PMID- 33613628
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20210223
IS  - 1664-8021 (Print)
IS  - 1664-8021 (Electronic)
IS  - 1664-8021 (Linking)
VI  - 12
DP  - 2021
TI  - Analysis of Structural Variants Reveal Novel Selective Regions in the Genome of 
      Meishan Pigs by Whole Genome Sequencing.
PG  - 550676
LID - 10.3389/fgene.2021.550676 [doi]
LID - 550676
AB  - Structural variants (SVs) represent essential forms of genetic variation, and 
      they are associated with various phenotypic traits in a wide range of important 
      livestock species. However, the distribution of SVs in the pig genome has not 
      been fully characterized, and the function of SVs in the economic traits of pig 
      has rarely been studied, especially for most domestic pig breeds. Meishan pig is 
      one of the most famous Chinese domestic pig breeds, with excellent reproductive 
      performance. Here, to explore the genome characters of Meishan pig, we construct 
      an SV map of porcine using whole-genome sequencing data and report 33,698 SVs in 
      305 individuals of 55 globally distributed pig breeds. We perform selective 
      signature analysis using these SVs, and a number of candidate variants are 
      successfully identified. Especially for the Meishan pig, 64 novel significant 
      selection regions are detected in its genome. A 140-bp deletion in the 
      Indoleamine 2,3-Dioxygenase 2 (IDO2) gene, is shown to be associated with 
      reproduction traits in Meishan pig. In addition, we detect two duplications only 
      existing in Meishan pig. Moreover, the two duplications are separately located in 
      cytochrome P450 family 2 subfamily J member 2 (CYP2J2) gene and phospholipase A2 
      group IVA (PLA2G4A) gene, which are related to the reproduction trait. Our study 
      provides new insights into the role of selection in SVs' evolution and how SVs 
      contribute to phenotypic variation in pigs.
CI  - Copyright (c) 2021 Du, Zheng, Zhao, Hu, Wang, Zhou and Liu.
FAU - Du, Heng
AU  - Du H
AD  - National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal 
      Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal 
      Science and Technology, China Agricultural University, Beijing, China.
FAU - Zheng, Xianrui
AU  - Zheng X
AD  - National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal 
      Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal 
      Science and Technology, China Agricultural University, Beijing, China.
FAU - Zhao, Qiqi
AU  - Zhao Q
AD  - National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal 
      Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal 
      Science and Technology, China Agricultural University, Beijing, China.
FAU - Hu, Zhengzheng
AU  - Hu Z
AD  - National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal 
      Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal 
      Science and Technology, China Agricultural University, Beijing, China.
FAU - Wang, Haifei
AU  - Wang H
AD  - College of Animal Science and Technology, Yangzhou University, Yangzhou, China.
FAU - Zhou, Lei
AU  - Zhou L
AD  - National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal 
      Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal 
      Science and Technology, China Agricultural University, Beijing, China.
FAU - Liu, Jian-Feng
AU  - Liu JF
AD  - National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal 
      Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal 
      Science and Technology, China Agricultural University, Beijing, China.
LA  - eng
PT  - Journal Article
DEP - 20210204
PL  - Switzerland
TA  - Front Genet
JT  - Frontiers in genetics
JID - 101560621
PMC - PMC7890942
OTO - NOTNLM
OT  - genome structural variants
OT  - pig
OT  - reproduction trait
OT  - selection signature
OT  - whole-genome sequencing
COIS- The authors declare that the research was conducted in the absence of any 
      commercial or financial relationships that could be construed as a potential 
      conflict of interest.
EDAT- 2021/02/23 06:00
MHDA- 2021/02/23 06:01
PMCR- 2021/02/04
CRDT- 2021/02/22 05:54
PHST- 2020/04/10 00:00 [received]
PHST- 2021/01/15 00:00 [accepted]
PHST- 2021/02/22 05:54 [entrez]
PHST- 2021/02/23 06:00 [pubmed]
PHST- 2021/02/23 06:01 [medline]
PHST- 2021/02/04 00:00 [pmc-release]
AID - 10.3389/fgene.2021.550676 [doi]
PST - epublish
SO  - Front Genet. 2021 Feb 4;12:550676. doi: 10.3389/fgene.2021.550676. eCollection 
      2021.