Evaluation and Utilization of Biodiversity in Triticeae for Wheat lmprovement

To adapt new varieties to a wide spectrum of environments breeders and farmers have emphasized the need for broadening the current narrow genetic base of modern varieties of important cereal crops such as wheat and barley. In response to this need, several thousand samples of indigenously cultivated Triticeae species and their wild relatives have been collected from the centers of diversity. However, gene bank collections are of little use if they are not evaluated and the information disseminated widely. Evaluation is essentially the link between conservation and use. Some of the collected material has been evaluated at the International Center for Agricultural Research in the Dry Areas (!CARDA) in Syria. In the past cereal breeders were averse to using germ plasm that after years of work yielded uncertain results. However, in recent years they have begun to successfully utilize non-conventional germplasm (wild/alien and obsolete forms) in their crossing blocks. The substantial progress at !CARDA in the evaluation and utilization of Triticeae germplasm for crop improvement in the low rainfall areas of West Asia and North Africa is described

Generation and exploitation of EST-derived SSR markers for assaying molecular diversity in durum wheat populations

Durum wheat [Triticum turgidum L. subsp. turgidum convar. durum (Desf.) MK] is an important cereal crop economically and nutritionally in the Central Asia and Caucasian, West Asia, and North Africa (CWANA) regions. Durum landraces and improved lines are largely grown in this region. Its genetic diversity has been studied using different molecular markers. The increasing availability of expressed sequence tags (ESTs) in wheat (Triticum aestivum) and related cereals provides a valuable resource of non-anonymous DNA markers to study durum diversity. In this study, a set of 517,319 Triticum aestivum EST sequences was employed for the identification of wheat simple sequence repeats called microsatellites (W-eSSRs) with the help of a PERL5 script called MISA. In comparison, barley microsatellites (B-eSSRs) have been used to exploit their transferability to durum wheat. Newly developed W-eSSR markers were probed on the 115 recombinant inbred lines (RIL) of the International Triticeae Mapping Initiative (ITMI) population (Opata 85 × Synthetic 7984). The polymorphic eSSRs were mapped. To examine the potential of the two types of eSSRs markers, 12 W-eSSR markers and 13 B-eSSR markers were used to fingerprint 153 wheat genotypes. Our results indicate that: (1) B-eSSRs show a high level of transferability to wheat, (2) the developed W-eSSRs are significantly polymorphic than those derived from genomic regions, (3) new W-eSSRs were identified and integrated in the ITMI genetic linkage map and, (4) B-eSSR and W-eSSRs are providing additional markers for comparative mapping following gene introgressions from wild species and carrying out evolutionary studies

Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage

Drought tolerance is a key trait for increasing and stabilizing barley productivity in dry areas worldwide. Identification of the genes responsible for drought tolerance in barley (Hordeum vulgare L.) will facilitate understanding of the molecular mechanisms of drought tolerance, and also facilitate the genetic improvement of barley through marker-assisted selection or gene transformation. To monitor the changes in gene expression at the transcriptional level in barley leaves during the reproductive stage under drought conditions, the 22K Affymetrix Barley 1 microarray was used to screen two drought-tolerant barley genotypes, Martin and Hordeum spontaneum 41-1 (HS41-1), and one drought-sensitive genotype Moroc9-75. Seventeen genes were expressed exclusively in the two drought-tolerant genotypes under drought stress, and their encoded proteins may play significant roles in enhancing drought tolerance through controlling stomatal closure via carbon metabolism (NADP malic enzyme, NADP-ME, and pyruvate dehydrogenase, PDH), synthesizing the osmoprotectant glycine-betaine (C-4 sterol methyl oxidase, CSMO), generating protectants against reactive-oxygen-species scavenging (aldehyde dehydrogenase,ALDH, ascorbate-dependent oxidoreductase, ADOR), and stabilizing membranes and proteins (heat-shock protein 17.8, HSP17.8, and dehydrin 3, DHN3). Moreover, 17 genes were abundantly expressed in Martin and HS41-1 compared with Moroc9-75 under both drought and control conditions. These genes were possibly constitutively expressed in drought-tolerant genotypes. Among them, seven known annotated genes might enhance drought tolerance through signalling [such as calcium-dependent protein kinase (CDPK) and membrane steroid binding protein (MSBP)], anti-senescence (G2 pea dark accumulated protein, GDA2), and detoxification (glutathione S-transferase, GST) pathways. In addition, 18 genes, including those encoding Δl-pyrroline-5-carboxylate synthetase (P5CS), protein phosphatase 2C-like protein (PP2C), and several chaperones, were differentially expressed in all genotypes under drought; thus they were more likely to be general drought-responsive genes in barley. These results could provide new insights into further understanding of drought-tolerance mechanisms in barley

