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

BMC Plant Biology Molecular evaluation of orphan Afghan common wheat (Triticum aestivum L.) landraces collected by Dr. Kihara using single nucleotide polymorphic markers Alagu Manickavelu 0 Abdulqader Jighly 1 Tomohiro Ban 0 0 Kihara Institute for Biological Research, Yokohama City University , Yokohama 244-0813 , Japan 1 International Centre for Agricultural Research in the Dry Areas (ICARDA) , P. O. Box 5466, Aleppo , Syria Background: Landraces 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. Results: A 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. Conclusion: The 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. Afghan wheat landraces; Botanical varieties; Genetic diversity; Population structure; Single nucleotide polymorphism - Background Wheat (Triticum aestivum) is the third most important cereal crop worldwide in terms of production and the most important in terms of calorie consumption, with overall production increasing year after year [1]. However, in developing countries such as Afghanistan, wheat production has declined steadily, an alarming trend in countries already struggling to meet basic food demands. 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 simply used elite varieties developed by private or international agricultural research centres. Regardless of the approach taken, identifying important alleles and other genetic information present in existing gene pools will be necessary to achieve optimal crop yields. Moreover, the establishment of self-driven germplasm activities is more sustainable, as this approach utilises native landraces, which are well suited to local environments. 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 not only to crop centres of origin, but also to new environments following transplantation. Afghanistan is the third largest centre of origin for domesticated crops worldwide [3], having played an important role in the domestication of wheat, barley (Hordeum vulgare), chickpeas (Cicer arietinum), peas (Pisum sativum), and rye (Secale cereale). However, frequent armed conflicts and other factors have led this country to lose all known germplasm collections developed to date. Fortunately, one long-running scientific expedition led by Dr. Hitoshi Kihara and others between 1950 and 1970 established an extensive Afghan wheat landraces collection, which is now housed in Japan. While other Afghan wheat collections do exist, the collection of landraces found in the Kihara Institute for Biological Research, Japan is thought to be unique in terms of the number of sites visited, the diversity of their environmental conditions, and the overall number of landraces collected [4]. Moreover, in contrast to other landraces, those of this collection are thought to be homozygous, since they were allowed to propagate by self-pollination over the course of several generations of genotypic studies. The genetic diversity contained within may therefore hold significant potential for both Afghanistan and beyond; however, significant work is needed to characterize these samples fully. The recent development of molecular markers and high throughput systems has revealed a wealth of genotypic information for a wide variety of crops and plants [5,6]. Among these, single nucleotide polymorphisms (SNPs) are the most common type of sequence variation in the genome [7], making them well suited for genomics approaches requiring a high number of markers, such as association mapping [8] and genomic selection [9]. High-throughput SNP genotyping platforms have long been available for diploid crops such as maize [10] and barley [11], and SNP arrays were developed recently for wheat [12,13]. SNP analysis has been used successfully to characterize rice landraces [14]; however, similar work in other landrace collections, such as wheat, has been minimal [15]. Here 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. Results and discussion The Kihara Afghan wheat landrace (KAWLR) collection and its importance Although 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 [16-18]. Over the past few decades, significant efforts (...truncated)