# GWAS and Selective Sweep Analysis Reveal the Genetic Basis of Papilla Number in the Sea Cucumber (Apostichopus japonicus)

## TL;DR

This study identifies genetic factors and biological pathways linked to papilla number variation in sea cucumbers, aiding breeding programs for this economically important trait.

## Contribution

The integration of GWAS and selective sweep analysis reveals novel candidate genes and pathways for papilla number in Apostichopus japonicus.

## Key findings

- GWAS identified two SNP loci and 48 candidate genes associated with papilla number in Group N1.
- Selective sweep analysis revealed 23 and 39 candidate genes in parental and offspring groups, respectively.
- The Calcium signaling pathway was significantly enriched, suggesting its role in papilla development.

## Abstract

The sea cucumber Apostichopus japonicus (A. japonicus) is a commercially valuable species due to its high nutritional and medicinal values. papilla number is one of the key economic traits in A. japonicus, closely associated with market grading standards in China. In the present study, reduced-representation genome sequencing (RRGS) and whole-genome resequencing (WGS) were conducted on A. japonicus collected from six geographically distinct populations in northern China (Group N1) and their offspring (Group N2), respectively. Subsequently, genome-wide association study (GWAS) and selective sweep analysis were integrated to identify candidate genes and biological pathways associated with papilla number in A. japonicus. GWAS identified two single-nucleotide polymorphism (SNP) loci and 48 candidate genes in Group N1. Selective sweep analysis identified 23 and 38 candidate genes in the parental group and offspring group, respectively. Functional enrichment analysis among these candidate genes highlighted six enriched biological pathways potentially involved in papilla number regulation in A. japonicus. These results provide a solid basis for revealing the papilla development mechanism of this species and open up new possibilities for developing papilla-rich breeding in sea cucumber.

Sea cucumber (Apostichopus japonicus) is a commercially important mariculture species in northern China. Papilla number has been recognized as a key economic trait in sea cucumbers. Notably, significant variation in papilla count exists among different populations. The genetic mechanisms controlling papilla development are not fully understood. In this study, 72 individuals from six geographically distinct sea cucumber populations (Group N1) and 35 individuals from their offspring (Group N2) were analyzed using reduced-representation genome sequencing (RRGS) and whole-genome resequencing (WGS), respectively. Genome-wide association studies (GWAS) and selective sweep analysis were conducted to identify the biological pathways and genetic basis underlying variation in papilla number. The GWAS analysis identified two single-nucleotide polymorphism (SNP) loci on chromosomes 4 and 14 in the Group N1 that were significantly associated with papilla number. Within the vicinity of two SNPs, 48 genes were annotated as putative candidate genes, six of which have been reported to be associated with growth in A. japonicus or other aquatic animals. Selective sweep analysis identified 23 candidate genes in the JZ vs. YT within Group N1 and 39 candidate genes in the G1 vs. G3 within Group N2. Notably, functional enrichment analysis revealed that the Calcium signaling pathway was significantly enriched in both Group N1 and Group N2. This pathway has been demonstrated to regulate key cellular processes such as cell proliferation and differentiation through the activation of downstream signaling cascades. The intersection of results from parental Group N1 and progeny Group N2 yielded a total of six key biological pathways, including biological process, cellular process, cellular anatomical entity, cellular component, membrane, and binding. Collectively, our findings contribute to a deeper understanding of the genetic mechanisms underlying papilla number variation in A. japonicus and provide valuable insights for genomic selection in breeding programs.