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.

Fig. 1

A consensus genetic map comprising 339 loci. Markers are shown on right side of the LG while map distances are indicated on left side. Each LG is divided into several bins based on 10-cM interval. The markers unique to mapping populations, common between two, three, four and five mapping populations have been shown by green, red, brown, blue and black colour, respectively. QTLs are indicated by bars with different colours. Blue, green, pink, white and yellow coloured bars were used to show the QTLs derived from populations TTB 7 × ICP 7035, ICPA 2039 × ICPR 2447, ICPA 2043 × ICPR 2671, ICPA 2043 × ICPR 3467 and ICP 8863 × ICPL 20097, respectively

Fig. 2

Scatter plots showing the extent of correlations among consensus genetic map and population-specific genetic maps. The marker integrated from different populations viz. ICP 8863 × ICPL 20097, ICPA 2039 × ICPR 2447, ICPA 2043 × ICPR 2671, ICPA 2043 × ICPR 3467, TTB 7 × ICP 7035 and ICPB 2049 × ICPL 99050 are shown by red triangles, pink triangles, purple squares, blue diamonds, light-green diamonds and yellow circles, respectively

Fig. 3

This depicts the marker-based correspondences for LG06, among consensus and individual genetic maps. Only common markers i.e. landmarks are included to visually asses the co-linearity of marker orders and marker positions. LGs are aligned together using comparative mapping programme CMap version 1.01. Figure can also be found at http://www.cmap.icrisat.ac.in/cmap/sm/pp/bohra/

Fig. 4

Comparison of marker order between the consensus and inter-specific genetic map based on ICP 28 × ICPW 94 mapping population. Consensus LGs are on left side while inter-specific LGs are on right side. Common loci are indicated by red colour, while unique loci are shown by blue colour