Artificial selection causes significant linkage disequilibrium among multiple unlinked genes in Australian wheat

Abstract

Australia has one of the oldest modern wheat breeding programs worldwide although the crop was first introduced to the country in 1788. Breeders selected wheat with high adaptation to different Australian climates, while ensuring satisfactory yield and quality. This artificial selection left distinct genomic signatures that can be used to retrospectively understand breeding targets, and to detect economically important alleles. To study the effect of artificial selection on modern cultivars and cultivars released in different Australian states, we genotyped 482 Australian cultivars representing the history of wheat breeding in Australia since 1840. Computer simulation showed that 86 genomic regions were significantly affected by artificial selection. Characterization of 18 major genes known to affect wheat adaptation, yield, and quality revealed that many were affected by artificial selection and contained within regions under selection. Similarly, many reported QTL and genes for yield, quality, and adaptation were also contained in regions affected by artificial selection. These included TaCwi‐A1, TaGw2‐6A, Sus‐2B, TaSus1‐7A, TaSAP1‐7A, Glu‐A1, Glu‐B1, Glu‐B3, PinA, PinB, Ppo‐D1, Psy‐A1, Psy‐A2, Rht‐A1, Rht‐B1, Ppd‐D1, Vrn‐A1, Vrn‐B1 , and Cre8 . Interestingly, 17 regions affected by artificial selection were in moderate‐to‐high linkage disequilibrium with each other with an average r 2 value of 0.35 indicating strong simultaneous selection on specific alleles. These regions included Glu‐B1, TaGw2‐6A, Cre8, Ppd‐D1, Rht‐B1, Vrn‐B1, TaSus1‐7A, TaSAP1‐7A , and Psy‐A1 plus multiple QTL affecting wheat yield and yield components. These results highlighted the effects of the long‐term artificial selection on Australian wheat germplasm and identified putative regions underlying important traits in wheat.

Allelic Variation at the Vernalization Response (Vrn-1) and Photoperiod Sensitivity (Ppd-1) Genes and Their Association With the Development of Durum Wheat Landraces and Modern Cultivars

“…Since breeders select directly for earliness, a single trait that is affected by both Vrn and Ppd genes, it is likely that alleles shortening cycle length at both loci were selected simultaneously in breeding programs. This has been shown to be the case in recent studies conducted with Australian bread wheat (Joukhadar et al, 2019) and Italian durum wheat (Taranto et al, 2020) which have demonstrated that artificial selection involved strong simultaneous selection on specific alleles for vernalization and photoperiod genes.…”

Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm

“…The selective pressure on these genes/QTLs marked the transition from LR, through OC, to MC. In particular, the locus Glu-1 was reported to be nearly fixed in modern bread (Joukhadar et al, 2019) and the durum wheat germplasm (Maccaferri et al, 2019).…”

Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review

“…Therefore, QTLs for plant height (PH) were also included ( Table S1 ). Using a large Australian wheat population, Joukhadar et al [ 23 ] showed that long-term artificial selection left distinct genomic signatures that can be used to retrospectively understand breeding targets, and to identify economically important alleles, such as the regions including Glu-B1 , TaGw2-6A , Cre8 , Ppd-D1 , Rht-B1 , Vrn-B1 , TaSus1-7A , TaSAP1-7A and Psy-A1 plus multiple QTLs affecting wheat yield and yield components. The recently assembled genome of the Italian durum wheat cv .…”

“…Different breeding approaches including quantitative trait loci (QTL) and genome-wide association studies (GWAS) are being applied to increase the grain yield potential of durum wheat through molecular marker-assisted selection (MAS). In fact, multiple QTLs with large and small effects have been mapped on all wheat chromosomes and they have been recently published [ 20 , 21 , 22 , 23 , 24 ]. Therefore, due to the importance of this complex trait and to summarize the available information on the genetics of grain yield in durum wheat, the objective of this review is to analyze in a comprehensive manner the most recent findings associated with the genetics, genomics and the identification of QTL for grain yield-related traits in durum wheat.…”