Genetic diversity status of Pacific white shrimp (Litopenaeus vannamei) using SSR markers in Iran

Rezaee, Saiwan; Farahmand, Hamid; Nematollahi, Mohammad Ali

doi:10.1007/s10499-015-9939-y

Cited by 11 publications

(6 citation statements)

References 16 publications

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“…The number of alleles for M. affinis over the five microsatellite loci ranged from 5 to 12, with varied in size from 120 to 434 bp (Table 2), which was similar to the number (2-13, 5-10, 3-12) reported by VallesJimenez et al (2005), Rezaee, Farahmand, and Nematollahi (2016), and Lima, Silva, Oliveira, Maggioni, and Coimbra (2010) for Pacific white shrimp (Litopenaeus vannamei) respectively, the number (6-14) that reported by Xu, Primavera, Pena, Pettit, Belak, and Warren (2001) for black tiger shrimp (Penaeus monodon), (5-16) by Zhang, Kong, Wang, and Wang (2010) for P. chinensis, and (5-15) by Gao et al (2008) for Chinese shrimp Fenneropenaeus chinensis. The tests for genetic differentiation showed significant allele frequency differences in all of the stock and suggested a moderate degree of similarity among the Bahrakan and Lifeh-Boosif populations of white shrimp (M. affinis) from the Persian Gulf evaluated in the current study.…”

Section: Discussionsupporting

confidence: 83%

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Shokoohmand¹,

Zolgharnein²,

Mashjoor³

et al. 2018

Turk. J. Fish. Aquat. Sci.

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We investigated the genetic structure of Metapenaeus affinis population from the northern coasts (Khuzestan Province: Bahrakan and Lifeh-Boosiaf region) of the Persian Gulf, using five microsatellite markers. The samples of pleopods tissue of shrimp were taken, DNA extracted and PCR was performed on microsatellite primers. The results revealed that all five microsatellite loci were polymorphic, the number of alleles (Na) ranged from 5 to 12 per locus, and the observed and effective number was 7 and 3.67, respectively, also the observed and expected heterozygosis was ranged from 0.1 to 0.77 and 0.1 and 0.83, respectively, which indicated that the two populations of M. affinis possessed a rich genetic diversity. The deviation from Hardy-Weinberg equilibrium (P<0.05) was observed that due to the heterozygote deficiency in populations. Based on the analysis of molecular variance (AMOVA), the genetic variation among stocks (17%) was much lower than that within stocks (83%), and Fst, Rst, and Nm were 0.107, 0.372 and 2.092, respectively. The highest genetic distance was 0.571 and the lowest was 0.561. Genetic distance and cluster analysis using UPGMA divided the two stocks into two groups. The present study showed that two different populations of M. affinis had a certain genetic diversity.

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Section: Discussionsupporting

confidence: 83%

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Shokoohmand¹,

Zolgharnein²,

Mashjoor³

et al. 2018

Turk. J. Fish. Aquat. Sci.

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“…Bacteria are the main microorganisms responsible for seafood fermentation. Research on the microbial diversity of shrimp paste has mostly concentrated on the culture environment of shrimp (20–22) and the chemical composition and sensory attributes of shrimp paste (23). There has been little research into the microbial community structure and diversity in shrimp paste.…”

Section: Introductionmentioning

confidence: 99%

Microbial Community Structure and Diversity of Shrimp Paste at Different Fermentation Stages

Dai

Wang

Sun

et al. 2018

Preprint

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9High-throughput sequencing was used to reveal the highly diverse bacterial 10 populations in shrimp paste at different fermentation stages. We studied three stages of 11 fermentation and obtained 448,916 reads. Using this approach, we revealed the presence 12 of 30 phyla, 55 classes, 86 orders, 206 families and 695 genera of bacteria in the shrimp 13 paste. Shrimp paste in fermentation metaphase had a more diverse microbiota than that in 14 fermentation prophase and fermentation anaphase. Diversity appeared greatest in 15 fermentation anaphase. The four dominant phyla were Proteobacteria, Firmicutes, 16 Actinobacteria, and Bacteroidetes. The most common genera were Psychrobacter, 17 Halomonas, Bacillus, Alteribacillus, and Lactococcus. Their content varied at different 18 stages of fermentation. All the microbiome presented a variety of changes in the 19 microbial diversity of shrimp paste. 20 Importance 21 Most research on the microbial diversity of shrimp paste has focused on the shrimp 22 culture environment, or the chemical composition and sensory attributes of the paste. 23 Applied and Environmental Microbiology 2 Little research has been conducted on the microbial diversity and composition of shrimp 24 paste. The relationship between microbes and the flavor and quality of shrimp paste has 25 thus been unknown. We therefore analyzed the microbial composition and variation of 26 shrimp paste at different stages of fermentation. The dominant bacteria in fermentation 27 prophase, metaphase, and anaphase were identified. Our preliminary findings give some 28 insight into which microbes contribute to the flavor of shrimp paste and suggest how to 29 improve its flavor. In addition, our findings are relevant to optimizing the production of 30 shrimp paste and guaranteeing its quality and safety.31

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“…The BMK and CP exhibit the lowest level of heterozygosity and high inbreeding coefficient, which is consistent with the ROH analysis. The observed heterozygosity levels are relatively lower than previous estimations (De Freitas and Galetti, 2005;Artiles et al, 2011;Rezaee et al, 2016;Perez-Enriquez et al, 2018a). The decay of LD provides important information about the historical recombination of population and is widely used to understand the evolutionary and demographic processes (Slatkin, 2008).…”

Section: Discussionmentioning

confidence: 80%

Selection Signatures of Pacific White Shrimp Litopenaeus vannamei Revealed by Whole-Genome Resequencing Analysis

Wang

Teng

et al. 2022

Front. Mar. Sci.

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The Pacific white shrimp Litopenaeus vannamei is among the top aquatic species of commercial importance around the world. Over the last four decades, the breeding works of L. vannamei have been carried out intensively and have generated multiple strains with improved production and performance traits. However, signatures of domestication and artificial selection across the L. vannamei genome remain largely unexplored. In the present study, we conducted whole genomic resequencing of 180 Pacific white shrimps from two artificially selective breeds and four market-leading companies. A total of 37 million single nucleotide polymorphisms (SNPs) were identified with an average density of 22.5 SNPs/Kb across the genome. Ancestry estimation, principal component analysis, and phylogenetic inference have all revealed the obvious stratifications among the six breeds. We evaluated the linkage disequilibrium (LD) decay in each breed and identified the genetic variations driven by selection. Pairwise comparison of the fixation index (Fst) and nucleotide diversity (θπ) has allowed for mining the genomic regions under selective sweep in each breed. The functional enrichment analysis revealed that genes within these regions are mainly involved in the cellular macromolecule metabolic process, proteolysis, structural molecule activity, structure of the constituent ribosome, and responses to stimulus. The genome-wide SNP datasets provide valuable information for germplasm resources assessment and genome-assisted breeding of Pacific white shrimps, and also shed light on the genetic effects and genomic signatures of selective breeding.

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Genetic diversity status of Pacific white shrimp (Litopenaeus vannamei) using SSR markers in Iran

Cited by 11 publications

References 16 publications

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Microbial Community Structure and Diversity of Shrimp Paste at Different Fermentation Stages

Selection Signatures of Pacific White Shrimp Litopenaeus vannamei Revealed by Whole-Genome Resequencing Analysis

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