Abstract
Key message
Structural variations are common in plant genomes, affecting meiotic recombination and distorted segregation in wheat. And presence/absence variations can significantly affect drought tolerance in wheat.
Abstract
Drought is a major abiotic stress limiting wheat production. Common wheat has a complex genome with three sub-genomes, which host large numbers of structural variations (SVs). SVs play critical roles in understanding the genetic contributions of plant domestication and phenotypic plasticity, but little is known about their genomic characteristics and their effects on drought tolerance. In the present study, high-resolution karyotypes of 180 doubled haploids (DHs) were developed. Signal polymorphisms between the parents involved with 8 presence-absence variations (PAVs) of tandem repeats (TR) distributed on the 7 (2A, 4A, 5A, 7A, 3B, 7B, and 2D) of 21 chromosomes. Among them, PAV on chromosome 2D showed distorted segregation, others transmit normal conforming to a 1:1 segregation ration in the population; and a PAVs recombination occurred on chromosome 2A. Association analysis of PAV and phenotypic traits under different water regimes, we found PAVs on chromosomes 4A, 5A, and 7B showed negative effect on grain length (GL) and grain width (GW); PAV.7A had opposite effect on grain thickness (GT) and spike length (SL), with the effect on traits differing under different water regimes. PAVs on linkage group 2A, 4A, 7A, 2D, and 7B associated with the drought tolerance coefficients (DTCs), and significant negative effect on drought resistance values (D values) were detected in PAV.7B. Additionally, quantitative trait loci (QTL) associated with phenotypic traits using the 90 K SNP array showed QTL for DTCs and grain-related traits in chromosomes 4A, and 5A, 3B were co-localized in differential regions of PAVs. These PAVs can cause the differentiation of the target region of SNP and could be used for genetic improvement of agronomic traits under drought stress via marker-assisted selection (MAS) breeding.
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Data availability
The datasets generated during the current study are available from the corresponding author on reasonable request.
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Acknowledgements
This project was supported by State Key Laboratory of Sustainable Dryland Agriculture (No. YJHZKF2107), National Natural Science Foundation of China (31871571), and Research Program of Shanxi Agricultural University (YBSJJ2006) Bioinformatics analyses were supported by the Bioinformatics Center of Nanjing Agricultural University, China. We thank the editor and anonymous reviewers for critical comments and suggestions for improving the manuscript.
Funding
This project was supported by State Key Laboratory of Sustainable Dryland Agriculture (No. YJHZKF2107), National Natural Science Foundation of China (31871571), and Research Program of Shanxi Agricultural University (YBSJJ2006).
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WDY and JZ planned and designed the experiments. JJZ, BBW, XWZ, and MJG performed the experiments. JJZ, ZJQ, LQ, and MCF analyzed the data. JJZ and XHL wrote the article. All authors read and commented on the final version for publication.
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Zhao, J., Li, X., Qiao, L. et al. Identification of structural variations related to drought tolerance in wheat (Triticum aestivum L.). Theor Appl Genet 136, 37 (2023). https://doi.org/10.1007/s00122-023-04283-4
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DOI: https://doi.org/10.1007/s00122-023-04283-4