Association studies and marker development for the fertility restorer gene Rf1 in sunflower

Abstract

Fertility restoration is an essential part of hybrid breeding based on cytoplasmic male sterility. In sunflower, the CMS PET1 originating from an interspecific hybridization between Helianthus petiolaris and H. annuus is world-wide used in hybrid breeding. The restorer gene Rf1 is responsible for restoring fertility in the hybrids by specifically reducing the co-transcript of atp1 and the CMS-specific orfH522 in the anthers. From the mode of action (differences in RNA stability) Rf1 could be a pentatricopeptide repeat gene. Blasting BAC-end sequences and sequences of markers linked to the restorer gene Rf1 two physical locations (encompassing 30 Mb and 3.9 Mb, respectively) on linkage group 13 could be identified in the sunflower genome sequence of HanXRQ. These two regions contained nine possible candidate genes for Rf1: seven pentatricopeptide repeat genes, one aldehyde dehydrogenase and one poly(A) polymerase 3 gene. Using a next generation sequencing approach, the nine candidate genes were sequenced with 120 x coverage in an association panel of 59 lines (27 maintainer and 32 restorer lines) and 210 single nucleotide polymorphisms (SNPs) as well as 67 insertions/deletions (InDels) could be identified.