Genetic Diversity Assessment of Bagrid Catfish ( Rita rita ) Using SSR Markers: Implications for Riverine Conservation

Genetic diversity and structure within and between wild and cultivated Saccharina japonica (Laminariales, Phaeophyta) revealed by SSR markers

Begonia versicolor Irmscher, a narrow endemic Begonia species in southeast Yunnan of China, is a wonderful ornamental plant with huge diversity in colored foliage. To investigate its variations, the genetic diversity and population structure were studied based on 56 individuals sampled from four localities using 12 polymorphic microsatellite loci transferred from other species of Begonia. The results showed a relatively low level of genetic diversity in B. versicolor comparing with other species of Begonia using microsatellite. Positive inbreeding coefficient (FIS) values were found in three populations (SWC, XPZ and DSD). AMOVA analysis indicated that genetic variations occurred mainly within populations (55.9%) rather than among populations (9.7%) and among groups (34.4%). Four populations were grouped into two clusters based on STRUCTURE. AMOVA and STRUCTURE analysis showed a high level and significant genetic differentiation in the populations of B. versicolor. Based on its genetic status and rarity in the wild, the sustainable in-situ and ex-situ conservation strategies should be urgently carried out to protect this species with high horticultural and scientific values.

Assessment of genetic variability among the Hypericum perforatum populations is critical to the development of effective conservation strategies in the Kashmir valley. To obtain accurate estimates of genetic diversity among and within populations of H. perforatum, inter-simple sequence repeats (ISSR) markers were used. The study was aimed to check, whether ISSR fingerprinting may be a useful tool for studying genetic variations among H. perforatum populations in the Kashmir valley (India). A total of 15 ISSR primers were tested with the 20 genotypes of H. perforatum. The ten informative primers were selected and used to evaluate the degree of polymorphism and genetic relationships within and among all the H. perforatum populations. ISSR of 20 genotypes analysis yielded 98 fragments that could be scored, of which 71 were polymorphic, with an average of 7.1 polymorphic fragments per primer. Number of amplified fragments varied in size from 150 to 1650 bp. Percentage of polymorphism ranged from 60% to a maximum of 100%. Resolving power ranged from a minimum of 7.7 to a maximum of 14.3. Shannon indexes ranges from 0.166 to 0.389 with an average of 0.198 and Nei’s genetic diversity (h) ranges from 6.98 to 9.8. Estimated value of gene flow (Nm = 0.579) indicated that there was limited gene flow among the populations. The genetic diversity (Ht) within the population of 0.245 was clearly higher than that of among population genetic diversity (Hs= 0.115), indicating an out-crossing predominance in the studied populations. Analysis of molecular variance by ISSR markers indicated that over half of the total variation in the studied populations (58%) could be accounted for by differences among the 8 divisions, with a further 42% being accounted for by the variation among populations within a division.The dendrogram grouping the populations by unweighted pair-group method with arithmetic averages (UPGMA) method revealed eight main clusters. In conclusion, combined analysis of ISSR markers and hypericin content is an optimal approach for further progress and breeding programs.   Key words:  Hypericum perforatum (St. John's Wort), inter-simple sequence repeats (ISSR) markers, unweighted pair-group method with arithmetic averages (UPGMA), Nei’s genetic diversity.

The genetic diversity and genetic structure of Trillium tschonoskii (Maxim) were investigated using amplified fragment length polymorphism markers. Eight primer combinations were carried out on 105 different individuals sampled from seven populations. Of the 619 discernible DNA fragments generated, 169 (27.3%) were polymorphic. The percentage of polymorphic bands within populations ranged from 4.52 to 10.50. Genetic diversity (H(E)) within populations ranged from 0.0130 to 0.0379, averaging 0.0536 at the species level. Genetic differentiation among populations was detected based on Nei's genetic diversity analysis (53.03%) and analysis of molecular variance (AMOVA) (52.43%). AMOVA indicated significant genetic differentiation among populations (52.43% of the variance) and within populations (47.57% of the variance) (p < 0.0002). Gene flow was low (0.4429) among populations. Species breeding system and limited gene flow among populations are plausible reasons for the high genetic differentiation observed for this species. We propose an appropriate strategy for conserving the genetic resources of T. tschonoskii in China.

