And Anoxic Germinability In A Diverse International Rice Collection

With the transfer of rural manpower to the second and third industries,lack of manpower has been one of the main problems in rice production.Development of light and simple techniques is the effective way to address this issue.Rice direct seeding has been well adopted in rice production because of its cost-effective and manpower saving compared with the traditional seedling transfer cultivation.However,direct seeding has not been largely applied in most of the areas in China.Poorer germinability of the rice cultivars under low temperature and anoxic condition is part of the factors affecting the application of this technique.In this study,a diverse rice collection with 379 rice accessions from 56 countries and regions and known genotypes determined by 700 k SNPs were used.Systematic evaluation of low temperature germination and anoxic germination of these rice materials has been conducted in order to screen for rice germplasm with strong low temperature germinability and anoxic germinability,respectively.Genome-wide association study was performed to map and identify the QTLs associated with low temperature and anoxic germinabiltiy in rice.The main results are followings:1.he distributions of low temperature germination and anoxic germinability in 379 rice accessions are normal or near normal,indicating the nature of quantitative trait controlled by multiple genes;2.The ANOVA revealed that significant difference was observed among rice accession.Ten rice accession with germination rate over 91% under 13? temperature and 10 rice accessions with strong anoxic germinability have been identified,respectively;3.The multiple range tests suggest that the low temperature germination rate and the anoxic germinability of indica group is significant higher and stronger than that of japonica and Aus groups,respectively(p<0.01),and low temperature germination rate of japonica group is significant higher than that of Aus group(p<0.05).However,the difference of anoxic germinability between japonica group and Aus group is not significant(p>0.05).Our finding that the cold tolerance of indica is better than that of japonica at germination stage is different with the previous conclusion that the cold tolerance of japonica is better4.Through genome-wide association study,we were able to identify 36 QTLs for low temperature germination and 31 QTLs for anoxic germinability in rice.Among the 36 QTLs for low temperature germination,6 QTLs are overlapped with the previous identified QTLs,30 QTLs are newly identified QTLs.Among the 31 QTLs for anoxic germinability,5 QTLs are overlapped with the previous identified QTLs,and 26 QTLs are newly identified QTLs.Interestingly,three QTLs for low temperature germination are overlapped with three QTLs for anoxic germinability in this study.In this study,we have obtained rice germplasm with strong low temperature germinability and anoxic germinability,and identified numerous QTLs for low temperature germination and anoxic germinability.Our results provide good basis for cloning of genes associated with low temperature and anoxic germinability,molecular breeding for direct seeding and facilitate molecular breeding for direct seeding.