The Genetic Analysis Of Heading Date Using A Rice Germplasm Collection And MAGIC Population

Rice?Oryza Sativa?is a short-day plant.Short-day length promotes the heading of rice,and long-day length suppresses the heading of rice.Many studies have evaluated rice heading date in field conditions in which some individuals in the population were exposed to various day lengths,including short and long days,prior to the growth phase transition.In this study,we investigated heading date under completely natural short-day conditions and long-day conditions for a diverse global collection of 529 O.sativa accessions and separately conducted genome-wide association studies within indica and japonica subpopulations.Using a four way Multi-parent Advanced Generation Inter-Cross?MAGIC?population,we dissected the genetic base of heading date under nature long-day conditions,and compared the QTL detecting power and resolution between GWAS at SNP level and at bin level.Under long-day conditions,three and four quantitative trait loci?QTLs?were identified in indica and japonica subpopulations,respectively,the lingkage disequlibrium?LD?intervals of two QTLs included the known genes Hd17 and Ghd7,respectively.Under short-day condition,six QTLs were detected in indica subpopulation,the LD intervals of three QTLs included the known heading date genes Ghd7,Ehd1 and RCN1,respectively.But there were no QTLs detected in japonica subpopulation under short-day condition.qHd3 under short-day condition and qHd4 under long-day condition were two novel major QTLs,which were deserved to be isolated and to be further studied in the future.To test the power of association mapping at the haplotype level,eleven known heading date genes Hd17,Ghd7,Ehd1,RCN1,Hd1,Ghd8,Ghd7.1,DTH2,Hd3 a,OsMADS50 and OsMADS56 were studied.By association mapping at haplotype level,Hd17,Ghd7,Ehd1 and RCN1 were again detected at more significant level,and three additional genes Hd3 a,OsMADS56 and Ghd7.1 were detected.However,of the detected seven genes,only one gene,Hd17,was commonly detected in both subpopulations,and the two genes Ghd7 and Ghd7.1 were detected in indica subpopulation under both long-day and short-day conditions.Furthermore,the comparison of the effects of alleles after the haplotype-level association mapping identified favorable haplotypes of Ghd7 and OsMADS56 for breeding design.Due to the low traceability of the history recombination events,it's hard to perform haplotype-level association mapping across the whole genome in nature populations.Whereas in MAGIC population,we can figure out the contributor of each genomic fragment by pedigree relationship,and the genotypes of bins can be identified.After the construction of bin map,a further comparison of detecting power between SNP-level and bin-level association mapping will be plausible in MAGIC population.A four way MAGIC population was constructed by paired crossing of four parents from three institutes/regions and selfing several generations by single seed descend?SSD?to create stable lines.1,231,431 high quality SNPs were identified by re-sequencing the four MAGIC parents and 248 lines.Neighbor-join tree and principle component analysis conducted by independent SNPs across genome indicate our MAGIC population have low level of population structure.We made a bin map by sliding window method together with identity by descend?IBD?and identity by state?IBS?.There are a total 4872 bins in this MAGIC population,each bin covers 88.9 kb on average.From this bin map,we found obvious repress of recombination around centromere region on all 12 chromosomes,and there are strong recombination hot spots at the end of chromosomes 2,7,12.QTL detecting for three sets of heading date in two years was conducted by both association mapping at SNP level and association mapping at bin level.Seven and twelve QTLs were detected by these two method,respectively.The known genes DTH3 and Ghd8 were detected in all the three sets of heading date by both methods,and they were confined in bins of size 120 kb and 330 kb by association mapping at bin level.Ghd7.1 and Ehd1 were detected by association mapping at SNP level alone,Hd3 a was detected by association mapping at bin level.The bin B11₃24 was associated with heading date in all the three sets of heading date.There are no known heading date genes reported at this locus before,so B11₃24 is a new heading date QTL.We further made multiple comparison for the bins of DTH3,Hd3 a,Ghd8 and B11₃24.Each of these four loci in population were contributed by all the four parents,and all the allele frequencies were high.Among them,Cypress contributed early heading date allele at DTH3 locus,whereas contributed late heading date allele at Ghd8 locus.Conclusion: Diverse heading date genes/QTLs between indica and japonica subpopulations responded to short-day and long-day length,and haplotype-level association mapping was more powerful than SNP-level association in nature population.The four way MAGIC population in our study have abundant genetic diversity,high allele frequency and low population structure.And the association mapping at bin level have more resolution compared with association mapping at SNP level.Our study illustrated MAGIC population was more valuable for breeding and genetic studies.