Fine-mapping and association analysis of candidate genes for papilla number in sea cucumber, .

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 ( < 1.25E-7) were located in the intergenic region near and the genic region of , 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 , , and . Potential SNPs with  < 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 , , and 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 (3.34-fold), (4.90-fold), and (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.