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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01023

A High-Density Genetic Linkage Map and QTL Mapping for Sex and Growth-Related Traits of Large-Scale Loach (Paramisgurnus dabryanus)

Jin Wei1, Yuanyuan Chen2 and  Weimin Wang1*
  • 1College of Fisheries, Huazhong Agricultural University, China
  • 2School of Life Sciences, Jianghan University, China

Large-scale loach (Paramisgurnus dabryanus) is a commercially important species in East Asia, however, the cultured population that exhibited degradation of germplasm resource cannot meet the market needs, and the genome resources for P. dabryanus are still lacking. In this study, the first high-density genetic map of P. dabryanus was constructed using 15,830 SNP markers based on high-throughput sequencing with an improved SLAF-seq strategy. The quantitative trait locus (QTL) mapping for sex, growth and morphology traits was performed for the first time. The genetic map spanned 4,657.64cM in length with an average inter-marker distance of 0.30 cM. QTL mapping and association analysis identified eight QTLs of growth traits, nine QTLs of morphology traits, and five QTLs of sex-related traits, respectively. Interestingly, the most significant QTLs for almost all the traits were concentrated on the same linkage group LG11. Seven candidate markers and 12 potentially key genes, which were associated with sex determination and growth, were identified within the overlapped QTL regions on LG11. Further, the first genome survey analysis of P. dabryanus was performed which represents the first step towards fully decoding the P. dabryanus genome. The genome scaffolds were anchored to the high-density linkage map, spanning 960.27 Mb of P. dabryanus reference genome. The collinearity analysis revealed a high level of collinearity between the genetic map and the reference genome of P. dabryanus. Moreover, a certain degree of homology was observed between large-scale loach and zebrafish using comparative genomic analysis. The constructed high-density genetic map was an important basis for QTL fine mapping, genome assembly, and genome comparison. The present study will provide a valuable resource for future marker-assisted breeding, and further genetic and genomic researches in P. dabryanus.

Keywords: large-scale loach, Genetic linkage map, QTL mapping, Growth, Sex, potentially key genes, genome survey analysis, genome scaffold anchoring

Received: 08 Jul 2019; Accepted: 24 Sep 2019.

Copyright: © 2019 Wei, Chen and Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Weimin Wang, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China, weijin@webmail.hzau.edu.cn