Comparative Transcriptome Analysis of Gossypium hirsutum Mutant (xin w 139) and Wild-Type (Xin W 139) Plants During Seed Embryo Development.

Background: Cotton seeds are the main byproduct of cotton crops. The phenomenon of plants failing to develop mature and full seeds is called seed embryo abortion, which leads to a decrease in seed yield and potentially causes economic losses.

Methods: We report a phenotypic evaluation of seed embryos from G. hirsutum mutant (xin w 139) and wild-type (Xin W 139) lines and a comparative RNA-seq study at four developmental stages.

Results: The field results from two years showed that the sterility rate and malformation rate of xin w 139 were significantly lower than those of Xin W 139, and the RNA-seq data revealed that the differences in the development of the seed embryos of the two lines mainly occurred after 20 days post anthesis (DPA). Differential analysis revealed a total of 29,151 differentially expressed genes (DEGs), including 2696 transcription factors (TFs), between the two lines, in which the fatty acid and glucose metabolism-related pathways were significantly enriched. These DEGs were divided into 8 clusters, with the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of each cluster being annotated. Furthermore, a gene regulatory network was built using weighted correlation network analysis (WGCNA), revealing 9 key genes that play crucial roles in shaping the developmental disparities of seed embryos between the two lines, among which 3 are TFs.

Conclusions: These findings offer a foundational framework for comprehending the molecular mechanisms underlying cottonseed embryo development, as well as presenting novel genetic reservoirs for further investigations into cottonseed embryo development.