Genome-wide Association Study For Loci Related To Cold Tolerance And Heterosis Of Rice

Low stress is one of the important abiotic factors to decrease the yield and quality of rice.The utilization of heterosis is an important way to increase rice yield.In this study,mapping cold tolerance and heterosis loci were carried out by developing different populations and using genome-wide association analysis.The results were as follows:Mapping cold tolerance loci.A IB population developed by crossing Huanghuazhan with eight varied donor was used to identify CT loci at booting stage.Both genotype and cold tolerance at booting stage of parents and IB population showed diversity.A total of 6 independent CT loci were identified under four environments.Most loci are detected out only in 1 to 2 environments,with a PVE of 4.0-8.5%.qCT-3-2,located on the short arm of chromosome 3,is a stable expression QTL with mean PVE of 6%under four environments.Furthermore,qCT-3-2 was mapped to the physical range of 192 kb by physical mapping,and its favorable allele came from recurrent parent HuangHuazhan.In addition,we found that qCT-3-2 also played a role in cold tolerance during rice seedling stage.Diversity analysis of indica restorer lines.The 56 K rice chip was adopted to genotyping 759 indica three-line restorer lines.The results showed that all the traits of restorer lines were varied and showed highly significant difference.PCA and cluster analysis showed that the restorer lines could be clearly divided into 4 subgroups and without obvious population structure.However,in different region of paddy,certain subgroup was mainstream along with other subgroups with lower proportion.It was far different in genetics between restorer lines from china and that imported from abroad.These results uncovered the distribution of diversity of indica restorer lines in china,indicating the genetic diversity had improved at a certain extent,but had significant difference in different planting regions.QTL mapping for heterotic loci.Mid-parents heterosis was used as an indix of heterosis.Analysis of variance showed that the heterosis of all traits except tiller number showed significant difference under four environments.The TN and FLL had negative heterosis,while the others showed stronger positive heterosis,especially PH,YD,GNPP,FGNPP and SR.A total of 51 independent heterosis loci were identified under four environments by GWAS.These loci distributed on 11 chromosome except chr.12,and the qHHD7.1 and qHHD7.2 were detected under four environments.Further,27 loci controlling different traits were found to distribute in ten enrichment regions,six of were reported previously many times,and one of were cloned(RH8).Integrating all loci identified from male population and mid-parents heterosis,we found twenty six loci were overlapped,and many were located in the enrichment regions of heterosis or containing known cloning genes controlling yield and yield-related such as GS3?GW5?RFL?NAL?Ghd7and Ghd8 et al,implying that these loci controlled simultaneously the phenotype of parents with homozygotic genotype and heterosis.In these hot regions,the two enrichment regions of heterosis simultaneously controlling some traits on the long arm of chr.7 and 8 were new and were identified from two population under many environments,implying that this new hot enrichment regions had important theoretical and applied value in conventional breeding,hybridization breeding or molecular breeding.In summary,our results not only provided important information for cloning the loci of cold tolerance and heterosis and understanding the mechanism of cold tolerance and heterosis,but also for breeding rice cultivation with low temperature resistance or super high yield.