Genetic diversity among five wild populations of Portunus trituberculatus

The fast development of aquaculture over the past decades has made it the main source of fish protein and led to its integration into the global food system. Mostly originating from inland production systems, aquaculture has emerged as strategy to decrease malnutrition in low-income countries. The Nile tilapia (Oreochromis niloticus) was introduced to Madagascar in the 1950s, and is now produced nationally at various scales. Aquaculture mostly relies on fry harvested from wild populations and grow-out in ponds for decades. It has recently been diversified by the introduction of several fast-growing strains. Little is known how local genetic diversity compares to recently introduced strains, although high and comparable levels of genetic diversity have previously been observed for both wild populations and local stocks. Our study compares DNA barcode genetic diversity among eight farms and several strains belonging to three species sampled. DNA-based lineage delimitation methods were applied and resulted in the detection of six well differentiated and highly divergent lineages. A comparison of DNA barcode records to sequences on the Barcode of Life Data System (BOLD) helped to trace the origin of several of them. Both haplotype and nucleotide diversity indices highlight high levels of mitochondrial genetic diversity, with several local strains displaying higher diversity than recently introduced strains. This allows for multiple options to maintain high levels of genetic diversity in broodstock and provides more options for selective breeding programs.

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Genetic Diversity of Salvia Species Assessed by ISSR and RAPD Markers

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha44210391 ◽

2016 ◽

Vol 44 (2) ◽

pp. 431-436 ◽

Cited By ~ 6

Author(s):

Masoumeh YOUSEFIAZARKHANIAN ◽

Ali ASGHARI ◽

Jafar AHMADI ◽

Behvar ASGHARI ◽

Ali Ashraf JAFARI

Keyword(s):

Genetic Diversity ◽

Genetic Polymorphisms ◽

Genomic Dna ◽

Rapd Markers ◽

Genetic Relationships ◽

Genetic Variations ◽

Molecular Techniques ◽

Wild Populations ◽

Similarity Coefficients ◽

The World

The genus Salvia includes an enormous assemblage of nearly 1,000 species dispersed around the world. Due to possible threats to this genus, there is an immediate requirement to evaluate the diversity of its wild populations. ISSR and RAPD molecular techniques were used to evaluate the genetic relationships among twenty-one ecotypes of eight Salvia species. Amplification of genomic DNA using 23 primers (15 RAPD and eight ISSR) produced 280 bands, of which 91% were polymorphic. The results of marker parameters showed no clear difference between two marker systems. It was generally observed that both ISSR and RAPD markers had similar efficiency in detecting genetic polymorphisms with remarkable ability to differentiate the closely related ecotypes of Salvia. Neiâ€™s similarity coefficients for these techniques ranged from 0.48 to 0.98. Based on the results of clustering, PCoA and AMOVA, the genetic diversity between and within species was confirmed. So, conservation and domestication of the genus Salvia must be due to levels of genetic variations.

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Genetic variation in native and farmed populations of Tambaqui (Colossoma macropomum) in the Brazilian Amazon: regional discrepancies in farming systems

Anais da Academia Brasileira de Ciências ◽

10.1590/0001-376520130007 ◽

2013 ◽

Vol 85 (4) ◽

pp. 1439-1447 ◽

Cited By ~ 8

Author(s):

Jonas Aguiar ◽

Horacio Schneider ◽

Fatima Gomes ◽

Jeferson Carneiro ◽

Simoni Santos ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Dna Sequences ◽

Amazon Basin ◽

Farming Systems ◽

Wild Populations ◽

The West ◽

Colossoma Macropomum ◽

Breeding Stock ◽

History Of

The tambaqui, Colossoma macropomum, is the most popular fish species used for aquaculture in Brazil but there is no study comparing genetic variation among native and farmed populations of this species. In the present study, we analyzed DNA sequences of the mitochondrial DNA to evaluate the genetic diversity among two wild populations, a fry-producing breeding stock, and a sample of fish farm stocks, all from the region of Santarém, in the west of the Brazilian state of Pará. Similar levels of genetic diversity were found in all the samples and surprisingly the breeding stock showed expressive representation of the genetic diversity registered on wild populations. These results contrast considerably with those of the previous study of farmed stocks in the states of Amapá, Pará, Piauí, and Rondônia, which recorded only two haplotypes, indicating a long history of endogamy in the breeding stocks used to produce fry. The results of the two studies show two distinct scenarios of tambaqui farming in the Amazon basin, which must be better evaluated in order to guarantee the successful expansion of this activity in the region, and the rest of Brazil, given that the tambaqui and its hybrids are now farmed throughout the country.

