Pudong White pig: a unique genetic resource disclosed by sequencing data

Xiao, Qiang; Zhang, Z.; Sun, Hao; Wang, Qishan; Pan, Yuchun

doi:10.1017/s1751731116002494

Cited by 12 publications

(11 citation statements)

References 28 publications

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“…The effective population size in the last five generations was about 88 and was about 3018 in the 1000th generation. This value was larger than that reported by Xiao et al (2017) for pig breeds in the Taihu region of China (ranging from 47 to 71) using the same method, therefore, this may indicate higher genetic diversity in Jinhua pigs.…”

Section: Resultscontrasting

confidence: 73%

“…SNP calling was performed using SAMTOOLS v0.1.19 and the missing genotypes were imputed using BEAGLE (Howie et al, 2009; Li et al, 2009). Additional quality controls were applied following Xiao et al (2017). These included a minimum number of samples genotyped > 30%, a calling quality > 20 (99% accuracy), and a minor allele frequency (MAF) ≥ 5%.…”

Section: Methodsmentioning

confidence: 99%

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Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data

Sun

Zhang

et al. 2019

Front. Genet.

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Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest. Here, we investigated the occurrence and distribution of ROH using next-generation sequencing data to characterize autozygosity in 202 Jinhua pigs, as well as to identify the genomic regions with high ROH frequencies within individuals. The average inbreeding coefficient, based on ROH longer than 1 Mb, was 0.168 ± 0.052. In total, 18,690 ROH were identified in all individuals, among which shorter segments (1–5 Mb) predominated. Individual ROH autosome coverage ranged from 5.32 to 29.14% in the Jinhua population. On average, approximately 16.8% of the whole genome was covered by ROH segments, with the lowest coverage on SSC11 and the highest coverage on SSC17. A total of 824 SNPs (about 0.5%) and 11 ROH island regions were identified (occurring in over 45% of the samples). Genes associated with reproduction ( HOXA3, HOXA7, HOXA10 , and HOXA11 ), meat quality ( MYOD1, LPIN3 , and CTNNBL1 ), appetite ( NUCB2 ) and disease resistance traits ( MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8 , and MYLK ) were identified in ROH islands. Moreover, several quantitative trait loci for ham weight and ham fat thickness were detected. Genes in ROH islands suggested, at least partially, a selection for economic traits and environmental adaptation, and should be subject of future investigation. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the pig genome.

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Section: Resultscontrasting

confidence: 73%

Section: Methodsmentioning

confidence: 99%

Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data

Sun

Zhang

et al. 2019

Front. Genet.

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“…; Xiao et al . ,b), except for Pietrain and Berkshire pigs. The Pietrain and Berkshire individuals were genotyped according to the protocol of GGRS (Chen et al .…”

Section: Methodsmentioning

confidence: 99%

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Zhang

Xiao

et al. 2018

Animal Genetics

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Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity (ROH) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reducedrepresentation sequencing method. After imputation and quality control, 60 850 highconfidence SNPs were retained for ROH detection. A simulation was performed to explore the reliability of ROH detection with imputed data. Different ROH-related variables were compared between imputed and non-missing genotypes used in ROH detection. Furthermore, ROH islands were evaluated and annotated to find genes influenced by inbreeding in these pigs. The simulation results showed that imputed data with 0.7 as the average missing genotype rate and three heterozygotes allowed in a sliding window have comparable ROH detected compared with data with no missing genotypes. Compared with Western pig breeds, Chinese pigs had more autosomes covered by ROH longer than 5 Mb, indicating higher inbreeding in Chinese pigs in recent times. Genes related to reproduction, immunity, meat quality and adaptability in Chinese pigs and several genes related to growth speed and immunity in Western pigs were observed in short ROH islands. The reproduction-related gene PRM1 was found to be located in the most frequent long ROH island in Chinese pigs, which might explain the decreasing fertility in Chinese pig breeds.

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“…We observed the lowest cross-validation error when K = 7 ( Figure 1B ), before PD separated from MMS into a different cluster. Suggesting a continuous gene flow between PD and the MMS breed ( Xiao et al, 2017a ). Consistent with previous findings and the genetic origins of worldwide pig breeds ( Fan et al, 2002 ; Ai et al, 2013 ; Zhang et al, 2018 ), K = 2 shows the ancient divergence between Asian and European pigs, indicating that the MMS breed was the ancestral population of the Chinese pigs examined in our study.…”

Section: Resultsmentioning

confidence: 99%

Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed

Oyelami

Zhao

et al. 2020

Front. Genet.

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The Jiangquhai (JQ) pig breed is one of the most widely recognized pig populations in China due to its unique and dominant characteristics. In this study, we examined the extent of Linkage disequilibrium (LD) and haplotype block structure of the JQ pig breed, and scanned the blocks for possible genes underlying important QTLs that could either be responsible for some adaptive features in these pigs or might have undergone some selection pressure. We compared some of our results with other Chinese and Western pig breeds. The results show that the JQ breed had the highest total block length (349.73 Mb ≈ 15% of its genome), and the coverage rate of blocks in most of its chromosomes was larger than those of other breeds except for Sus scrofa chromosome 4 (SSC4), SSC6, SSC7, SSC8, SSC10, SSC12, SSC13, SSC14, SSC17, SSC18, and SSCX. Moreover, the JQ breed had more SNPs that were clustered into haplotype blocks than the other breeds examined in this study. Our shared and unique haplotype block analysis revealed that the Hongdenglong (HD) breed had the lowest percentage of shared haplotype blocks while the Shanzhu (SZ) breed had the highest. We found that the JQ breed had an average r 2 > 0.2 at SNPs distances 10–20 kb and concluded that about 120,000–240,000 SNPs would be needed for a successful GWAS in the breed. Finally, we detected a total of 88 genes harbored by selected haplotype blocks in the JQ breed, of which only 4 were significantly enriched ( p-value ≤ 0.05). These genes were significantly enriched in 2 GO terms ( p-value < 0.01), and 2 KEGG pathways ( p-value < 0.02). Most of these enriched genes were related to health. Also, most of the overlapping QTLs detected in the haplotype blocks were related to meat and carcass quality, as well as health, with a few of them relating to reproduction and production. These results provide insights into the genetic architecture of some adaptive and meat quality traits observed in the JQ pig breed and also revealed the pattern of LD in the genome of the pig. Our result provides significant guidance for improving the statistical power of GWAS and optimizing the conservation strategy for this JQ pig breed.

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Pudong White pig: a unique genetic resource disclosed by sequencing data

Cited by 12 publications

References 28 publications

Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data

Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed

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