A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus)

- A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp ( Cyprinus carpio haematopterus.
- The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China.
- Results: A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C.
- The length of the map was 4586.56 cM with an average marker interval of 0.57 cM.
- haematopterus and another common carp strain (subspecies) C.
- A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2..
- Conclusions: We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high- density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp.
- This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp..
- 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0.
- With the development of the next- generation sequencing technologies (NGS), a variety of genotyping-by-sequencing (GBS) methods have been de- veloped and applied for rapidly and cost-effectively de- veloping and genotyping thousands of single nucleotide polymorphism (SNP) markers which are available for constructing high-resolution linkage maps [7].
- Among those available GBS techniques, restriction site- associated DNA (RAD) sequencing [8] and its derivative methods, such as ddRAD [9], GGRS [10], SLAF [11] and 2b-RAD [12], are reduced representation approaches that construct sequencing libraries from a fraction of the genome produced by using restriction enzymes.
- Growth, one of the most important economic traits for aquaculture fish, is a quantitative trait that controlled by multi-gene QTLs across the genome and environ- mental effects.
- associated with the genetic variation for important traits but also to identify the candidate genes involving physio- logical processes of the traits [23], showing its strong ap- plication potential in MAS program.
- QTL analyses of growth-related traits have been conducted in some aqua- culture fishes, such as Atlantic salmon [24], rainbow trout (Oncorhynchus mykiss) [25], tilapia [26], Asian sea- bass [18], Japanese flounder [27] and half-smooth tongue sole (Cynoglossus semilaevis) [28].
- Common carp (Cyprinus carpio), one of the most important cyprinid species, is mainly cultured in Europe and Asia with a culture history of several thousand years, and contributes an annual production of 4.1 million metric tons in the world (FAO, 2013).
- Based on morphological characters, common carp was classi- fied into three subspecies: C.
- Owing to the important roles of common carp in aquaculture industry and bio- logical studies, various genetic and genomic resources, such as genetic linkage maps [31], transcriptome [32], microRNA [33] and genome sequence [34] have been developed in the Songpu mirror carp strain which be- longs to the subspecies C.
- haema- topterus and as one of the most important aquacul- tured strains in China, has quite limited genetics and genomics resources for analysis of economic traits so far.
- Construction of the high-resolution map for the Yangtze River strain of common carp would provide more information to understand the genome structure and gene rearrangement between the two subspecies..
- QTLs for growth-related traits have been identified by several studies in the Songpu mirror carp strain mainly based on microsatellite markers [36 –38].
- However, the density of the map base on microsatellites is generally medium or low, which is not suitable for fine mapping of QTL..
- The main objectives of this study include: (1) con- struction of a high-resolution genetic linkage map based on 2b-RAD markers and microsatellite markers in the Yangtze River common carp C.
- carpio, zebrafish (Danio rerio) and grass carp (Ctenopharyngodon idellus), (3) performing fine QTL mapping for growth-related traits and sex, and (4) identification of candidate genes associated with growth-related traits..
- Characteristics of the phenotypic traits.
- These growth-related traits showed a strong correlation with each other (r P <.
- By phenotype sexing in the mapping family, 50 and 54 individuals were identified as males and females, respectively, with a sex ratio of 1:1.08..
- Finally, a total of 19,839 polymorphic markers including 12,084 codominant (parent-shared) markers and 7755 dominant (parent-specific) markers were het- erozygous in at least one parent and genotyped in at least 80% of the offspring..
- Construction of the high-resolution linkage map.
- The sex- averaged genetic map spanned 4586.56 cM with an aver- age marker interval of 0.57 cM.
- Table 1 Pearson correlation coefficients (r) for all pairwise combinations of the five growth-related traits (P <.
- Of the 667 markers uniquely anchored to the assembled LGs of C.
- Fine QTL mapping for growth-related traits and sex The chromosome-wide and genome-wide LOD significance thresholds for growth-related traits varied from 3.3 to 6.2.
- 1 The sex-averaged genetic linkage map of the Yangtze River common carp C.
