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.)

• Published in: Rice (New York, N.Y.) N.Y.), 2020-02, Vol.13 (1), p.11-11, Article 11
• Main Authors: Li, Pingbo, Zhou, Hao, Yang, Hanyuan, Xia, Duo, Liu, Rongjia, Sun, Ping, Wang, Quanxiu, Gao, Guanjun, Zhang, Qinglu, Wang, Gongwei, He, Yuqing
• Format: Article
• Language: English
• Subjects: Agriculture; Biomedical and Life Sciences; Cloning; CMS-HL; CMS-WA; Cytoplasmic male sterility; Fertility; Genes; Genomes; Germplasm; GWAS; Haplotype analysis; Haplotypes; Life Sciences; Loci; Male sterility; Original; Original Article; Plant breeding; Plant Breeding/Biotechnology; Plant Ecology; Plant Genetics and Genomics; Plant Sciences; Population studies; Populations; Restoration; Rf genes; Rice; Subgroups
• ISSN: 1939-8425; 1939-8433; 1934-8037
• DOI: 10.1186/s12284-020-0372-0

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.