Genetic Diversity within Snap Beans and Their Relation to Dry Beans.

Lyle Wallace,Haidar Arkwazee,James Myers,Kelly Vining

doi:10.3390/genes9120587

Lyle Wallace, Haidar Arkwazee + Show 2 more

Open Access

https://doi.org/10.3390/genes9120587

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Journal: Genes	Publication Date: Nov 28, 2018
Citations: 29	License type: CC BY 4.0

Affiliation: Oregon State University, University of Sulaymaniyah

Abstract

Two hundred forty-six snap bean genotypes and 49 dry beans representing both centers of domestication and six bean races with materials from Europe, Asia, and the Americas were genotyped using a single nucleotide polymorphism (SNP) array. The data was analyzed for expected heterozygosity, K-means clustering, principal components, phylogenetic relationships, and population substructure. When all gene pools of snap bean were assembled, the expected heterozygosity was roughly equivalent to a carefully chosen panel of dry beans representing all bean races and centers of domestication demonstrating the genetic richness of snap materials in total. K-means clustering and K = 2 structure analysis showed significant mixing of gene pools in the European and American commercial snap materials and the dominance of the Andean center of domestication among commercial contemporary snap beans. Conversely, the same analysis showed that Chinese, Iberian, and heirloom materials were underrepresented in contemporary materials. Further, Structure analysis revealed eight distinct groups within snap beans. Two showed strong kinship to the Middle American center of domestication, three to the Andean center of domestication, and three showed admixture between the two centers. Snap beans may have been independently derived from dry beans more than once and from both centers. Overall, we identified eight potential germplasm pools for snap bean.

Highlights

Phaseolus vulgaris appears to have split from its nearest relatives approximately 1.3 million years ago (MYA) based on ribosomal internal transcribed spacer sequence data [1]
The first source of materials was the Common Bean Coordinated Agricultural Project (BeanCAP) snap bean diversity panel [24], consisting of 141 bush habit snap beans and 8 pole habit snap beans that were mostly derived from commercial bean lines in North America and Europe
There is a surprising degree of agreement between the deep basal branching of phylogenetic trees, Structure analysis, and multiple other clustering methods regarding the splitting of genotypes into either the Andean or Middle American gene pools, much of the other basal branching can be confused

Summary

Introduction

Phaseolus vulgaris appears to have split from its nearest relatives approximately 1.3 million years ago (MYA) based on ribosomal internal transcribed spacer sequence data [1]. The available evidence strongly points towards Middle America as the ultimate origin of P. vulgaris where all the nearest relatives of P. vulgaris are localized. This origin hypothesis has been complicated by new evidence that P. vulgaris may have originated in Middle America but the ancestral form of the species underwent further speciation through allopatry in the Amotape–Huancabamba Depression of the Andes [2]. Humans domesticated P. vulgaris within each of these gene pools nearly simultaneously in a dual event at ~8000 BP These concurrent domestications of the same species in two geographically distinct regions has resulted in a great phylogenetic divide in domesticated beans whose existence is supported by evidence from multiple sources.

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