The need for allele mining: perspectives of the System-wide Genetic Resources Programme (SGRP)

The SGRP is a consortium of all CGIAR gene banks. These banks aim to (1) conserve diversity efficiently, including and especially rare alleles and genotypes; (2) ensure efficient use of collection by delivering appropriately selected subsets of germplasm to users, maximizing the chance of giving users the set of alleles or genotypes that they need; and (3) ensure that the entire collection remains available for use. The SGRP exists to ensure a consistent, integrated, system-wide approach to the efficient achievement of these goals

Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley

A ‘core set’ of 28 simple sequence repeat (SSR) and 28 single nucleotide polymorphism (SNP) markers for barley was developed after screening six diverse genotypes (DGs) representing six countries (Afghanistan, Pakistan, Algeria, Egypt, Jordan and Syria) with 50 SSR and 50 SNP markers derived from expressed sequence tags (ESTs). The markers of the core set are single locus with very high quality amplifications, high polymorphism information content (PIC) and are distributed across the barley genome. PIC values for the selected SSR and SNP markers ranged between 0.32–0.72 (average 0.58) and 0.28–0.50 (average 0.42), respectively. To make the SNP genotyping cost effective, CAPS (cleaved amplified polymorphic sequence) and indel assays were developed for 23 markers and the remaining 5 SNP markers were optimized for pyrosequencing. A high coefficient of correlations (r = 0.96, P < 0.005) between the genetic similarity matrices of SSR and SNP genotyping data of the core set on diverse genotypes (DGs) and their similar groupings according to the geographical distribution in both SSR and SNP phenograms with high bootstrap values underline the utility and reliability of the core set. A comparative allelic and sequence diversity for SSR and SNP markers between the DGs and six elite parental genotypes (PGs) of mapping populations showed comparable diverse nature of two germplasm sets. However, unique SNPs and indels were observed in both germplasm sets providing more datapoints for analysing haplotypes in a better way for the corresponding SNP marke

Mining the chickpea composite collection for allelic variation

Chickpea, Cicer arietinum L., is believed to have originated in south-east Turkey. However, at present, the major chickpea-growing countries are India, Pakistan, Iran, Turkey, Australia, Ethiopia, and Mexico. Chickpea is a leguminous food crop, self-pollinating, and diploid. Its gene pool consists of 43 species: one annual cultivated (i.e. chickpea), eight annual wild, and 34 perennial wild species. Two types of chickpea are known: desi types with coloured flowers, and angular-shaped and dark-coloured seeds, primarily grown in South Asia and Africa; and kabuli types with white flowers, owl’s head-shaped and beige-coloured seeds, and grown mostly in Mediterranean countries. To study the allelic richness and diversity associated with beneficial traits, a composite set of 3000 chickpea germplasm accessions was constituted. This set included the chickpea core collection, old and new cultivars and traitspecific germplasm accessions from ICRISAT and accessions representing the ICARDA collection

Assessment of EST-microsatellites markers for discrimination and genetic diversity in bread and durum wheat landraces from Afghanistan

Accurate and reliable means for identification are necessary to assess the discrimination between landraces of tetraploid wheat [T.␣turgidum L. subsp. durum (Desf.) Husn.] and hexaploid wheat (T. aestivum L. em. Thell.). In Afghanistan, farmers usually cultivate mixed landraces, and thus distinction between bread and durum is difficult. A set of 18 microsatellites derived from the DuPont EST-database were used to describe genetic diversity in a sample of 82 Afghan wheat landraces. A total of 101 alleles were detected, with allele number per locus ranging from 2 to 13, and a mean allele number of 6.31. The percentage of polymorphic loci was 89%. The EST-SSRs markers showed different level of gene diversity: the highest Polymorphism Information Content value (0.921) was observed with DuPw 221. Our results demonstrated that with a reasonable number of expressed sequences target microsatellites (EST-SSRs) it is possible to discriminate between T. durum and T. aestivum species of wheat germplasm. Our results showed that EST-databases could be a useful source for species-specific markers and have the potential for new genic microsatellites markers that could enhance screening germplasm in gene banks