Interspecific breeding in cotton takes advantage of genetic recombination among desirable genes from different parental lines. However, the expression new alleles (ENAs) from crossovers within genic regions and their significance in fibre length (FL) improvement are currently not understood. Here, we generated resequencing genomes of 191 interspecific backcross inbred lines derived from CRI36 (Gossypium hirsutum) × Hai7124 (Gossypium barbadense) and 277 dynamic fibre transcriptomes to identify the ENAs and extremely expressed genes (eGenes) potentially influencing FL, and uncovered the dynamic regulatory network of fibre elongation. Of 35 420 eGenes in developing fibres, 10 366 ENAs were identified and preferentially distributed in chromosomes subtelomeric regions. In total, 1056–1255 ENAs showed transgressive expression in fibres at 5–15 dpa (days post-anthesis) of some BILs, 520 of which were located in FL-quantitative trait locus (QTLs) and GhFLA9 (recombination allele) was identified with a larger effect for FL than GhFLA9 of CRI36 allele. Using ENAs as a type of markers, we identified three novel FL-QTLs. Additionally, 456 extremely eGenes were identified that were preferentially distributed in recombination hotspots. Importantly, 34 of them were significantly associated with FL. Gene expression quantitative trait locus analysis identified 1286, 1089 and 1059 eGenes that were colocalized with the FL trait at 5, 10 and 15 dpa, respectively. Finally, we verified the Ghir_D10G011050 gene linked to fibre elongation by the CRISPR-cas9 system. This study provides the first glimpse into the occurrence, distribution and expression of the developing fibres genes (especially ENAs) in an introgression population, and their possible biological significance in FL.

中文翻译：

---

纤维伸长过程中表达的基因及其新的等位基因鉴定揭示了棉花纤维长度改善的遗传因素

棉花种间育种利用来自不同亲本系的理想基因之间的基因重组。然而，来自基因区域内交叉的新等位基因 (ENA) 的表达及其在纤维长度 (FL) 改善中的意义目前尚不清楚。在这里，我们生成了来自 CRI36 ( Gossypium hirsutum ) × Hai7124 ( Gossypium barbadense )的 191 个种间回交自交系的重测序基因组。) 和 277 个动态纤维转录组来识别可能影响 FL 的 ENA 和极度表达的基因 (eGenes)，并揭示了纤维伸长的动态调控网络。在发育中的纤维中的 35 420 个 eGenes 中，10 366 个 ENA 被鉴定并优先分布在染色体亚端粒区域。总共有 1056-1255 个 ENAs 在一些 BILs 的 5-15 dpa（开花后天数）的纤维中表现出海侵表达，其中 520 个位于 FL 数量性状基因座（QTLs）和GhFLA9（重组等位基因）被鉴定为对 FL 的影响比GhFLA9 大CRI36 等位基因。使用 ENA 作为一种标记，我们鉴定了三个新的 FL-QTL。此外，还鉴定了 456 个极端 eGene，它们优先分布在重组热点中。重要的是，其中 34 个与 FL 显着相关。基因表达数量性状基因座分析鉴定了 1286、1089 和 1059 个 eGene，它们分别在 5、10 和 15 dpa 时与 FL 性状共定位。最后，我们通过 CRISPR-cas9 系统验证了与纤维伸长相关的Ghir_D10G011050基因。本研究首次揭示了渐渗种群中发育中的纤维基因（尤其是 ENA）的发生、分布和表达，以及它们在 FL 中可能的生物学意义。