PMID- 36553577
OWN - NLM
STAT- MEDLINE
DCOM- 20221226
LR  - 20230109
IS  - 2073-4425 (Electronic)
IS  - 2073-4425 (Linking)
VI  - 13
IP  - 12
DP  - 2022 Dec 8
TI  - Detection of Selection Signatures in Anqing Six-End-White Pigs Based on 
      Resequencing Data.
LID - 10.3390/genes13122310 [doi]
LID - 2310
AB  - As a distinguished Chinese indigenous pig breed that exhibits disease resistance 
      and high meat quality, the Anqing six-end-white (AQ) pig represents a valuable 
      germplasm resource for improving the quality of the pig breeding industry. In 
      this study, 24 AQ pigs that were distantly blood-related and 6 Asian Wild Boar 
      (AWB) were selected for 10x deep-genome resequencing. The signatures of the 
      selection were analyzed to explore the genetic basis of their germplasm 
      characteristics and to identify excellent germplasm-related functional genes 
      based on NGS data. A total of 49,289,052 SNPs and 6,186,123 indels were detected 
      across the genome in 30 pigs. Most of the genetic variations were synonym 
      mutations and existed in the intergenic region. We identified 275 selected 
      regions (top 1%) harboring 85 genes by applying a crossover approach based on 
      genetic differentiation (F(ST)) and polymorphism levels (pi ratio). Some genes 
      were found to be positively selected in AQ pigs' breeding. The SMPD4 and DDX18 
      genes were involved in the immune response to pseudorabies virus (PRV) and 
      porcine reproductive and respiratory syndrome virus (PRRSV). The BCL6 and P2RX6 
      genes were involved in biological regulation of immune T cells and phagocytes. 
      The SLC7A4 and SPACA4 genes were related to reproductive performance. The MSTN 
      and HIF1A genes were related to fat deposition and muscle development. Moreover, 
      138 overlapping regions were detected in selected regions and ROH islands of AQ 
      pigs. Additionally, we found that the QTLs with the most overlapping regions were 
      related to back fat thickness, meat color, pH value, fatty acid content, immune 
      cells, parasitic immunity, and bacterial immunity. Based on functional enrichment 
      analysis and QTLs mapping, we conducted further research on the molecular genetic 
      basis of germplasm traits (disease resistance and excellent meat quality). These 
      results are a reliable resource for conserving germplasm resources and exploiting 
      molecular markers of AQ pigs.
FAU - Chen, Yige
AU  - Chen Y
AD  - College of Animal Science and Technology, Anhui Agricultural University, Hefei 
      230036, China.
FAU - Wu, Xudong
AU  - Wu X
AD  - Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety 
      Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy 
      of Agricultural Sciences, Hefei 230031, China.
FAU - Wang, Jinglin
AU  - Wang J
AD  - College of Animal Science and Technology, Anhui Agricultural University, Hefei 
      230036, China.
FAU - Hou, Yinhui
AU  - Hou Y
AD  - College of Animal Science and Technology, Anhui Agricultural University, Hefei 
      230036, China.
FAU - Liu, Ying
AU  - Liu Y
AD  - College of Animal Science and Technology, Anhui Agricultural University, Hefei 
      230036, China.
FAU - Wang, Bo
AU  - Wang B
AD  - College of Animal Science and Technology, Anhui Agricultural University, Hefei 
      230036, China.
FAU - Hu, Xiaojing
AU  - Hu X
AD  - College of Animal Science and Technology, Anhui Agricultural University, Hefei 
      230036, China.
FAU - Zheng, Xianrui
AU  - Zheng X
AD  - College of Animal Science and Technology, Anhui Agricultural University, Hefei 
      230036, China.
FAU - Zhang, Xiaodong
AU  - Zhang X
AD  - College of Animal Science and Technology, Anhui Agricultural University, Hefei 
      230036, China.
FAU - Ding, Yueyun
AU  - Ding Y
AD  - College of Animal Science and Technology, Anhui Agricultural University, Hefei 
      230036, China.
FAU - Yin, Zongjun
AU  - Yin Z
AD  - College of Animal Science and Technology, Anhui Agricultural University, Hefei 
      230036, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20221208
PL  - Switzerland
TA  - Genes (Basel)
JT  - Genes
JID - 101551097
SB  - IM
MH  - Swine/genetics
MH  - Animals
MH  - *Sus scrofa/genetics
MH  - *Disease Resistance/genetics
MH  - Sequence Analysis, DNA
MH  - Phenotype
MH  - Quantitative Trait Loci/genetics
PMC - PMC9777694
OTO - NOTNLM
OT  - Anqing six-end-white pig
OT  - gene enrichment analyses
OT  - genetic diversity
OT  - positive selection
OT  - single nucleotide polymorphism
COIS- The authors declare no conflict of interest.
EDAT- 2022/12/24 06:00
MHDA- 2022/12/27 06:00
PMCR- 2022/12/08
CRDT- 2022/12/23 01:22
PHST- 2022/11/15 00:00 [received]
PHST- 2022/12/02 00:00 [revised]
PHST- 2022/12/04 00:00 [accepted]
PHST- 2022/12/23 01:22 [entrez]
PHST- 2022/12/24 06:00 [pubmed]
PHST- 2022/12/27 06:00 [medline]
PHST- 2022/12/08 00:00 [pmc-release]
AID - genes13122310 [pii]
AID - genes-13-02310 [pii]
AID - 10.3390/genes13122310 [doi]
PST - epublish
SO  - Genes (Basel). 2022 Dec 8;13(12):2310. doi: 10.3390/genes13122310.