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Background  Wild-abortive cytoplasmic male sterility (CMS-WA) and Honglian CMS (CMS-HL) are the two main CMS types utilized in production of three-line hybrid rice in  xian / indica  ( XI ) rice. Dissection of the genetic basis of fertility restoration of CMS-WA and CMS-HL in the core germplasm population would provide valuable gene and material resources for development of three-line hybrid combinations.    Results  In this study, two F 1  populations with CMS-WA and CMS-HL background respectively were developed using 337  XI  and  aus  accessions being paternal parents. Genome-wide association studies on three fertility-related traits of the two populations for two consecutive years revealed that both fertility restoration of CMS-WA and CMS-HL were controlled by a major locus and several minor loci respectively. The major locus for fertility restoration of CMS-WA was co-located with  Rf4 , and that for fertility restoration of CMS-HL was co-located with  Rf5 , which are cloned major  restorer of fertility  ( Rf ) genes. Furthermore, haplotype analysis of  Rf4 ,  Rf5  and  Rf6 , the three cloned major  Rf  genes, were conducted using the 337 paternal accessions. Four main haplotypes were identified for  Rf4 , and displayed different subgroup preferences. Two main haplotypes were identified for  Rf5 , and the functional type was carried by the majority of paternal accessions. In addition, eight haplotypes were identified for  Rf6 .    Conclusions  Haplotype analysis of three  Rf  genes,  Rf4 ,  Rf5  and  Rf6 , could provide valuable sequence variations that can be utilized in marker-aided selection of corresponding genes in rice breeding. Meanwhile, fertility evaluation of 337 accessions under the background of CMS could provide material resources for development of maintainer lines and restorers.

rice

Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.)