Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map

Abstract

BackgroundPearl millet (Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) R. Br) is an important cereal and fodder crop in hot and arid environments. There is great potential to improve pearl millet production through hybrid breeding. Cytoplasmic male sterility (CMS) and the corresponding nuclear fertility restoration / sterility maintenance genes (Rfs) are essential tools for economic hybrid seed production in pearl millet. Mapping the Rf genes of the A4 CMS system in pearl millet would enable more efficient introgression of both dominant male-fertility restoration alleles (Rf) and their recessive male-sterility maintenance counterparts (rf).ResultsA high density linkage map based on single nucleotide polymorphism (SNP) markers was generated using an F2 mapping population and genotyping-by-sequencing (GBS). The parents of this cross were ‘ICMA 02777’ and ‘ICMR 08888’, which segregate for the A4 Rf locus. The linkage map consists of 460 SNP markers distributed mostly evenly and has a total length of 462 cM. The segregation ratio of male-fertile and male-sterile plants (3:1) based on pollen production (presence/absence) indicated monogenic dominant inheritance of male-fertility restoration. Correspondingly, a major quantitative trait locus (QTL) for pollen production was found on linkage group 2, with cross-validation showing a very high QTL occurrence (97%). The major QTL was confirmed using selfed seed set as phenotypic trait, though with a lower precision. However, these QTL explained only 14.5% and 9.9% of the phenotypic variance of pollen production and selfed seed set, respectively, which was below expectation. Two functional KASP markers were developed for the identified locus.ConclusionThis study identified a major QTL for male-fertility restoration using a GBS-based linkage map and developed KASP markers which support high-throughput screening of the haploblock. This is a first step toward marker-assisted selection of A4 male-fertility restoration and male-sterility maintenance in pearl millet.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1267-8) contains supplementary material, which is available to authorized users.

A unified strategy for West African pearl millet hybrid and heterotic group development

“…The A 4 male-fertility restoration genes are most likely dominantly monogenically inherited, according to Gupta et al (2012) and phenotypic data from Pucher et al (2018). However, the same study of Pucher et al (2018) identified major fertility restoration and maintenance QTLs for pollen production and selfed seed set, which explained only 14.5 and 9.9% of the phenotypic variance, respectively. This led to the conclusion that minor or modifying genes are also present.…”

“…However, screening of OPVs for fertility restoration ability is challenging and still incomplete (Rai, Kulkarni, Thakur, Haussmann, & Mgonja, 2006). More recently published research suggests screening WA germplasm for A 4 male-fertility restoration genes or transferring them via backcrossing into WA-adapted material with pure phenotypic or better marker-assisted selection (Gupta, Rai, Govindaraj, & Rao, 2012;Pucher et al, 2018). The A 4 male-fertility restoration genes are most likely dominantly monogenically inherited, according to Gupta et al (2012) and phenotypic data from Pucher et al (2018).…”

“…More recently published research suggests screening WA germplasm for A 4 male-fertility restoration genes or transferring them via backcrossing into WA-adapted material with pure phenotypic or better marker-assisted selection (Gupta, Rai, Govindaraj, & Rao, 2012;Pucher et al, 2018). The A 4 male-fertility restoration genes are most likely dominantly monogenically inherited, according to Gupta et al (2012) and phenotypic data from Pucher et al (2018). However, the same study of Pucher et al (2018) identified major fertility restoration and maintenance QTLs for pollen production and selfed seed set, which explained only 14.5 and 9.9% of the phenotypic variance, respectively.…”

“…This led to the conclusion that minor or modifying genes are also present. Nevertheless, Pucher et al (2018) developed Kompetitive allele specific polymerase chain reaction (KASP) markers for male fertility restoration in the A 4 CMS system that can be applied in marker-assisted pearl millet hybrid breeding.…”

“…Pearl millet breeders can already use a few A 4 maintainer hybrid parents that are available for WA (Pucher et al, 2018). The fertility restoration KASP markers still need to be validated but have the potential to facilitate the development of distinct male and female heterotic groups by allowing the breeder to focus on other relevant restorer and maintainer characteristics like pollen shedding and seed set or seed size.…”