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Wheat cultivar Zhongmai 895 was earlier found to carry YR86 in an 11.6 Mb recombination-suppressed region on chromosome 2AL when crossed with Yangmai 16. To fine-map the YR86 locus, we developed two large F2 populations from crosses Emai 580/Zhongmai 895 and Avocet S/Zhongmai 895. Remarkably, both populations exhibited suppressed recombination in the same 2AL region. Collinearity analysis across Chinese Spring, Aikang 58, and 10+ wheat genomes revealed a 4.1 Mb chromosomal inversion spanning 708.5-712.6 Mb in the Chinese Spring reference genome. Molecular markers were developed in the breakpoint and were used to assess a wheat cultivar panel, revealing that Chinese Spring, Zhongmai 895, and Jimai 22 shared a common sequence named InvCS, whereas Aikang 58, Yangmai 16, Emai 580, and Avocet S shared the sequence named InvAK58. The inverted configuration explained the suppressed recombination observed in all three bi-parental populations. Normal recombination was observed in a Jimai 22/Zhongmai 895 F2 population, facilitating mapping of YR86 to a genetic interval of 0.15 cM corresponding to 710.27-712.56 Mb falling within the inverted region. Thirty-three high-confidence genes were annotated in the interval using the Chinese Spring reference genome, with six identified as potential candidates for YR86 based on genome and transcriptome analyses. These results will accelerate map-based cloning of YR86 and its deployment in wheat breeding. [ABSTRACT FROM AUTHOR]

Waterlogging is a growing threat to wheat production in high-rainfall areas. In this study, a doubled haploid (DH) population developed from a cross between Yangmai 16 (waterlogging-tolerant) and Zhongmai 895 (waterlogging-sensitive) was used to map quantitative trait loci (QTL) for waterlogging tolerance using a high-density 660K single-nucleotide polymorphism (SNP) array. Two experimental designs, waterlogging concrete tank (CT) and waterlogging plastic tank (PT), were used to simulate waterlogging during anthesis in five environments across three growing seasons. Waterlogging significantly decreased thousand-kernel weight (TKW) relative to non-waterlogged controls, although the degree varied across lines. Three QTL for waterlogging tolerance were identified on chromosomes 4AL, 5AS, and 7DL in at least two environments. All favorable alleles were contributed by the waterlogging-tolerant parent Yangmai 16. QWTC.caas-4AL exhibited pleiotropic effects on both enhancing waterlogging tolerance and decreasing plant height. Six high-confidence genes were annotated within the QTL interval. The combined effects of QWTC.caas-4AL and QWTC.caas-5AS greatly improved waterlogging tolerance, while the combined effects of all three identified QTL (QWTC.caas-4AL, QWTC.caas-5AS, and QWTC.caas-7DL) exhibited the most significant effect on waterlogging tolerance. Breeder-friendly kompetitive allele-specific PCR (KASP) markers (K_AX_111523809, K_AX_108971224, and K_AX_110553316) flanking the interval of QWTC.caas-4AL, QWTC.caas-5AS, and QWTC.caas-7DL were produced. These markers were tested in a collection of 240 wheat accessions, and three superior polymorphisms of the markers distributed over 67 elite cultivars in the test population, from the Chinese provinces of Jiangsu, Anhui, and Hubei. The three KASP markers could be used for marker-assisted selection (MAS) to improve waterlogging tolerance in wheat. [ABSTRACT FROM AUTHOR]