Genetic diversity assessment of 48 Tanzanian sweetpotato genotypes was conducted using nine polymorphic simple sequence repeat markers to determine genetic relationship and select unique parents which could be used for future breeding. Genetic diversity parameters, cluster analysis, and analysis of molecular variance were calculated to determine genetic diversity and relationships. Results showed that the SSR markers used had the mean PIC of 0.78, allelic richness per locus ranged from 4–17 with a mean of 10.0 and the number of effective alleles varied from 2.2–6.1 with a mean value 3.5. The un-weighted pair group method with arithmetic mean allocated the germplasm collection into three major genetic clusters. The greatest genetic distance was identified between the genotypes sourced from Kagera, Temeke, Mkuranga and Kisarawe areas of Tanzania. The study identified genetically unrelated and complementary sweetpotato genotypes such as Ex-Ramadhani, Kibakuli, Mkombozi, Mjomba mkwe, Ex-Halima-3 and Kabuchenji which are recommended for future breeding programmes.

Genetic diversity and differentiation of the endangered tree Elaeagnus mollis Diels (Elaeagnus L.) as revealed by Simple Sequence Repeat (SSR) Markers

Variation in genetic diversity of tree sparrow (Passer montanus) population in long-term environmental heavy metal polluted areas

BackgroundKorarima (Aframomum corrorima) is a perennial and aromatic herb native and widely distributed in southwestern Ethiopia. It is known for its fine flavor as a spice in various Ethiopian traditional dishes. Few molecular studies have been performed on this species so far. In the present paper, the ISSR technique was employed to study the genetic diversity in populations of cultivated A. corrorima.ResultsSeven ISSR primers produced a total of 86 clearly scorable DNA bands. High levels of genetic diversity were detected in cultivated A. corrorima (percentage of polymorphic bands = 97.67%, gene diversity = 0.35, Shannon’s information index = 0.52). Analysis of molecular variance (AMOVA) showed that 27.47% of the variation is attributed to the variation among populations and 72.53% to the variation within populations. The Fst (0.28) value showed a significant (p < 0.0001) genetic differentiation among populations. This was supported by the high coefficient of gene differentiation (Gst = 0.32) and low estimated gene flow (Nm = 1.08). A neighbor-joining dendrogram showed that the thirteen cultivated populations were separated into three clusters, which was in good accordance with the results provided by the two dimensional and three dimensional coordinate analyses. However, the clusters did not reveal clear pattern of populations clustering according to their geographic origin. This could be due to human mediated transfer of genetic material among different localities.ConclusionThe genetic diversity in populations of A. corrorima from the southwestern part of Ethiopia was relatively high. This finding should be taken into account when conservation actions, management policies for the species and site identification for in situ and ex situ conservation strategies are developed. Mizan Teferi II population displayed the highest genetic diversity; this population should be considered as the key site in designing conservation strategies for this crop. In addition, Jimma I and Jimma II populations with lowest genetic diversity, should also be considered due to the putative risk of extinction that they face because of the low genetic diversity.

The pacu (Piaractus mesopotamicus) is a Neotropical fish with remarkable productive performance for aquaculture. Knowledge of genetic resources in Neotropical fish is essential for their applications in breeding programs. The aim of this study was to characterize the genetic diversity of seven farmed populations of pacu which will constitute the basis for a broodstock foundation for coming breeding programs in Brazil. Analysis of one wild population (Paraná River) was used as a reference to compare genetic parameters in the farmed populations. The analyses were performed using 32 single-nucleotide polymorphisms (SNP) and 8 simple sequence repeat (SSR) markers. No significant differences in genetic diversity between populations estimated through the number of alleles and allelic richness, observed heterozygosity, expected heterozygosity, and minimum allele frequency were detected (p > 0.05). Low genetic diversity was observed in all farmed stocks and the wild population. Moreover, we detected low genetic structure when comparing farmed and wild populations for SNPs (FST = 0.07; K = 3) and SSRs (FST = 0.08; K = 2). Analysis of molecular variance (AMOVA) demonstrated that genetic variation was mostly within populations. Kinship analysis showed that most fish farms included related individuals at a proportion of at least 25%. Our results suggest that the basal broodstock for pacu breeding programs should be founded with individuals from different fish farms for higher genetic diversity and to avoid inbreeding risks.

