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Mar Life Sci Technol
2022 Aug 01;43:343-355. doi: 10.1007/s42995-022-00139-w.
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Fine-mapping and association analysis of candidate genes for papilla number in sea cucumber, Apostichopus japonicus.
Zhu X
,
Ni P
,
Sturrock M
,
Wang Y
,
Ding J
,
Chang Y
,
Hu J
,
Bao Z
.
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UNLABELLED: The papilla number is one of the most economically important traits of sea cucumber in the China marketing trade. However, the genetic basis for papilla number diversity in holothurians is still scarce. In the present study, we conducted genome-wide association studies (GWAS) for the trait papilla number of sea cucumbers utilizing a set of 400,186 high-quality SNPs derived from 200 sea cucumbers. Two significant trait-associated SNPs that passed Bonferroni correction (P < 1.25E-7) were located in the intergenic region near PATS1 and the genic region of EIF4G, which were reported to play a pivotal role in cell growth and proliferation. The fine-mapping regions around the top two lead SNPs provided precise causative loci/genes related to papilla formation and cellular activity, including PPP2R3C, GBP1, and BCAS3. Potential SNPs with P < 1E-4 were acquired for the following GO and KEGG enrichment analysis. Moreover, the two lead SNPs were verified in another population of sea cucumber, and the expressive detection of three potential candidate genes PATS1, PPP2R3C, and EIF4G that near or cover the two lead SNPs was conducted in papilla tissue of TG (Top papilla number group) and BG (Bottom papilla number group) by qRT-PCR. We found the significantly higher expression profile of PATS1 (3.34-fold), PPP2R3C (4.90-fold), and EIF4G (4.23-fold) in TG, implying their potential function in papilla polymorphism. The present results provide valuable information to decipher the phenotype differences of the papilla trait and will provide a scientific basis for selective breeding in sea cucumbers.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-022-00139-w.
Fig. 1. The phenotypic and genetic analysis of papilla number trait. A Papilla number (left) and linkage disequilibrium (LD) decay analysis (right). B Quantile–quantile (QQ) plots. C Genetic clustering analysis. D The Manhattan plots for papilla trait in the sea cucumber, where the red line indicates the Bonferroni cut-off (P < 1.25E−7) and the blue line indicates the conventional threshold (P < 1E−5)
Fig. 2. Fine-mapping result of the top two causative SNPs. A Fine-mapping the chromosome 10: region. B Fine-mapping in the chromosome 9: region
Fig. 3. The bioinformatic enrichment and expression analysis of candidate genes. A The summary of GO function annotation analysis and each term described the function of gene cluster and the length of colored bars represent the P value. B The summary of KEGG pathway enrichment analysis and the bubble size and color represented gene numbers and Q values in certain pathway. C Relative expression levels of PATS1, PPP2R3C and EIF4G in papilla of TG and BG sea cucumbers. Three replicates were performed for each papillae tissue, and three technical replicates were conducted for each PCR. The comparison of the expression levels as performed using an independent sample t test. ‘*’ indicates differences that are statistically significant (P < 0.05)
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