Construction of a High-Density Genetic Linkage Map for the Mapping of QTL Associated with Growth-Related Traits in Sea Cucumber (Apostichopus japonicus)

Genetic linkage maps have become an indispensable tool for genetics and genomics research. Sea cucumber (Apostichopus japonicus), which is an economically important mariculture species in Asia, is an edible echinoderm with medicinal properties. In this study, the first SNP-based high-density genetic linkage map was constructed by sequencing 132 A. japonicus individuals (2 parents and 130 offspring) according to a genotyping-by-sequencing (GBS) method. The consensus map was 3181.54 cM long, with an average genetic distance of 0.52 cM. A total of 6144 SNPs were assigned to 22 linkage groups (LGs). A Pearson analysis and QTL mapping revealed the correlations among body weight, body length, and papillae number. An important growth-related candidate gene, protein still life, isoforms C/SIF type 2 (sif), was identified in LG18. The gene was significantly highly expressed during the larval developmental stages. Its encoded protein reportedly functions as a guanine nucleotide exchange factor. These results would facilitate the genetic analysis of growth traits and provide valuable genomic resources for the selection and breeding of new varieties of sea cucumbers with excellent production traits.

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A genetic linkage map of the sea cucumber,Apostichopus japonicus(Selenka), based on AFLP and microsatellite markers

Animal Genetics ◽

10.1111/j.1365-2052.2009.01900.x ◽

2009 ◽

Vol 40 (5) ◽

pp. 678-685 ◽

Cited By ~ 29

Author(s):

Q. Li ◽

L. Chen ◽

L. Kong

Keyword(s):

Microsatellite Markers ◽

Linkage Map ◽

Genetic Linkage ◽

Sea Cucumber ◽

Genetic Linkage Map ◽

Apostichopus Japonicus

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A genetic linkage map of the sea cucumber (Apostichopus japonicus) based on microsatellites and SNPs

Aquaculture ◽

10.1016/j.aquaculture.2013.04.011 ◽

2013 ◽

Vol 404-405 ◽

pp. 1-7 ◽

Cited By ~ 8

Author(s):

Jingjing Yan ◽

Jing Jing ◽

Xiaoyu Mu ◽

Huixia Du ◽

Meilin Tian ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Sea Cucumber ◽

Genetic Linkage Map ◽

Apostichopus Japonicus

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Construction of a high-density genetic linkage map and mapping of quantitative trait loci for growth-related traits in silver carp (Hypophthalmichthys molitrix)

Scientific Reports ◽

10.1038/s41598-019-53469-8 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Xinhua Wang ◽

Haiyang Liu ◽

Meixia Pang ◽

Beide Fu ◽

Xiaomu Yu ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Linkage Map ◽

Quantitative Trait ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Growth Traits ◽

Silver Carp ◽

High Density ◽

Potential Candidate ◽

Hypophthalmichthys Molitrix

AbstractHigh-density genetic map and quantitative trait loci (QTL) mapping are powerful tools for identifying genomic regions that may be responsible for such polygenic trait as growth. A high-density genetic linkage map was constructed by sequencing 198 individuals in a F1 family of silver carp (Hypophthalmichthys molitrix) in this study. This genetic map spans a length of 2,721.07 cM with 3,134 SNPs distributed on 24 linkage groups (LGs). Comparative genomic mapping presented a high level of syntenic relationship between silver carp and zebrafish. We detected one major and nineteen suggestive QTL for 4 growth-related traits (body length, body height, head length and body weight) at 6, 12 and 18 months post hatch (mph), explaining 10.2~19.5% of phenotypic variation. All six QTL for growth traits of 12 mph generally overlapped with QTL for 6 mph, while the majority of QTL for 18 mph were identified on two additional LGs, which may reveal a different genetic modulation during early and late muscle growth stages. Four potential candidate genes were identified from the QTL regions by homology searching of marker sequences against zebrafish genome. Hepcidin, a potential candidate gene identified from a QTL interval on LG16, was significantly associated with growth traits in the analyses of both phenotype-SNP association and mRNA expression between small-size and large-size groups of silver carp. These results provide a basis for elucidating the genetic mechanisms for growth and body formation in silver carp, a world aquaculture fish.

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