Candidate sex-associated gene identification in Trachinotus ovatus (Carangidae) using an integrated SLAF-seq and bulked segregant analysis approach

Pingping He; Pinyuan Wei; Yuan Ma; Shenhua Hu; Jiuxiang Yao; Xiaozhen Jiang; Youhou Xu; Peng Zhu; Mingli Wei; Weiming Jiang; Jinxia Peng

doi:10.1016/j.gene.2021.146026

Candidate sex-associated gene identification in Trachinotus ovatus (Carangidae) using an integrated SLAF-seq and bulked segregant analysis approach

Gene. 2022 Jan 30:809:146026. doi: 10.1016/j.gene.2021.146026. Epub 2021 Oct 20.

Authors

Pingping He¹, Pinyuan Wei¹, Yuan Ma², Shenhua Hu¹, Jiuxiang Yao¹, Xiaozhen Jiang³, Youhou Xu², Peng Zhu², Mingli Wei¹, Weiming Jiang⁴, Jinxia Peng⁵

Affiliations

¹ Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China.
² Beibu Gulf University, Qinzhou 535000, China.
³ Guangxi Agricultural Vocational College, Nanning 530007, China.
⁴ Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China. Electronic address: [email protected].
⁵ Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning 530021, China. Electronic address: [email protected].

PMID: 34687789
DOI: 10.1016/j.gene.2021.146026

Abstract

It is difficult to distinguish the sexes of Trachinotus ovatus based on appearance, and little data about sex-determining genes are available for this species. Here, we generated 200 F2 individuals using the parents R404 and R403. DNA samples were collected from 50 individuals of each sex and aggregated into sex-specific DNA pools. Specific-locus amplified fragment sequencing was integrated with bulked segregant analysis to detect candidate sex-associated genes. Approximately 3,153,153 high-quality single-nucleotide polymorphism (SNP) markers and 135,363 high-quality insertion-deletion (Indel) markers were generated. Six candidate regions within chromosome 14, encompassing 132 candidate genes, were identified as closely related to sex. Based on annotations, six genes (EVM0019817, EVM0004192, EVM0001445, EVM0005260, EVM0014734, and EVM0009626) were predicted to be closely associated with sex. These results present an efficient genetic mapping approach that lays a foundation for molecular sex discrimination in T. ovatus.

Keywords: BSA; Chromosome; SLAF-seq; SNP; Sex-related; Trachinotus ovatus.

MeSH terms

Animals
Chromosome Mapping / methods
Female
Fish Proteins / genetics*
Fishes / genetics*
INDEL Mutation
Male
Polymorphism, Single Nucleotide*
Sequence Analysis, DNA
Sex Determination Analysis / methods*

Substances

Fish Proteins