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Barley yellow dwarf (BYD) is one of the most serious viral diseases in cereal crops worldwide. Identification of quantitative trait loci (QTLs) underlining wheat resistance to barley yellow dwarf virus (BYDV) is essential for breeding BYDV-tolerant wheat cultivars. In this study, a recombinant inbred line (RIL) population was developed from the cross between Jagger (PI 593688) and a Jagger mutant (JagMut1095). A linkage map of 3106 cM consisting of 21 wheat chromosomes was developed using 1003 unique single nucleotide polymorphisms (SNPs) from the RIL population and was used to identify QTLs for BYDV resistance and yield-related traits, including 1000-kernel weight (TKW), kernel area (KA), kernel width (KW), and kernel length (KL). QByd.hwwg-2DL, a QTL on chromosome arm 2DL for BYDV resistance, was consistently identified in three field experiments and explained 11.6%-44.5% of the phenotypic variation. For yield-related traits, six major and repeatable QTLs were identified on 1AS (QKa.hwwg-1AS), 2DL (QTkw.hwwg-2DL, QKa.hwwg-2DL, QKw.hwwg-2DL, and QKl.hwwg-2DL), and 5AL (QKw.hwwg-5AL). The major QTLs on chromosome 2DL for TKW, KA, KW, and KL were mapped between 621 and 643 Mb, overlapping with QByd.hwwg-2DL with all the favorable alleles from Jagger. This study reports the first native BYDV resistance QTL (QByd.hwwg-2DL) originating from common wheat and tightly linked markers to the QTL for improvement of wheat BYDV resistance in wheat breeding., (Published 2025. This article is a U.S. Government work and is in the public domain in the USA. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Background: Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome., Results: Although open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs' chromosomal position and proximity to genes. While the chromatin accessibility of genes is influenced by proximity to TEs, and not by their position on the chromosomes, we observe a negative chromatin accessibility gradient along the telomere-centromere axis in the intergenic regions, positively correlated with the distance between genes. Both gene expression levels and homoeologous gene expression bias are correlated with chromatin accessibility in promoter regions. The differential nuclease sensitivity assay accurately predicts previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within more closed chromatin., Conclusions: Chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.

Background: Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines., Results: A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies., Conclusions: Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.