Abstract
Body weight is one of the most important quantitative traits with high heritability in chicken. We previously mapped a quantitative trait locus (QTL) for body weight by genome-wide association study (GWAS) in an F2 chicken resource population. To identify the causal mutations linked to this QTL, expression profiles were determined on livers of high-weight and low-weight chicken lines by microarray. Combining the expression pattern with SNP effects by GWAS, miR-16 was identified as the most likely potential candidate with a 3.8-fold decrease in high-weight lines. Re-sequencing revealed that a 54-bp insertion mutation in the upstream region of miR-15a-16 displayed high allele frequencies in high-weight commercial broiler line. This mutation resulted in lower miR-16 expression by introducing three novel splicing sites instead of the missing 5′ terminal splicing of mature miR-16. Elevating miR-16 significantly inhibited DF-1 chicken embryo cell proliferation, consistent with a role in suppression of cellular growth. The 54-bp insertion was significantly associated with increased body weight, bone size and muscle mass. Also, the insertion mutation tended towards fixation in commercial broilers (Fst > 0.4). Our findings revealed a novel causative mutation for body weight regulation that aids our basic understanding of growth regulation in birds.
Highlights
A short insertion mutation disrupts genesis of miR-16 and causes increased body weight in domesticated chicken
To identify the causal mutations linked to this quantitative trait locus (QTL), expression profiles were determined on livers of high-weight and low-weight chicken lines by microarray
A genome-wide association study (GWAS) was performed to determine the genetic architecture of body weight in an F2 intercross, resulting in a 3 Mb QTL region on Chromosome 1, which contains most the significant single nucleotide polymorphisms (SNP) effects on body weight[10]
Summary
A short insertion mutation disrupts genesis of miR-16 and causes increased body weight in domesticated chicken. We previously mapped a quantitative trait locus (QTL) for body weight by genome-wide association study (GWAS) in an F2 chicken resource population. To identify the causal mutations linked to this QTL, expression profiles were determined on livers of high-weight and low-weight chicken lines by microarray. Re-sequencing revealed that a 54-bp insertion mutation in the upstream region of miR-15a-16 displayed high allele frequencies in high-weight commercial broiler line. High density SNP panels (60 K and 600 K SNP-Chip) have been successfully used to study distinct natural and experimental chicken populations, resulting in identification of many quantitative trait loci (QTL) and candidate genes for body weight[7,8,9]. It remains a challenging task to search for the causal mutations linked to observed QTLs responsible for complex biologic traits
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