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

被引：41

作者：

You, Jiaqi ^{[1
]}

Liu, Zhenping ^{[1
]}

Qi, Zhengyang ^{[1
]}

Ma, Yizan ^{[1
]}

Sun, Mengling ^{[1
]}

Su, Ling ^{[1
]}

Niu, Hao ^{[1
]}

Peng, Yabing ^{[1
]}

Luo, Xuanxuan ^{[1
]}

Zhu, Mengmeng ^{[1
]}

Huang, Yuefan ^{[1
]}

Chang, Xing ^{[1
]}

Hu, Xiubao ^{[1
]}

Zhang, Yuqi ^{[1
]}

Pi, Ruizhen ^{[1
]}

Liu, Yuqi ^{[1
]}

Meng, Qingying ^{[1
]}

Li, Jianying ^{[1
]}

Zhang, Qinghua ^{[1
]}

Zhu, Longfu ^{[1
]}

Lin, Zhongxu ^{[1
]}

Min, Ling ^{[1
]}

Yuan, Daojun ^{[1
]}

Grover, Corrinne E. ^{[2
]}

Fang, David D. ^{[3
]}

Lindsey, Keith ^{[4
]}

Wendel, Jonathan F. ^{[2
]}

Tu, Lili ^{[1
]}

Zhang, Xianlong ^{[1
]}

Wang, Maojun ^{[1
]}

机构：

[1] Huazhong Agr Univ, Hubei Hongshan Lab, Natl Key Lab Crop Genet Improvement, Wuhan, Peoples R China

[2] Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA USA

[3] USDA ARS, Cotton Fiber Biosci Res Unit, Southern Reg Res Ctr, New Orleans, LA USA

[4] Univ Durham, Dept Biosci, Durham, England

来源：

NATURE GENETICS | 2023年 / 55卷 / 11期

基金：

中国国家自然科学基金;

关键词：

CELL ELONGATION; MODELS; DOMESTICATION; TRANSCRIPTOME; POLYPLOIDY; SELECTION; QUALITY;

D O I：

10.1038/s41588-023-01530-8

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between coresident subgenomes in polyploids remains to be understood. Here we document the genetic regulation of fiber development in allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes and 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 genetic modules that control staged fiber development and uncover genetic components governing their partitioned expression relative to subgenomic duplicated genes (homoeologs). Only about 30% of fiber quality-related homoeologs show phenotypically favorable allele aggregation in cultivars, highlighting the potential for subgenome additivity in fiber improvement. We envision a genome-enabled breeding strategy, with particular attention to 48 favorable alleles related to fiber phenotypes that have been subjected to purifying selection during domestication. Our work delineates the dynamics of gene regulation during fiber development and highlights the potential of subgenomic coordination underpinning phenotypes in polyploid plants.

引用

页码：1987 / +

页数：34

共 65 条

[1] Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation [J].

Baca, Sylvan C. ;

Singler, Cassandra ;

Zacharia, Soumya ;

Seo, Ji-Heui ;

Morova, Tunc ;

Hach, Faraz ;

Ding, Yi ;

Schwarz, Tommer ;

Huang, Chia-Chi Flora ;

Anderson, Jacob ;

Fay, Andre P. ;

Kalita, Cynthia ;

Groha, Stefan ;

Pomerantz, Mark M. ;

Wang, Victoria ;

Linder, Simon ;

Sweeney, Christopher J. ;

Zwart, Wilbert ;

Lack, Nathan A. ;

Pasaniuc, Bogdan ;

Takeda, David Y. ;

Gusev, Alexander ;

Freedman, Matthew L. .

NATURE GENETICS, 2022, 54 (09) :1364-+

[2] Unraveling cis and trans regulatory evolution during cotton domestication [J].

Bao, Ying ;

Hu, Guanjing ;

Grover, Corrinne E. ;

Conover, Justin ;

Yuan, Daojun ;

Wendel, Jonathan F. .

NATURE COMMUNICATIONS, 2019, 10 (1)

[3] Emergence of scaling in random networks [J].

Barabási, AL ;

Albert, R .

SCIENCE, 1999, 286 (5439) :509-512

[4]

Bastian M., 2009, INT AAAI C WEBL SOC, DOI [DOI 10.13140/2.1.1341.1520, 10.13140/2.1.1341.1520]

[5] The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation [J].

Birchler, James A. ;

Yang, Hua .

PLANT CELL, 2022, 34 (07) :2466-2474

[6] Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus [J].

Bird, Kevin A. ;

Niederhuth, Chad E. ;

Ou, Shujun ;

Gehan, Malia ;

Pires, J. Chris ;

Xiong, Zhiyong ;

VanBuren, Robert ;

Edger, Patrick P. .

NEW PHYTOLOGIST, 2021, 230 (01) :354-371

[7] Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy [J].

Blischak, Paul D. ;

Mabry, Makenzie E. ;

Conant, Gavin C. ;

Pires, J. Chris .

ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 49, 2018, 49 :253-278

[8] Trimmomatic: a flexible trimmer for Illumina sequence data [J].

Bolger, Anthony M. ;

Lohse, Marc ;

Usadel, Bjoern .

BIOINFORMATICS, 2014, 30 (15) :2114-2120

[9] Gene Expression Dominance in Allopolyploids: Hypotheses and Models [J].

Bottani, Samuel ;

Zabet, Nicolae Radu ;

Wendel, Jonathan F. ;

Veitia, Reiner A. .

TRENDS IN PLANT SCIENCE, 2018, 23 (05) :393-402

[10] The miR319-Targeted GhTCP4 Promotes the Transition from Cell Elongation to Wall Thickening in Cotton Fiber [J].

Cao, Jun-Feng ;

Zhao, Bo ;

Huang, Chao-Chen ;

Chen, Zhi-Wen ;

Zhao, Ting ;

Liu, Hong-Ru ;

Hu, Guan-Jing ;

Shangguan, Xiao-Xia ;

Shan, Chun-Min ;

Wang, Ling-Jian ;

Zhang, Tian-Zhen ;

Wendel, Jonathan F. ;

Guan, Xue-Ying ;

Chen, Xiao-Ya .

MOLECULAR PLANT, 2020, 13 (07) :1063-1077

← 1 2 3 4 5 6 7 →