Genome-wide association study reveals genomic regions and candidate genes for head size and shape in bighead carp (Hypophthalmichthys nobilis)

Abstract

Head-related traits are economically important in fish because they will essentially affect fillet yields. Bighead carp (Hypophthalmichthys nobilis) is an important aquaculture fish, and interestingly its head has higher culinary and market values than its fillet in China. In this study, using 776 bighead carp individuals and high-throughput SNP genotyping technology, we performed genome-wide association study (GWAS) to identify genomic regions and candidate genes potentially associated with head-size and head-shape traits such as head length (HL), head width (HW), head height (HH), head length/head height ratio (HL/HH), head length/head width ratio (HL/HW) and head length/body length ratio (HL/BL). The morphometrics of most of these traits were significantly correlated (P < 0.01). GWAS detected eleven significant SNPs and twelve suggestive SNPs associated with head size of bighead carp, which were mainly located on linkage group (LG) 16 and four of these SNPs were commonly shared among three head-size traits. For HL, four significant and three suggestive SNPs were on LG16. For HW, five significant and four suggestive SNPs were identified on LG3, LG16 and LG21, respectively. For HH, two significant and five suggestive SNPs were detected on LG11 and LG16. Genes involved in cell proliferation and bone development, such as cc2b, prdm1b, fndc5b, lbr, bmp8a and ATP6v1cb, were found surrounding SNPs in the QTL regions. For head shape, seventeen and six SNPs were significantly related to HL/HH and HL/HW, respectively, and underlying candidate genes were identified from genomic regions of bighead carp surrounding these SNPs, including ptch1, col9a1a, tgfbr2, hecw2a, zbtb42 and sema7a. This study shed lights on understanding genetic architecture of head size/shape traits in fish and facilitated to identify candidate genes for marker-assisted selection towards breeding bigger headed carp in future.