Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.)

Varshney, R K and Paulo, M J and Grando, S and Eeuwijk, F A van and Keizer, L C P and Ceccarelli, S and Kilian, A and Baum, M and Graner, A (2012) Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.). Field Crops Research, 126 (1). 171-180 . ISSN 0378-4290

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Abstract

Genome wide association (GWA) analysis of yield, yield components, developmental, physiological and anatomical traits was conducted for a barley germplasm collection consisting of 185 cultivated (Hordeum vulgare L.) and 38 wild (Hordeum spontaneum L.) genotypes, originating from 30 countries of four continents. Phenotypic evaluations were performed at a dry (Breda) and wet (Tel Hadya) location in Syria. Genome wide association study was done with 816 markers comprised of 710 diversity array technology (DArT), 61 single nucleotide polymorphism (SNP) and 45 microsatellite or simple sequence repeat (SSR) markers. Diversity analysis revealed 5 groups of germplasm, related to origin (Middle East, North Africa), structural information (two-rows), and domestication (wild versus domesticated). Linkage disequilibrium (LD) decayed after 3 cM with a few exceptions at 10 and 15 cM. Although a few QTLs were identified that differed between the dry and wet site, these QTLs explained low phenotypic variation and could not unequivocally be related to drought tolerance when compared to earlier linkage mapping based QTL analysis studies. Therefore, GWA analysis seems to be not very effective for identification of major QTLs for complex traits like drought tolerance in highly structured germplasm collections.

Item Type:	Article
Divisions:	UNSPECIFIED
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Genome wide association analysis; Diversity Array Technology (DArT); Single nucleotide polymorphisms (SNPs); Simple sequence repeats (SSRs); Barley
Subjects:	Others > Genetics and Genomics
Depositing User:	Users 6 not found.
Date Deposited:	29 Nov 2011 06:18
Last Modified:	16 Sep 2013 09:54
URI:	http://oar.icrisat.org/id/eprint/4456
Official URL:	http://dx.doi.org/10.1016/j.fcr.2011.10.008
Projects:	GTZ project
Funders:	Bundesministerium für Wirtschaftliche Zusammenarbeit und Entwicklung, Centre for BioSystems Genomics, Generation Challenge Programme
Acknowledgement:	Thanks are due to Ms. U. Beier for her excellent technical assistance. This research work was financially supported by a GTZ project (no. 2002.7860.6-001.00 and contract no. 1060503) sponsored by BMZ (Bundesministerium für Wirtschaftliche Zusammenarbeit und Entwicklung), Germany. Work by M.J. Paulo and F.A. van Eeuwijk was (co)financed by the Centre for BioSystems Genomics (CBSG) which is part of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research, and by the Generation Challenge Program/IBP project 2.2.1.
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