- A genome-wide significant QTL was finely mapped on LG50 with the confidence interval ranging from 12.25 cM to 40.75 cM, and explained 38.1% of the phenotypic variance (LOD = 10.83) (Fig.
- A total of 15 markers were identified in this QTL region, among them, nine continuous markers (from ref-20,177 to ref- 119,060) with the average LOD score of 7.12 were all heterozygous in female parent and homozygous in male parent.
- The confidence interval of the QTL (qHL5-a) on LG5 was mapped to a 0.87 M region on chromosome 3 of Table 2 Summary of the sex-averaged genetic linkage map of C.
- genotyped in this study, and 14% of them were parent- shared markers which help us to construct the first high- density sex-averaged genetic map of the Yangtze River common carp (C.
- 1) is in agreement with the haploid chromo- some number of common carp [48].
- Common carp is believed to have undergone a fourth round of genome duplication [34, 52], which was also vali- dated in this study.
- Strong correlations among the five growth-related traits (BW, TL, BL, BH and HL) have been reported in some aquaculture species, such as Atlantic salmon [57],.
- On LG27, a QTL-containing interval was identified for all growth- related traits, suggesting the influence of one QTL on all growth-related traits in the Yangtze River carp.
- Fur- ther studies are necessary to verify the associations be- tween polymorphisms in these two genes with growth traits in common carp..
- The sex determination of common carp is male- dominant (XX/XY) since sex ratios in conventional diploid offspring approximate 1:1 and gynogenetic offspring are all female [62].
- Chen et al.
- An earlier discovery has provided evidence for autosomal influ- ences on sex determination in common carp [66].
- The sex-determining loci identified in this study would be useful for MAS breeding in the Yangtze River common carp..
- A high-density genetic linkage map of the Yangtze River carp (C.
- A total of 21 QTLs for growth-related traits were identified on 12 LGs..
- These genetic markers or candidate genes associated with growth traits provide a basis for marker-assisted selection (MAS) in the Yangtze River carp and/or other common carp strains..
- Two wild populations of common carp were collected from two geographic areas (Jingzhou and Wuhan) along the Yangtze River, and were used to produce F1 popula- tions.
- Five parameters of growth-related traits including BW, TL, BL, BH and HL were recorded.
- Phenotype sexing was performed for each progeny of the F2 family by gently press abdomen of the fish in late April 2012.
- The distribution patterns (normal or nonnormal) of growth-related traits were determined by the Kolmogorov- Smirnov tests.
- Before the library preparation, potential restriction sites were calculated based on the assembled genome se- quence of common carp (http://www.carpbase.org).
- Libraries were pooled with equal amount to make the final library which was sequenced in a lane of the Illumina HiSeq2500 SE50 platform (Illu- mina, USA)..
- A total of 1500 genomic and transcript-associated SSR markers previously published for common carp [73, 74].
- Segregating markers that could not be genotyped in at least 20% of the offspring were removed.
- Freq.” func- tion was used for a chi-square test to assess the good- ness of fit to the expected segregation ratios for each locus at the confidence level of 0.05.
- Linkage between markers was exam- ined by estimating logarithm of the odds (LOD) scores for recombination fraction.
- Markers were grouped at a LOD threshold score of 11.0 and a maximum recombin- ation fraction of 0.35.
- MapChart 2.2 software was used for graphical visualization of the link- age groups (LGs) [75]..
- To perform comparative analysis, sequences of the markers on the genetic map were aligned to the assem- bled genomes of C.
- QTL analysis of growth-related traits and sex.
- utilized to detect any significant association between growth-related traits and marker loci in the data sets..
- Cofactors for MQM analyses were automatically selected with a p-value of 0.02.
- Calculation of the percentage of phenotypic variance explained (PVE) by a QTL was per- formed on the basis of the population variance found within the progeny..
- Information of markers located in the high- resolution genetic linkage map of the Yangtze River common carp (Cyprinus carpio haematopterus), and their aligned positions in genomes of C.
- The markers within confidence intervals of QTLs for growth traits in the Yangtze River common carp (Cyprinus carpio haematopterus), and their aligned positions in genomes of C.
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