Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton

Authors: YOU, JIAQI - Huazhong Agricultural University; LIU, ZHENPING - Huazhong Agricultural University; QI, ZHENGYANG - Huazhong Agricultural University; MA, YIZAN - Huazhong Agricultural University; SUN, MENGLING - Huazhong Agricultural University; CHEN, XINYUAN - Huazhong Agricultural University; SU, LING - Iowa State University; NIU, HAO - Huazhong Agricultural University; PENG, YABING - Huazhong Agricultural University; Fang, David; LUO, XUANXUAN - Huazhong Agricultural University; ZHU, MENGMENG - Huazhong Agricultural University; HUANG, YUEFAN - Huazhong Agricultural University; CHANG, XING - Huazhong Agricultural University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/14/2023
Publication Date: 10/16/2023
Citation: You, J., Liu, Z., Qi, Z., Ma, Y., Sun, M., Chen, X., Su, L., Niu, H., Peng, Y., Fang, D.D., Luo, X., Zhu, M., Huang, Y., Chang, X. 2023. Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton. Nature Genetics. https://doi.org/10.1038/s41588-023-01530-8.
DOI: https://doi.org/10.1038/s41588-023-01530-8

Interpretive Summary: Cotton is a tetraploid which means to have four sets of chromosomes. This can have certain survival and competitive advantages but also complicate synergic regulation among genes especially among those with similar function but residing in different chromosomes. Although this research subject is important to our fundamental understanding about cotton fiber development, yet it is a poorly studied. In this research, we present a genetic regulome in fiber development of Upland cotton by sequencing the genomes of 376 accessions and transcriptomes of 2,215 time-series developing fibers. We characterized 1,258 fiber quality-related genes constituting 36 genetic modules that empower staged fiber development, and uncovered genetic components governing their partitioned expression relative to subgenomic counterparts. No more than 30% of homoeologous genes show favorable allele aggregation in both subgenomes, illuminating the considerable potential of subgenome additivity in fiber improvement. We envision a genomic design strategy for fiber improvement, with a particular attention to 50 favorable alleles that have been subjected to high pressure selection during long-period of domestication. Our work delineates dynamic genetic regulation in cotton and highlights the significance of subgenome coordination in genomics-based breeding of polyploid plants.

Technical Abstract: Genome polyploidy complicates transcription regulation and increases the capacity establishing phenotypic advantages in organisms. However, dynamic genetic regulation of gene expression between co-existing subgenomes for a specific trait in polyploids remains poorly understood. We present a genetic regulome in fiber development of allotetraploid cotton Gossypium hirsutum by sequencing the genomes of 376 accessions and transcriptomes of 2,215 time-series developing fibers. We characterized 1,258 fiber quality-related genes constituting 36 genetic modules that empower staged fiber development, and uncovered genetic components governing their partitioned expression relative to subgenomic counterparts. No more than 30% of homoeologous genes show favorable allele aggregation in both subgenomes, illuminating the considerable potential of subgenome additivity in fiber improvement. We envision a genomic design strategy for fiber improvement, with a particular attention to 50 favorable alleles that have been subjected to high pressure selection during long-period of domestication. Our work delineates dynamic genetic regulation in cotton and highlights the significance of subgenome coordination in genomics-based breeding of polyploid plants.