Unraveling cis and trans regulatory evolution during cotton domestication

• Published in: Nature communications Vol. 10; no. 1; pp. 5399 - 12
• Main Authors: Bao, Ying, Hu, Guanjing, Grover, Corrinne E., Conover, Justin, Yuan, Daojun, Wendel, Jonathan F.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 27.11.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 38/90; 38/91; 631/181/2474; 631/208/182; 631/449/2491/3933; Complexity; Cotton; Cotton Fiber; Divergence; Domestication; Evolution; Evolution, Molecular; Gene expression; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genome, Plant; Genomes; Gossypium - genetics; Gossypium hirsutum; Heredity; Humanities and Social Sciences; Hybrids; multidisciplinary; Polyploidy; Redundancy; Regulatory sequences; Regulatory Sequences, Nucleic Acid; Science; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-13386-w

Cis and trans regulatory divergence underlies phenotypic and evolutionary diversification. Relatively little is understood about the complexity of regulatory evolution accompanying crop domestication, particularly for polyploid plants. Here, we compare the fiber transcriptomes between wild and domesticated cotton ( Gossypium hirsutum ) and their reciprocal F 1 hybrids, revealing genome-wide (~15%) and often compensatory cis and trans regulatory changes under divergence and domestication. The high level of trans evolution (54%–64%) observed is likely enabled by genomic redundancy following polyploidy. Our results reveal that regulatory variation is significantly associated with sequence evolution, inheritance of parental expression patterns, co-expression gene network properties, and genomic loci responsible for domestication traits. With respect to regulatory evolution, the two subgenomes of allotetraploid cotton are often uncoupled. Overall, our work underscores the complexity of regulatory evolution during fiber domestication and may facilitate new approaches for improving cotton and other polyploid plants. Relatively little is known about the complexity of regulatory evolution accompanying polyploid crop domestication. Here, using reciprocal hybrids between wild and domesticated allotetraploid cotton lines, the authors catalog cis and trans regulatory variants and show their equivalent effects on cotton fiber domestication.