Genome‐wide association study reveals structural chromosome variations with phenotypic effects in wheat (Triticum aestivum L.)

Abstract

SUMMARY Structural chromosome variations (SCVs) are large‐scale genomic variations that can be detected by fluorescence in situ hybridization (FISH). SCVs have played important roles in the genome evolution of wheat (Triticum aestivum L.), but little is known about their genetic effects. In this study, a total of 543 wheat accessions from the Chinese wheat mini‐core collection and the Shanxi Province wheat collection were used for chromosome analysis using oligonucleotide probe multiplex FISH. A total of 139 SCVs including translocations, pericentric inversions, presence/absence variations (PAVs), and copy number variations (CNVs) in heterochromatin were identified at 230 loci. The distribution frequency of SCVs varied between ecological regions and between landraces and modern cultivars. Structural analysis using SCVs as markers clearly divided the landraces and modern cultivars into different groups. There are very clear instances illustrating alien introgression and wide application of foreign germplasms improved the chromosome diversity of Chinese modern wheat cultivars. A genome‐wide association study (GWAS) identified 29 SCVs associated with 12 phenotypic traits, and five (RT4AS•4AL‐1DS/1DL•1DS‐4AL, Mg2A‐3, Mr3B‐10, Mr7B‐13, and Mr4A‐7) of them were further validated using a doubled haploid population and advanced sib‐lines, implying the potential value of these SCVs. Importantly, the number of favored SCVs that were associated with agronomic trait improvement was significantly higher in modern cultivars compared to landraces, indicating positive selection in wheat breeding. This study demonstrates the significant effects of SCVs during wheat breeding and provides an efficient method of mining favored SCVs in wheat and other crops.

Towards carotenoid biofortification in wheat: identification of XAT-7A1, a multicopy tandem gene responsible for carotenoid esterification in durum wheat

“…Large-scale structural variations have been also identified through bread wheat pangenome studies. For instance, a translocation between chromosomes 5B and 7B was detected in 66% of the 538 common wheat lines analyzed [ 47 , 49 ]. Unfortunately, a durum wheat pangenome is still in progress.…”

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“…Chromosome number variation involves euploidy and aneuploidy variation (Guerra, 2008). Structural chromosome variations (SCVs) are large‐scale genomic variations that can be detected by fluorescence in situ hybridization (FISH) (Zhao et al, 2022). SCVs include deletions, duplications, inversions, translocations, and more complex rearrangements (Alkan et al, 2011; Lei et al, 2021).…”

Genetic dissection for seedling root-related traits using multiple-methods in bread wheat (Triticum aestivum L.)

“…For example, Zhao et al (2023) found three SCVs on chromosomes 4A, 5A, and 7B, which were signi cantly associated with wheat grain length, grain width, and spike length. Zhao et al (2022) analyzed 12 agronomic traits of wheat, including 1000-grain weight, grain length, and grain width, and identi ed 29 signi cantly associated SCVs, with R 2 ranging from 1.10 % to 37.19 %.…”

“…. A total of 74 polymorphic SCVs were identi ed by FISH in the association panel, which were located on 17 chromosomes, including 1A, 1B and 1D(Zhao et al 2022). In the DH population, 13 polymorphic SCVs located on 11 chromosomes were identi ed by FISH.…”

“…In of chromosomal structural variants can provide new insights for the genetic characterization of root traits. In wheat, the genetic effects of SCVs have been studied rarely, and only SCVs associated to agronomic traits have been reported(Zhao et al 2022;Zhao et al 2023…”