Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat's wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterize introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilization of introgression pre-breeding material in wheat breeding programmes.

中文翻译：

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全基因组测序揭示了六倍体小麦/Ambylopyrum muticum 基因渗入系的结构和转录组学景观

小麦是一种全球重要的作物，但其有限的遗传变异给旨在随着时间的推移维持或加速农业改良的育种者带来了挑战。通过渐渗线将小麦野生近缘种的新基因和等位基因引入小麦育种库是克服这种低变异的重要组成部分，但受到基因组分辨率差和对渐渗育种计划的基因组影响的理解有限的限制。通过对 17 个六倍体小麦/ Ambylopyrum muticum基因渗入系和亲本系进行测序，我们精确定位了基因渗入片段的边界，其中大部分发生在基因内。我们报告了 Am 的基因组组装和注释。有助于识别的muticum是。muticum抗性基因通常渗入到抗条锈病品系中。我们的分析已经确定了基因渗入线中大量的结构破坏和同源配对，这可能是由抑制的Ph1引起的轨迹。对其中 6 个基因渗入系的 mRNAseq 分析表明，新的基因渗入基因很少表达，那些直接取代小麦直向同源基因的基因有下调的趋势，在同源拷贝的表达中没有明显的补偿。本研究探讨了基因渗入育种的基因组影响，并提供了一个示意图，可以遵循该示意图来表征基因渗入系并识别表型下的片段和候选基因。这将有助于在小麦育种计划中更有效地利用基因渗入预育种材料。