Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.)

Abstract

BackgroundFrost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure.ResultsGWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress.ConclusionsHaplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance.

Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley

“…The germplasm panel consisted of 41 six-and two-row type varieties with different growth habit that were previously characterized for response to low-temperature stress in several field and laboratory experiments (Rizza et al 2011). Moreover, some of them were already characterized for adaptation to Mediterranean environments (Visioni et al 2013). The majority of genotypes originated from 11 European countries while ten were from Australia (1), Syria (2), Turkey (5) and USA (2) (Supplementary Table 1).…”

“…In temperate cereals serious damages to plant cells and tissues are caused by intracellular or extracellular ice formation during the freeze events (Levitt 1980), and cold winters with large temperature fluctuations may result in severe winterkill. In view of possibly higher and faster temperature variations, expectedly due to climate change, improving fast resilience to frost is fundamental for minimizing the so-called yield gap (the gap between potential and actual yield), increasing yield stability, and guaranteeing crop sustainability (Rizza et al 2011;Visioni et al 2013). During the last 10 years, barley has been extensively used as a model system for genetic dissection of low temperature tolerance in fall-sown cereals (Pecchioni et al 2012).…”

Haplotype‐based genotyping‐by‐sequencing in oat genome research

“…Hence, the testing of combinations of multiple marker systems is the most pragmatic approach (Hamblin and Jannink, 2011). Similar empirical GWAS comparisons between haplotype and SNP markers in other crops and animal studies showed mixed results, but the majority of studies reported that haplotype-based GWAS was superior (Hamblin and Jannink, 2011;Lorenz et al, 2010;Visioni et al, 2013).…”

Systematic selection and validation of appropriate reference genes for gene expression studies by quantitative real-time PCR in pear

“…Increasing the stress resistance of pear will improve its production and quality (Chang et al 2012b). However, studies on plant stress resistance have focused on crops including Arabidopsis, tomato and barley (Jakab et al 2005;Jiang et al 2012;Pandey et al 2011;Visioni et al 2013). Understanding the expression patterns of some key genes in the stress tolerance pathway of the pear would give insight into the mechanisms that underlie the processes from germination to harvest, and may help to reveal the changes in gene expression under various conditions.…”