Earlham Institute, Norwich, Norfolk, NR4 7UZ, UK.
USDA-ARS Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, 66506, USA.
Plant Biotechnol J. 2023 Mar;21(3):482-496. doi: 10.1111/pbi.13859. Epub 2023 Jan 24.
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.
小麦是一种全球重要的作物，但由于其遗传变异有限，给希望随着时间的推移保持或加速农业改良的培育者带来了挑战。通过导入系将小麦野生近缘种的新基因和等位基因引入小麦育种群体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导入育种计划基因组影响的理解有限的限制。通过对 17 个六倍体小麦/长穗偃麦草导入系及其亲本进行测序，我们精确地确定了导入片段的边界，其中大多数位于基因内。我们报告了长穗偃麦草的基因组组装和注释，这有助于鉴定在抗条锈病的系中常见的长穗偃麦草抗性基因。我们的分析鉴定了大量的结构破坏和同源配对在导入系中发生，这可能是由被抑制的 Ph1 基因座引起的。对这六个导入系的 mRNAseq 分析表明，很少有新的导入基因表达，而那些直接替代小麦同源物的基因往往会下调，同源拷贝的表达没有明显的补偿。本研究探讨了导入系的基因组影响，并提供了一个可以遵循的示意图，用于描述导入系和鉴定导致表型的片段和候选基因。这将促进在小麦育种计划中更有效地利用导入前育种材料。
