Association Mapping Of QTL For Heading Date And Plant Height Using Magic Populations And Germplasm Of Rice

The heading date(HD)and plant height(PH)are important agronomic traits in rice.HD determines the regional adaptability and seasonal adaptability of rice in different ecological regions.Appropriate growth of PH can effectively improve biomass thus further increase rice yield on the base of keeping lodging resistance in the stage of maturity.Association analysis was performed to map QTL for HD and PH using 3 multi-parents advanced generation inter-cross(MAGIC)populations including 2 four parents-and 1 eight parents-derived populations(DC1,DC2 and 8way)and their compound populations(DC12=DC1+DC2,RMPRIL=DC12+8way)derived from 8 elite indica lines,and SNP genotypic data of Rice 55 K SNP chips.A total of 2412 germplasm materials(including 1386 indica and 674 japonica rice)which were selected from 3000 rice germplasm resources collected from 89 countries and regions,and 400,000 SNP markers were used for association analysis to verify the mapping results of MAGIC populations.The main results in this study were summarized as follows:1.Using the phenotypic data of HD and PH collected from two sites(Jiangxi and Shenzhen)in consecutive two years(2015 and 2016),and SNP genotypic data of Rice 55 K SNP chips,3 HD QTL(qHD3,qHD6 and qHD8)were identified and located in the same regions of DTH3,Hd3 a and Ghd8,respectively.And 5 PH QTL(qPH1.1,qPH1.2,qPH1.3,qPH4 and qPH6)were also identified,of which qPH1.1and qPH1.2 were located in the adjacent regions of Psd1 and sd1.The other 3 PH QTL were new loci which were detected only in one population and one environment.Different MAGIC populations differed in mapping efficacy for HD and PH,i.e.,eight parents-derived populations such as 8way,DC12 and RMPRIL not only detected more HD and PH QTL(5,5 and 6)than four parents-derived populations such as DC1 and DC2(2 and 4),but also had higher mapping resolution than the four parents-derived populations did,showing obvious advantage in two aspects of QTL detection: more highly significant level and more close to the known genes.Especially,joint analyses of different populations such as DC12 and RMPRIL had significant advantage in QTL mapping over other populations.Therefore,for further gene cloning and marker-assisted breeding of previously identified QTL,it is a preferred alternative to choose more parents-derived population.2.Genome-wide association analysis were conducted using the phenotypic data of HD and PH collected from two sites(Hainan and Shenzhen)in consecutive two years(2015 and 2016),and genotypic data of 400,000 SNP.We identified 13 QTL associated with HD and 12 QTL associated with PH.And the number of QTL in the whole population were significantly higher than those in indica(1386)and japonica(687).Mapping results of PH and HD differed in subgroups and whole natural population,probably resulting from:(1)different regulation pathways of HD and PH in different subgroups;and(2)sample size and population structure.3.Three major QTL,q HD3,qHD6 and qHD8 affecting HD,which were simultaneously detected in the MAGIC population and germplasm resources,were located in the same regions of the known HD genes DTH3,Hd3 a and Ghd8,respectively.Similarly,two QTL qPH1.1 and qPH1.2,which were detected in the MAGIC population and germplasm resources,were adjacent to the known genes Psd1 and sd1,respectively.Above mentioned five QTL were identified in different populations and environments,showing independence of the genetic background and environment and great usefulness in marker-assisted selection of rice variety with suitable PH and HD.