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Identifcation of KASP markers and candidate genes for drought tolerance in wheat using 90K SNP array genotyping of near isogenic lines targeting a 4BS quantitative trait locus
Tuesday, 2023/09/19 | 08:11:39

Guannan Liu, Dongcheng Liu, Aimin Zhang, Hui Liu, Md Sultan Mia, Daniel Mullan, Guijun Yan

Theoretical and Applied Genetics; September 2023; vol. 136:190



Key message

This study identifed a novel SNP and developed a highly efcient KASP marker for drought tolerance in wheat by genotyping NILs targeting a major QTL for drought tolerance using an SNP array and validation with commercial varieties.


Common wheat (Triticum aestivum L.) is an important winter crop worldwide and a typical allopolyploid with a large and complex genome. With global warming, the environmental volatility and incidence of drought in wheat-producing areas will increase. Molecular markers for drought tolerance are urgently needed to enhance drought tolerance breeding. Here, we genotyped four near-isogenic line (NIL) pairs targeting a major QTL qDSI.4B.1 on wheat chromosome arm 4BS for drought tolerance using the 90K SNP Illumina iSelect array and discovered a single nucleotide polymorphism (SNP) (Excalibur_c100336_106) with consistent genotype–phenotype associations among all four NIL pairs and their parents. Then, we converted the SNP into a Kompetitive Allele-Specifc PCR (KASP) marker, with an accuracy of 100% for the four NIL pairs and their parents and as high as 81.8% for the 44 tested wheat lines with known phenotypes collected from Australia and China. Two genes near this SNP were suggested as candidate genes for drought tolerance in wheat after checking the Chinese Spring reference genome annotation version 1.1. One gene, TraesCS4B02G085300, encodes an F-box protein reportedly related to the ABA network, a main pathway for drought tolerance, and another gene, TraesCS4B02G085400, encodes a calcineurin-like metallophos-phoesterase transmembrane protein, which participates in Ca2+-dependent phosphorylation regulatory system. Based on this work and previous research on pre-harvest sprouting, we established a quick and efcient general SQV-based approach for KASP marker development, integrating genotyping by SNP arrays (S) using NILs targeting major QTL for a specifc trait (Q) and validating them with commercial varieties (V). The identifed SNP and developed KASP marker could be applied to marker-assisted selection in drought breeding, and further study of the candidate genes may improve our understanding of drought tolerance in wheat.


See https://link.springer.com/article/10.1007/s00122-023-04438-3

Fig. 1: Locations of the six selected SNPs with their physical positions on chromosome 4B. SNP marked as bold shows genotype–phenotype associations in all four NIL pairs; red line is the peak region of the target QTL (qDSI.4B.1); QTL markers are bolded; the details of each SNP’s physical distance (based on Chinese Spring genome version 1.1) were listed in the embedded table


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