Dataset Information

Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs.

ABSTRACT: Birth weight of pigs is an important economic factor in the livestock industry. The identification of the genes and variants that underlie birth weight is of great importance. In this study, we integrated two genotyping methods, single nucleotide polymorphism (SNP) chip analysis and restriction site associated DNA sequencing (RAD-seq) to genotype genome-wide SNPs. In total, 45,175 and 139,634 SNPs were detected with the SNP chip and RAD-seq, respectively. The genome-wide association study (GWAS) of the combined SNP panels identified two significant loci located at chr1: 97,745,041 and chr4: 112,031,589, that explained 6.36% and 4.25% of the phenotypic variance respectively. To reduce interval containing causal variants, we imputed sequence-level SNPs in the GWAS identified regions and fine-mapped the causative variants into two narrower genomic intervals: a ?100 kb interval containing 71 SNPs and a broader ?870 kb interval with 432 SNPs. This fine-mapping highlighted four promising candidate genes, SKOR2, SMAD2, VAV3, and NTNG1. Additionally, the functional genes, SLC25A24, PRMT6 and STXBP3, are also located near the fine-mapping region. These results suggest that these candidate genes may have contribute substantially to the birth weight of pigs.

SUBMITTER: Li Y

PROVIDER: S-EPMC7118202 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs.

Li Yong Y Li Bin B Yang Manman M Han Hu H Chen Tao T Wei Qiang Q Miao Zepu Z Yin Lilin L Wang Ran R Shen Junran J Li Xinyun X Xu Xuewen X Fang Ming M Zhao Shuhong S

Frontiers in genetics 20200327

Birth weight of pigs is an important economic factor in the livestock industry. The identification of the genes and variants that underlie birth weight is of great importance. In this study, we integrated two genotyping methods, single nucleotide polymorphism (SNP) chip analysis and restriction site associated DNA sequencing (RAD-seq) to genotype genome-wide SNPs. In total, 45,175 and 139,634 SNPs were detected with the SNP chip and RAD-seq, respectively. The genome-wide association study (GWAS) ...[more]

PMID: 32292414

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Project description:As a result of selecting for increased litter size, newborn piglets are being born lighter and have a lower chance of survival. Raising fewer pigs to market weight would have a negative impact on the industry and farmer profitability; thus, understanding the genetics of individual growth performance traits will determine whether these traits will play an important role in pig breeding schemes. This study aimed to estimate genetic parameters for individual birth weight (BW), weaning weight (WW), and probe weight (PW) in Canadian-purebred Yorkshire and Landrace pigs. PW is a live weight taken at the time of the ultrasound measurements, when pigs weigh about 100 kg. Data were collected from 2 large and related breeding herds from 2003 to 2015. Four linear animal models were used, which included the following: Model 1-direct additive genetic effect; Model 2-direct additive genetic and maternal genetic effect; Model 3-direct additive genetic and common litter effect; and Model 4-direct additive genetic, maternal genetic, and common litter effect. The model which included all 3 random effects (Model 4) was determined to be the best fit to the data. Low to moderate direct heritability estimates were observed as follows: 0.15 ± 0.03 for BW, 0.04 ± 0.01 for WW, and 0.33 ± 0.03 for PW for the Yorkshire breed; and 0.05 ± 0.01 for BW, 0.01 ± 0.01 for WW, and 0.27 ± 0.03 for PW in the Landrace breed. As expected, the direct heritability estimates increased with age as a result of decreased maternal influence on the trait. Bivariate animal models were also used to estimate genetic and environmental correlations between traits. Strong direct genetic correlations were observed between BW and WW in both breeds. Based on the estimates of genetic parameters, individual BW could be evaluated and considered in breeding programs aiming to increase BW and improve subsequent performance. Different selection emphasis could also be applied on direct and maternal additive genetic effects on BW to optimize the breeding programs and improve selection efficiency.

Project description:The highly polymorphic swine major histocompatibility complex (MHC), termed swine leukocyte antigen (SLA), is associated with different levels of immunologic responses to infectious diseases, vaccines, and transplantation. Pig breeds with known SLA haplotypes are important genetic resources for biomedical research. Canadian Yorkshire and Landrace pigs represent the current specific pathogen-free (SPF) breeding stock maintained in the isolation environment at the Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences. In this study, we identified 61 alleles at five polymorphic SLA loci (SLA-1, SLA-2, SLA-3, DRB1, and DQB1) representing 17 class I haplotypes and 11 class II haplotypes using reverse transcription-polymerase chain reaction (RT-PCR) sequence-based typing and PCR-sequence specific primers methods in 367 Canadian SPF Yorkshire and Landrace pigs. The official designation of the alleles has been assigned by the SLA Nomenclature Committee of the International Society for Animal Genetics and released in updated Immuno Polymorphism Database-MHC SLA sequence database [Release 2.0.0.3 (2016-11-03)]. The submissions confirmed some unassigned alleles and standardized nomenclatures of many previously unconfirmed alleles in the GenBank database. Three class I haplotypes, Hp-37.0, 63.0, and 73.0, appeared to be novel and have not previously been reported in other pig populations. One crossover within the class I region and two between class I and class II regions were observed, resulting in three new recombinant haplotypes. The presence of the duplicated SLA-1 locus was confirmed in three class I haplotypes Hp-28.0, Hp-35.0, and Hp-63.0. Furthermore, we also analyzed the functional diversities of 19 identified frequent SLA class I molecules in this study and confirmed the existence of four supertypes using the MHCcluster method. These results will be useful for studying the adaptive immune response and immunological phenotypic differences in pigs, screening potential T-cell epitopes, and further developing the more effective vaccines.

Dataset Information

Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs.

Publications

Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs.

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