Common wheat (Triticum aestivum L.) is the most important crop in the world and a typical allopolyploid with a large and complex genome. Pre-harvest sprouting (PHS) leads to a significant reduction in grain quality worldwide. PHS is a complex trait with related QTL located on different chromosomes. However, the study of markers and genes related to PHS resistance is limited especially for white-grained wheat. Four pairs of near isogenic lines (NILs) from a white-grained wheat cross of Chara × DM5637B*8 targeting a major QTL for PHS resistance (Qphs.ccsu-3A.1) on wheat chromosme 3AL were genotyped using the 90K SNP Illumina iSelect array. Ten SNPs were identified, with a 75%–100% consistency between genotype and phenotype in the resistant or susceptible isolines. The 10 SNPs were converted to cost-effective kompetitive allele-specific PCR (KASP) markers. Screening of 48 wheat cultivars with different phenotypes of PHS identified four KASP markers with 81.3%–85.4% conformity between genotype and phenotype. Further investigation revealed that the four SNPs (BS00022245_51, Kukri_c49927_151, BS00022884_51 and BS00110550_51) corresponding to the four validated KASP markers are residing in three independent genes (TraesCS3A03G1072800, TraesCS3A03G1072400, TraesCS3A03G1071800) close to each other with a distance of 4.28–4.48 Mb to the targeted QTL. These three annotated genes have potential functions related to PHS resistance. Our study revealed that combined use of NILs and the 90K SNP chip is a powerful approach for developing KASP markers and mining functional genes in wheat. The KASP markers for PHS resistance on chromosome 3AL are useful for high-throughput evaluation and marker-assisted selection, and the three identified genes could lead to a better understanding of the genetic pathways controlling PHS.

Wheat production is seriously influenced by extreme hot weather, which has attracted increasing attention. It is important to compare wheat responses to heat at seedling and reproductive stages, to explore the potential relationship between the performances at different growing stages and the possibility of early selection to accelerate heat tolerance breeding. In this study, forty wheat genotypes were screened under heat stress at both seedling and adult stages. It was found that root lengths at seedling stage were severely reduced by heat stress with significant variations among wheat genotypes. Heat-tolerant genotypes at seedling stage showed less root length decrease than susceptible ones. Wheat genotypes tolerant at seedling stage showed higher yield at adult stage after heat treatment. The performances of wheat genotypes screened under heat stress at seedling and adult stages were ranked by seedling damage index and adult damage index. A significant positive relationship was found between heat tolerance at seedling stage and at adult stage (r = 0.6930), suggesting a similar tolerant/susceptible mechanism at different plant growth stages and the possibility of early selection at seedling stage for breeding heat tolerance. Extremely tolerant and susceptible genotypes with consistent performances at seedling and adult stages were genetically compared and associated SNP markers and linked candidate genes were identified.