Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L

Authors: MING, QINGYING - Huazhong Agricultural University; XIE, PEIHAO - Huazhong Agricultural University; XU, ZHONGPING - Huazhong Agricultural University; TANG, JIWEI - Huazhong Agricultural University; HUI, LIUYANG - Huazhong Agricultural University; GU, JIAQI - Huazhong Agricultural University; GU, XINXIN - Huazhong Agricultural University; JIANG, SHIHE - Huazhong Agricultural University; RONG, YUXUAN - Huazhong Agricultural University; ZHANG, JIE - Huazhong Agricultural University; Udall, Joshua; GROVER, CORRINNE - Iowa State University; WENDELL, JONATHAN - Iowa State University; ZHENG, KAI - Xinjiang Agricultural University; CHEN, QUANJIA - Xinjiang Agricultural University; KONG, JIE - Xinjiang Agricultural University; WANG, MAOJUN - Huazhong Agricultural University; LIN, ZHONGXU - Huazhong Agricultural University; JIN, SHUANGXIA - Huazhong Agricultural University; ZHANG, XIANLONG - Huazhong Agricultural University; YUAN, DAOJUN - Huazhong Agricultural University

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/19/2025
Publication Date: 5/29/2025
Citation: Ming, Q., Xie, P., Xu, Z., Tang, J., Hui, L., Gu, J., Gu, X., Jiang, S., Rong, Y., Zhang, J., Udall, J.A., Grover, C.E., Wendell, J., Zheng, K., Chen, Q., Kong, J., Wang, M., Lin, Z., Jin, S., Zhang, X., Yuan, D. 2025. Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L. Nature Communications. 16. Article 4995. https://doi.org/10.1038/s41467-025-60254-x.
DOI: https://doi.org/10.1038/s41467-025-60254-x

Interpretive Summary: This work defined the genetic makeup of Gossypium barbadense, which is one of the cotton species used to make high-quality fabrics. Genome sequences of 12 varieties of this cotton were created, capturing a wide range from wild types to those bred for farming, to construct a detailed genetic map called a pangenome. This pangenome will help scientists understand all the genetic variations that exist within the species, not just in a single individual, and will be useful in developing new and superior cotton types for productive use by farmers in cotton production regions worldwide.

Technical Abstract: Pangenome analysis has the potential to provide insight into causal genomic variation underlying agronomic traits in crop species. To date, pangenome analyses in Gossypium barbadense have been based on limited genome assemblies and have identified few causal variants related to fiber length, fiber strength, and lint percentage. We de novo assembled 12 G. barbadense accessions that span the wild-to-domesticated continuum, and constructed a graph-based pangenome. Whole genome comparative analyses identified 350,995 non-redundant structural variations (SVs) by integrating 16 G. barbadense and 12 other tetraploid cotton accessions. We clarified genetic relationships within G. barbadense and identified putative selection signals using 671 G. barbadense genomes for which re-sequencing data were available. A large introgression segment on chromosome A01 was identified, which we identified as having originated from interspecific gene flow in the Caribbean from G. hirsutum. Species-specific SVs were discovered related to differentiation of fiber quality and yield between G. barbadense and G. hirsutum.SV-based genome-wide association study (GWAS) analysis identified four, three, and seven causal structural variations for fiber length, fiber strength and lint percentage, respectively. To confirm these genomic inferences, two pleiotropic favorable alleles were combined into Xinhai cotton (Xinjiang cultivar) to significantly improve fiber length and fiber strength, and three favorable alleles were combined into Pima cotton through the interspecific hybrid, which significantly improved lint percentage. In this study, twelve G. barbadense genomes were newly de novo assembled and a graph-based pangenome was constructed for tetraploid cotton. Causal structural variations for fiber length, fiber strength, and lint percentage were identified in G. barbadense. These trait-associated SVs provide insight into and resources for improving cotton fiber quality.