Significant association of the novel Rf4-targeted SNP marker with the restorer for WA-CMS in different rice backgrounds and its utilization in molecular screening

Abstract

In the rice cytoplasmic-genetic male sterility (CMS) system, the combination of a CMS line, maintainer line and restorer line carrying the restorer gene to restore fertility, is indispensable for the development of hybrids. However, the process of screening for the trait of fertility restoration is laborious and time consuming. In the present study, we analyzed the nucleotide sequence of the Rf4 gene, which is the major locus controlling fertility restoration, to identify allele-specific variation. A SNP A/C at +474 in the CDS was found to be capable of strictly distinguishing groups of alleles Rf4 (A) and rf4 (C). Using KASP genotyping, this valuable SNP was converted to an allele-specific PCR marker. We evaluated and validated the marker among three-line parents with different backgrounds, and the results revealed a complete correlation between SNP alleles and the fertility restoration phenotype. Molecular screening was subsequently carried out for the presence of alleles of Rf4 and Rf3 among 328 diverse rice cultivars with worldwide distribution. The results demonstrate that this SNP marker could be the optimal choice for the molecular identification of potential restorers.

Choice of microsatellite markers for isolation of fertility restorers of wild abortive (WA) type cytoplasmic male sterility in rice

“…These four primer pairs are specific to the chromosomes known to harbor fertility restorer genes. Among the two fertility restorer genes known to be involved infertility restoration of WA type CMS system in rice, the effect of Rf4 located on chromosome 10 is stronger than the effect of Rf3 located on chromosome 1 and additive effect of these two fertility restorer genes leads to effective fertility restoration (Cai et al 2013;Huang et al 2014;Chen et al 2017). Some of these primers in combinations with other primer pairs have also been used in earlier studies for classification of fertility restorers from non-restorers (Alavi et al 2009;Ghara et al 2012).…”

“…The pollen parents are considered as fertility restorers, if a high level of pollen fertility and spikelet fertility restoration is observed in test crosses (Priyanka et al 2016). Recently, molecular markers have also been used by several researchers for tagging of fertility restorer genes and classification of pollen parents into the categories of sterility maintainers and fertility restorers (Huang et al 2014;Chen et al 2017). Amongst the several classes of molecular markers, microsatellite markers are regarded as the most amenable markers for various applications in rice due to their extensive genome coverage, multi-allelic nature, high reproducibility, codominant inheritance, abundance and simple reproducible assays.…”

A review of rice male sterility types and their sterility mechanisms

“…At present, the sown area of three-line hybrid rice based on cytoplasmic male sterility accounts for more than half of the sown area of hybrid rice. However, the backbone male sterile lines and restorer lines of Chinese three-line hybrid rice mainly belong to two heterosis groups, such as South Asia, Southeast Asia medium indica ecotype and South China early indica ecotype, and the recovery spectrum is narrow [ 104 ]. Recently reported that FA182 is a new cytoplasmic source which is different from the existing restoration and maintenance relationship, and has the characteristics of complete sporophytic sterility and single fertility restoration gene [ 105 , 106 ].…”

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.)

“…Therefore, selection of Rf genes is of great importance in development of threeline hybrid rice. Some markers have been developed for Rf4 in previous studies (Chen et al 2017, Suresh et al 2012, Tang et al 2014. In this study, the haplotypes of three Rf genes viz Rf4, Rf5 and Rf6 have been systematically classified using 337 accessions that covering the majority variation of XI and aus accessions worldwide, providing valuable sequence variations for the development of co-segregating markers (Additional file 2: Table S3-S4, Fig.…”