Research Article: Genome-wide association mapping of grain yield in a diverse collection of spring wheat (Triticum aestivum L.) evaluated in southern Australia

Date Published: February 4, 2019

Publisher: Public Library of Science

Author(s): Melissa Garcia, Paul Eckermann, Stephan Haefele, Sanjiv Satija, Beata Sznajder, Andy Timmins, Ute Baumann, Petra Wolters, Diane E. Mather, Delphine Fleury, Aimin Zhang.


Wheat landraces, wild relatives and other ‘exotic’ accessions are important sources of new favorable alleles. The use of those exotic alleles is facilitated by having access to information on the association of specific genomic regions with desirable traits. Here, we conducted a genome-wide association study (GWAS) using a wheat panel that includes landraces, synthetic hexaploids and other exotic wheat accessions to identify loci that contribute to increases in grain yield in southern Australia. The 568 accessions were grown in the field during the 2014 and 2015 seasons and measured for plant height, maturity, spike length, spike number, grain yield, plant biomass, HI and TGW. We used the 90K SNP array and two GWAS approaches (GAPIT and QTCAT) to identify loci associated with the different traits. We identified 17 loci with GAPIT and 25 with QTCAT. Ten of these loci were associated with known genes that are routinely employed in marker assisted selection such as Ppd-D1 for maturity and Rht-D1 for plant height and seven of those were detected with both methods. We identified one locus for yield per se in 2014 on chromosome 6B with QTCAT and three in 2015, on chromosomes 4B and 5A with GAPIT and 6B with QTCAT. The 6B loci corresponded to the same region in both years. The favorable haplotypes for yield at the 5A and 6B loci are widespread in Australian accessions with 112 out of 153 carrying the favorable haplotype at the 5A locus and 136 out of 146 carrying the favorable haplotype at the 6A locus, while the favorable haplotype at 4B is only present in 65 out of 149 Australian accessions. The low number of yield QTL in our study corroborate with other GWAS for yield in wheat, where most of the identified loci have very small effects.

Partial Text

Wheat is the second most important cereal crop worldwide [1]. It is also the most important crop in Australia, with grain production of about 25 million tonnes per year. With a growing world population and increasing consumption per capita, food production needs to increase by 70% to be able to meet the demands projected for 2050[2]. This would require increasing annual wheat yield by at least 1.6% per year, which is substantially higher than historical rates of yield increase for wheat, estimated at about 1% per year. Given that climate change is expected to significantly increase temperatures in wheat production regions [3–4], it is critical to improve the crop’s ability to increase grain yield with less water [5]. This is particularly challenging in regions where drought and heat are endemic, such as southern Australia.

Many studies aimed at mapping yield related QTL in wheat biparental populations in dry and hot climates (reviewed in [6]), and there have been several attempts to map yield loci through GWAS [40–43]. Domestication and selection create a genetic bottleneck by removing low-frequency alleles, decreasing variation, increasing LD and creating linkage drag [44]. This is particularly true for self-pollinating species like wheat. By exploiting broad genetic diversity, GWAS attempts to overcome this problem.




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