An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations

Abstract

Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750 kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59–140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6 cM have been constructed. Using these four genetic maps together with two recently published intra-specific genetic maps, a consensus map was constructed, comprising of 339 SSR loci spanning a distance of 1,059 cM. Furthermore, quantitative trait loci (QTL) analysis for fertility restoration (Rf) conducted in three mapping populations identified four major QTLs explaining phenotypic variances up to 24 %. To the best of our knowledge, this is the first report on construction of a consensus genetic map in pigeonpea and on the identification of QTLs for fertility restoration. The developed consensus genetic map should serve as a reference for developing new genetic maps as well as correlating with the physical map in pigeonpea to be developed in near future. The availability of more informative markers in the bins harbouring QTLs for sterility mosaic disease (SMD) and Rf will facilitate the selection of the most suitable markers for genetic analysis and molecular breeding applications in pigeonpea.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-012-1916-5) contains supplementary material, which is available to authorized users.

Molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea (Cajanus cajan (L.) Millsp.)

“…In order to compare QTLs detected in Bohra et al (2012) with the present findings, we have extracted bacterial artificial chromosome (BAC)-end sequences for corresponding SSRs and mapped to present GBS data. Interestingly majority of the major QTLs detected in Bohra et al (2012) were collocated with the present study on CcLG08 (ESM Table 4). Comparative analysis between above-mentioned studies has further enhanced our confidence in this region at CcLG08.…”

“…Subsequently SSR marker-based genetic map was developed by Bohra et al (2011). Soon after this, intra-specific genetic maps were also generated using SSR markers with relatively very low marker density (Gnanesh et al 2011; Bohra et al 2012). SNP-based genotyping assays were also deployed for genetic map construction using inter-specific (Saxena et al 2012) and intra-specific mapping populations (Kumawat et al 2012).…”

“…Previously published results of mapping the restoration of fertility in A4 cytoplasm were achieved with the use of three F 2 mapping populations comprising of 188 individuals each (Bohra et al 2012). A similar number of F 2 individuals were used for the development of GBS-based genetic map in the present study.…”

“…Further identification of molecular markers tightly linked to Rf would enhance the breeding efficiency by enabling the classification of inbred lines or germplasm as either maintainer (B-line) or restorer (R-line) without field evaluation of their test crosses; and it would also permit their rapid backcross transfer of Rf in elite inbred lines. A simple sequence repeat (SSR) marker-based study has reported the identification of QTLs for Rf in pigeonpea with large inter-marker distance in low-density genetic maps (Bohra et al 2012). Therefore, it is highly required to develop a moderate-density genetic map that can provide tightly associated markers with Rf.…”

Conventional and Molecular Approaches towards Genetic Improvement in Pigeonpea for Insects Resistance

“…The large numbers of SSR markers [2,68,69], DArT markers [31], SNPs [70] and ESTs [68] hold high promise for improvement of a number of economic traits in pigeonpea. Availability of more than 3000 SSR markers facilitated development of inter-as well as intra-specific genetic maps using several F 2 mapping populations [69,71]. This represents the first instance of merging multiple genetic maps in pigeonpea.…”