Genome-wide association analysis of Russian wheat aphid (Diuraphis noxia) resistance in Dn4 derived wheat lines evaluated in South Africa

Abstract

Russian wheat aphid (RWA; Diuraphis noxia Kurdjumov) resistance on the 1D chromosome of wheat has been the subject of intensive research. Conversely, the deployment of the Dn4 derived RWA resistant varieties diminished in recent years due to the overcoming of the resistance it imparts in the United States of America. However, this resistance has not been deployed in South Africa despite reports that Dn4 containing genotypes exhibited varying levels of resistance against the South African RWA biotypes. It is possible that there may be certain genetic differences within breeding lines or cultivars that influence the expression of resistance. The aim of this study was to identify single nucleotide polymorphism (SNP) markers associated with resistance to South African RWA biotypes. A panel of thirty-two wheat lines were phenotyped for RWA resistance using four South African RWA biotypes and a total of 181 samples were genotyped using the Illumina 9K SNP wheat chip. A genome wide association study using 7598 polymorphic SNPs showed that the population was clustered into two distinct subpopulations. Twenty-seven marker trait associations (MTA) were identified with an average linkage disequilibrium of 0.38 at 10 Mbp. Four of these markers were highly significant and three correlated with previously reported quantitative trait loci linked to RWA resistance in wheat. Twenty putative genes were annotated using the IWGSC RefSeq, three of which are linked to plant defence responses. This study identified novel chromosomal regions that contribute to RWA resistance and contributes to unravelling the complex genetics that control RWA resistance in wheat.

Unravelling the novel genetic diversity and marker-trait associations of corn leaf aphid resistance in wheat using microsatellite markers

“…Comparing these findings with the study by Li and Peng [ 59 ], two distinct groups were identified in the wheat germplasm using the STRUCTURE Bayesian analysis, with the highest ΔK value obtained at 2 suggesting the wheat germplasm could be divided into two groups. Following a population structure study, Kisten et al [ 35 ] separated the wheat panel into two unique clusters. Cluster 2 featured 67 bulked samples of spring-type breeding lines created in Montana, United States, whereas Cluster 1 contained 102 bulked samples of winter-type cultivars and breeding lines from the United States and Turkey.…”

“…For instance, Xgwm111 , which is linked to other resistance-related genes, has been reported to be associated with aphid resistance [ 63 , 64 ]. Previous association mapping studies by Peng et al [ 58 ], Dahleen et al [ 65 ], Li and Peng [ 59 ], and Kisten et al [ 35 ] have also identified significant associations between SSR loci or SNP markers and aphid resistance or related traits in wheat germplasm. The results obtained from association mapping provide valuable insights into the genetic basis of aphid resistance mechanism in wheat, contributing towards understanding of the underlying loci and potential markers associated with resistance traits.…”

“…The use of molecular genetic diversity and marker-trait associations has proven to be valuable in choosing better parental materials for breeding aphid-resistant wheat varieties [ 7 ]. In this context, SSR markers have played a crucial role in various aspects of wheat breeding, such as genomic mapping, marker-assisted breeding, genetic analyses, and assessing the diversity and polymorphism of wheat germplasm [ 35 ]. A large number of SSR markers have been extensively utilized in wheat improvement programs.…”

Integrated genome‐wide association study and QTL mapping reveals qSa‐3A associated with English grain aphid, Sitobion avenae (Fabricius) resistance in wheat

“…GWAS has been successfully used to identify loci associated with resistance to Aphid glycines, Spodoptera litura and Heterodera glycines in soybean, Ostrinia furnacalis in maize, Melanaphis sorghi in Sorghum, Sitodiplosis mosellana and Diuraphis noxia in wheat at the whole-genome level. [16][17][18][19][20][21][22] However, GWAS for S. avenae resistance in wheat has not yet been reported.…”

Evaluation of Russian wheat resistance sources with the spectrum of South African Diuraphis noxia biotypes

“…The exact nature of the genetic control of RWA resistance is not yet fully understood. A recent genome wide association study (Kisten et al., 2020) validated that QTL Xgwm 1017 (on 6A) (Castro et al., 2008), Xwmc 264 (on 3A), and Xbarc 109 (on 5B) (Riccardi et al., 2010), which were reported to be associated with resistance gene DnCI2401 on chromosome 7D (Tulpová et al., 2019), were also associated with Dn4 located on chromosome 1D (Dong et al., 1997).…”