Genetic Diversity Assessment of MPOB-Senegal Oil Palm Germplasm Using Microsatellite Markers.
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ABSTRACT:
SUBMITTER: Myint KA
PROVIDER: S-EPMC8116142 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.
| S-EPMC3760190 | biostudies-literature
Project description:Xanthoceras sorbifolium Bunge has great potential for producing biodiesel. In order to select and evaluate appropriate germplasm to produce biodiesel, we analyzed the genetic diversity of Xanthoceras sorbifolium Bunge germplasm based on morphological traits and simple sequence repeats (SSRs) in this study. Fifty-six germplasm samples were evaluated using nine morphological traits and 23 SSR loci. Significant differences among germplasms were observed in eight morphological characters. The SSR markers analysis showed high genetic diversity among the germplasms. All SSRs had polymorphisms, and we detected 77 alleles in total. The number of alleles at each locus ranged from two to six, averaging 3.35 per marker. The polymorphic information content values ranged from 0.36 to 0.61, averaging 0.49. Expected heterozygosity, observed heterozygosity, and Shannon's information index calculations detected large genetic variations among germplasms. The high average number of alleles per locus and the allelic diversity observed in the set of genotypes analyzed indicated that the genetic base of this species is relatively wide. Thus, microsatellite markers can be used to efficiently distinguish Xanthoceras sorbifolium Bunge germplasms and assess their genetic diversity. Hundred-grain weight and lateral diameter were positively correlated with monounsaturated fatty acids and depended on genotype. These results suggest that seeds with higher hundred-grain weight and lateral diameter could be more suitable to produce biodiesel. Our data will lay a foundation for selecting appropriate germplasm to produce biodiesel based on seed phenotype and will contribute to the conservation and management of this important plant genetic resource.
| S-EPMC5453433 | biostudies-literature
Project description:A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2-5). The average polymorphic information content (PIC) was 0.69 (range, 0.29-0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44-0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin.
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Project description:Improved knowledge of the diversity within and among local animal populations is increasingly necessary for their sustainable management. Accordingly, this study assessed the genetic diversity and structure of the indigenous goat population of Benin. Nine hundred and fifty-four goats were sampled across the three vegetation zones of Benin [i.e., Guineo-Congolese zone (GCZ), Guineo-Sudanian zone (GSZ), and Sudanian zone (SZ)] and genotyped with 12 multiplexed microsatellite markers. The genetic diversity and structure of the indigenous goat population of Benin were examined using the usual genetic indices (number of alleles Na, expected and observed heterozygosities He and Ho, Fixation index FST, coefficient of genetic differentiation GST), and three different methods of structure assessment [Bayesian admixture model in STRUCTURE, self-organizing map (SOM), and discriminant analysis of principal components (DAPC)]. The mean values of Na (11.25), He (0.69), Ho (0.66), FST (0.012), and GST (0.012) estimated in the indigenous Beninese goat population highlighted great genetic diversity. STRUCTURE and SOM results showed the existence of two distinct goat groups (Djallonké and Sahelian) with high crossbreeding effects. Furthermore, DAPC distinguished four clusters within the goat population descending from the two ancestry groups. Clusters 1 and 3 (most individuals from GCZ) respectively showed a mean Djallonké ancestry proportion of 73.79% and 71.18%, whereas cluster 4 (mainly of goats from SZ and some goats of GSZ) showed a mean Sahelian ancestry proportion of 78.65%. Cluster 2, which grouped almost all animals from the three zones, was also of Sahelian ancestry but with a high level of interbreeding, as shown by the mean membership proportion of only 62.73%. It is therefore urgent to develop community management programs and selection schemes for the main goat types to ensure the sustainability of goat production in Benin.
| S-EPMC10064012 | biostudies-literature
Project description:BACKGROUND:Currently about 26,000 horses are breeding in Korea and 57.2% (14,776 horses) of them are breeding in Jeju island. According to the statistics published in 2010, the horses breeding in Jeju island are subdivided into Jeju horse (6.1%), Thoroughbred (18.8%) and Halla horse (75.1%). Halla horses are defined as a crossbreed between Jeju and Thoroughbred horses and are used for horse racing, horse riding and horse meat production. However, little research has been conducted on Halla horses because of the perception of crossbreed and people's weighted interest toward Jeju horses. METHOD:Using 17 Microsatellite (MS) Markers recommended by International Society for Animal Genetics (ISAG), genomic DNAs were extracted from the hair roots of 3,880 Halla horses breeding in Korea and genetic diversity was identified by genotyping after PCR was performed. RESULTS AND CONCLUSION:In average, 10.41 alleles (from 6 alleles in HTG7 to 17 alleles in ASB17) were identified after the analysis using 17 MS Markers. The mean value of Hobs was 0.749 with a range from 0.612(HMS1) to 0.857(ASB2). Also, it was found that Hexp and PIC values were lowest in HMS1 (0.607 and 0.548, respectively), and highest in LEX3(0.859 and 0.843, respectively), and the mean value of Hexp was 0.760 and that of PIC was 0.728. 17 MS markers used in this studies were considered as appropriate markers for the polymorphism analysis of Halla horses. The frequency for the appearance of identical individuals was 5.90?×?10-20 when assumed as random mating population and when assumed as half-sib and full-sib population, frequencies were 4.08?×?10-15 and 3.56?×?10-8, respectively. Based on these results, the 17 MS markers can be used adequately for the Individual Identification and Parentage Verification of Halla horses. Remarkably, allele M and Q of ASB23 marker, G of HMS2 marker, H and L of HTG6 marker, L of HTG7 marker, E of LEX3 marker were the specific alleles unique to Halla horses.