The Durian Tengkurak ( Durio tanjungpurensis Navia) is one of the endangered exotic species in the Malvaceae family. The species is important for conservation of the germplasm and is considered a potential genetic resource for the development of durian in the future. The objective of this research project was to assess the molecular diversity of D. tanjungpurensis in West Kalimantan, based on Inter Simple Sequence Repeat (ISSR) markers. We applied ten ISSR primers to reveal the genetic diversity of 60 individuals from six natural endemic D. tanjungpurensis populations. The genetic diversity parameters were estimated based on binary data about PCR products (present or absent bands). The results showed that the mean number of observed alleles, the mean number of effective alleles, the genetic diversity, the Shannon’s Information Index score, the number of polymorphic loci, and the percentage of polymorphic loci were 1.53, 1.29, 0.17, 0.26, 77.83, and 52.59, respectively. An analysis of molecular variance (AMOVA) showed that the genetic diversity within a population (65%) was higher than that found between the populations (35%). UPGMA clustering and principal coordinate analysis, based on the DICE similarity matrix, were used to classify the populations into three groups: 1) Hutan Rejunak and Tembaga, 2) Bukit Merindang, and 3) Hutan Rawak, Bukit Sagu 1, and Bukit Sagu 2. Further analysis of the population structure using STRUCTURE software was used to classify all the individuals into two major categories, thus uniting Groups 2 and 3 as one major category. In conclusion, a high level of genetic diversity in the Durian Tengkurak was revealed utilizing the ISSR markers employed in the study.

Artemisia annua is an important medicinal plant valued all over the world. Genetic characterization of 20 genotypes of A. annua collected from two valleys viz. Nubra (9,600 ft) and Leh (11,500 ft) of the Trans-Himalayan (Ladakh, India) region were analyzed using 37 polymerase chain reaction (PCR) markers (20 random amplification of polymorphic deoxyribonucleic acid. (RAPDs) and 17 inter simple sequence repeats) (ISSRs). RAPD analysis yielded 124 polymorphic fragments (96.9%), with an average of 6.2 polymorphic fragments per primer. ISSR analysis produced 85 bands, of which 78 were polymorphic (86.1%), with an average of 4.58 polymorphic fragments per primer. The primers based on (CT) n produced maximum number of bands (nine) while, (AT) n and many other motifs gave no amplification. The genetic diversity was high among the genotypes (Nei’s genetic diversity = 0.336 and Shannon’s information index = 0.495) as measured by combination of both RAPD and ISSR markers. The mean coefficient of gene differentiation (Gst) was 0.145, indicating 85.5% of the genetic diversity resided within the genotypes. RAPD markers were found more efficient with respect to polymorphism detection, as they detected 96.9% in comparison to 86.1% for ISSR markers. It was found that the genetic diversity among genotypes from Nubra valley was narrow than that of Leh valley, suggesting the importance and feasibility of introducing elite genotypes from different origins for Artemisia germplasm conservation and breeding programs. Key words: Artemisia annua, Ladakh, genetic diversity, random amplification of polymorphic deoxyribonucleic acid (RAPD), inter simple sequence repeats (ISSR), analysis of molecular variance (AMOVA).

