Insight into the genetic basis of ammonia tolerance in razor clam Sinonovacula constricta by genome-wide association study

Abstract

With the development of high-density integrated farming model, the razor clam Sinonovacula constricta faces severe pressures from environmental factors, especially ammonia nitrogen, which is the top factor threaten the growth and survival of aquatic animals. Hence, ammonia tolerance has been one of the most important economic traits for razor clam. To cultivate new strains with ammonia tolerance trait, it is necessary to dissect genetic basis comprehensively underlying ammonia tolerance of S. constricta. In this study, we performed a genome wide association study (GWAS) to identify the single nucleotide polymorphisms (SNPs) and genes associated with ammonia tolerance through whole genome resequencing of 231 individuals. As a result, 56 associated SNPs (-log10P = 5) which were embedded in or adjacent to 236 genes were identified among a total of 4,577,102 SNPs. Most of these genes were related to various processes of metabolism, homeostasis, response to stress and apoptosis, suggesting that the polygenic architecture in the trait of ammonia tolerance was complex in razor clam. Among these sites, 11 genome-wide significant associated SNPs (-log10P = 6.66) adjacent to five candidate genes, including beta-galactosidase (glb1), tetratricopeptide repeat protein 28 (ttc28), Na+/K+-ATPase alpha-1 (nka), tubulin beta (tubb) and elongation factor 1-alpha (eef1a). In particular, NKA has been demonstrated to be involved in NH4+ excretion to reduce ammonia accumulation in mollusca. Our results provide insight into genetic basis of ammonia tolerance, and the SNPs would be valuable markers for selective breeding of ammonia-tolerant strain in S. constricta.