Lessons from a GWAS study of a wheat pre-breeding program: pyramiding resistance alleles to Fusarium crown rot

Abstract

Much has been published on QTL detection for complex traits using bi-parental and multi-parental crosses (linkage analysis) or diversity panels (GWAS studies). While successful for detection, transferability of results to real applications has proven more difficult. Here, we combined a QTL detection approach using a pre-breeding populations which utilized intensive phenotypic selection for the target trait across multiple plant generations, combined with rapid generation turnover (i.e. “speed breeding”) to allow cycling of multiple plant generations each year. The reasoning is that QTL mapping information would complement the selection process by identifying the genome regions under selection within the relevant germplasm. Questions to answer were the location of the genomic regions determining response to selection and the origin of the favourable alleles within the pedigree. We used data from a pre-breeding program that aimed at pyramiding different resistance sources to Fusarium crown rot into elite (but susceptible) wheat backgrounds. The population resulted from a complex backcrossing scheme involving multiple resistance donors and multiple elite backgrounds, akin to a MAGIC population (985 genotypes in total, with founders, and two major offspring layers within the pedigree). A significant increase in the resistance level was observed (i.e. a positive response to selection) after the selection process, and 17 regions significantly associated with that response were identified using a GWAS approach. Those regions included known QTL as well as potentially novel regions contributing resistance to Fusarium crown rot. In addition, we were able to trace back the sources of the favourable alleles for each QTL. We demonstrate that QTL detection using breeding populations under selection for the target trait can identify QTL controlling the target trait and that the frequency of the favourable alleles was increased as a response to selection, thereby validating the QTL detected. This is a valuable opportunistic approach that can provide QTL information that is more easily transferred to breeding applications.

Mining for New Sources of Resistance to Powdery Mildew in Genetic Resources of Winter Wheat

“…Apart from potential false positives associations, several factors limit the usability of GWAS and QTL analysis for downstream breeding and scientific applications. To transfer QTL mapped with biparental populations is difficult when the genetic backgrounds of mapping and breeding populations differ significantly (Melchinger et al, 1998 ; Utz et al, 2000 ; Malosetti et al, 2020 ). Another limitation to the transferability of results is population size and composition.…”

GmFtsH25 overexpression increases soybean seed yield by enhancing photosynthesis and photosynthates

“…Photosynthesis is precisely regulated and is a complex quantitative trait controlled by multiple genes (Fracheboud et al, 2002; Wang et al, 2020). With the rapid development of molecular techniques, linkage mapping and genome‐wide association studies (GWASs) have become effective approaches to identify and explore genetic variation and important genes that regulate quantitative traits, such as stress tolerance, and quality and yield (Pantalião et al, 2016; Zhang et al, 2019; Malosetti et al, 2020; Rashid et al, 2020; Wu et al, 2020; Hu et al, 2022). Major quantitative trait loci (QTLs) controlling photosynthesis have been identified in rice and wheat ( Triticum aestivum ) (Teng et al, 2004; Bhusal et al, 2018).…”

Screening Fungicides for Controlling Wheat Crown Rot Caused by Fusarium pseudograminearum across Hebei Province in China

“…There are different methods for controlling FCR. Resistant cultivars [19], management of crop residues and rotation [20,21], and fertilizers have been shown to be effective in controlling FCR disease to some extent [22][23][24]. The lack of high resistance germplasms to wheat FCR is a specific challenge for breeding resistant cultivars [25,26].…”