Resequencing the barley exome to identify genes controlling plant adaptation to environment.

Barley development and actual yield is strongly affected by a number of environmental stress factors that can prevent the plant from expressing its maximum genetic potential. Indeed abiotic stresses (temperatures, drought, anaerobiosis and soil salinity) are often responsible for severe grain losses although they have driven the evolution and the wide distribution of the genus Hordeum in temperate, subtropical and arctic areas. We present a new resource to dissect natural allelic variation at candidate genes controlling key adaptive traits in barley, based on a collection of 500 accessions assembled in the context of the EU-FP7-WHEALBI (Wheat and Barley Legacy for Breeding Improvement) project. The collection comprises 227 old and elite cultivars, 238 landraces and 35 wild barleys (H. spontaneum) from a wide geographical range. Winter and spring nurseries (common garden trials) have been carried out in 4 contrasting environments (Scotland, North Italy, Hungary and Central Anatolia in Turkey, in this last site under both rainfed and irrigated conditions) and several phenological and morphological traits have been evaluated. Moreover, a comprehensive molecular variant analysis by exome sequencing (exome capture arrays) has been carried out, resulting in more than 2 million SNPs and InDels. Plant growth habit and heading-date are the basic traits involved in barley adaptation to the environment since they allow synchronize life cycle with seasonal changes. Several genes involved in these key adaptive traits have been characterized and they can serve as a proof of concept to validate the effectiveness of WHEALBI resource in mining new functional alleles. To this purpose allelic diversity of candidate genes has been evaluated in wild, landraces and cultivated barley to determine the extent of haplotype diversity and build haplotype networks. The genetic diversity of barley CBF and Vrn-H1, two key loci responsible for frost tolerance, have been explored in 403 barley accessions using the exome sequencing information. This dataset along with curated annotation of the CBF genes provided the means to identify unique SNP variants in HvCBF genes and predict functional effects at the protein level. A large proportion of these SNPs were observed in the gene pool of barley landraces and wild relatives, only being fixed in the cultivated germplasm. Similarly, examining diversity at the winter allele of Vrn-H1, from Hordeum vulgare cv. Strider, as reference, several unknown deletions of this gene were identified as well as one accession with two copies of Vrn-H1 gene. To date, the genetic variants (SNPs and CNVs) of coding sequences developed and validated in this project are a snapshot of the existing genetic variability of barley, which will enable the research community to mine interesting alleles for other traits and exploit the untapped genetic diversity of barley. [ABSTRACT FROM AUTHOR]