Extension of the core map of common bean with EST-SSR, RGA, AFLP, and putative functional markers

Abstract

Microsatellites and gene-derived markers are still underrepresented in the core molecular linkage map of common bean compared to other types of markers. In order to increase the density of the core map, a set of new markers were developed and mapped onto the RIL population derived from the ‘BAT93’ × ‘Jalo EEP558’ cross. The EST-SSR markers were first characterized using a set of 24 bean inbred lines. On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7. In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced. With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust. The distribution of the markers over 11 linkage groups is discussed and a newer version of the common bean core linkage map is proposed.

Saturation of an Intra-Gene Pool Linkage Map: Towards a Unified Consensus Linkage Map for Fine Mapping and Synteny Analysis in Common Bean

“…Also, a consensus map using three populations of Brassica napus producing a highly saturated map with 5,162 genetic markers [54]. In addition, the length of our consensus map is 2,041 cM, slightly higher than single maps of DB and BJ populations and previous maps reports [6], [7], [8], [9], [27], [28]. Consensus maps with increased map size have been reported with other species [23], [55], [56].…”

Linkage disequilibrium based association mapping of micronutrients in common bean (Phaseolus vulgaris L.): a collection of Jammu & Kashmir, India

“…74 SSRs (Genomic and Geneic) with known positions on 11 chromosomes were used (Yu et al 2000;Gaitan-Solis et al 2002;Grisi et al 2007;Hanai et al 2010;Co´rdoba et al 2010). Out of 74 SSRs only 55 SSRs were polymorphic and these 55 SSRs were considered for further analysis (Supplementary Table 1).…”

Morphological and genetic diversity among and within common bean (Phaseolus vulgaris L.) landraces from the Campania region (Southern Italy)

“…We analyzed three plants per landrace. Ten SSR loci were used for PCR amplification (Buso et al, 2006;Gaitan-Solis et al, 2002;Grisi et al, 2007;Hanai et al, 2010;Yu et al, 2000). SSR features, primer sequences and annealing temperature (T a ) are reported in Supplementary Table 1.…”