Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers.

Haiping Qiang,Zhengli Zhang,Zhihong Chen,Zan Wang,Xuemin Wang,Hongwen Gao,Zhengfeng Wang

doi:10.1371/journal.pone.0124592

Haiping Qiang, Zhengli Zhang + Show 5 more

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https://doi.org/10.1371/journal.pone.0124592

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Abstract

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding.

Highlights

Cultivated tetraploid alfalfa (Medicago sativa subsp. sativa L.), a perennial autotetraploid (2n = 4x = 32) and cross-pollinated forage legume, is the most important cultivated forage plant in the world [1]
Nine accessions from China were obtained from National Herbage Germplasm Bank of China; two accessions from Syria, one from Libya and one accession from Sudan were provided by the Institute of Animal Science, Chinese Academy of Agricultural Science (Beijing, China); the other 62 accessions were provided by the USDA National Plant Germplasm System (NPGS)
Bf111 and bf644149, both located on the chromosome 2, shared the highest and lowest genetic diversity respectively, with the value of 0.901 and 0.283 in the He while 0.893 and 0.273 in polymorphism information content (PIC) (S2 Table)

Summary

Introduction

The objectives of this study were to estimate the genetic diversity, and population structure of a worldwide collection of cultivated tetraploid alfalfa. Chromosomes 2 and 3 had the highest genetic diversity which revealed by the allele number, He and PIC (Table 1). A Neighbor-joining tree of 336 alfalfa genotypes was constructed using Nei’s genetic distance and five clusters I, II, III, IX, and V were identified (Fig 3).

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