An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigs

Xu, Pao; Li, Desen; Wu, Zhongping; Ni, Lubin; Liu, Jiaxing; Tang, Ying; Yu, Tongshun; Ren, Jun; Zhao, Xiaoyan; Huang, Min

doi:10.1016/j.animal.2022.100591

Cited by 3 publications

(1 citation statement)

References 34 publications

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“…LD analysis of the significant continuous regions in the imputed data detected three LD blocks, with the largest linkage block being 49 kb and containing the PLAG1 gene. PLAG1 is mainly expressed during embryonic development (Pan et al, 2022) and is a candidate gene strongly associated with pig growth traits (Qiao et al, 2015;Xu et al, 2022). Rubin et al (2012) found that LCORL and PLAG1 can explain 18.4% of the residual variation in BL in wild boar hybrid offspring.…”

Section: Gwas and Candidate Genesmentioning

confidence: 99%

Genomic prediction and genome‐wide association studies for additive and dominance effects for body composition traits using 50 K and imputed high‐density SNP genotypes in Yunong‐black pigs

Wu,

Dou,

Bai

et al. 2023

J Animal Breeding Genetics

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Body composition traits are complex traits controlled by minor genes and, in hybrid populations, are impacted by additive and nonadditive effects. We aimed to identify candidate genes and increase the accuracy of genomic prediction of body composition traits in crossbred pigs by including dominance genetic effects. Genomic selection (GS) and genome‐wide association studies were performed on seven body composition traits in 807 Yunong‐black pigs using additive genomic models (AM) and additive‐dominance genomic models (ADM) with an imputed high‐density single nucleotide polymorphism (SNP) array and the Illumina Porcine SNP50 BeadChip. The results revealed that the additive heritabilities estimated for AM and ADM using the 50 K SNP data ranged from 0.20 to 0.34 and 0.11 to 0.30, respectively. However, the ranges of additive heritability for AM and ADM in the imputed data ranged from 0.20 to 0.36 and 0.12 to 0.30, respectively. The dominance variance accounted for 23% and 27% of the total variance for the 50 K and imputed data, respectively. The accuracy of genomic prediction improved by 5% on average for 50 K and imputed data when dominance effect were considered. Without the dominance effect, the accuracies for 50 K and imputed data were 0.35 and 0.38, respectively, and 0.41 and 0.43, respectively, upon considering it. A total of 12 significant SNP and 16 genomic regions were identified in the AM, and 14 significant SNP and 21 genomic regions were identified in the ADM for both the 50 K and imputed data. There were five overlapping SNP in the 50 K and imputed data. In the AM, a significant SNP (CNC10041568) was found in both body length and backfat thickness traits, which was in the PLAG1 gene strongly and significantly associated with body length and backfat thickness in pigs. Moreover, a significant SNP (CNC10031356) with a heterozygous dominant genotype was present in the ADM. Furthermore, several functionally related genes were associated with body composition traits, including MOS, RPS20, LYN, TGS1, TMEM68, XKR4, SEMA4D and ARNT2. These findings provide insights into molecular markers and GS breeding for the Yunong‐black pigs.

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Section: Gwas and Candidate Genesmentioning

confidence: 99%

Genomic prediction and genome‐wide association studies for additive and dominance effects for body composition traits using 50 K and imputed high‐density SNP genotypes in Yunong‐black pigs

Wu,

Dou,

Bai

et al. 2023

J Animal Breeding Genetics

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Assessing Population Structure and Signatures of Selection in Wanbei Pigs Using Whole Genome Resequencing Data

Zhang

Liu

et al. 2022

Animals

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Wanbei pig (WBP) is one of the indigenous pig resources in China and has many germplasm characteristics. However, research on its genome is lacking. To assess the genomic variation, population structure, and selection signatures, we resequenced 18 WBP for the first time and performed a comprehensive analysis with resequenced data of 10 Asian wild boars. In total, 590.03 Gb of data and approximately 41 million variants were obtained. Polymorphism level (θπ) ratio and genetic differentiation (fixation index)-based cross approaches were applied, and 539 regions, which harbored 176 genes, were selected. Functional analysis of the selected genes revealed that they were associated with lipid metabolism (SCP2, APOA1, APOA4, APOC3, CD36, BCL6, ADCY8), backfat thickness (PLAG1, CACNA2D1), muscle (MYOG), and reproduction (CABS1). Overall, our results provide a valuable resource for characterizing the uniqueness of WBP and a basis for future breeding.

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A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology

Liu,

Chen,

Chen

et al. 2023

Genes

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Animal genotyping by means of genome-wide association studies is important for connecting phenotypes of interest with their underlying genetics in livestock. However, the use of whole genome sequencing to investigate chest circumference (CC) in donkeys has rarely been reported. We aimed to use the genome-wide association study approach to detect significant single nucleotide polymorphisms (SNPs) and key genes associated with chest circumference traits in Xinjiang donkeys. We assessed 112 Xinjiang donkeys in this study. The chest circumference of each was measured 2 h before milking. We re-sequenced blood samples from the Xinjiang donkeys, and genome-wide association study analyses were performed using a mixed model with the PLINK, GEMMA, and REGENIE programs. We tested 38 donkeys for candidate SNPs for genome-wide association study using three software programs. Additionally, 18 SNP markers reached genome-wide significance (p < 1.61 × 10−9). On the basis of these, 41 genes were identified. Previously proposed candidate genes for CC traits were supported by this study, including NFATC2 (Nuclear Factor of Activated T Cells 2), PROP1 (PROP Paired-Like Homeobox 1), UBB (Ubiquitin B), and HAND2 (Heart and Neural Crest Derivatives Expressed 2). These promising candidates provide a valuable resource for validating potential meat production genes and will facilitate the development of high-yielding Xinjiang donkey breeds through marker-assisted selection or gene editing.

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An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigs

Cited by 3 publications

References 34 publications

Genomic prediction and genome‐wide association studies for additive and dominance effects for body composition traits using 50 K and imputed high‐density SNP genotypes in Yunong‐black pigs

Genomic prediction and genome‐wide association studies for additive and dominance effects for body composition traits using 50 K and imputed high‐density SNP genotypes in Yunong‐black pigs

Assessing Population Structure and Signatures of Selection in Wanbei Pigs Using Whole Genome Resequencing Data

A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology

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