Molecular evaluation of orphan Afghan common wheat (Triticum aestivum L.) landraces collected by Dr. Kihara using single nucleotide polymorphic markers.

Alagu Manickavelu,Abdulqader Jighly,Tomohiro Ban

doi:10.1186/s12870-014-0320-5

Abstract

BackgroundLandraces are an important source of genetic diversity in common wheat, but archival collections of Afghan wheat landraces remain poorly characterised. The recent development of array based marker systems, particularly single nucleotide polymorphism (SNP) markers, provide an excellent tool for examining the genetic diversity of local populations. Here we used SNP analysis to demonstrate the importance of Afghan wheat landraces and found tremendous genetic diversity and province-specific characteristics unique to this geographic region.ResultsA total of 446 Afghan wheat landraces were analysed using genotype by sequencing (GBS) arrays containing ~10 K unique markers. Pair-wise genetic distance analyses revealed significant genetic distances between landraces, particularly among those collected from distanced provinces. From these analyses, we were able to divide the landraces into 14 major classes, with the greatest degree of diversity evident among landraces isolated from Badakhshan province. Population-based analyses revealed an additional 15 sub-populations within our germplasm, and significant correlations were evident in both the provincial and botanical varieties. Genetic distance analysis was used to identify differences among provinces, with the strongest correlations seen between landraces from Herat and Ghor province, followed closely by those between Badakhshan and Takhar provinces. This result closely resembles existing agro-climatic zones within Afghanistan, as well as the wheat varieties commonly cultivated within these regions. Molecular variance analysis showed a higher proportion of intra-province variation among landraces compared with variation among all landraces as a whole.ConclusionThe SNP analyses presented here highlight the importance and genetic diversity of Afghan wheat landraces. Furthermore, these data strongly refute a previous analysis that suggested low genetic diverse within this germplasm. Ongoing analyses include phenotypic characterisation of these landraces to identify functional traits associated with individual genotypes. Taken together, these analyses can be used to help improve wheat cultivation in Afghanistan, while providing insights into the evolution and selective pressures underlying these distinct landraces.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0320-5) contains supplementary material, which is available to authorized users.

Highlights

Landraces are an important source of genetic diversity in common wheat, but archival collections of Afghan wheat landraces remain poorly characterised
We examined a large, yet poorly characterized wheat landrace collection from Afghanistan to determine the genetic diversity, population structure, and other characteristics associated with genetic polymorphisms
The Kihara Afghan wheat landrace (KAWLR) collection and its importance the importance of landraces in terms of both conservation and utilisation remain controversial [2], much of this uncertainty stems from the lack of reliable data regarding the use and implementation of these resources [16,17,18]

Summary

Introduction

Landraces are an important source of genetic diversity in common wheat, but archival collections of Afghan wheat landraces remain poorly characterised. In order to achieve sustainable production goals, most national programs have begun either exploiting existing natural diversity to identify strains suitable for specific regions or climates or have used elite varieties developed by private or international agricultural research centres. Landraces have been identified as distinct, locallyadapted species with a high capacity to tolerate biotic and abiotic stresses, resulting in higher sustainable yields, as well as intermediate yields under low input agricultural conditions [2]. Populations such as these arose as a result of both natural and artificial selection, adapting to crop centres of origin, and to new environments following transplantation

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