Elite allele mining for growth rate traits in common carp ( Cyprinus carpio ) by association analysis

Abstract

Growth is one of the important economic traits to be improved in the breeding of common carp, yet the genetic basis in it remains unclear. In this study, a GoldenGate assay containing 1,536 SNP was used to genotype a full‐sib panel of 68 individuals of mirror carp Cyprinus carpio. Association studies were carried out between SNP and growth rate for three consecutive months of the panel. 15 loci significantly associated with growth rate were identified using the general linear model and the mixed linear model, which located in eight chromosomes (chr6, 8, 9, 11, 20, 28, 32 and 35) and four scaffolds (scaffold902, 28835, 29008 and 29015). The phenotypic variance of these associated loci ranged from 6.4% to 19.2%. The elite alleles were mined based on the average phenotypic allele effect (AAE) of each allele. 15 elite alleles were screened out with 6.60% higher than the average phenotypic allele and 16.88% higher than the non‐elite ones among the four traits. Meanwhile, 15 candidate genes were scanned and annotated. The loci and elite alleles of growth rate identified may facilitate marker‐based breeding for rapid growth in common carp.

Mapping Growth-Related Quantitative Trait Locus (QTL) in Commercial Yellow River Carp (Cyprinus carpio haematopterus) during Overwintering

“…For example, Sauvage et al [31] tagged brook charr (Salvelinus fontinalis) with PIT at the age of 5 months, collected the growth data of four different growth periods (May 2009, July 2009, August 2009, and November 2009), and mapped the growth rate-related QTLs in different growth periods. Zhang et al [32] measured the growth rate of common carp at three time points (3,4, and 5 MAH) and identified 15 genomic regions associated with growth rate. Wang et al [13] carried out a QTL mapping study on four growth traits of Yellow River carp at the age of 13, 17, and 13-17 months.…”

A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp (Cyprinus carpio)

“…Most economically important traits of fish such as growth, disease resistance, and flesh quality are controlled by multiple genes, environmental factors, and their interactions ( Song et al, 2012 ; Shao et al, 2015 ; Peng et al, 2016 ; Zheng et al, 2016 ). Phenotypic variation of these traits is thought to be caused by quantitative genetic variation that results from the segregation of alleles at multiple quantitative trait loci (QTL) ( Mackay et al, 2009 ; Zhang et al, 2021 ). The purpose of QTL mapping is to understand the number and effect of genes that determine traits and to assist in the selection of breeding to accelerate the genetic improvement of important traits ( Doerge, 2002 ; Naish and Hard 2008 ).…”

Table2.XLSX

“…Most economically important traits of fish such as growth, disease resistance, and flesh quality are controlled by multiple genes, environmental factors, and their interactions (Song et al, 2012;Shao et al, 2015;Peng et al, 2016;Zheng et al, 2016). Phenotypic variation of these traits is thought to be caused by quantitative genetic variation that results from the segregation of alleles at multiple quantitative trait loci (QTL) (Mackay et al, 2009;Zhang et al, 2021). The purpose of QTL mapping is to understand the number and effect of genes that determine traits and to assist in the selection of breeding to accelerate the genetic improvement of important traits (Doerge, 2002;Naish and Hard 2008).…”