The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

中文翻译：

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异源四倍体种间CSSL的遗传解剖指导棉花的种间遗传和育种。

陆地棉遗传多样性低，限制了遗传改良的潜力。充分利用海岛棉的遗传资源，将有助于广泛种植的陆地棉品种的遗传改良。染色体区段替换系（CSSL）为在种间杂交中定位数量性状基因座（QTL）提供了理想的策略。在这项研究中，CSSL人群是通过基于PCR的标记辅助选择（MAS）开发的，该标记首先来自陆地棉（Gh）和巴巴德氏酵母（Gb）的杂交和回交。然后，通过全基因组重测序，鉴定出11,653,661个高质量的单核苷酸多态性（SNP），其最终从Gb构建了1211个重组染色体渐渗区段。与基于PCR的标记相比，基于测序的物理图谱提供了更准确的基因渗入。通过利用具有突变形态特征的CSSL，鉴定了对Gb中的叶片形状和无绒毛突变有响应的基因。基于高分辨率重组bin图以揭示确定Gh和Gb之间表型差异的遗传位点，针对14个农艺性状鉴定了64个QTL，间隔长度为158 kb至27 Mb。令人惊讶的是，Gb的多个等位基因在提高棉籽油含量（SOC）方面显示出极高的价值。这项研究为研究种间遗传，特别是育种研究者，为将来在CSSLs研究中使用传统的基于PCR的分子标记和高通量重测序技术提供了指导。可用资源包括控制棉花质量和数量性状的候选职位，以及优良的育种材料。总的来说，我们的结果为Gb等位基因对Gh的遗传效应提供了见识，并为种间育种中Gb等位基因的利用提供了指导。