Development of novel SSR markers and validation by assessing the genetic diversity of endangered Deccan mahseer, Tor khudree

Gargee Das; Sofia Priyadarsani Das; Amrita Bit; Lakshman Sahoo; Subrat Kumar Swain; Channaveer Huchappa Raghavendra; N P Krishnaprasoon; Sangram Ketan Sahoo; Paramananda Das

doi:10.1007/s11033-023-09188-5

Development of novel SSR markers and validation by assessing the genetic diversity of endangered Deccan mahseer, Tor khudree

Mol Biol Rep. 2024 Feb 8;51(1):290. doi: 10.1007/s11033-023-09188-5.

Authors

Gargee Das¹, Sofia Priyadarsani Das², Amrita Bit¹, Lakshman Sahoo¹, Subrat Kumar Swain³, Channaveer Huchappa Raghavendra⁴, N P Krishnaprasoon⁵, Sangram Ketan Sahoo^{1

6}, Paramananda Das⁷

Affiliations

¹ Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India.
² Department of Aquaculture, National Taiwan Ocean University, Keelung City, 202, Taiwan.
³ Institute of Medical Sciences & SUM Hospital, Siksha O Anusandhan University, Bhubaneswar, India.
⁴ ICAR- Central Institute of Freshwater Aquaculture, RRC, Bengaluru, India.
⁵ PMFGR Centre of ICAR-National Bureau of Fish Genetic Resources, CMFRI Campus, Kochi, India.
⁶ Aquaculture Productions and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India.
⁷ Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India. pdas77@hotmail.com.

PMID: 38329563
DOI: 10.1007/s11033-023-09188-5

Abstract

Background: The Deccan mahseer, Tor khudree (Sykes, 1839) is a potential game and food fish species belonging to the family cyprinidae and is categorized as endangered. Its distribution is restricted to southern part of India, specifically to Peninsular Rivers. This study is first to assess the genetic diversity and differentiation in Tor khudree by developing novel simple sequence repeat (SSR) markers.

Methods and results: Low depth next generation sequencing followed by sequence analysis in MISA software identified 187,649 SSRs. The novel fourteen validated SSR loci were used for population genetic analysis. All of the SSR loci were highly informative with mean PIC > 0.5. High mean allelic richness (9.29) observed heterozygosity (0.98) and expected heterozygosity (0.79) were observed across the loci. However, genetic differentiation was low but significant (0.052). Negative F_IS values were observed in both locus-wise and populations indicating the presence of high heterozygosity. Intrapopulation variation was found to be high (96.29%). The population structure revealed two genetic stocks.

Conclusions: The results from the present study including the highly polymorphic markers developed would be a useful resource for further research on population genetics and conservation genetics of the species.

Keywords: Deccan mahseer. Next generation sequencing. SSR. Population diversity.

MeSH terms

Alleles
Animals
Cyprinidae* / genetics
Food
Genetic Variation / genetics
Microsatellite Repeats / genetics