ASSOCIATION GENETICS APPROACHES FOR THE IDENTIFICATION OF GENES ASSOCIATED TO BARLEY AGRONOMIC TRAITS IN A MEDITERRANEAN ENVIRONMENT
Creators: name: MOHAMMED MOHAMMED ELBADRY, NADER
Publisher: name: Universit� degli Studi di Milano
Year: 2013

description: Barley (Hordeum vulgare) is one of the four most economically important cereal crops worldwide. It serves as a major animal feed crop, with smaller amounts used for malting and in health food. Among environmental factors influencing barley production, drought is recognized as the most common in the Mediterranean area and this problem is expected to worsen with on-going climate changes. Breeding for drought resistance is therefore an important objective to ensure stable crop yields. In this context, genetic and molecular dissection of drought tolerance is expected to lead to the identification of key genes/loci and favourable alleles through exploration of biodiversity. Association genetics focuses on the identification of links between phenotypic traits and genetic markers with the aim to identify QTLs and locate the underlying genes in the genome. In general, different barley genotypes are expected to carry different loci at genomic regions of interest. The probability of chromosomal recombination between two loci is proportional to the physical distance between those loci. General objective of this project was the identification of loci subtending major agronomic traits under different water regimes, using an association genetics approach. To this end, we considered a phenotypic panel consisting of 83 barley cultivars representing European diversity for drought tolerance. This germplasm collection included 2 and 6 rows winter and spring barleys, that were previously evaluated for plant height, flowering time and yield under irrigated and rainfed conditions over three successive years (Rizza et al., 2004). At the beginning of this project, an initial objective was to evaluate the potential association between allelic variants of candidate genes (CGs) selected for their known roles in drought responses and phenotypic variation for barley grain yield under different watering regimes. Thus, we re-sequenced an initial set of 3 CGs -HvCbf2, HvCbf4a and HvCbf7- and we identified 4 Single Nucleotide Polymorphisms (SNPs) in the coding region of HvCbf4a. In parallel, we tried to assess the genetic diversity and structure of our barley panel by utilizing the low cost molecular marker approach of Amplified Fragment Length Polymorphism (AFLP). Incorporation of structure information in association analysis is important to prevent recovery of false associations. However, when we run structure analyses using our AFLP data, we failed to recover the classical barley subdivisions reported in the literature indicating that these markers may not be reliable for our purposes. For this reason and considering the limited chances of detecting association with few CGs, we took advantage of the recently established iSELECT Infinium� Illumina 9k SNP platform (Comadran et al., 2012) to carry out a Genome Wide Association Study (GWAS) on our barley panel. Filtering out the monomorphic and failed-genotyped markers resulted in the identification of a total of 4,661 SNPs distributed over the 7 barley chromosomes. Population stratification was investigated with a subset of 260 SNPs selected as highly informative using admixture model implemented in Structure software. Accordingly, three main subgroups were identified corresponding to winter-2rows, winter-6rows and spring-2rows barleys, respectively. Association between barley genotypic data and flowering date (FD) was processed using general linear model and afterward compared with mixed linear model. Quantitative Trait Loci (QTLs) controlling grain yield (GY), flowering date (FD), and plant height (PH) were identified using the general linear model. Our results provide a starting point for the identification of potentially useful genes and markers for future applications in barley breeding schemes.