Development and use of chloroplast microsatellites in Phaseolus spp. and other legumes

Abstract

Chloroplast microsatellites (cpSSRs) provide a powerful tool to study the genetic variation and evolution of plants. We have investigated the usefulness of 39 primer pairs tagging cpSSR loci on a set of eight different genera of Leguminosae (Papilionoideae subfamily) and five species belonging to the genus Phaseolus. Thirty-six 'universal' primer pairs were retrieved from the literature, one was re-designed and a further two were designed de novo. The cpSSR loci analysed were highly polymorphic across the individuals examined. Twenty-seven primer pairs were polymorphic in the overall sample, 18 within Phaseolus, and 16 in both P. vulgaris and P. coccineus. Analysis of the plastome sequences of four Leguminosae species (obtained from GenBank) showed that in the loci targeted by universal primer pairs: (i) the originally tagged cpSSRs can be lost; (ii) other cpSSRs can be present; and (iii) polymorphism arises not only from differences in the numbers of cpSSR repeats, but often from other insertion/deletion events. Multilocus linkage disequilibrium analysis suggests that homoplasy is not a major problem in our dataset, and principal component analysis indicates intelligible relationships among the species considered. Our study demonstrates that this set of chloroplast markers provides a useful tool to study the diversity and the evolution of several legumes, and particularly P. vulgaris and P. coccineus.

Origin of year-long bean (Phaseolus dumosusMacfady, Fabaceae) from reticulated hybridization events between multiplePhaseolusspecies

“…It should be noted that there is a discrepancy between the numbers of markers analysed in each genome, with fewer derived from the cpDNA. However, our results are in agreement with those proposed following analysis of cpSSRs (Angioi et al, 2009;Desiderio et al, 2013), which suggests that our study assessed sufficient plastid markers to draw valid inferences. Interestingly, results based on the nuclear genome reflect sympatric associations: wild P. dumosus more closely resembles the Guatemalan accessions of P. coccineus than those of any other locality.…”

Genomics of Origin, Domestication and Evolution of Phaseolus vulgaris

“…Two independent domestication events in the Americas have been documented in several studies, and a large set of coherent data have been obtained using different approaches based on molecular markers and morphological characteristics (Gepts et al 1986;Gepts and Bliss 1988;Koenig and Gepts 1989;Gepts and Debouk 1991;Singh et al 1991a, b, c;Becerra Velasquez and Gepts 1994;Freyre et al 1996;Tohme et al 1996;Gepts 1998;Delgado-Salinas et al 1999;Papa and Gepts 2003;Blair et al 2006a, b;Diaz and Blair 2006;Angioi et al 2009a;Rossi et al 2009;Nanni et al 2011;Blair et al 2012;Bitocchi et al 2013). These two independent domestication events, one in Mesoamerica and one in the Andes, gave origin to two major domesticated gene pools (Papa et al 2006;Acosta-Gallegos et al 2007;Angioi et al 2009a). Following domestication, the domesticated gene pools of the common bean appear to have been organized into four Mesoamerican (Durango, Jalisco, Mesoamerica, Guatemala) and three Andean (Nueva Granada, Peru, Chile) races (Singh et al 1991c;Beebe et al 2000Beebe et al , 2001.…”

“…The lack of a cytoplasmic bottleneck in Europe is somewhat surprising, because cpSSR markers are very sensitive indicators of such phenomena, due to their uniparental inheritance, hypervariabilty and haploidy (Provan et al 2001;Ebert and Peakall 2009;Angioi et al 2009a). The most likely explanation for this is that the founding common bean populations that colonized Europe were highly variable in their cytoplasmic DNA or that different releases may have had different source populations.…”

“…A powerful method for the detection of hybridization events is the integration of cytoplasmic and nuclear analyses (Provan et al 2001;Ebert and Peakall 2009;Angioi et al 2009a). Using this approach Angioi et al (2010) found that at least 33 % of the landraces in the collection were hybrids.…”

Mesoamerican origin of the common bean ( Phaseolus vulgaris L.) is revealed by sequence data

“…These two gene pools are characterized by partial reproductive isolation (3,4), and they are seen in both wild and domesticated materials. They have been recognized in several studies based on morphology (5-7), agronomic traits (7), seed proteins (8), allozymes (9), and different types of molecular markers (10)(11)(12)(13)(14)(15), which have given the overall indication of the occurrence of at least two independent domestication events in the two different hemispheres. The existence of these two geographically distinct and isolated evolutionary lineages that predate the domestication of the common bean represents a unique scenario among crops.…”