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Association genetics in elite cultivated barleys

Accurate knowledge of the genomic location of genes controlling important agronomic traits is a prerequisite for the successful deployment of molecular marker technology within a breeding programme. Barley cultivated germplasm has accumulated a large phenotypic and genetic variation through generations of crossing and selection during the breeding process. Our strategy is to use such a wealth of biodiversity stored in populations of barley to fine-map traits of economic and agronomic interest. Our major focus is to precisely locate genomic regions underlying complex traits such as yield and grain quality, thus helping breeders to produce new cultivars better adapted to growing conditions.

Figure 1: Barley trials for the AGOUEB project at the Institute (2008)

Figure 1: Barley trials for the AGOUEB project at the Institute (2008)

The majority of important agronomic traits are controlled by Quantitative Trait Loci (QTL). Classic approaches to QTL mapping involve bi-parental populations developed specifically for the occasion and benefit from large Linkage Disequilibrium (LD) expanding several cM. However, by using only two parental lines, results are difficult to extrapolate to current cultivated germplasm and large progenies are needed in order to precisely locate the genomic regions controlling QTLs of interest.

QTL mapping can also be done in natural populations (association genetics) representative of the cultivated gene-pool. In order to fine-map traits of interest association genetics benefits from the break-down of LD through the recombination events accumulated during decades of breeding practise. In bi-parental populations, association between loci (LD) is mainly caused by genetic linkage while in natural populations other forces, such as subjacent population structure, are also involved shaping LD between markers and the phenotype. These forces have to be identified and corrected for in the analysis as they can cause false positives. To achieve our goals, appropriate statistical approaches, good marker genome coverage, and bioinformatics tools are used.

Evaluation and understanding of the forces that have generated and shaped present genetic and phenotypic diversity in UK and European elite barley germplasm.
Use and evaluation of distinct statistical resources for whole genome association scans to fine map quantitative trait loci, QTLs, for agronomic traits of interest.
Use and develop genetics and genomics resources to produce molecular markers to use in molecular breeding framework.

Figure 2: Whole genome scan for yield.

Figure 2: Whole genome scan for yield. Barley chromosomes on the X-axis and LOD scores (strength of the association) on the Y-axis.

We have three main distinct association mapping approaches with distinct purposes, although all of them have used the same high-throughput genotyping platform (1536 Single Nucleotide Polymorphism molecular markers). Therefore, the three projects are interconnected and will benefit from each others results.

1) AGOUEB (Association Genetics of UK and European Barley). The main aim of this proposal is the detailed genetic resolution of the genomic regions that control economically important traits in elite UK barley through association mapping to link phenotypic data to marker genotypes. The project takes advantage of recent developments in barley genomic research and modern marker technology to rapidly generate genotypic data that can be related to the wealth of phenotypic data that has been generated through the official UK barley trialling system since the unified testing system was introduced with effect from 1993.

2) MABDE (Mapping Adaptation of Barley to Drought Environments). A sample of barley cultivars and landraces representative of the cultivated barley within the Mediterranean rim has been used to identify genomic regions involved in yield adaptability and abiotic stress adaptation. Extensive phenotypic and environmental data has been collected for a series of 28 trials in Italy, Spain, UK, Jordan, Turkey, Syria, Algeria and Morocco in 2004 and 2005.

3) ExBARDIV (Genomics-Assisted Analysis and Exploitation of Barley Diversity). The central goal of this project is to establish an incremental association mapping approach based different population types for the discovery of new gene alleles in wild barley (Hordeum vulgare ssp. spontaneum), which can be exploited for crop breeding. Genomic regions of interest will be firstly identified in a collection of elite barley cultivars, to proceed with map saturation and fine-mapping in wild barley germplasm.


Areas of Interest

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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.