Genome‐wide association studies for growth‐related traits in a crossbreed pig population

Xue, Yansong; Li, C.; Duan, Dongdong; Wang, M.; Han, Xuelei; Wang, K.; Qiao, Ruimin; Li, X.‐J.

doi:10.1111/age.13032

Cited by 22 publications

(18 citation statements)

References 31 publications

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“…The top 99.8th genome window on OCU2 includes the mitochondrial ribosomal protein L33 (MRPL33) gene, which has been reported to be a candidate gene for muscle development in ducks [69]. The second top genomic window on OCU15 contains the coiled-coil serine rich protein 1 (CCSER1), which has been suggested to be involved in fat deposition in pigs [70]. Another important candidate gene in a window that was identified on OCU9, protein tyrosine phosphatase non-receptor type 2 (PTPN2), confirms the results of the PCAdapt analysis (see Additional file 2: Fig.…”

Section: Tablementioning

confidence: 99%

Genomic diversity and signatures of selection in meat and fancy rabbit breeds based on high-density marker data

et al. 2022

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Background Domestication of the rabbit (Oryctolagus cuniculus) has led to a multi-purpose species that includes many breeds and lines with a broad phenotypic diversity, mainly for external traits (e.g. coat colours and patterns, fur structure, and morphometric traits) that are valued by fancy rabbit breeders. As a consequence of this human-driven selection, distinct signatures are expected to be present in the rabbit genome, defined as signatures of selection or selective sweeps. Here, we investigated the genome of three Italian commercial meat rabbit breeds (Italian Silver, Italian Spotted and Italian White) and 12 fancy rabbit breeds (Belgian Hare, Burgundy Fawn, Champagne d’Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex, Rhinelander and Thuringian) by using high-density single nucleotide polymorphism data. Signatures of selection were identified based on the fixation index (FST) statistic with different approaches, including single-breed and group-based methods, the latter comparing breeds that are grouped based on external traits (different coat colours and body sizes) and types (i.e. meat vs. fancy breeds). Results We identified 309 genomic regions that contained signatures of selection and that included genes that are known to affect coat colour (ASIP, MC1R and TYR), coat structure (LIPH), and body size (LCORL/NCAPG, COL11A1 and HOXD) in rabbits and that characterize the investigated breeds. Their identification proves the suitability of the applied methodologies for capturing recent selection events. Other regions included novel candidate genes that might contribute to the phenotypic variation among the analyzed breeds, including genes for pigmentation-related traits (EDNRA, EDNRB, MITF and OCA2) and body size, with a strong candidate for dwarfism in rabbit (COL2A1). Conclusions We report a genome-wide view of genetic loci that underlie the main phenotypic differences in the analyzed rabbit breeds, which can be useful to understand the shift from the domestication process to the development of breeds in O. cuniculus. These results enhance our knowledge about the major genetic loci involved in rabbit external traits and add novel information to understand the complexity of the genetic architecture underlying body size in mammals.

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Section: Tablementioning

confidence: 99%

Genomic diversity and signatures of selection in meat and fancy rabbit breeds based on high-density marker data

et al. 2022

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“…A total of 572 Yunong‐black pigs weighing 95–105 kg were selected from a pig farm in Henan province, consisting of 526 females and 46 males for this study. The Yunong‐black pig is a crossbred population formed by the hybridization of Duroc, Erhualian, Laiwu, Lulai, Nanyang and Yunan pigs (Xue et al, 2021). Phenotypic data were collected from 2018 to 2021, and the statistics of the seven body traits were calculated (Table 1).…”

Section: Traits (Cm) N Mean ± Sda Median Cvb 50k H2 ± Sec Imputed H...mentioning

confidence: 99%

An association study on imputed whole‐genome resequencing from high‐throughput sequencing data for body traits in crossbred pigs

