Functional mapping in pea, as an aid to the candidate gene selection and for investigating synteny with the model legume Medicago truncatula

Abstract

The identification of the molecular polymorphisms giving rise to phenotypic trait variability-both quantitative and qualitative-is a major goal of the present agronomic research. Various approaches such as positional cloning or transposon tagging, as well as the candidate gene strategy have been used to discover the genes underlying this variation in plants. The construction of functional maps, i.e. composed of genes of known function, is an important component of the candidate gene approach. In the present paper we report the development of 63 single nucleotide polymorphism markers and 15 single-stranded conformation polymorphism markers for genes encoding enzymes mainly involved in primary metabolism, and their genetic mapping on a composite map using two pea recombinant inbred line populations. The complete genetic map covers 1,458 cM and comprises 363 loci, including a total of 111 gene-anchored markers: 77 gene-anchored markers described in this study, 7 microsatellites located in gene sequences, 16 flowering time genes, the Tri gene, 5 morphological markers, and 5 other genes. The mean spacing between adjacent markers is 4 cM and 90% of the markers are closer than 10 cM to their neighbours. We also report the genetic mapping of 21 of these genes in Medicago truncatula and add 41 new links between the pea and M. truncatula maps. We discuss the use of this new composite functional map for future candidate gene approaches in pea.

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

“…With advances in model legume sequencing and genomic knowledge, there has been a switch to gene-based markers in pea (Aubert et al, 2006;Jing et al, 2007;Deulvot et al, 2010;Bordat et al, 2011). Recently, a comprehensive transcriptome of pea was published (Franssen et al, 2011), and another RNA-seq atlas is being established at INRA, France (http://bios.dijon.inra.fr).…”

EARLY FLOWERING3 Redundancy Fine-Tunes Photoperiod Sensitivity

“…Several markers used for linkage analysis were modified from gene-based markers described by Aubert et al (2006) and Bordat et al (2011). These markers were supplemented by newly designed markers targeted to introns of appropriate genes identified in the relevant interval of the Medicago truncatula genome (v4.0; www.jcvi.org/medicago/) and also present in pea sequence databases in GenBank (www.ncbi.nlm.nih.gov).…”

Evaluation of SRAP markers for mapping of Pisum sativum L.

“…The length of our map (528.8 cM) is shorter than that of previous ones generated with other molecular markers, which covered 1430, 1458, and 1283 cM, respectively (Loridon et al 2005, Aubert et al 2006, Barilli et al 2010. All these genetic maps were constructed using mapping populations with different sizes, derived from different crosses.…”

“…Different kinds of markers, such as simple sequence repeats (SSR; Loridon et al 2005), single nucleotide polymorphisms (SNP; Deulvot et al 2010), inter simple sequence repeats (ISSR; Mishra et al 2009), and sequence tagged sites (STS; Barilli et al 2010) have been used to develop moderate density linkage maps in pea. Several markers were common in different maps corresponding to different crosses; this allowed an integration of these maps (Loridon et al 2005, Aubert et al 2006, as well as the development of consensus linkage maps for the species (Weeden et al 1998, Bordat et al 2011.…”