Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain

Abstract

Common carp is one of the oldest and most popular cultured freshwater fish species both globally and in China. In a previous study, we used a carp strain with a long breeding tradition in China, named Huanghe, to create a new fast-growing strain by selection for fast growth for 6 years. The growth performance at 8 months of age has been improved by 20.84%. To achieve this, we combined the best linear unbiased prediction with marker-assisted selection techniques. Recent progress in genome-wide association studies and genomic selection in livestock breeding inspired common carp breeders to consider genome-based breeding approaches. In this study, we developed a 2b-RAD sequence assay as a means of investigating the quantitative trait loci in common carp. A total of 4,953,017,786 clean reads were generated for 250 specimens (average reads/specimen = 19,812,071) with BsaXI Restriction Enzyme. From these, 56,663 SNPs were identified, covering 50 chromosomes and 3,377 scaffolds. Principal component analysis indicated that selection and control groups are relatively clearly distinct. Top 1% of Fst values was selected as the threshold signature of artificial selection. Among the 244 identified loci, genes associated with sex-related factors and nutritional metabolism (especially fat metabolism) were annotated. Eighteen QTL were associated with growth parameters. Body length at 3 months of age and body weight (both at 3 and 8 months) were controlled by polygenic effects, but body size (length, depth, width) at 8 months of age was controlled mainly by several loci with major effects. Importantly, a single shared QTL (IGF2 gene) partially controlled the body length, depth, and width. By merging the above results, we concluded that mainly the genes related to neural pathways, sex and fatty acid metabolism contributed to the improved growth performance of the new Huanghe carp strain. These findings are one of the first investigations into the potential use of genomic selection in the breeding of common carp. Moreover, our results show that combining the Fst, QTL mapping and CRISPR–Cas9 methods can be an effective way to identify important novel candidate molecular markers in economic breeding programs.

Association and Functional Analyses Revealed That PPP1R3B Plays an Important Role in the Regulation of Glycogen Content in the Pacific Oyster Crassostrea gigas

“…SNPs from this study could account for 1.4–6.3% of the PVE, which is comparable to the GWAS results for host resistance to Ostreid herpesvirus of oyster, with the top 10 markers ranging between 1.9 and 4.7% (Gutierrez et al, 2018a) as well as GWAS result of growth traits in juvenile farmed Atlantic salmon, with the top SNP explain ∼7% of the additive genetic variation. However, the use of selected fast growing lines may contribute to the high phenotypic variation of 7–52% PVE of growth traits in common carp (Su et al, 2018). Moreover, minor alleles were the favorable allele for 8 of the 10 SNPs, indicating that we should pay more attention to the minor alleles.…”

Genome Wide Analysis for Growth at Two Growth Stages in A New Fast-Growing Common Carp Strain (Cyprinus carpio L.)

“…Xu et al relied on QTL mapping to identify a number of growth performance regulators, including those associated with cell-proliferation (IGF1) and growth and energy metabolism (ERBB4, BMPR1B, SMTLB, GS, KISS2 and NPFFR1) 52 . In our previous genome-wide analysis of the Xinlong strain, we found a number of genes associated with growth parameters at the early grow-out stage, including those related to neural pathways (RHEB, MDGA2, NRXN1a, BDNF, SHANK2 and REEP2), sex dimorphism (NRXN1A, SMOC2, RAB10 and HSD17B), and fatty acid metabolism (RAB10, TNMD, VPAC2 and ACSF2) 18 . However, it remained unknown which candidate genes or loci contribute to the growth performance during later growth stages.…”

“…AGPAT2 enzyme catalyzes the acylation of lysophosphatidic acid to form phosphatidic acid, a key intermediate in the biosynthesis of triacylglycerol and glycerophospholipids 64 . Therefore, regulation of biosynthesis of triacylglycerol and glycerophospholipids may be the genetic explanaiton behind higher content of polyunsaturated fatty acids in the muscle of the Jinlong carp 18 .…”

“…In order to construct the 2b-RAD libraries for each of the 123 individuals, we followed a simplified RAD (restriction site-associated DNA) genotyping method, as described by Su et al 18 , with minor modifications. This method is based on sequencing of uniform fragments produced by type IIB restriction endonucleases 8 , as described in the 2b-RAD protocol 3 .…”

“…After six years of continuous selection, its growth rate improvement (compared to the Huanghe strain) was 20.84% after an 8 months-long growth trial 16 . In order to explore the genetic basis for this fast-growing phenotype, we previously conducted a genome-wide association study using 2b-RAD sequence assay for four growth-related traits at 3 and 8 months of age, and found that genes contributing to this improvement are related to sex, neural pathways and fatty acid metabolism 18 . However, for the aquaculture industry purposes, growth performance at the end of the culture period, i.e.…”