After polyploidization originated from one interspecific hybridization event in Gossypium, Gossypium barbadense evolved to produce extra-long staple fibres than Gossypium hirsutum (Upland cotton), which produces a higher fibre yield. The genomic diversity between G. barbadense and G. hirsutum thus provides a genetic basis for fibre trait variation. Recently, rapid accumulation of gene disruption or deleterious mutation was reported in allotetraploid cotton genomes, with unknown impacts on fibre traits. Here, we identified gene disruptions in allotetraploid G. hirsutum (18.14%) and G. barbadense (17.38%) through comparison with their presumed diploid progenitors. Relative to conserved genes, these disrupted genes exhibited faster evolution rate, lower expression level and altered gene co-expression networks. Within a module regulating fibre elongation, a hub gene experienced gene disruption in G. hirsutum after polyploidization, with a 2-bp deletion in the coding region of GhNPLA1D introducing early termination of translation. This deletion was observed in all of the 34 G. hirsutum landraces and 36 G. hirsutum cultivars, but not in 96% of 57 G. barbadense accessions. Retrieving the disrupted gene GhNPLA1D using its homoeolog GhNPLA1A achieved longer fibre length in G. hirsutum. Further enzyme activity and lipids analysis confirmed that GhNPLA1A encodes a typical phospholipase A and promotes cotton fibre elongation via elevating intracellular levels of linolenic acid and 34:3 phosphatidylinositol. Our work opens a strategy for identifying disrupted genes and retrieving their functions in ways that can provide valuable resources for accelerating fibre trait enhancement in cotton breeding.

中文翻译：

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检索编码磷脂酶 A 的破坏基因以增强异源四倍体栽培棉花的纤维

多倍化起源于棉属中的一种种间杂交事件后，有刺棉进化为产生比陆地棉（陆地棉）更长的短纤维，从而产生更高的纤维产量。因此， G. barbadense和G. hirsutum之间的基因组多样性为纤维性状变异提供了遗传基础。最近，在异源四倍体棉花基因组中报道了基因破坏或有害突变的快速积累，对纤维性状的影响未知。在这里，我们发现了异源四倍体G. hirsutum (18.14%) 和G. barbadense的基因破坏(17.38%) 通过与假定的二倍体祖细胞进行比较。相对于保守基因，这些被破坏的基因表现出更快的进化速度、更低的表达水平和改变的基因共表达网络。在调节纤维伸长的模块中，一个枢纽基因在多倍化后在陆地棉中经历了基因破坏，在GhNPLA1D的编码区有 2 bp 的缺失导致翻译提前终止。在所有 34 个G. hirsutum地方品种和 36 个 G. hirsutum栽培品种中都观察到了这种缺失 ，但在 96% 的 57 个 G. barbadense种质中没有观察到。使用其同源物 GhNPLA1A检索被破坏的基因GhNPLA1D在G. hirsutum中获得了更长的纤维长度。进一步的酶活性和脂质分析证实，GhNPLA1A编码典型的磷脂酶 A，并通过提高细胞内亚麻酸和 34:3 磷脂酰肌醇的水平来促进棉纤维伸长。我们的工作开启了一种识别被破坏基因并恢复其功能的策略，从而为加速棉花育种中的纤维性状增强提供宝贵资源。