Genome-wide recombination rate variation in a recombination map of cotton

被引:23
作者
Shen, Chao [1 ]
Li, Ximei [1 ,2 ]
Zhang, Ruiting [1 ]
Lin, Zhongxu [1 ]
机构
[1] Huazhong Agr Univ, Coll Plant Sci & Technol, Natl Key Lab Crop Genet Improvement, Wuhan, Hubei, Peoples R China
[2] Qingdao Agr Univ, Coll Agron & Plant Protect, Shandong Key Lab Dryland Farming Technol, Qingdao, Shandong, Peoples R China
来源
PLOS ONE | 2017年 / 12卷 / 11期
基金
中国国家自然科学基金;
关键词
MEIOTIC RECOMBINATION; PROVIDES INSIGHTS; EVOLUTION; SEQUENCE; GENES; RESISTANCE; DATABASE; MAIZE; TOOL; HOT;
D O I
10.1371/journal.pone.0188682
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Recombination is crucial for genetic evolution, which not only provides new allele combinations but also influences the biological evolution and efficacy of natural selection. However, recombination variation is not well understood outside of the complex species' genomes, and it is particularly unclear in Gossypium. Cotton is the most important natural fibre crop and the second largest oil-seed crop. Here, we found that the genetic and physical maps distances did not have a simple linear relationship. Recombination rates were unevenly distributed throughout the cotton genome, which showed marked changes along the chromosome lengths and recombination was completely suppressed in the centromeric regions. Recombination rates significantly varied between A-subgenome (At) (range = 1.60 to 3.26 centimorgan/megabase [cM/Mb]) and D-subgenome (Dt) (range = 2.17 to 4.97 cM/Mb), which explained why the genetic maps of At and Dt are similar but the physical map of Dt is only half that of At. The translocation regions between A02 and A03 and between A04 and A05, and the inversion regions on A10, D10, A07 and D07 indicated relatively high recombination rates in the distal regions of the chromosomes. Recombination rates were positively correlated with the densities of genes, markers and the distance from the centromere, and negatively correlated with transposable elements (TEs). The gene ontology (GO) categories showed that genes in high recombination regions may tend to response to environmental stimuli, and genes in low recombination regions are related to mitosis and meiosis, which suggested that they may provide the primary driving force in adaptive evolution and assure the stability of basic cell cycle in a rapidly changing environment. Global knowledge of recombination rates will facilitate genetics and breeding in cotton.
引用
收藏
页数:15
相关论文
共 50 条
[41]   Genome-wide analysis of human hotspot intersected genes highlights the roles of meiotic recombination in evolution and disease [J].
Tao Zhou ;
Zhibin Hu ;
Zuomin Zhou ;
Xuejiang Guo ;
Jiahao Sha .
BMC Genomics, 14
[42]   Genome-wide characterization and expression analysis of Erf gene family in cotton [J].
Zafar, Muhammad Mubashar ;
Rehman, Abdul ;
Razzaq, Abdul ;
Parvaiz, Aqsa ;
Mustafa, Ghulam ;
Sharif, Faiza ;
Mo, Huijuan ;
Youlu, Yuan ;
Shakeel, Amir ;
Ren, Maozhi .
BMC PLANT BIOLOGY, 2022, 22 (01)
[43]   Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation [J].
Pinosio, Sara ;
Giacomello, Stefania ;
Faivre-Rampant, Patricia ;
Taylor, Gail ;
Jorge, Veronique ;
Le Paslier, Marie Christine ;
Zaina, Giusi ;
Bastien, Catherine ;
Cattonaro, Federica ;
Marroni, Fabio ;
Morgante, Michele .
MOLECULAR BIOLOGY AND EVOLUTION, 2016, 33 (10) :2706-2719
[44]   Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis [J].
Lee, Isaiah Paolo A. ;
Andam, Cheryl P. .
SCIENTIFIC REPORTS, 2022, 12 (01)
[45]   Genome-wide analysis of the WRKY gene family in cotton [J].
Dou, Lingling ;
Zhang, Xiaohong ;
Pang, Chaoyou ;
Song, Meizhen ;
Wei, Hengling ;
Fan, Shuli ;
Yu, Shuxun .
MOLECULAR GENETICS AND GENOMICS, 2014, 289 (06) :1103-1121
[46]   Genome-Wide Variation in Betacoronaviruses [J].
LaTourrette, Katherine ;
Holste, Natalie M. ;
Rodriguez-Pena, Rosalba ;
Leme, Raquel Arruda ;
Garcia-Ruiz, Hernan .
JOURNAL OF VIROLOGY, 2021, 95 (15)
[47]   A Sequence-Anchored Linkage Map of the Plant-Parasitic Nematode Meloidogyne hapla Reveals Exceptionally High Genome-Wide Recombination [J].
Thomas, Varghese P. ;
Fudali, Sylwia L. ;
Schaff, Jennifer E. ;
Liu, Qingli ;
Scholl, Elizabeth H. ;
Opperman, Charles H. ;
Bird, David McK. ;
Williamson, Valerie M. .
G3-GENES GENOMES GENETICS, 2012, 2 (07) :815-824
[48]   Elite durum wheat genetic map and recombination rate variation in a multiparental connected design [J].
Vaissayre, Laurence ;
Ardisson, Morgane ;
Borries, Christiane ;
Santoni, Sylvain ;
David, Jacques ;
Roumet, Pierre .
EUPHYTICA, 2012, 185 (01) :61-75
[49]   A genome-wide map of circular RNAs in adult zebrafish [J].
Sharma, Disha ;
Sehgal, Paras ;
Mathew, Samatha ;
Vellarikkal, Shamsudheen Karuthedath ;
Singh, Angom Ramcharan ;
Kapoor, Shruti ;
Jayarajan, Rijith ;
Scaria, Vinod ;
Sivasubbu, Sridhar .
SCIENTIFIC REPORTS, 2019, 9 (1)
[50]   Genomic prediction of the recombination rate variation in barley - A route to highly recombinogenic genotypes [J].
Casale, Federico ;
Van Inghelandt, Delphine ;
Weisweiler, Marius ;
Li, Jinquan ;
Stich, Benjamin .
PLANT BIOTECHNOLOGY JOURNAL, 2022, 20 (04) :676-690