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Sci Rep
2015 Oct 06;5:14852. doi: 10.1038/srep14852.
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Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus.
Tian M
,
Li Y
,
Jing J
,
Mu C
,
Du H
,
Dou J
,
Mao J
,
Li X
,
Jiao W
,
Wang Y
,
Hu X
,
Wang S
,
Wang R
,
Bao Z
.
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Genetic linkage maps are critical and indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density and high-resolution linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as echinoderms. In this study, high-density, high-resolution genetic map was constructed for a sea cucumber species, Apostichopus japonicus, utilizing the 2b-restriction site-associated DNA (2b-RAD) method. A total of 7839 markers were anchored to the linkage map with the map coverage of 99.57%, to our knowledge, this is the highest marker density among echinoderm species. QTL mapping and association analysis consistently captured one growth-related QTL located in a 5 cM region of linkage group (LG) 5. An annotated candidate gene, retinoblastoma-binding protein 5 (RbBP5), which has been reported to be an important regulator of cell proliferation, was recognized in the QTL region. This linkage map represents a powerful tool for research involving both fine-scale QTL mapping and marker assisted selection (MAS), and will facilitate chromosome assignment and improve the whole-genome assembly of sea cucumber in the future.
Figure 1. Recombination rate of shared markers between sex-specific maps and consensus map.This diagram was constructed using the recombination rate of 162 shared markers shared by sex-specific maps and consensus map. The left Y-axis represents shared marker interval in female map and right Y-axis represents the shared marker interval in male map, the X-axis stands for shared marker interval in consensus map. The blue dots stand for shared marker interval ratio between female map and consensus map (F:C ratio), while the red dots represent shared marker interval ratio between male map and consensus map (M:C ratio). *F:C ratio represents the recombination rate correlation of shared markers between female map and consensus map; M:C ratio stands for the recombination rate ratio between male map and consensus map.
Figure 2. The high-density consensus linkage map of A. japonicus.The consensus map which contained 7839 markers in 22 linkage groups was constructed through combing the male and female linkage maps (Supplementary Figure F2 and F3).
Figure 3. Growth-related QTL mapping and association analysis in A. japonicus among all linkage groups (a) and the candidate region of the major QTL in LG5 (b).The dashed line indicates the genome-wide significance threshold where LOD = 3.7. The vertical dashed line stands for the growth trait related QTL window (82.45 ± 2.5 cM).
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