The conservation and sustainable utilization of cattle genetic resources necessitate a comprehensive understanding of their genetic diversity and population structure. This study provides an analysis of five native Turkish cattle breeds: Anatolian Black (ANB), Turkish Grey (TUR), Anatolian Southern Yellow (ASY), East Anatolian Red (EAR), and South Anatolian Red (SAN) using 50 K SNP data. These breeds were compared with three European breeds, Simmental (SIM), Holstein (HOL), and Jersey (JER), and three Asian Zebu breeds: Arabic Zebu (ZAR), Nelore (NEL), and Red Sindhi (RSI). Genetic diversity indices demonstrated moderate heterogeneity among the breeds, with TUR exhibiting the highest observed heterozygosity (Ho = 0.35). Wright's Fst values indicated significant genetic differentiation, particularly between Turkish breeds and both European (Fst = 0.035-0.071) and Asian breeds (Fst = 0.025-0.150). Principal component analysis distinguished the unique genetic profiles of each breed cluster. Admixture analysis revealed degrees of shared genetic ancestry, suggesting historical gene flow between Turkish, European, and Asian breeds. Analysis of molecular variance (AMOVA) attributed approximately 58% of the variation to population differences. Nei's genetic distances highlighted the closer genetic relatedness within Turkish breeds (distance ranges between 0.032 and 0.046) and suggested a more relative affinity of TUR with European breeds. The study's phylogenetic assessments elucidate the nuanced genetic relationships among these breeds, with runs of homozygosity (ROH) analysis indicating patterns of ancestral relatedness and moderate levels of inbreeding, particularly evident in Turkish breeds. Our findings provide valuable insights into the genetic landscape of Turkish cattle, offering a crucial foundation for informed conservation and breeding strategies aimed at preserving these breeds' genetic integrity and heritage.

In the present study, we employed microsatellite DNA markers to analyze the genetic diversity and differentiation between and within cultured stocks and wild populations of the orange-spotted grouper originating from the South China Sea and Southeast Asia. Compared to wild populations, genetic changes including reduced genetic diversity and significant differentiation have taken place in cultured grouper stocks, as shown by allele richness and heterozygosity studies, pairwise Fst, structure, molecular variance analysis, as well as multidimensional scaling analysis. Although two geographically adjacent orange-spotted grouper populations in China showed negligible genetic divergence, significant population differentiation was observed in wild grouper populations distributed in a wide geographical area from China, through Malaysia to Indonesia. However, the Mantel test rejected the isolation-by-distance model of genetic structure, which indicated the genetic differentiation among the populations could result from the co-effects of various factors, such as historical dispersal, local environment, ocean currents, river flows and island blocks. Our results demonstrated that microsatellite markers could be suitable not only for genetic monitoring cultured stocks but also for revealing the population structuring of wild orange-spotted grouper populations. Meanwhile, our study provided important information for breeding programs, management of cultured stocks and conservation of wild populations of the orange-spotted grouper.

To investigate the germplasm differences between northern and southern populations of Parabramis pekinensis and analyze their genetic diversity and population structure, this study employed 10 developed microsatellite markers to analyze 133 individuals collected from the Yangtze River Basin (Jiangsu JS, Hunan HN) and the Amur River Basin (Jilin JL, Heilongjiang HLJ). The HLJ population is considered a wild stock, while the other three groups are classified as cultured populations. The analysis revealed that four Parabramis pekinensis populations exhibited high levels of genetic diversity, with polymorphic information content (PIC) ranging from 0.5130 to 0.6142. A total of 249 alleles were detected, among which the HN population showed the highest genetic diversity (Na = 8.0 ± 4.59). The analysis of molecular variance (AMOVA) revealed significant genetic differentiation among populations, with 34% of gene variation attributed to inter-population differences (Fst = 0.337). The UPGMA clustering and STRUCTURE analysis (optimal K = 3) grouped the JL and HLJ populations into a single cluster, which subsequently merged with the JS population to form a larger clade. In contrast, the HN population was distinctly separated as an independent branch. The study demonstrates that the HN population of P. pekinensis should be prioritized for conservation as a distinct genetic unit, with the enhancement of habitat connectivity among northern populations could effectively mitigate genetic diversity loss. These findings provide a scientific foundation for the preservation of P. pekinensis germplasm resources.

Genetic diversity and structure of the endemic and endangered species Aristolochia delavayi growing along the Jinsha River