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Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China

PeerJ ◽

10.7717/peerj.8304 ◽

2020 ◽

Vol 8 ◽

pp. e8304 ◽

Cited By ~ 2

Author(s):

Biao Xiong ◽

Limei Zhang ◽

Shubin Dong ◽

Zhixiang Zhang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Isolation By Distance ◽

Sex Ratios ◽

Mainland China ◽

Small Sample ◽

Chloroplast Microsatellites ◽

Wild Populations ◽

Haplotype Networks ◽

Low Levels

Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqing, and southwest China (population GJS). It is suggested that few wild male individuals should be conserved in order to maintain overall genetic diversity in the wild populations of this species. These findings provide important information for the sustainable utilization and preservation of the overall genetic diversity of L. glauca.

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Genetic Diversity and Disease Resistance of Wild Malus orientalis from Turkey and Southern Russia

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.133.3.383 ◽

2008 ◽

Vol 133 (3) ◽

pp. 383-389 ◽

Cited By ~ 19

Author(s):

Gayle M. Volk ◽

Christopher M. Richards ◽

Ann A. Reilley ◽

Adam D. Henk ◽

Patrick A. Reeves ◽

...

Keyword(s):

Genetic Diversity ◽

Disease Resistance ◽

Venturia Inaequalis ◽

Apple Scab ◽

The Black Sea ◽

Wild Populations ◽

Southern Russia ◽

Sib Families ◽

Small Clusters ◽

Malus Orientalis

Genetic diversity and disease resistance are described for 496 seedlings from wild populations of Malus orientalis Uglitzh. collected in southern Russia and Turkey in 1998 and 1999. Eighty-five half-sib families were genotyped using seven microsatellite markers, and disease resistance was determined for apple scab (Venturia inaequalis Cooke), cedar apple rust (Gymnosporangium juniperi-virginianae Schwein), and fire blight (Erwinia amylovora Burrill). Individuals from the two Russian Caucasus collection locations were homogeneous compared with populations from the four Turkish collection locations. Within three of the Turkish collection locations, some half-sib families were highly diverse and several of these families had unusually high levels of disease resistance. In all, twenty individuals exhibited resistance to all three diseases. Bayesian analyses of the population structure revealed six distinct clusters. Most of the individuals segregated into two clusters, one containing individuals primarily from southern Russia and the other containing individuals from both Russia and northern Turkey. Individuals in the four small clusters were specific to Turkish collection locations. These data suggest wild populations of M. orientalis from regions around the Black Sea are genetically distinguishable and show high levels of diversity.

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Genealogical relationship inference to identify areas of intensive poaching of the Orange-fronted Parakeet (Eupsittula canicularis)

BMC Zoology ◽

10.1186/s40850-021-00080-y ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Gabriela Padilla-Jacobo ◽

Tiberio C. Monterrubio-Rico ◽

Horacio Cano-Camacho ◽

María Guadalupe Zavala-Páramo

Keyword(s):

