Genome-wide association studies demonstrate that TASP1 contributes to increased muscle fiber diameter

Abstract

Muscle fiber diameter is an economically important trait because it affects meat yield and quality. However, the genetic basis underlying muscle fiber diameter has not been determined. In this study, we collected THREE muscular histological phenotypes in 479 ducks from an F₂ segregating population generated by mallard × Pekin duck crosses. We performed genome-wide association studies (GWAS) and identified a quantitative trait locus (QTL) significantly associated with muscle fiber diameter on chromosome 3. Then, we discovered the selection signatures using the fixation index among 40 mallards and 30 Pekin ducks in this QTL region. Furthermore, we characterized the recombination event in this QTL region and identified a 6-kb block located on TASP1 that was significantly associated with muscle fiber diameter. Finally, five SNPs were screened as potential causative mutations within the 6-kb block. In conclusion, we demonstrated that TASP1 contributes to an increase in muscle fiber diameter, which helps to characterize muscle development and contributes to the genetic improvement of meat yield and quality in livestock.

Fig. 1. Pekin duck and mallard and their muscle fiber histomorphological data.

a The distribution of muscle fiber diameter is presented under the muscle fiber images. Blue and red refer to the mallard and Pekin duck at 8 weeks, respectively. b Pekin duck and mallard muscle fiber histomorphological data at 8 weeks, including muscle fiber area, muscle fiber diameter, and muscle fiber density. c F₂ population muscle fiber histomorphological and heritability. d A heatmap depicting Pearson’s correlation coefficients between phenotype means (low triangle) and genetic correlations (upper triangle). Asterisks indicate significant correlations using a two-tailed t-test (**P < 0.001 and ***P < 0.0001), and the values between parenthesis indicate SE.

Fig. 2. GWAS for muscle fiber diameter and selective sweep analyses for the QTL region.

a GWAS analyses of muscle fiber diameter. The gray horizontal dashed lines indicate the Bonferroni significance threshold of the GWAS (−log₁₀ P > 8.164). b Regional plots for the loci ranging from 11.00 to 11.50 Mbp associated with muscle fiber diameter trait. All genotyped SNPs are color-coded according to their pairwise LD with the leader SNP (Chr3:11396601) calculated in the F₂ population. SNPs are colored based on the strength of LD values (r² values) considering the most strongly associated SNP and the other SNPs in the region. c Fixation index (Fst, blue dot) for chr3:10.00–12.50-Mbp SNP between Pekin duck and mallard. d Nucleotide diversity (π) for chr3:11.35–11.45-Mbp SNP between Pekin duck (red line) and mallard (blue line). e Extended haplotype homozygosity for core haplotype (chr3:11396601) to assess the age of each core haplotype by the decay of its association to alleles at various distances from the locus in Pekin duck (red line) and mallard (blue line).

Fig. 3. Fine-mapping of the QTL region.

a Recombination event analyses are shown in schematic form in this plot. Red bars refer to chromosomal segments originating from Pekin ducks, purple bars refer to segments originating from mallards, and orange bars refer to segments originating from heterozygotes. R1–10 refer to ten recombinant types. The left box plot refers to muscle fiber diameter. The numbers of individuals are given in brackets. The indicated P values are based on one-way ANOVA. Box plots denote median (centerline), 25–75th percentile (limits), the minimum and maximum values without outliers, and outliers (gray dots). The right breast muscle image shows F₂ population muscle fiber diameter segregation of mallard, Pekin duck, and heterozygotic haplotypes of TASP1. b. The locations of all five candidate SNPs in the TASP1 gene and these contribute to muscle fiber diameter in block 2. Box plots denote median (centerline), 25–75th percentile (limits), minimum and maximum values without outliers, and outliers (gray dots).

Fig. 4. The hypothesis that TASP1 regulation affects muscle fiber diameter: TASP1 encodes an endopeptidase to cleave MLL.

The variation in TASP1 might influence its enzymatic activity, causing the appearance of unprocessed MLL and the loss of proper HOX gene expression, which in turn induces developmental pathways inhibiting SC function and muscle regeneration. Combined with the gene mRNA expression, the expression levels of both HOXA9 and KAT2B were higher in mallards than in Pekin ducks at 8 weeks. The expression levels of the other genes (AFF1, MLLT1, KDM6A, KMT2A) were lower in mallards than in Pekin ducks at 8 weeks. The 2- to 8-week CPM of Pekin ducks (orange line) and mallards (blue line).