Duan

Xue

et al. 2022

Animal Genetics

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Body traits are important economic factors in the pig industry. Genome‐wide association studies (GWASs) have been widely applied using high‐density genotype data to detect QTL in pigs. The aim of the present study was to detect the genetic variants significantly associated with body traits in crossbred pigs using the Illumina Porcine SNP50 BeadChip and imputed whole‐genome sequence data. A set of seven body traits – body length, body height, chest circumference, cannon bone circumference, leg buttock circumference, back fat thickness and loin muscle depth – were measured. Moderate to high heritabilities were obtained for most traits (from 0.14 to 0.46), and significant genetic and phenotypic correlations among them were observed. GWAS identified 714 significantly associated SNPs located at 39 regions on all autosomes for body traits, and a total of seven functionally related candidate genes: PIK3CD, HOXA, PCGF2, CHST11, COL2A1, BMI1 and OSR2. Functional enrichment analysis revealed that candidate genes were enriched in the estrogen signaling pathway, embryonic skeletal system morphogenesis and embryonic skeletal system development. These results aim to uncover the genetic mechanisms underlying body development and marker‐assisted selection programs focusing on body traits in pigs.

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“…Based on the density, the porcine SNP arrays were split into 50K ( 12 ), 60K ( 13 ), and 80K ( 14 ). The beadchips have been widely used for genomic selection ( 15 ), selection signature research ( 14 ), and genome-wide association studies ( 16 ). The array can be used to complete population genetics research ( 17 ) and CNV detection ( 18 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Studies, Runs of Homozygosity Analysis, and Copy Number Variation Detection to Identify Reproduction-Related Genes in Bama Xiang Pigs

Lu²,

Zhu³

et al. 2022

Front. Vet. Sci.

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Litter size and teat number are economically important traits in the porcine industry. However, the genetic mechanisms influencing these traits remain unknown. In this study, we analyzed the genetic basis of litter size and teat number in Bama Xiang pigs and evaluated the genomic inbreeding coefficients of this breed. We conducted a genome-wide association study to identify runs of homozygosity (ROH), and copy number variation (CNV) using the novel Illumina PorcineSNP50 BeadChip array in Bama Xiang pigs and annotated the related genes in significant single nucleotide polymorphisms and common copy number variation region (CCNVR). We calculated the ROH-based genomic inbreeding coefficients (FROH) and the Spearman coefficient between FROH and reproduction traits. We completed a mixed linear model association analysis to identify the effect of high-frequency copy number variation (HCNVR; over 5%) on Bama Xiang pig reproductive traits using TASSEL software. Across eight chromosomes, we identified 29 significant single nucleotide polymorphisms, and 12 genes were considered important candidates for litter-size traits based on their vital roles in sperm structure, spermatogenesis, sperm function, ovarian or follicular function, and male/female infertility. We identified 9,322 ROHs; the litter-size traits had a significant negative correlation to FROH. A total of 3,317 CNVs, 24 CCNVR, and 50 HCNVR were identified using cnvPartition and PennCNV. Eleven genes related to reproduction were identified in CCNVRs, including seven genes related to the testis and sperm function in CCNVR1 (chr1 from 311585283 to 315307620). Two candidate genes (NEURL1 and SH3PXD2A) related to reproduction traits were identified in HCNVR34. The result suggests that these genes may improve the litter size of Bama Xiang by marker-assisted selection. However, attention should be paid to deter inbreeding in Bama Xiang pigs to conserve their genetic diversity.

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Genome‐wide association studies for growth‐related traits in a crossbreed pig population

Cited by 22 publications

References 31 publications

Genomic diversity and signatures of selection in meat and fancy rabbit breeds based on high-density marker data

Genomic diversity and signatures of selection in meat and fancy rabbit breeds based on high-density marker data

An association study on imputed whole‐genome resequencing from high‐throughput sequencing data for body traits in crossbred pigs

Genome-Wide Association Studies, Runs of Homozygosity Analysis, and Copy Number Variation Detection to Identify Reproduction-Related Genes in Bama Xiang Pigs

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