Genetic Diversity ◽

Dna Sequences ◽

Haplotype Diversity ◽

Coastal Region ◽

Central American ◽

Illegal Trade ◽

Wild Populations ◽

High Genetic Diversity ◽

Genealogical Relationship ◽

Genetic Pool

Abstract Background The Orange-fronted Parakeet (Eupsittula canicularis) is the Mexican psittacine that is most captured for the illegal pet trade. However, as for most wildlife exploited by illegal trade, the genetic diversity that is extracted from species and areas of intensive poaching is unknown. In this study, we analyzed the genetic diversity of 80 E. canicularis parakeets confiscated from the illegal trade and estimated the level of extraction of genetic diversity by poaching using the mitochondrial DNA sequences of cytochrome b (Cytb). In addition, we analyzed the genealogical and haplotypic relationships of the poached parakeets and sampled wild populations in Mexico, as a strategy for identifying the places of origin of poached parakeets. Results Poached parakeets showed high haplotype diversity (Hd = 0.842) and low nucleotide diversity (Pi = 0.00182). Among 22 haplotypes identified, 18 were found exclusively in 37 individuals, while four were detected in the remaining 43 individuals and shared with the wild populations. A rarefaction and extrapolation curve revealed that 240 poached individuals can include up to 47 haplotypes and suggested that the actual haplotype richness of poached parakeets is higher than our analyses indicate. The geographic locations of the four haplotypes shared between poached and wild parakeets ranged from Michoacan to Sinaloa, Mexico. However, the rare haplotypes detected in poached parakeets were derived from a recent genetic expansion of the species that has occurred between the northwest of Michoacan and the coastal region of Colima, Jalisco and southern Nayarit, Mexico. Conclusions Poached parakeets showed high genetic diversity, suggesting high extraction of the genetic pool of the species in central Mexico. Rarefaction and extrapolation analyses suggest that the actual haplotype richness in poached parakeets is higher than reflected by our analyses. The poached parakeets belong mainly to a very diverse genetic group of the species, and their most likely origin is between northern Michoacan and southern Nayarit, Mexico. We found no evidence that poachers included individuals from Central American international trafficking with individuals from Mexico in the sample.

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Temporal stability of genetic diversity revealed by microsatellite markers in restocked populations of Caspian roach, Rutilus caspicus (Yakovlev, 1870)

Animal Biology ◽

10.1163/15707563-17000081 ◽

2019 ◽

Vol 69 (3) ◽

pp. 327-347

Author(s):

Hadiseh Kashiri ◽

Ali Shabani ◽

Saeed Gorgin ◽

Mohamad Rezaei ◽

Ahmadreza Jabale

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Economic Value ◽

Temporal Stability ◽

Time Frame ◽

Wild Populations ◽

The Caspian Sea ◽

Sequential Bonferroni Correction ◽

The Stability ◽

Caspian Roach

Abstract Rutilus caspicus is considered one of the most important bony fish with high economic value in the Caspian Sea. Since the population size of Caspian roach has decreased during recent decades, restocking of the populations is done through releasing hatchery-produced larvae into the wild. In the present study, the genetic diversity of wild and hatchery populations of R. caspicus was investigated using ten microsatellite loci. Also, microsatellite analysis was performed to compare the population structure of Caspian roach over a time frame of about 11 years. Although the allelic and gene diversity of hatchery populations tended to be lower than those of the wild populations, no significant differences in genetic diversity parameters were observed among the wild and hatchery populations. Similar variation levels were noticed among temporal samples of the same population, suggesting temporal stability in the genetic diversity of the wild populations. In most cases, significant departure from the Hardy-Weinberg equilibrium was observed after sequential Bonferroni correction. Results from analysis showed that a captive hatchery population was the most differentiated group. Also, the UPGMA dendrogram showed that the captive population was the most distant group. The stability of genetic composition between the two periods was noticed by the low and non-significant and estimates. The results from this study are anticipated to provide important information for setting up more efficient strategies for the conservation and restocking of R. caspicus.

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Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers

Forests ◽

10.3390/f10111019 ◽

2019 ◽

Vol 10 (11) ◽

pp. 1019 ◽

Cited By ~ 1

Author(s):

Zhong ◽

Yang ◽

Li ◽

Zhang ◽

Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

South China ◽

Expressed Sequence Tag ◽

Gene Diversity ◽

Jiangxi Province ◽

Group Method ◽

Cinnamomum Camphora ◽

Wild Populations ◽

Arithmetic Means

Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.

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