Genome-wide association study of production and stability traits in barley cultivated under future climate scenarios

Abstract

Future barley cultivars will have to produce under the constraints of higher temperature in combination with increased concentrations of atmospheric carbon dioxide and ozone as a consequence of climate change. A diverse set of 167 spring barley genotypes was cultivated under elevated levels of temperature (?5°C) and [CO 2 ] (700 ppm) as single factors and in combination as well as under elevated [O 3 ] (100-150 ppb) as single factor. The setting in general resembled changes projected by IPCC (AR5) to take place at the end of this century. A genome-wide association study (GWAS) was performed to identify markers for increased primary production under climate change conditions and reveal possible genes of interest. Phenotyped traits included grain yield, number of grains, number of ears per plant, aboveground vegetative biomass, harvest index and stability of the production parameters over the five applied treatments. The GWAS encompassed 7864 SNP markers (Illumina iselect), a compressed mixed linear model with the GAPIT package, and conservative validation of markers. A total of 60 marker-trait associations [-log 10 (P value) 2.97-5.58] were identified, e.g. grain yield under elevated temperature on barley chromosome 2H, static stability of grain yield on 7H, sites for exploitation of elevated [CO 2 ] on 4H Electronic supplementary material The online version of this article (

Growth response of 98 barley (Hordeum vulgare L.) genotypes to elevated CO2 and identification of related quantitative trait loci using genome‐wide association studies

“…This is partly comparable to the results found by Ingvordsen, Backes, Lyngkjaer, Peltonen‐Sainio, Jahoor, et al. () in their phytotron experiment with potted spring barley genotypes, where the authors found significantly associated loci for possible exploitation of future CO 2 levels on chromosomes 4H and 7H. The vast majority of the markers in our study could be aligned to already mapped barley coding sequences and their known or predicted functions.…”

“…As QTL and gene detection are no longer limited to biparental populations due to the development of high‐throughput genotyping platforms for barley (Waugh, Jannink, Muehlbauer, & Ramsay, ), using GWAS for these purposes became popular in recent years (Rode et al., ; Zhou, Johnson, Ryan, Delhaize, & Zhou, ). With respect to possible growth effects of future atmospheric CO 2 levels GWAS have only recently been applied for barley in a growth chamber experiment (Ingvordsen, Backes, Lyngkjaer, Peltonen‐Sainio, Jahoor, et al., ). As the global CO 2 distribution is homogenous, and as no information about the response of barley to eCO 2 was available, a primary pool of 321 barley accessions was analysed with the 9k iSelect chip (Comadran et al., ).…”

“…With respect to possible growth effects of future atmospheric CO 2 levels GWAS have only recently been applied for barley in a growth chamber experiment (Ingvordsen, Backes, Lyngkjaer, Peltonen-Sainio, Jahoor, et al, 2015). As the global CO 2 distribution is homogenous, and as no information about the response of barley to eCO 2 was available, a primary pool of 321 barley accessions was analysed with the 9k iSelect chip (Comadran et al, 2012).…”

“…GWAS is now commonly used in plant genetic studies to identify Quantitative Trait Loci (QTL) involved in traits of major agronomic importance in barley (Cockram et al., ; Lex, Ahlemeyer, Friedt, & Ordon, ; Rode, Ahlemeyer, Friedt, & Ordon, ) and other major crop species such as soybean (Hwang et al., ), wheat (Edae, Byrne, Haley, Lopes, & Reynolds, ) or maize (Li et al., ). Recently, in a growth chamber study with 167 potted spring barley genotypes, GWAS was performed to identify markers for increased primary production under conditions of changes in climate variables including eCO 2 (Ingvordsen, Backes, Lyngkjaer, Peltonen‐Sainio, Jahoor, et al., ).…”

Genetic studies towards elucidation of drought tolerance of potato

“…The principle of genome wide association mapping is to associate phenotypic variation with genetic markers in populations of unrelated genotypes by exploiting linkage disequilibrium (LD) between markers and QTLs (Malosetti et al 2007;Ersoz et al 2007). Successful application of association mapping for complex traits was demonstrated for amongst others drought tolerance , salt tolerance , and higher temperature and CO2 (Ingvordsen et al 2015). The feasibility of association mapping in tetraploid potato was shown by the detection of marker trait associations for quality traits in potato ).…”