A whole genome sequence association study of muscle fiber traits in a White Duroc×Erhualian F2 resource population

Abstract

Objective: Muscle fiber types, numbers and area are crucial aspects associated with meat production and quality. However, there are few studies of pig muscle fibre traits in terms of the detection power, false discovery rate and confidence interval precision of whole-genome quantitative trait loci (QTL). We had previously performed genome scanning for muscle fibre traits using 183 microsatellites and detected 8 significant QTLs in a White Duroc× Erhualian F2 population. The confidence intervals of these QTLs ranged between 11 and 127 centimorgan (cM), which contained hundreds of genes and hampered the identification of QTLs. A whole-genome sequence imputation of the population was used for fine mapping in this study.Methods: A whole-genome sequences association study was performed in the F2 population. Genotyping was performed for 1,020 individuals (19 F0, 68 F1, and 933 F2). The whole-genome variants were imputed and 21,624,800 single nucleotide polymorphisms (SNPs) were identified and examined for associations to 11 longissimus dorsi muscle fiber traits.Results: A total of 3,201 significant SNPs comprising 7 novel QTLs showing associations with the relative area of fiber type I (I_RA), the fiber number per square centimeter (FN) and the total fiber number (TFN). Moreover, one QTL on pig chromosome 14 was found to affect both FN and TFN. Furthermore, four plausible candidate genes associated with FN (kinase non-catalytic C-lobe domain containing [KNDC1]), TFN (KNDC1), and I_RA (solute carrier family 36 member 4, contactin associated protein like 5, and glutamate metabotropic receptor 8) were identified.Conclusion: An efficient and powerful imputation-based association approach was utilized to identify genes potentially associated with muscle fiber traits. These identified genes and SNPs could be explored to improve meat production and quality via marker-assisted selection in pigs.

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

“…GATM and SEMA5A are involved in placental development and embryonic development, respectively [ 51 , 52 ]. HDAC9 and GRM8 are associated with eye muscle area and the relative area of type I fibers, respectively [ 53 , 54 ]. ITGAL is immune-related and involved in leukocyte recruitment processes [ 55 ].…”

Genome-wide association study reveals genetic loci and candidate genes for meat quality traits in a four-way crossbred pig population

“…In previous studies, most of the SNPs and candidate genes for important economic traits of pigs identified based on GWAS mainly used F2 generation populations, which were generated by crossbreeding local pig breeds from different countries with Western lean pig breeds ( Liu et al, 2014 ; Zhang et al, 2014 ; Cho et al, 2015 ; Guo et al, 2020 ; Liu et al, 2020 ) and purebred pigs ( Xiong et al, 2015 ; Ding et al, 2019 ; Fabbri et al, 2020 ; Fu et al, 2020 ). The F2 generation population is characterized by segregation of traits, large phenotypic variation and more genetic diversity, which is suitable for GWAS.…”

“…The F2 generation population is characterized by segregation of traits, large phenotypic variation and more genetic diversity, which is suitable for GWAS. Some studies use white Duroc × Erhualian F2 hybrid pig population to conduct GWAS on growth, fat, meat quality, muscle fiber, body size and body weight traits ( Ma et al, 2013 ; Qiao et al, 2015 ; Guo et al, 2017 ; Ji et al, 2017 ; Guo et al, 2020 ), and obtained a large number of mutation sites and candidate genes related to the research traits. Besides, two studies used Large White × Minzhu F2 generation population to perform GWAS on meat quality and external traits ( Luo et al, 2012 ; Wang et al, 2014 ), and identified some SNP loci and candidate genes related to meat quality and external traits.…”

“…A study finds that GRM8 is a porcine candidate gene related to muscling and a SNP in the GRM8 gene also displayed a strong association with the loin eye area of pigs ( Li et al, 2011 ). GRM8 was also associated with the relative area of longissimus dorsi muscle fiber type I and was considered a plausible candidate gene for this trait ( Guo et al, 2020 ). Perhaps, the GRM8 gene expressed in longissimus dorsi muscle may be a potential candidate gene for porcine pH traits.…”