Genetic diversity and population structure analysis based on the high density SNP markers in Ethiopian durum wheat (Triticum turgidum ssp. durum)

Admas Alemu,Tileye Feyissa,Tesfaye Letta,Bekele Abeyo

doi:10.1186/s12863-020-0825-x

Abstract

BackgroundEthiopia has been considered as a center of diversity and the second possible center of domestication of durum wheat. Genetic diversity and population structure analysis in the existing Ethiopian durum wheat germplasm have enormous importance in enhancing breeding effort and for sustainable conservation. Hence, 192 Ethiopian durum wheat accessions comprising 167 landraces collected from major wheat-growing areas of the country and 25 improved varieties released from Debre Zeit and Sinana Agricultural Research Centers, Ethiopia in different years (1994–2010) were assembled for the current study.ResultsThe panel was genotyped with a High-density 90 K wheat SNP array by Illumina and generated 15,338 polymorphic SNPs that were used to analyze the genetic diversity and to estimate the population structure. Varied values of genetic diversity indices were scored across chromosomes and genomes. Genome-wide mean values of Nei’s gene diversity (0.246) and polymorphism information content (0.203) were recorded signifying the presence of high genetic diversity within this collection. Minor allele frequency of the genome varied with a range of 0.005 to 0.5 scoring a mean value of 0.175. Improved varieties clustered separately to landraces in population structure analysis resulted from STRUCTURE, PCA and neighbor joining tree. Landraces clustering was irrespective of their geographical origin signifying the presence of higher admixture that could arise due to the existence of historical exchanges of seeds through informal seed system involving regional and countrywide farming communities in Ethiopia.ConclusionsSustainable utilization and conservation of this rich Ethiopian durum wheat genetic resource is an irreplaceable means to cope up from the recurrent climate changes and biotic stresses happening widely and thereby able to keep meeting the demand of durum productivity for the ever-growing human population.

Highlights

Ethiopia has been considered as a center of diversity and the second possible center of domestication of durum wheat
Higher number polymorphic Single nucleotide polymorphism (SNP) markers were recorded on B genome (9013 SNPs) than the A genome (6325 SNPs) in Ethiopian durum wheat accessions (Fig. 1-b)
Clustering analysis showed a higher genetic admixture between landraces despite their geographic origin resulted from the existence of higher rate of historical seed exchange throughout the country

Summary

Introduction

Ethiopia has been considered as a center of diversity and the second possible center of domestication of durum wheat. 192 Ethiopian durum wheat accessions comprising 167 landraces collected from major wheat-growing areas of the country and 25 improved varieties released from Debre Zeit and Sinana Agricultural Research Centers, Ethiopia in different years (1994–2010) were assembled for the current study. Up to recent time, agricultural research centers and institutions have been involved in collecting and conserving Ethiopian durum wheat landrace accessions in the country. Vavilov [4] and Zohary [15] reported the presence of high genetic diversity in Ethiopian durum wheat and recent studies specified uniqueness of Ethiopian durum landraces form the Fertile Crescent collections (primary center of domestication) and considered as the possible second center of domestication for the crop [3]. In Ethiopia, durum wheat is commonly planted on heavy black clay soils (vertisols) of the highlands between 1800 and 2800 masl [23]

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Conclusion