| The reciprocal introgression lines(ILs)and recombinant inbred lines(RILs)developed from the cross between Xuishui09,a high quality late japonica variety,and IR2061,a drought resistant indica variety,were genotyped by 55 K SNP chip and evaluated grain quality including milling quality,appearance quality,cooking and eating quality and nutritional quality traits in Sanya and Shenzhen to dissect population genetic structure,and to identify genetic background independent and environment stable QTL that would be benefical for molecular breeding of rice quality.At same time,we also carried out an association analysis to identify QTL affecting nine rice grain appearance and milling quality traits using a diverse panel of 258 accessions selected from 3K Rice Genome Project and evaluated in Sanya and Shenzhen and take advantage of high density of SNP data from 3K RGP to infer candidate genes.The main studied results are summarized as follows:1.The genetic structure of XS09-ILs and IR2061-ILs.The introgression frequency reciprocal ILs population including XS09 background introgression lines(XS09-ILs)population and IR2061 background introgression lines(IR2061-ILs)population was analyzed by 25,206 polymorphic SNP markers from a 55 K SNP chip.The results indicated that more than half of the SNP markers were distorted segregated.The average introgression frequency of donor allele in both two populations was lower than the expected value,and the average introgression frequency in IR2061-ILs was higher than in XS09-ILs.The donor alleles can be introgressed at all marker loci.However,the introgression frequency between different chromosomes and the different loci within each chromosome were inconsistent.The result provided valuable information of the introgression characters of target region that should be considered in breeding practice.2.QTL identification for rice quality traits using XS09-ILs,IR2061-ILs and RILs.QTL linkage mapping was conducted for rice quality related traits evaluated in Sanya(SY)and Shenzhen(SZ)using 237 XS09-ILs,240 IR2061-ILs and 235 RILs genotyped by 25,206 polymorphic SNP.In total,71 QTL were detected in three populations across two environments,including 57 QTL for rice milling and appearance quality traits and 14 QTL for rice eating and cooking and nutritional traits.Among them,38 QTL(53.5%)were commonly detected in both SY and SZ,which indicated that around half QTL for rice quality related traits appeared to be more or less environment-specific.In XS09-ILs,IR2061-ILs and RILs populations,19(54%),24(52%)and 16(40%)QTL were commonly dectected in both environments,respectively,indicating QTL for rice quality related traits had strong genetic background effect.Seven QTL affecting rice quality related traits including qGL5,qGL7.2,qGW12,qGW2/qGLWR2.2,qGW5/qGLWR5/qPGWC5,qGLWR2.1,qAC6/qGC6/qDEC6/qPGWC6 were commonly detected under three populations in both environments.These genetic background independent and environmental stable QTL could be used to marker assisted breeding of rice quality through genetic selection or pyramiding.3.GWAS and gene-based association mapping for rice quality traitsWe carried out an association analysis to identify QTL affecting rice quality traits using a diverse panel of 258 accessions and evaluated in two environments SY and SZ.Using 22,488 high quality SNP,in total,91 QTL affecting rice grain quality traits were identified.Combined gene-based association and haplotype analyses plus functional annotation allowed us to shortlist 28 candidate genes for 11 important QTL regions.The candidate genes included four cloned genes(GS3,TUD1,Wx and ALK)and two fine mapped QTL(qGRL7.1 and q PGWC7).This research demonstrated the superior power to shortlist candidate genes affecting complex phenotypes by the strategy of combined GWAS,gene-based association coupled with haplotype analyses.The identified candidate genes provided valuable sources for future functional characterization and genetic improvement of rice quality. |
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