Identifying the unique characteristics of the Chinese indigenous pig breeds in the Yangtze River Delta region for precise conservation

Zhao, Qi; Oyelami, Favour Oluwapelumi; Qadri, Qamar Raza; Sun, Hao; Xu, Zhi-Hong; Wang, Qishan; Pan, Yuchun

doi:10.1186/s12864-021-07476-7

Cited by 13 publications

(10 citation statements)

References 22 publications

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“…The data analyzed in this study were derived from a 62,822 SNP genotype file for 24 pig breeds, including 159 individuals from 5 cosmopolitan breeds and 910 individuals from 19 indigenous breeds in the Yangtze River region of China. The data were generated by Zhao et al [ 1 ] and are publicly available at the website ( , accessed on 6 June 2022). In order to keep the number of individuals involved in the analysis above 20 for each Chinese indigenous pig breed, we removed the data from the genotype file for one breed (Dongchuan pigs, DC) because it contained only 10 individuals.…”

Section: Methodsmentioning

confidence: 99%

“…There are many indigenous pig breeds in China; according to statistics, there are about 108 local pig breeds or strains. For example, the Taihu pig, known for its high fertility, can be divided into seven breeds based on its unique characteristics or traits [ 1 ]. However, due to a small population size, some breeds are gradually inbreeding and becoming degraded or even extinct.…”

Section: Introductionmentioning

confidence: 99%

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Screening Discriminating SNPs for Chinese Indigenous Pig Breeds Identification Using a Random Forests Algorithm

Gao

Sun

Zhang

et al. 2022

Genes

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Chinese indigenous pig breeds have unique genetic characteristics and a rich diversity; however, effective breed identification methods have not yet been well established. In this study, a genotype file of 62,822 single-nucleotide polymorphisms (SNPs), which were obtained from 1059 individuals of 18 Chinese indigenous pig breeds and 5 cosmopolitan breeds, were used to screen the discriminating SNPs for pig breed identification. After linkage disequilibrium (LD) pruning filtering, this study excluded 396 SNPs on non-constant chromosomes and retained 20.92~−27.84% of SNPs for each of the 18 autosomes, leaving a total of 14,823 SNPs. The principal component analysis (PCA) showed the largest differences between cosmopolitan and Chinese pig breeds (PC1 = 10.452%), while relatively small differences were found among the 18 indigenous pig breeds from the Yangtze River Delta region of China. Next, a random forest (RF) algorithm was used to filter these SNPs and obtain the optimal number of decision trees (ntree = 1000) using corresponding out-of-bag (OOB) error rates. By comparing two different SNP ranking methods in the RF analysis, the mean decreasing accuracy (MDA) and mean decreasing Gini index (MDG), the effects of panels with different numbers of SNPs on the assignment accuracy, and the statistics of SNP distribution on each chromosome in the panels, a panel of 1000 of the most breed-discriminative tagged SNPs were finally selected based on the MDA screening method. A high accuracy (>99.3%) was obtained by the breed prediction of 318 samples in the RF test set; thus, a machine learning classification method was established for the multi-breed identification of Chinese indigenous pigs based on a low-density panel of SNPs.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Screening Discriminating SNPs for Chinese Indigenous Pig Breeds Identification Using a Random Forests Algorithm

Gao

Sun

Zhang

et al. 2022

Genes

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“…NY pigs were collected from Xichuan County; QS pigs from Queshan County; HN pigs from Gushi County; and YX pigs from Luanchuan County of Henan Province, China. Total DNA of these individuals was extracted using the phenol–chloroform method (Zhao et al, 2021) and qualified by Nanodrop 1000 and 1% agarose gel electrophoresis.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds

Zhang

et al. 2022

Animal Genetics

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Mitochondria follow non‐Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities.

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“…Yunnan Province is located in southwest China, with unique geographical and climatic characteristics and abundant genetic resources of pig breeds. Protecting these native breeds is of great importance for the sustainable development of the pig industry and for global genetic diversity (Zhao et al, 2021). At present, there are no reports on the use of antibiotics in different local pig breeds.…”

Section: Introductionmentioning

confidence: 99%

Comparative Analyses of Antibiotic Resistance Genes in Jejunum Microbiota of Pigs in Different Areas

Yang²,

Ma³

et al. 2022

Front. Cell. Infect. Microbiol.

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Antibiotic resistance genes (ARGs) are emerging environmental contaminants that threaten human and animal health. Intestinal microbiota may be an important ARGs repository, and intensive animal farming is a likely contributor to the environmental burden of ARGs. Using metagenomic sequencing, we investigated the structure, function, and drug resistance of the jejunal microbial community in Landrace (LA, Kunming), Saba (SB, Kunming), Dahe (DH, Qujing), and Diannan small-ear piglets (DS, Xishuangbanna) from different areas in Yunnan Province, China. Remarkable differences in jejunal microbial diversity among the different pig breeds, while the microbial composition of pig breeds in close areas tends to be similar. Functional analysis showed that there were abundant metabolic pathways and carbohydrate enzymes in all samples. In total, 32,487 ARGs were detected in all samples, which showed resistance to 38 categories of drugs. The abundance of ARGs in jejunum was not significantly different between LA and SB from the same area, but significantly different between DS, DH and LA or SB from different areas. Therefore, the abundance of ARGs was little affected by pig breeds and microorganism community structure, but it was closely related to geographical location. In addition, as a probiotic, Lactobacillus amylovorus is also an important ARGs producing bacterium. Our results revealed the antibiotic exposure and intestinal microbial resistance of farms in the study areas, which could provide basic knowledge and potential strategies for rational use of antibiotics and reducing the risk of ARGs transmission in animal husbandry.

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Identifying the unique characteristics of the Chinese indigenous pig breeds in the Yangtze River Delta region for precise conservation

Cited by 13 publications

References 22 publications

Screening Discriminating SNPs for Chinese Indigenous Pig Breeds Identification Using a Random Forests Algorithm

Screening Discriminating SNPs for Chinese Indigenous Pig Breeds Identification Using a Random Forests Algorithm

Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds

Comparative Analyses of Antibiotic Resistance Genes in Jejunum Microbiota of Pigs in Different Areas

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