Research Article: Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris)

Date Published: January 31, 2019

Publisher: Public Library of Science

Author(s): Tania Gioia, Giuseppina Logozzo, Stefania Marzario, Pierluigi Spagnoletti Zeuli, Paul Gepts, Tzen-Yuh Chiang.


Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA and include both dry bean and snap beans for the fresh and processing markets. Through population structure, principal components analyses, cluster analysis, and discriminant analysis of principal components (DAPC), Andean and Mesoamerican genotypes as well as most American commercial type classes could be distinguished. The genetic relationship among the commercial cultivars revealed by the SSR markers was generally in agreement with known pedigree data. The Mesoamerican cultivars were separated into three major groups—black, small white, and navy accessions clustered together in a distinct group, while great northern and pinto clustered in another group, showing mixed origin. The Andean cultivars were distributed in two different groups. The kidney market classes formed a single group, while the green bean accessions were distributed between the Andean and Mesoamerican groups, showing inter-gene pool genetic admixture. For a subset of 24 SSR markers, we compared and contrasted the genetic diversity of the commercial cultivars with those of wild and domesticated landrace accessions of common bean. An overall reduction in genetic diversity was observed in both gene pools, Andean and Mesoamerican, from wild to landraces to advanced cultivars. The limited diversity in the commercial cultivars suggests that an important goal of bean breeding programs should be to broaden the cultivated gene pool, particularly the genetic diversity of specific commercial classes, using the genetic variability present in common bean landraces.

Partial Text

Common bean (Phaseolus vulgaris L.) is a crop plant cultivated worldwide and one of the most important grain legumes in terms of total yield and cultivated area (Food and Agriculture Organization of the United Nations (FAO) It is grown for its green pods and immature and/or dry seeds and is a primary source of protein in the human diet in both developing and developed countries. According to FAO data (, common bean world production in 2016 was estimated at 27 million metric t for dry bean production, and at 23.5 million t for green bean. In the United States, dry bean is grown on about 630,743 ha with a total annual production of 1,269,916 t and an average yield of 2.01 t ha-1, while green bean is grown on about 11,330 ha with a total annual production of 41,640 t and an average yield of 3.67 t ha-1 (

This is the first report of the analysis of genetic relationships among a large sample of common bean advanced cultivars widely grown in North America using SSR markers. SSR markers used in the present study were appropriate to provide a first overview of the genetic diversity levels and of the population structure within the common bean cultivars.




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