Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information.

Muhammad Azhar Nadeem,Sezai Ercişli,Rüştü Hatipoğlu,Faheem Shehzad Baloch,Tolga Karaköy,Gonul Comertpay,Ephrem Habyarimana,Muhammad Qasim Shahid,Mehmet Zahit Yeken,Vahdettin Çiftçi,Muhammad Amjad Nawaz,Fawad Ali,Gyuhwa Chung,Zhengfeng Wang

doi:10.1371/journal.pone.0205363

Abstract

Turkey presents a great diversity of common bean landraces in farmers’ fields. We collected 183 common bean accessions from 19 different Turkish geographic regions and 5 scarlet runner bean accessions to investigate their genetic diversity and population structure using phenotypic information (growth habit, and seed weight, flower color, bracteole shape and size, pod shape and leaf shape and color), geographic provenance and 12,557 silicoDArT markers. A total of 24.14% markers were found novel. For the entire population (188 accessions), the expected heterozygosity was 0.078 and overall gene diversity, Fst and Fis were 0.14, 0.55 and 1, respectively. Using marker information, model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 188 accessions into two main populations A (predominant) and B, and 5 unclassified genotypes, representing 3 meaningful heterotic groups for breeding purposes. Phenotypic information clearly distinguished these populations; population A and B, respectively, were bigger (>40g/100 seeds) and smaller (<40g/100 seeds) seed-sized. The unclassified population was pure and only contained climbing genotypes with 100 seed weight 2–3 times greater than populations A and B. Clustering was mainly based on A: seed weight, B: growth habit, C: geographical provinces and D: flower color. Mean kinship was generally low, but population B was more diverse than population A. Overall, a useful level of gene and genotypic diversity was observed in this work and can be used by the scientific community in breeding efforts to develop superior common bean strains.

Highlights

Common bean (Phaseolus vulgaris L.) is one of the most ancient grain legumes of America [1,2–3], and is an important proteinaceous staple food for more than 300 million people [4]
P. coccineus commonly known as scarlet runner bean is close relative of common [7] and 3rd most economically important bean species after common bean and P. lunatus [8]
A diversity panel was assembled consisting of natural populations of 177 common bean landraces and 6 commercial cultivars with 5 scarlet runner bean landraces collected by a group of researchers (Baloch FS and Ciftci V) from various farmers’ fields in different geographical provinces across Turkey

Summary

Introduction

Common bean (Phaseolus vulgaris L.) is one of the most ancient grain legumes of America [1,2–3], and is an important proteinaceous staple food for more than 300 million people [4]. It is a self-pollinated crop with a small genome size of 587 Mbs [5]. P. coccineus commonly known as scarlet runner bean is close relative of common [7] and 3rd most economically important bean species after common bean and P. lunatus [8]. Runner bean is a climbing perennial crop but often grown as annual crop for green pod production [6]

Objectives

Methods

Findings

Conclusion