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Identification of a large SNP dataset in Larimichthys crocea using specific‐locus amplified fragment sequencing
Author(s) -
Chen Y.,
Wang Y.,
Jiang S.,
Zhang J.,
Lü Z.,
Deng S.
Publication year - 2018
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12676
Subject(s) - biology , snp , locus (genetics) , genetics , sciaenidae , germplasm , single nucleotide polymorphism , overfishing , population , fishery , genotype , gene , fish <actinopterygii> , botany , demography , sociology
Summary The large yellow croaker, Larimichthys crocea , is a commercially important drum fish (Family: Sciaenidae) native to the East and South China Sea. Habitat deterioration and overfishing have led to significant population decline and the collapse of its fishery over the past decades. Today, the market supply of L. crocea depends solely on stocks produced in hatcheries and farms. Common issues that occur in the culture of L. crocea include germplasm degradation, precocious puberty, elevated disease susceptibility and growth retardation. In this study, we employed SLAF ‐seq (specific‐locus amplified fragment sequencing) technology to identify single nucleotide polymorphism ( SNP ) loci across the L. crocea genome. Sixty samples were selected for SLAF analysis out of 1000 progeny in the same cohort of a cultured stock. Our analysis obtained a total of 151 253 SLAF s, of which 65.88% (99 652) were identified to be polymorphic, scoring a total of 710 567 putative SNP s. Further filtration resulted in a final panel of 1782 SNP loci. The data derived from this work could be beneficial for understanding the genetics of complex phenotypic traits as well as for developing marker‐selection‐assisted breeding programs in L. crocea .