Abstract
Head size is important economic trait for many aquaculture fish which is directly linked to their carcass yield. The genetic basis of head size trait remains unclear in many widely cultured fish species. Common carp (Cyprinus carpio) is one of the most widely studied fish due to its importance on both economic and environmental aspects. In this study, we performed genome-wide association study using 433 Yellow River carp individuals from multiple families to identify loci and genes potentially associated with head size related traits including head length (HL), head length/body length ratio (HBR), eye diameter (ED), and eye cross (EC). QTL mapping was utilized to filter the effects of population stratification and improve power for the candidates identification in the largest surveyed family with a published genetic linkage map. Twelve SNPs showed significant for head size traits in GWAS and 18 QTLs were identified in QTL mapping. Our study combining both GWAS and QTL mapping could compensate the deficiency from each other and advance our understanding of head size traits in common carp. To acquire a better understanding of the correlation between head size and body growth, we also performed comparisons between QTLs of head size traits and growth-related traits. Candidate genes underlying head size traits were identified surrounding the significant SNPs, including parvalbumin, srpk2, fsrp5, igf1, igf3, grb10, igf1r, notch2, sfrp2. Many of these genes have been identified with potential functions on bone formation and growth. Igf1 was a putative gene associated with both head size and body growth in Yellow River carp. The teleost-specific igf3 was a candidate head size related gene, related to both HL and HBR. Our study also indicated the importance of Igf signaling pathway for both growth and head size determination in common carp, which could be potentially used in future selective breeding in common carp as well as other species.
Highlights
Head size related traits such as head length (HL), head length/body length ratio (HBR), eye diameter (ED) and eye cross (EC) are important morphological indicators for fish taxonomy, and play important roles in fish behaviors and environmental adaptation like locomotion
No strong phenotypic correlations were observed within head size traits, including a moderate correlation between HL and ED (r = 0.498, p < 0.01), a weak correlation between HL and EC (r = 0.312, p < 0.01) and a weak correlation between ED and EC (r = 0.247, p < 0.05)
We identified igf1 in the region of HBR8, which was previously reported to be possibly associated with body weight (BW) in common carp (Peng et al, 2016), revealing the genetic overlap between growth related traits and head size traits
Summary
Head size related traits such as head length (HL), head length/body length ratio (HBR), eye diameter (ED) and eye cross (EC) are important morphological indicators for fish taxonomy, and play important roles in fish behaviors and environmental adaptation like locomotion. Head size is important economic trait in fish because of the direct effect on carcass yield. Dog is Genetic Mapping of Head Size another representative species with various strains distinguished by head size. Because of the great value of head size in biology and economics, researchers have attempted to unravel the genetic basis of head size determination for many years, with the final goal of the development of molecular markers suitable for phenotype prediction and eventually used in molecular marker-assisted breeding (MAS). Understanding the associations between effect loci or genes and head size related traits is still at the early stage. It is of great value to investigate the genetic architecture responsible for head size traits with the final goal to produce fish with extreme big or small head for ornamental or economic reasons
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