Scientia Agricultura Sinica ›› 2017, Vol. 50 ›› Issue (5): 802-810.doi: 10.3864/j.issn.0578-1752.2017.05.003

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-Wide Association Study of the Fertility Restorer Loci for pol CMS in Rapeseed (Brassica napus L.)

WEI DaYong, TAN ChuanDong, CUI YiXin, WU DaoMing, LI JiaNa, MEI JiaQin, QIANWei   

  1. College of Agronomy and Biotechnology, Southwest University/Chongqing Engineering Research Center for Rapeseed, Chongqing 400716
  • Received:2016-09-23 Online:2017-03-01 Published:2017-03-01

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Abstract: 【Objective】 Polima system of cytoplasmic male sterility (pol CMS) in Brassica napus (rapeseed), controlled by a major gene as well as polygenes, has been widely used in China for hybrid rapeseed breeding. Genome-wide association study (GWAS) was performed in a rapeseed population to identify genetic loci and candidate genes for fertility restorer of pol CMS. 【Method】 301A, a rapeseed pol CMS line, was chosen as the female parent to cross with a panel of 308 accessions in natural population of rapeseed which has been genotyped previously using the 60 K Brassica SNP array. The F1 hybrids were grown for fertility evaluation in 2013 and 2014, respectively, with two replications each year. The fertility of F1 was classified according to pollen fertility and performance of pistil and stamen, and population structure and relative kinship of 308 male accessions were analyzed. GWAS was conducted by associating the fertility of F1 with the single nucleotide polymorphisms (SNPs) of males. Candidate genes was identified from the region of 100 kb each side of the peak SNP or trait-associated SNPs at LD (R2＞0.5). Comparative analysis of QTL and haplotype effect evaluation for candidate genes were performed. 【Result】 A significant difference (P＜0.01) was found in the fertility of F1 between two years, but a high correlation was detected in it between two years (r = 0.52, P＜0.001). The population structure analysis classified the 308 male accessions into three genetic groups (winter, spring and semi-winter). The relative kinships analysis found that 73% of the kinship coefficients between lines were ＜0.1 and 53% were equal to 0. A total of 13 SNPs were detected to be with significant association with the fertility of F1, formed six genetic intervals on chromosomes A01, A09, C03, C06 and C08. Six genes related to fertility were predicted from the six intervals, and four of these could encode the PPR type proteins which is a conserve structure encoded by fertility restorer genes. Collinearity analysis revealed two PPR type candidate genes (BnaA09g46700D and BnaC08g40710D) detected in homoeologous regions between chromosome A09 and C08 were homology with ORF2, an open reading frame functioning as the reported rapeseed nuclear restorer gene of pol CMS. The other two PPR type candidates (BnaC03g45840D and BnaC06g13000D) were novel candidate restorer genes for rapeseed pol CMS, of which the linked alleles or haplotypes of SNPs were found to significantly associated with the fertility level of the F1 (P＜0.001).【Conclusion】The present study identified several fertility restorer genes for pol CMS in rapeseed from both A and C subgenomes. Developing functional markers from the alleles or SNPs linked with the candidate genes will benefit the screening of restorer and maintainer lines in the pol CMS system.

Key words: Brassica napus, polima CMS, fertility restorer gene, GWAS, SNP

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