Abstract：
Structural variations (SVs) are critical factors affecting genome evolution and important traits. However, identification results and functional analyses of SVs in upland cotton are rare. Here, based on the genetic relationships, breeding history and cumulative planting area of upland cotton in China, nine predominant cultivars from the past 60 years (1950s-2010s) were selected for long read sequencing to uncover genic variations and breeding improvement targets for this crop. Based on the ZM24 reference genome, 0.88-1.47 × 104 SVs per cultivar were identified, and an SV set was constructed. SVs affected the expression of a large number of genes during fiber elongation, and a transposable element insertion resulted in the glandless phenotype in upland cotton. Six widespread inversions were identified based on nine draft genomes and high-throughput chromosome conformation capture data. Multiple haplotype blocks that were always associated with aggregated SVs were demonstrated to play a pivotal role in the agronomic traits of upland cotton and drove its adaptation to the northern planting region. Exotic introgression was the source of these haplotype blocks and increased the genetic diversity of upland cotton. Our results enrich the genome resources of upland cotton, and the identified SVs will promote genetic and breeding research in cotton.
摘要：
结构变异（SVs）是影响基因组进化和重要性状的关键因素。然而,陆地棉SVs的鉴定结果和功能分析很少见。这里,基于遗传关系，中国陆地棉育种史和累计种植面积,选择了过去60年（1950年代至2010年代）的9个主要品种进行长读数测序，以揭示该作物的基因变异和育种改良目标。基于ZM24参考基因组，每个品种鉴定出0.88-1.47×104SV，并建造了一套SV。SVs影响纤维伸长过程中大量基因的表达，转座因子的插入导致了陆地棉的无腺表型。基于九个草图基因组和高通量染色体构象捕获数据，确定了六个广泛的倒置。事实证明，始终与聚集的SV相关的多个单倍型区块在陆地棉的农艺性状中起着关键作用，并推动了其对北部种植区的适应。外来渗入是这些单倍型区块的来源，并增加了陆地棉的遗传多样性。我们的研究结果丰富了陆地棉的基因组资源,确定的SVs将促进棉花的遗传和育种研究。
