Although pork quality traits are important commercially, genome-wide association studies (GWASs) have not well considered Landrace and Yorkshire pigs worldwide. Landrace and Yorkshire pigs are important pork-providing breeds. Although quantitative trait loci of pigs are well-developed, significant genes in GWASs of pigs in Korea must be studied. Through a GWAS using the PLINK program, study of the significant genes in Korean pigs was performed. We conducted a GWAS and surveyed the gene ontology (GO) terms associated with the backfat thickness (BF) trait of these pigs. We included the breed information (Yorkshire and Landrace pigs) as a covariate. The significant genes after false discovery rate (<0.01) correction were
Landrace and Yorkshire pigs are commercial breeds used for pork production. The Landrace pig is a long, white pig with 16 or 17 ribs. Landrace pigs are utilized as Grandparents in the production of F1 parent stock females in a terminal crossbreeding (
In Korea, the Landrace and Yorkshire breeds in Korea are used for commercial pork production. Pork quality traits are polygenic and quantitative trait loci (QTL) are associated with pork quality traits. In this regard, we analyzed genome-wide association studies (GWASs) for backfat thickness (BF) for these breeds. BF is an important trait in pork production. Despite the importance of BF, there have not been in-depth GWAS of the BF in the Landrace and Yorkshire breeds.
Rohrer
The number of Landrace individuals was 1,041 and the number of Yorkshire individuals was 836. Their BF were measured and the genomic DNA of each individual Landrace or Yorkshire pig was genotyped using an Illumina Porcine 60 K SNP Beadchip (Illumina, San Diego, CA, USA). Total number of single nucleotide polymorphisms (SNPs) was 62,551 and 62,551 in the Landrace and Yorkshire breeds, respectively. After quality control (minor allele frequency <0.05, Hardy-Weinberg equilibrium p < 0.0001 and genotyping rate threshold < 0.05), the number of SNPs in the Landrace and Yorkshire breeds was 42,654 and 57,799, respectively. After merging the data of the two breeds, the number of SNPs was 38,002.
A GWAS using BF of Landrace and Yorkshire pigs was performed. The PLINK program was used for the GWAS [
where
We analyzed the GO of the top 5% genes (p-value order) associated with BF in Landrace and Yorkshire pigs. Because the test result with a p-value < 0.05 in our study was very genial and multiple testing such as the Bonferroni correction and the false discovery rate (FDR) of our study result was very restrictive, we performed the GO analysis with the top 5% genes. The gene catalogue was retrieved from Ensemble database (
The BF statistics for Landrace pigs were 7.22 (minimum), 19.42 (maximum), 11.89 (average), and 1.54 (standard deviation). The BF statistics for Yorkshire pigs were 8.44 (minimum), 18.04 (maximum), 12.70 (average), and 1.49 (standard deviation). The average value of Yorkshire BF was greater than that of Landrace BF, while the maximum value of Yorkshire BF was less than that of Landrace pig BF.
The GWAS was performed and the p-values were FDR-corrected.
A GO analysis was performed in Landrace and Yorkshire pigs in Korea.
The commercial pig breeds in Korea are mainly the Landrace, Yorkshire, Duroc and Berkshire breeds. Among these breeds, we analyzed GWASs of backfat thickness using the Landrace and Yorkshire breeds. Although there is a pig QTL database (QTL DB,
It was reported that neuronal genes are closely related to fat accumulation [
Among the actin cytoskeleton organization genes and cell morphogenesis genes,
Conceptualization: YSL, DS
Data curation: DS
Formal analysis: YSL
Methodology: YSL, DS
Writing – original draft: YSL
Writing – review & editing: YSL, DS
This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (No. NRF-2017R1A6A3A11033784 & NRF-2017R1C1B3007144).
Mahattan plot showing the −log10(p-value) for backfat thickness across chromosomes in Landrace and Yorkshire pigs in Korea. The horizontal dotted line represents an false discovery rate of 0.01.
Boxplots of sex and parity in Landrace pigs.
Boxplots of sex and parity in Yorkshire pigs.
