Skip to main content
SpringerLink
Log in

QTL mapping for economically important traits of common carp (Cyprinus carpio L.)

  • Animal Genetics • Original Paper
  • Published:
Journal of Applied Genetics Aims and scope Submit manuscript

Abstract

Quantitative trait loci (QTL) were analyzed for three economically important traits, i.e., body weight (BW), body length (BL), and body thickness (BT), in an F1 family of common carp holding the 190 progeny. A genetic linkage map spanning 3,301 cM in 50 linkage groups with 627 markers and an average distance of 5.6 cM was utilized for QTL mapping. Sixteen QTLs associated with all three growth-related traits were scattered across ten linkage groups, LG6, LG10, LG17, LG19, LG25, LG27, LG28, LG29, LG30, and LG39. Six QTLs for BW and five each for BL and BT explained phenotypic variance in the range 17.0–32.1 %. All the nearest markers of QTLs were found to be significantly (p ≤ 0.05) related with the trait. Among these QTLs, a total of four, two (qBW30 and qBW39) related with BW, one (qBL39) associated with BL, and one (qBT29) related to BT, were found to be the major QTLs with a phenotypic variance of >20 %. qBW30 and qBW39 with the nearest markers HLJ1691 and HLJ1843, respectively, show significant values of 0.0038 and 0.0031, correspondingly. QTLs qBL39 and qBT29 were found to have significant values of 0.0047 and 0.0015, respectively. Three QTLs (qBW27, qBW30, qBW39) of BW, two for BL (qBL19, qBL39), and two for BT (qBT6, qBT25) found in this study were similar to populations with different genetic backgrounds. In this study, the genomic region controlling economically important traits were located. These genomic regions will be the major sources for the discovery of important genes and pathways associated with growth-related traits in common carp.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Ashley PJ (2007) Fish welfare: current issues in aquaculture. Appl Anim Behav Sci 104:199–235

    Article  Google Scholar 

  • Castelloe JM (2000) Sample size computations and power analysis with the SAS system. In: Proceedings of the Twenty-fifth Annual SAS Users Group International Conference, paper 265-25. SAS Institute Inc., Cary

    Google Scholar 

  • Cheng L, Liu L, Yu X, Wang D, Tong J (2010) A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers. Anim Genet 41:191–198

    Article  CAS  PubMed  Google Scholar 

  • Food and Agriculture Organization of the United Nations (FAO) (2012) World review of fisheries and aquaculture. The State of World Fisheries and Aquaculture 2012

  • Geldermann H (1975) Investigations on inheritance of quantitative characters in animals by gene markers I. Methods. Theor Appl Genet 46:319–330

    Article  CAS  PubMed  Google Scholar 

  • Jin S, Zhang X, Jia Z, Fu H, Zheng X, Sun X (2012) Genetic linkage mapping and genetic analysis of QTL related to eye cross and eye diameter in common carp (Cyprinus carpio L.) using microsatellites and SNPs. Aquaculture 358–359:176–182

    Article  Google Scholar 

  • Laghari MY, Zhang Y, Lashari P, Zhang X, Xu P, Xin B, Sun X (2013) Quantitative trait loci (QTL) associated with growth rate trait in common carp (Cyprinus carpio). Aquaculture Int 21:1373–1379. doi:10.1007/s10499-013-9639-4

    Article  Google Scholar 

  • Li O, Cao D, Zhang Y, Gu Y, Zhang X, Lu C, Sun X (2009) Studies on feed conversion ratio trait of common carp (Cyprinus carpio L.) using EST-SSR marker. J Fisheries China 33:624–631

    CAS  Google Scholar 

  • Liu ZJ (2001) Gene mapping, marker-assisted selection, gene cloning, genetic engineering and integrated genetic improvement programs at Auburn University, p. 109–118. In: Gupta MV, Acosta BO (eds) Fish genetics research in member countries and institutions of the International Network on Genetics in Aquaculture. ICLARM conference proceedings 64, 179 pp

  • Liu Z (2007) Aquaculture genome technologies. Detection and analysis of quantitative trait loci (QTL) for economic traits in aquatic species. Blackwell Publishing, pp 169–198

  • Liu JH, Zhang Y, Chang YM, Liang LQ, Lu CY, Zhang XF, Xu MJ, Sun XW (2009) Mapping QTLs related to head length, eye diameter and eye cross of common carp (Cyprinus carpio L.). Yi Chuan 31:508–514 (in Chinese)

    Article  CAS  PubMed  Google Scholar 

  • Mao RX, Liu FJ, Zhang XF, Zhang Y, Cao DC, Lu CY, Liang LQ, Sun X (2009) Studies on quantitative trait loci related to activity of lactate dehydrogenase in common carp (Cyprinus carpio). Yi Chuan 31:407–411 (in Chinese)

    Article  CAS  PubMed  Google Scholar 

  • Naish KA, Hard JJ (2008) Bridging the gap between the genotype and the phenotype: linking genetic variation, selection and adaptation in fishes. Fish Fisheries 9:396–422

    Article  Google Scholar 

  • Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234

    Article  CAS  PubMed  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: Join Map. Plant J 3:739–744

    Article  CAS  Google Scholar 

  • Sun X, Liang L (2004) A genetic linkage map of common carp (Cyprinus carpio L.) and mapping of a locus associated with cold tolerance. Aquaculture 238:165–172

    Article  CAS  Google Scholar 

  • Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H, Xu C, Song J, Huang L, Wang C, Shi J, Wang R, Zheng X, Lu C, Wang X, Zheng H (2013) SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One 8(3):e58700. doi:10.1371/journal.pone.0058700

