113 / 2024-10-31 10:40:49

Genomic Inversions and Topological Associations in Gossypium hirsutumshaping modern cultivars

Genomic inversions; Topologically associating domains (TADs); Gossypium hirsutum; Comparative genomics

Genomic inversions and topologically associating domains (TADs) play pivotal roles in shaping the genomic architecture and regulatory landscapes of plants. This study explores the structural variations in Gossypium hirsutum, focusing on the landrace G. hirsutum purpurascens (GhP) and the advanced line ZMS637-9. Through a combination of comparative genomics, population genetics, and transcriptomics approaches, we identify significant chromosomal inversions and their impacts on gene expression and phenotypic variation. Our findings reveal extensive chromosomal rearrangements in GhP, highlighting its potential as a reservoir of genetic diversity for cotton breeding. Notably, we identified large inversions on chromosomes A02, A05, A06, A08, A11, A13, and D03 which significantly disrupt TAD boundaries and alter gene expression. For example, the inversion on chromosome A05 resulted in the reconfiguration of TADs, leading to differential expression of genes such as A05.g22621 and A05.g24002. Furthermore, the study uncovered specific inversions on chromosome A06 correlating with haplotypes associated with early flowering and photoperiod sensitivity, involving genes like A06.g27636 and A06.g27643. The analysis of chromosome A08 revealed three significant inversions, uniquely present in ZMS, which encompass 241 genes with distinct expression patterns. These inversions include genes such as A08.g40334 and A08.g39443, impacting ubiquitin conjugation and ribosomal protein synthesis relevant to flowering and photoperiod sensitivity.The study also identified significant genomic differentiation between wild and domesticated cotton groups. Our findings emphasize the role of chromosomal inversions in preserving adaptive gene complexes crucial for cotton's resilience and adaptability. These results provides valuable insights into the evolutionary dynamics of cotton genomes and lays the foundation for targeted genetic improvements.