The quantile-quantile plot (QQ-plot) of genome-wide association study p-values. It represents the normality of our results.
Principal component analysis in Landrace and Yorkshire pigs to check the population stratification problem between Landrace and Yorkshire pigs.
Summary statistics of backfat thickness in the two pig breeds
Breed | Min | Max | Average | Standard deviation |
---|---|---|---|---|
Landrace | 7.22 | 19.42 | 11.89 | 1.54 |
Yorkshire | 8.44 | 18.04 | 12.70 | 1.49 |
The significant SNPs and those-containing genes associated with BF after FDR correction
Chr | SNP | Base pair | Beta | FDR | Gene |
---|---|---|---|---|---|
1 | ALGA0003992 | 74,391,668 | 0.5628 | 0.0010 | |
1 | ALGA0006854 | 185,048,329 | 0.5478 | 0.0016 | |
1 | ALGA0003716 | 65,086,290 | 0.4237 | 0.0027 | |
1 | ALGA0003091 | 52,127,592 | 0.7812 | 0.0029 | |
7 | ASGA0032161 | 30,521,413 | 0.6079 | 0.0029 | |
1 | CASI0007774 | 71,401,555 | 0.4248 | 0.0029 | |
1 | H3GA0001881 | 71,455,634 | 0.4248 | 0.0029 | |
1 | DRGA0002197 | 265,831,621 | 0.3553 | 0.0069 | |
1 | MARC0031246 | 231,303,178 | 0.4662 | 0.0072 | |
7 | ASGA0031143 | 10,707,229 | −0.3348 | 0.0072 | |
9 | ALGA0104955 | 33,658,036 | −0.348 | 0.0076 | |
13 | MARC0056987 | 206,756,876 | 0.3341 | 0.0084 | |
7 | ASGA0031992 | 27,352,011 | 0.3849 | 0.0097 |
Most of the significant SNPs belonged to chromosome 1.
SNP, single nucleotide polymorphism; BF, backfat thickness; FDR, false discovery rate; AFG1L, AFG1 like ATPase; RIMS1, regulating synaptic membrane exocytosis 1; SPDEF, SAM pointed domain containing ETS transcription factor; SCAI, suppressor of cancer cell invasion.
GO terms of the top 5% genes associated with backfat thickness
Term | Count | p-value | Gene | Fold enrichment |
---|---|---|---|---|
GO:0031532~actin cytoskeleton reorganization | 5 | 8.26E-04 | 11.67 | |
GO:0040011~locomotion | 15 | 0.01 | 2.03 | |
GO:0030036~actin cytoskeleton organization | 9 | 0.01 | 2.90 | |
GO:0000902~cell morphogenesis | 14 | 0.01 | 2.11 | |
GO:0000904~cell morphogenesis involved in differentiation | 10 | 0.02 | 2.55 | |
GO:1901187~regulation of ephrin receptor signaling pathway | 2 | 0.02 | 107.38 | |
GO:0030182~neuron differentiation | 13 | 0.02 | 2.11 | |
GO:0048666~neuron development | 11 | 0.02 | 2.29 | |
GO:0032989~cellular component morphogenesis | 14 | 0.02 | 1.99 | |
GO:0050804~modulation of synaptic transmission | 5 | 0.02 | 4.67 | |
GO:0030030~cell projection organization | 13 | 0.02 | 2.03 | |
GO:0030029~actin filament-based process | 9 | 0.03 | 2.51 | |
GO:0010455~positive regulation of cell fate commitment | 2 | 0.03 | 71.59 | |
GO:0048699~generation of neurons | 13 | 0.04 | 1.90 | |
GO:0048667~cell morphogenesis involved in neuron differentiation | 7 | 0.04 | 2.77 | |
GO:1903047~mitotic cell cycle process | 8 | 0.04 | 2.48 | |
GO:0031175~neuron projection development | 9 | 0.04 | 2.26 |
The major gene ontology (GO) terms were neuron-related, cell morphogenesis, and actin cytoskeleton organization, and reorganization.