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Van Ooijen JW (2006) JoinMap 4. Software for the calculation of genetic linkage maps in experimental populations. Plant Research International, Wageningen

    Google Scholar 

  • Van Ooijen JW, Boer MP, Jansen RC, Maliepaard C (2002) MapQTL 4.0: software for the calculation of QTL positions on genetic maps. Plant Research International, Wageningen

  • Wang CM, Lo LC, Zhu ZY, Yue GH (2006) A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer). BMC Genomics 7:274

    Article  PubMed Central  PubMed  Google Scholar 

  • Wang LQ, Liu WJ, Xu Y, He YQ, Luo LJ, Xing YZ, Xu CG, Zhang Q (2007) Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain. Theor Appl Genet 115:463–476

    Article  CAS  PubMed  Google Scholar 

  • Wang CH, Li SF, Nagy ZT, Lehoczky I, Huang L, Zhao Y, Song X, Jeney Z (2010) Molecular genetic structure and relationship of Chinese and Hungarian common carp (Cyprinus carpio L.) strains based on mitochondrial sequence. Aquaculture Res 41:1339–1447

    Article  CAS  Google Scholar 

  • Wang J, He A, Ma Y, Wang C (2012) Genetic map construction and quantitative trait locus (QTL) analysis on growth-related traits in common carp (Cyprinus carpio L.). African J Biotech 11(30):7874–7884

    CAS  Google Scholar 

  • Yue GH (2014) Recent advances of genome mapping and marker-assisted selection in aquaculture. Fish Fisheries 15:376–396. doi:10.1111/faf.12020

    Article  Google Scholar 

  • Zhang Y, Liang LQ, Chang YM, Hou N, Lu CY, Sun XW (2007) Mapping and genetic effect analysis of quantitative trait loci related to body size in common carp (Cyprinus carpio L.). Yi Chuan 29:1243–1248 (in Chinese)

    Article  CAS  PubMed  Google Scholar 

  • Zhang YF, Zhang Y, Lu CY, Cao DC, Sun XW (2008) Correlation analysis of microsatellite DNA markers with body weight, length and height of common carp (Cyprinus carpio L.). Yi Chuan 30:613–619 (in Chinese)

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Xu P, Lu C, Kuang Y, Zhang X, Cao D, Li C, Chang Y, Hou N, Li H, Wang S, Sun X (2011) Genetic linkage mapping and analysis of muscle fiber-related QTLs in common carp (Cyprinus carpio L.). Mar Biotechnol (NY) 13:376–392

    Article  CAS  Google Scholar 

  • Zhang X, Zhang Y, Zheng X, Kuang Y, Zhao Z, Zhao L, Li C, Jiang L, Cao D, Lu C, Xu P, Sun X (2013a) A consensus linkage map provides insights on genome character and evolution in common carp (Cyprinus carpio L.). Mar Biotechnol (NY) 15:275–312. doi:10.1007/s10126-012-9485-9

    Article  CAS  Google Scholar 

  • Zhang Y, Wang S, Li J, Zhang X, Jiang L, Xu P, Lu C, Wan Y, Sun X (2013b) Primary genome scan for complex body shape-related traits in the common carp Cyprinus carpio. J Fish Biol 82:125–140. doi:10.1111/j.1095-8649.2012.03469.x

    Article  CAS  PubMed  Google Scholar 

  • Zhao L, Zhang Y, Ji P, Zhang X, Zhao Z, Hou G, Huo L, Liu G, Li C, Xu P, Sun X (2013) A dense genetic linkage map for common carp and its integration with a BAC-based physical map. PLoS One 8(5):e63928. doi:10.1371/journal.pone.0063928

    Article  PubMed Central  PubMed  Google Scholar 

  • Zheng X, Kuang Y, Lv W, Cao D, Zhang X, Li C, Lu C, Sun X (2013) A consensus linkage map of common carp (Cyprinus carpio L.) to compare the distribution and variation of QTLs associated with growth traits. Sci China Life Sci 56:351–359. doi:10.1007/s11427-012-4427-3

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This study was supported by the National High-tech R&D Program of China (2011AA100401), Key Project of Chinese National Programs for Fundamental Research and Development (2010CB126305), the Introduction of Advanced Agricultural Science and Technology Key Project (“948” Project: 2011-G12), and Special Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Sciences (2012C013).

Conflict of interest

It is declared here that the experiment was conducted complying with the current laws of the People’s Republic of China and there is no conflict of interest.

Author information

Authors and Affiliations

  1. School of Chemical Engineering and Environment, Beijing Institute of Technology, 100081, Beijing, China

    Muhammad Younis Laghari & Baoping Xin

  2. Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, 100141, Beijing, China

    Muhammad Younis Laghari, Punhal Lashari, Xiaofeng Zhang, Peng Xu, Yan Zhang & Xiaowen Sun

  3. Department of Fresh Water Biology and Fisheries, University of Sindh, 76080, Jamshoro, Pakistan

    Muhammad Younis Laghari, Punhal Lashari & Naeem Tariq Narejo

Authors
  1. Muhammad Younis Laghari
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Punhal Lashari
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiaofeng Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Peng Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Naeem Tariq Narejo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Baoping Xin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yan Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Xiaowen Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Yan Zhang or Xiaowen Sun.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Laghari, M.Y., Lashari, P., Zhang, X. et al. QTL mapping for economically important traits of common carp (Cyprinus carpio L.). J Appl Genetics 56, 65–75 (2015). https://doi.org/10.1007/s13353-014-0232-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13353-014-0232-y

Keywords

Search

Navigation