Genetic population analysis of jinga shrimp (Metapenaeus affinis) in Persian Gulf

Jinga shrimp Metapenaeus affinis is one of the most important penaeide shrimp species in Persian Gulf that has the highest amount of shrimp catch after banana shrimp in Hormozgan province. Regarding the importance of Jinga shrimp in fisheries of this province, genetic diversity and population structure of this species was assessed for the first time by mitochondrial 16SrRNA sequencing. A number of 18 shrimps were collected from the regions of Bandar Abbas, Bushehr and Khuzestan (six samples each region). DNA Extraction was performed using phenolchloroform and by optimizing the PCR for amplification of 16SrRNA, the most suitable temperature for primer binding was 48 °C. Analysis of 18 sequenced samples including 486 aligned base pairs of 16SrRNA yielded 480 monomorphic loci, 6 polymorphic loci and 2 transitions. No insertions and deletions were observed. 9 haplotypes were identified from the 18 samples. Mean haplotype diversity in each region was recorded from 0.0 ± 0.0 (Bandar Abbas) to 0.333 ± 0.215 (Bushehr) and 0.333 ± 0.215 (Khuzestan), and mean nucleotide diversity from 0.0 ± 0.0 (Bandar Abbas) to 0.003 ± 0.003 (Bushehr) and 0.001 ± 0.001 (Khuzestan). Haplotype and nucleotide diversity of all samples were 0.608 ± 0.007 and 0.002 ± 0.003, respectively. The maximum amount of F- statistic parameter was 0.750 between samples of Bandar Abbas and Khuzestan and the minimum amount between Bushehr and Khuzestan (-0.105). At probability level of 0.05, population differentiation was significant between Bandar Abbas and two other regions of Bushehr and Khuzestan but not significant between regions of Bushehr and Khuzestan. Test of exact p values within population confirmed the difference of Bandar Abbas population from the two other populations. Phylogenetic trees showed the differentiation of Bandar Abbas population from the two other regions. The results of this study using mitochondrial 16SrRNA sequencing revealed that the Jinga shrimp population of Bandar Abbas is a differentiated and separated gene pool from the two other regions, and although the populations of Bushehr and Khuzestan seem not genetically separated, molecular diversity of this species is acceptable in these two regions.