Population structure and genetic diversity of four Henan pig populations

Qiao, Ruimin; Han, Xuelei; Wang, K.; Lv, Guoguo; Ren, Guoqing; Li, Xiuling

doi:10.1111/age.12775

Cited by 18 publications

(14 citation statements)

References 24 publications

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“…Three indigenous pig breeds, the Nanyang Black pig (NY), the Huainan pig (HN), and the Queshan black pig (QS), have been named based on the classification scheme from the National Commission of Animal Genetics resource book (2011). These three pig breeds exhibited strong disease-resistance, high meat yield and early maturation (Qiao et al, 2019). Low density SNP analysis revealed that there has been admixture between Henan indigenous pigs and European commercial pigs (Qiao et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…These three pig breeds exhibited strong disease-resistance, high meat yield and early maturation (Qiao et al, 2019). Low density SNP analysis revealed that there has been admixture between Henan indigenous pigs and European commercial pigs (Qiao et al, 2019). However, the genomic differences and potential role of introgression in Henan indigenous pigs is still unclear.…”

Section: Introductionmentioning

confidence: 99%

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Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

et al. 2021

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Introgression of genetic features from European pigs into Chinese pigs was reported possibly contributing to improvements in productivity traits, such as feed conversion efficiency and body size. However, the genomic differences from European pigs and the potential role of introgression in Henan indigenous pigs remains unclear. In this study, we found significant introgression from European pigs into the genome of Chinese indigenous pigs, especially in Henan indigenous pigs. The introgression in Henan indigenous pigs, particularly in the Nanyang black pig, was mainly derived from Duroc pigs. Most importantly, we found that the NR6A1, GPD2, and CSRNP3 genes were introgressed and reshaped by artificial selection, and these may have contributed to increases in pig body size and feed conversion efficiency. Our results suggest that human-mediated introgression and selection have reshaped the genome of Henan pigs and improved several of their desired traits. These findings contribute to our understanding of the history of Henan indigenous pigs and provide insights into the genetic mechanisms affecting economically important traits in pig populations.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

et al. 2021

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“…The Nanyang black breed of pig is indigenous to the central region of China [ 13 ]. Mineral content, marble stripes, meat color, and IMF content in Nanyang black pigs is significantly higher than those in imported breeds ( P < 0.01) [ 14 – 16 ]. The Nanyang black pig is, thus, an ideal research model for lipid deposition.…”

Section: Introductionmentioning

confidence: 99%

Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs

Wang

Zhang

et al. 2021

BMC Genomics

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Background Lower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence. One such breed, the Nanyang black pig, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model in which to investigate lipid position trait mechanisms in pigs. An understanding of lipid deposition in pigs might improve pig meat traits in future breeding and promote the selection progress of pigs through modern molecular breeding techniques. Here, transcriptome and tandem mass tag-based quantitative proteome (TMT)-based proteome analyses were carried out using longissimus dorsi (LD) tissues from individual Nanyang black pigs that showed high levels of genetic variation. Results A large population of Nanyang black pigs was phenotyped using multi-production trait indexes, and six pigs were selected and divided into relatively high and low lipid deposition groups. The combined transcriptomic and proteomic data identified 15 candidate genes that determine lipid deposition genetic divergence. Among them, FASN, CAT, and SLC25A20 were the main causal candidate genes. The other genes could be divided into lipid deposition-related genes (BDH2, FASN, CAT, DHCR24, ACACA, GK, SQLE, ACSL4, and SCD), PPARA-centered fat metabolism regulatory factors (PPARA, UCP3), transcription or translation regulators (SLC25A20, PDK4, CEBPA), as well as integrin, structural proteins, and signal transduction-related genes (EGFR). Conclusions This multi-omics data set has provided a valuable resource for future analysis of lipid deposition traits, which might improve pig meat traits in future breeding and promote the selection progress in pigs, especially in Nanyang black pigs.

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“…Exploring the genetic characterization of DSE pigs could help for preserving genomic variability, advancing scientific conservation, and contributing to sustainability ( Weitzman, 1993 ). Population genetic data, such as single-nucleotide polymorphism (SNP), are often used to demonstrate population structure and genetic diversity in some other Chinese indigenous pigs, such as Jiangxi native pigs, Henan native pigs, Taihu native pigs, and so on ( Wang et al, 2018 ; Qiao et al, 2019 ; Zhao et al, 2019 ). But limited genetic information–associated literatures were reported about DSE pigs, which reflected that people know little about genetic characteristics of DSE pigs.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing

Sun

et al. 2020

Front. Genet.

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Genetic characterization of Chinese indigenous pig breeds is essential to promote scientific conservation and sustainable development of pigs. Here, we systematically surveyed the genomes of 75 unrelated Diannan small-ear (DSE) pigs from three diverse regions (Yingjiang County, Jinping County, and Sipsongpanna in Yunnan Province) to describe their population structures, genetic diversity, inbreeding coefficients, and selection signatures. First, these individuals were sequenced and genotyped using the genome reducing and sequencing (GGRS) protocol. A total of 438,038 autosomal single-nucleotide polymorphisms (SNPs) were obtained and used for subsequent statistical analysis. The results showed that these DSE pigs were clearly differentiated into three separate clades revealed by the population structure and principal component analysis, which is consistent with their geographical origins. Diannan small-ear pigs owned lower genetic diversity when compared with some other pig breeds, which demonstrated the need to strengthen the conservation strategies for DSE pigs. In addition, the inbreeding coefficients based on runs of homozygosity (ROH) length (F ROH) were calculated in each ROH length categories, respectively. And the results indicated that the ancient (up to 50 generations ago) inbreeding had greater impacts than recent (within the last five generations) inbreeding within DSE pigs. Some candidate selection signatures within the DSE pig population were detected through the ROH islands and integrated haplotype homozygosity score (iHS) methods. And genes associated with meat quality (COL15A1, RPL3L, and SLC9A3R2), body size (PALM2-AKAP2, NANS, TRAF7, and PACSIN1), adaptability (CLDN9 and E4F1), and appetite (GRM4) were identified. These findings can help to understand the genetic characteristics and provide insights into the molecular background of special phenotypes of DSE pigs to promote conservation and sustainability of the breed.

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Population structure and genetic diversity of four Henan pig populations

Cited by 18 publications

References 24 publications

Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs

Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing

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