Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Wang, Shiyuan; Yang, Jie; Li, Guixin; Ding, Rongrong; Zhuang, Zhanwei; Ruan, Donglin; Wu, Jie; Yang, Huaqiang; Zheng, Enqin; Cai, Guangyan; Wang, Xiaopeng; Wu, Zhenfang

doi:10.3389/fvets.2022.855933

Cited by 3 publications

(3 citation statements)

References 67 publications

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“…Demographic events like population bottlenecks, genetic drift, and inbreeding primarily contribute to the formation of ROH [ 10 , 11 ]. These homogenous DNA segments are instrumental in the analysis of inbreeding in livestock species [ 12 , 13 , 14 ]. In livestock, the length of ROH segments serves as an indicator of the level of inbreeding, with longer ROH segments denoting recent inbreeding events and shorter segments indicating inbreeding that occurred earlier in the generations [ 15 , 16 ].…”

Section: Introductionmentioning

confidence: 99%

Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China

Huang,

Zhao,

Chen

et al. 2024

Genes

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Runs of Homozygosity (ROH) are continuous homozygous DNA segments in diploid genomes, which have been used to estimate the genetic diversity, inbreeding levels, and genes associated with specific traits in livestock. In this study, we analyzed the resequencing data from 10 local goat breeds in Yunnan province of China and five additional goat populations obtained from a public database. The ROH analysis revealed 21,029 ROH segments across the 15 populations, with an average length of 1.27 Mb, a pattern of ROH, and the assessment of the inbreeding coefficient indicating genetic diversity and varying levels of inbreeding. iHS (integrated haplotype score) was used to analyze high-frequency Single-Nucleotide Polymorphisms (SNPs) in ROH regions, specific genes related to economic traits such as coat color and weight variation. These candidate genes include OCA2 (OCA2 melanosomal transmembrane protein) and MLPH (melanophilin) associated with coat color, EPHA6 (EPH receptor A6) involved in litter size, CDKAL1 (CDK5 regulatory subunit associated protein 1 like 1) and POMC (proopiomelanocortin) linked to weight variation and some putative genes associated with high-altitude adaptability and immune. This study uncovers genetic diversity and inbreeding levels within local goat breeds in Yunnan province, China. The identification of specific genes associated with economic traits and adaptability provides actionable insights for utilization and conservation efforts.

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Section: Introductionmentioning

confidence: 99%

Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China

Huang,

Zhao,

Chen

et al. 2024

Genes

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“…As one of the world's most popular commercial pig breeds, the Duroc pig has undergone intense artificial selection to improve its commercial productivity and product quality ( 1 ). In recent years, Duroc pigs have gained popularity as the terminal sire in many mixed commercial lean types due to their superior performance in growth, feed conversion efficiency and conformation, along with carcass and other beneficial characteristics ( 2 , 3 ). For example, Duroc × (Landrace × Yorkshire) (DLY) commercial pigs account for the majority of the current hog production market in China.…”

Section: Introductionmentioning

confidence: 99%

Genetic evaluation for production and body size traits using different animal models in purebred-Duroc pigs

Zhou,

Lin,

Dong

et al. 2023

Front. Vet. Sci.

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Duroc pigs are popular crossbred terminal sires, and accurate assessment of genetic parameters in the population can help to rationalize breeding programmes. The principle aim of this study were to evaluate the genetic parameters of production (birth weight, BW; age at 115 kg, AGE; feed conversion ratio, FCR) and body size (body length, BL; body height, BH; front cannon circumference, FCC) traits of Duroc pigs. The second objective was to analyze the fit of different genetic assessment models. The variance components and correlations of BW (28,348 records), AGE (28,335 records), FCR (11,135 records), BL (31,544 records), BH (21,862 records), and FCC (14,684 records) traits were calculated by using DMU and AIREMLF90 from BLUPF90 package. In the common environment model, the heritability of BW, AGE, FCR, BL, BH, and FCC traits were 0.17 ± 0.014, 0.30 ± 0.019, 0.28 ± 0.024, 0.16 ± 0.013, 0.14 ± 0.017, and 0.081 ± 0.016, with common litter effect values of 0.25, 0.20, 0.18, 0.23, 0.19, and 0.16, respectively. According to the results of the Akaike information criterion (AIC) calculations, models with smaller AIC values have a better fit. We found that the common environment model with litter effects as random effects for estimating genetic parameters had a better fit. In this Model, the estimated genetic correlations between AGE with BW, FCR, BL, BH, and FCC traits were −0.28 (0.040), 0.76 (0.038), −0.71 (0.036), −0.44 (0.060), and −0.60 (0.073), respectively, with phenotypic correlations of −0.17, 0.52, −0.22, −0.13 and −0.24, respectively. In our analysis of genetic trends for six traits in the Duroc population from 2012 to 2021, we observed significant genetic trends for AGE, BL, and BH. Particularly noteworthy is the rapid decline in the genetic trend for AGE, indicating an enhancement in the pig's growth rate through selective breeding. Therefore, we believe that some challenging-to-select traits can benefit from the genetic correlations between traits. By selecting easily measurable traits, they can gain from synergistic selection effects, leading to genetic progress. Conducting population genetic parameter analysis can assist us in devising breeding strategies.

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“…Wu et al [ 11 ] found some candidate selection signatures within the DSE pig population were detected through the ROH islands. Wang et al [ 12 ] used Duroc (American origin) and Duroc (Canadian origin) pigs to investigate the harmful ROH regions on five economic traits. Xu et al [ 13 ] described the occurrence and distribution of ROH in the genome of Jinhua pigs and found several genes within ROH.…”

Section: Introductionmentioning

confidence: 99%

Genomic Scan for Runs of Homozygosity and Selective Signature Analysis to Identify Candidate Genes in Large White Pigs

Yin,

Wang,

Zhou

et al. 2023

IJMS

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Large White pigs are extensively utilized in China for their remarkable characteristics of rapid growth and the high proportion of lean meat. The economic traits of pigs, comprising reproductive and meat quality traits, play a vital role in swine production. In this study, 2295 individuals, representing three different genetic backgrounds Large White pig populations were used: 500 from the Canadian line, 295 from the Danish line, and 1500 from the American line. The GeneSeek 50K GGP porcine HD array was employed to genotype the three pig populations. Firstly, genomic selective signature regions were identified using the pairwise fixation index (FST) and locus-specific branch length (LSBL). By applying a top 1% threshold for both parameters, a total of 888 candidate selective windows were identified, harbouring 1571 genes. Secondly, the investigation of regions of homozygosity (ROH) was performed utilizing the PLINK software. In total, 25 genomic regions exhibiting a high frequency of ROHs were detected, leading to the identification of 1216 genes. Finally, the identified potential functional genes from candidate genomic regions were annotated, and several important candidate genes associated with reproductive traits (ADCYAP1, U2, U6, CETN1, Thoc1, Usp14, GREB1L, FGF12) and meat quality traits (MiR-133, PLEKHO1, LPIN2, SHANK2, FLVCR1, MYL4, SFRP1, miR-486, MYH3, STYX) were identified. The findings of this study provide valuable insights into the genetic basis of economic traits in Large White pigs and may have potential use in future pig breeding programs.

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Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Cited by 3 publications

References 67 publications

Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China

Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China

Genetic evaluation for production and body size traits using different animal models in purebred-Duroc pigs

Genomic Scan for Runs of Homozygosity and Selective Signature Analysis to Identify Candidate Genes in Large White Pigs

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