A consensus linkage map of common carp (Cyprinus carpio L.) to compare the distribution and variation of QTLs associated with growth traits

Zheng, Xianhu; Kuang, Youyi; Lv, Wenjing; Cao, Dan; Zhang, Xiaofeng; Li, Chao; Lu, Cuiyun; Sun, Xiaowen

doi:10.1007/s11427-012-4427-3

Cited by 23 publications

(15 citation statements)

References 36 publications

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“…Growth-related traits (e.g., body weight and length) constitute the main purpose of genetic breeding projects in aquaculture. Earlier studies on common carp have confirmed a heritable basis in these traits [ 37 ], and some QTLs affecting growth-related traits have been reported [ 32 – 35 , 38 , 39 ]. For example, Laghari et al [ 32 ] performed analysis looking for BW, TL, and condition factor (K) based on a backcross common carp family, they detected 12 QTLs associated with BW and TL on ten LGs.…”

Section: Discussionmentioning

confidence: 96%

“…The study also revealed that both major and minor genes differ in their genetic performance. Therefore, we concluded that the major genes are undergoing change and remain unfixed in these families [ 35 ]. Further investigation is needed to identify shared and overlapping QTLs in either populations or families to understand quantitative genetic variation.…”

Section: Introductionmentioning

confidence: 99%

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QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio)

Zheng

Kuang

et al. 2016

BMC Genet

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BackgroundComparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families.ResultsWe completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sib-pair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in marker-assisted selection.ConclusionA large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs affecting body growth. Discovery of these common QTLs between families and growth-related traits represents an important step towards understanding of quantitative genetic variation in common carp.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0370-9) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio)

Zheng

Kuang

et al. 2016

BMC Genet

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“…Other linkage mapping studies for carps have estimated map lengths of widely differing sizes. For example, common carp map sizes range from 1852 cM to 5506 cM (between 161 and 719 and markers were used in these studies generating between 42 and 64 linkage groups [13-16]). Many of these size estimates are likely to be inaccurate due to poor coverage.…”

Section: Discussionmentioning

confidence: 99%

A linkage map of transcribed single nucleotide polymorphisms in rohu (Labeo rohita) and QTL associated with resistance to Aeromonas hydrophila

Robinson

Baranski²,

Mahapatra

et al. 2014

BMC Genomics

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BackgroundProduction of carp dominates world aquaculture. More than 1.1 million tonnes of rohu carp, Labeo rohita (Hamilton), were produced in 2010. Aeromonas hydrophila is a bacterial pathogen causing aeromoniasis in rohu, and is a major problem for carp production worldwide. There is a need to better understand the genetic mechanisms affecting resistance to this disease, and to develop tools that can be used with selective breeding to improve resistance. Here we use a 6 K SNP array to genotype 21 full-sibling families of L. rohita that were experimentally challenged intra-peritoneally with a virulent strain of A. hydrophila to scan the genome for quantitative trait loci associated with disease resistance.ResultsIn all, 3193 SNPs were found to be informative and were used to create a linkage map and to scan for QTL affecting resistance to A. hydrophila. The linkage map consisted of 25 linkage groups, corresponding to the number of haploid chromosomes in L. rohita. Male and female linkage maps were similar in terms of order, coverage (1384 and 1393 cM, respectively) and average interval distances (1.32 and 1.35 cM, respectively). Forty-one percent of the SNPs were annotated with gene identity using BLAST (cut off E-score of 0.001). Twenty-one SNPs mapping to ten linkage groups showed significant associations with the traits hours of survival and dead or alive (P <0.05 after Bonferroni correction). Of the SNPs showing significant or suggestive associations with the traits, several were homologous to genes of known immune function or were in close linkage to such genes. Genes of interest included heat shock proteins (70, 60, 105 and “small heat shock proteins”), mucin (5b precursor and 2), lectin (receptor and CD22), tributyltin-binding protein, major histocompatibility loci (I and II), complement protein component c7-1, perforin 1, ubiquitin (ligase, factor e4b isoform 2 and conjugation enzyme e2 c), proteasome subunit, T-cell antigen receptor and lymphocyte specific protein tyrosine kinase.ConclusionsA panel of markers has been identified that will be validated for use with both genomic and marker-assisted selection to improve resistance of L. rohita to A. hydrophila.

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“…Because of the economic importance of C. carpio for the global aquaculture industry, as well as its importance as a model species for ecology, physiology, and evolutionary studies, over the past decade, researchers have developed a variety of genetic and genomics tool and resources. A large number of genetic markers have been developed, including microsatellites [ 3 , 4 ], and single nucleotide polymorphisms (SNPs) [ 5 , 6 ]. A number of genetic linkage maps have been constructed based on these markers [ 7 - 10 ].…”

Section: Introductionmentioning

confidence: 99%

“…A number of genetic linkage maps have been constructed based on these markers [ 7 - 10 ]. The markers have also been used to identify quantitative trait loci (QTLs) associated with economically important traits including growth rate, body shape, and meat quality [ 4 , 11 , 12 ]. A large set of expressed sequence tags (ESTs) have been generated using traditional cloning and Sanger sequencing methods, or next-generation transcriptome sequencing, and a cDNA microarray has been designed and constructed [ 13 - 17 ].…”

Section: Introductionmentioning

confidence: 99%

Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio)

et al. 2014

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BackgroundA large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio.ResultsThe SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster.ConclusionsThe Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species.

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A consensus linkage map of common carp (Cyprinus carpio L.) to compare the distribution and variation of QTLs associated with growth traits

Cited by 23 publications

References 36 publications

QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio)

QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio)

A linkage map of transcribed single nucleotide polymorphisms in rohu (Labeo rohita) and QTL associated with resistance to Aeromonas hydrophila

Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio)

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