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

Abstract

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.

Novel Alleles for Combined Drought and Heat Stress Tolerance in Wheat

“…Three of the genomic regions, located on chromosome 4A, 6B, and 7B, were associated with grain weight for the heat response under drought, harvest index, biomass, screenings, and leaf water potential. QTL for grain weight under single and combined drought and heat stress colocated with the QTL on chromosomes 6B and 7B (Valluru et al, 2017;Garcia et al, 2019;Qaseem et al, 2019) and QTL for harvest index and biomass were previously found under heat conditions on chromosome 7B (Qaseem et al, 2019). Using two QTL were reported, mainly wheat accessions from China, for grain number at all three regions (Shi et al, 2017;Sun et al, 2017).…”

“…Six other QTL associated with grain weight were detected under well-watered, rainfed, or heat conditions Valluru et al, 2017;Wang et al, 2017;Qaseem et al, 2018) and coincided with the QTL for grain weight under DH and the heat response under drought on chromosome 3B, 5B, and the long arm of chromosome 6B (QGWp.adh-3B.1, QGWp.adh-3B.2, QGWp.adh-5B, QGWt.ara-6B.7, QGWp.ara-6B.3). The QTL on the long arm of chromosome 6B also co-located with QTL for harvest index under combined drought and heat stress (Garcia et al, 2019) as well as single grain weight and leaf chlorophyll content under heat (Shirdelmoghanloo et al, 2016). Regions on chromosome 3B co-located with QTL for tiller number under combined drought and heat stress, grain number, biomass, and harvest index under well-watered conditions (Qaseem et al, 2018), while the region on chromosome 7A coincided with QTL for spike length and water-soluble carbohydrates (Gao et al, 2015;Dong et al, 2016;Sun et al, 2017).…”

“…For the GWAS, diversity panels composed of a total of 315 spring wheat accessions were evaluated in two independent experiments in 2016 and 2017. The two panels represented a reduced set of the panel described in Garcia et al (2019) and differed in 110 accessions between both years due to identity issues, missing genotypic data, or late maturing types in 2016 ( Supplementary Table 1). Accessions with uncertain identity were excluded from the analysis in 2016, resulting in a subset of 273 lines.…”

“…Genotyping and the population structure analysis of the original diversity panel are described in Garcia et al (2019). A total of 563 accessions were genotyped using the wheat iSelect 90K SNP genotyping array (Wang et al, 2014).…”

Gains through selection for grain yield in a winter wheat breeding program

“…Grain yield is a complex trait controlled mainly by many loci with small effects [11–13] and this makes yield more difficult to examine than disease resistance. Improvement in grain yield, however, remains the prime emphasis of many wheat breeding programs [14], and with that, it is necessary to measure gains achieved through different breeding and selection strategies.…”