Genome Data Uncover Conservation Status, Historical Relatedness and Candidate Genes Under Selection in Chinese Indigenous Pigs in the Taihu Lake Region

Liu, Chenxi; Li, Pinghua; Zhou, Wuduo; Ma, Xianlei; Wang, Xiaopeng; Xu, Yan; Jiang, Nengjing; Zhao, Moran; Zhou, Tianwei; Yin, Yanzhen; Ren, Jun; Huang, Ruihua

doi:10.3389/fgene.2020.00591

Cited by 18 publications

(24 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The LD extent (r 2 = 0.3) in Xidu black pigs was about 25 Kb. This value was less than 79.54 Kb (r 2 = 0.3) for Meishan pigs (one of the original parental breed) obtained by the same method (Liu et al, 2020). The effectiveness of GWAS and genomic selection (GS) relies on the LD between the markers.…”

Section: Linkage Disequilibriummentioning

confidence: 86%

Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed

Mei

Zhou

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

The primary purpose of the current study was to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore hotspot regions for traces of selection. First, we estimated the length, number, and frequency of ROH in 262 Xidu black pigs using the Porcine SNP50 BeadChip and compared the estimates of inbreeding coefficients, which were calculated based on ROHs (FROH) and homozygosity (FHOM). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In addition, Sus scrofa chromosome (SSC) 8 and SSC10, respectively, has the highest and lowest chromosome coverage by ROH. These results suggest that inbreeding estimation based on total ROH may be a useful method, especially for crossbreed or composite populations. We also calculated an inbreeding coefficient of 0.077 from the total ROH. Eight ROH islands were found in this study. These ROH islands harbored genes associated with fat deposition, muscular development, reproduction, ear shape, and adaptation, such as TRAF7, IGFBP7, XPO1, SLC26A8, PPARD, and OR1F1. These findings may help to understand the effects of environmental and artificial selection on the genome structure of composite pigs. Our results provide a basis for subsequent genomic selection (GS), and provides a reference for the hybrid utilization of other pig breeds.

show abstract

Section: Linkage Disequilibriummentioning

confidence: 86%

Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed

Mei

Zhou

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

show abstract

“…Both Meishan and Erhualian were representative breeds of the Taihu Lake (TL) region of Eastern China. These breeds have been documented with exceptional prolificacy [ 37 ] and were also part of our clustered heatmap result. There was a vast difference between the highly prolific Chinese Taihu breeds and European breeds [ 38 ] in relation to the litter size.…”

Section: Discussionmentioning

confidence: 87%

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes

D’Alessandro

Asare

Zheng

et al. 2022

Genes

View full text Add to dashboard Cite

Retrotransposons account for more than one-third of the pig reference genome. On account of the genome variability in different breeds, structural variation (SV) caused by retrotransposon-generated deletion or insertion may have a function in the genome. Litter size is one of the most important reproductive traits and significantly impacts profitability in terms of pig production. We used the method of bioinformatics, genetics, and molecular biology to make an analysis among different pig genomes. Predicted 100 SVs were annotated as retrotransposon in 20 genes related to reproduction. The PCR detection based on these predicted SVs revealed 20 RIPs in 20 genes, that most RIPs (12) were generated by SINE insertion or deletion (indel), and nine RIPs were generated by the ERV indel. We selected 12 RIPs to make the second PCR detection in 24 individuals among nine pig breeds. The PCR detection results revealed that the RIP-A1CF-4 insertion in the breed of Bama, Large White, and Meishan only had the homozygous genotype but low to moderately polymorphisms were present in other breeds. We found that RIP-CWH43-9, RIP-IDO2-9, RIP-PRLR-6, RIP-VMP1-12, and RIP-OPN-1 had a rich polymorphism in the breed of Large White pigs. The statistical analysis revealed that RIP-CWH43-9 had a SINE insertion profitable to the reproductive traits of TNB and NBA but was significantly affected (p < 0.01) and (p < 0.05) in the reproductive traits of litter birthweight (LW) in Large White. On the other hand, the SINE insertion in IDO2-9 may be a disadvantage to the reproductive trait of LW, which was significantly affected (p < 0.05) in Large White. These two RIPs are significant in pig genome research and could be useful molecular markers in the breeding system.

show abstract

“…Laiwu pig (He = 0.380) [19], Erhualian pig (He = 0.378) and Meishan pig (He = 0.382) [20]. The low expected heterozygosity of the Min pig conserved population indicates that many SNPs loci have tended to be pure, and may be undergoing inbred…”

Section: Genetic Diversity Of the Min Pig Conserved Populationmentioning

confidence: 99%

Single nucleotide polymorphism-based analysis of the genetic structure of the Min pig conserved population

Meng

Cai²,

Wang³

et al. 2022

Anim Biosci

View full text Add to dashboard Cite

Objective:The study aims toIn order to protect and utilize the genetic resources of Min pig, this paper uncovered the genetic diversity and unique genetic structure of the Min pig conserved population, divided the nucleus conservation population, and constructed the molecular pedigree. Methods: We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂，63♀) in the Min pig conserved population from Lanxi breeding Farm.A c c e p t e d A r t i c l e 3 Results: We showed that tThe polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335 and 0.330, respectively. The pedigree-based inbreeding coefficients (FPED) was significantly different from those estimated from runs of homozygosity (FROH) and single nucleotide polymorphism (FSNP) based on genome, . but Tthe pearson correlation coefficient between FROH and FSNP was significant (P < 0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40 < r < 1.50), and increased significantly in the last 5 generations (r = 2.6). According to the composition of Chinese lineage, we separated the nucleus conservation population (81 individuals) and the candidate conservation population (13 individuals) of Min pig, then the nucleus conservation population of Min pig was divided into 9 families by genomic information matrix. Conclusion:The results illuminated thatOur study indicated that the genetic diversity of the Min pig conserved population was inadequate. Due to the introgression of European commercial pig breeds and the unscientific breeding process, it is necessary for Min pig to construct the molecular pedigree of the nucleus conservation population.

show abstract

Genome Data Uncover Conservation Status, Historical Relatedness and Candidate Genes Under Selection in Chinese Indigenous Pigs in the Taihu Lake Region

Cited by 18 publications

References 52 publications

Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed

Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes

Single nucleotide polymorphism-based analysis of the genetic structure of the Min pig conserved population

Contact Info

Product

Resources

About