| S-EPMC5114825 | biostudies-literature
Project description:Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright's fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei's genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.
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Project description:The state of the local breeds of farm animals is increasingly precarious worldwide because of the aggressive introduction of breeds with improved economical traits. The preference of the breeders for local breeds is due to their higher adaptability to the particular climate and relief conditions of the mountain areas, to the high rate of assimilation of the feeds from these regions and to their increased resistance to diseases. This study analyzes the genetic variation of the main four local Romanian sheep breeds (Tsurcana, Tsigai, Ratska and Teleorman Blackhead) in terms of stock and economic importance, using 18 microsatellite markers. The mean number of alleles per locus was of 9.764. The values of genetic diversity parameters exhibited a high degree of polymorphism for the analyzed breeds, although inbreeding was highlighted particularly in Tsurcana and Tsigai. These breeds also showed an intense gene flow among them and were less differentiated in comparison with Ratska and Teleorman Blackhead. The results of this study may be useful for breeding programs and conservation plans since the genetic resources of the local breeds must be preserved so as to maintain an adequate level of biodiversity in animal husbandry.
| S-EPMC7059605 | biostudies-literature
Project description:The trend of microsatellite marker discovery and development revolved as a result of the advancement of next generation sequencing (NGS) technology as it has developed numerous microsatellites within a short period of time at a low cost. This study generated microsatellite markers using RAD sequencing technologies for the understudied Nephelium lappaceum. A total of 1403 microsatellite markers were successfully designed, which consisted of 853 di-, 525 tri-, 17 tetra-, 5 penta-, and 3 hexanucleotide microsatellite markers. Subsequently, selection of 39 microsatellites was made for the evaluation of genetic diversity of the selected 22 rambutan varieties. Twelve microsatellites, which exhibited high call rates across the samples, were used to assess the diversity of the aforementioned rambutan varieties. The analysis of 12 microsatellites revealed the presence of 72 alleles and six alleles per locus in average. Furthermore, the polymorphic information content (PIC) value ranged from 0.326 (NlaSSR20) to 0.832 (NlaSSR32), which included an average of 0.629 per locus, while the generated Neighbour Joining dendrogram showed two major clusters. The pairwise genetic distance of shared alleles exhibited a range of values from 0.046 (R134↔R170) to 0.818 (R5↔R170), which suggested highest dissimilarity detected between R5 and R170. Notably, these research findings would useful for varietal identification, proper management and conservation of the genetic resources, and exploitation and utilization in future breeding programs.
| S-EPMC7527576 | biostudies-literature
Project description:Donkeys are one important livestock in China because of their nourishment and medical values. To investigate the genetic diversity and phylogenetic relationships of Chinese donkey breeds, a panel of 25 fluorescently labeled microsatellite markers was applied to genotype 504 animals from 12 Chinese donkey breeds. A total of 226 alleles were detected, and the expected heterozygosity ranged from 0.6315 (Guanzhong) to 0.6999 (Jiami). The mean value of the polymorphism information content, observed number of alleles, and expected number of alleles for all the tested Chinese donkeys were 0.6600, 6.890, and 3.700, respectively, suggesting that Chinese indigenous donkeys have relatively abundant genetic diversity. Although there were abundant genetic variations found, the genetic differentiation between the Chinese donkey breeds was relatively low, which displayed only 5.99?% of the total genetic variance among different breeds. The principal coordinates analysis clearly splits 12 donkey breeds into two major groups. The first group included Xiji, Xinjiang, Liangzhou, Kulun, and Guanzhong donkey breeds. In the other group, Gunsha, Dezhou, Biyang, Taihang, Jiami, Qingyang, and Qinghai donkeys were clustered together. This grouping pattern was further supported by structure analysis and neighbor-joining tree analysis. Furthermore, genetic relationships between different donkey breeds identified in this study were corresponded to their geographic distribution and breeding history. Our results provide comprehensive and precise baseline information for further research on preservation and utilization of Chinese domestic donkeys.
| S-EPMC6853031 | biostudies-literature
Project description:In this study, indigenous chickens were collected from eight different regions in Kenya and kept at InCIP-Egerton University. These were studied using eighteen microsatellite markers to determine genetic variation. Statistics related to genetic variation were estimated using GenALEx6. Mean percentage polymorphic loci (PPL) was 96.71% and 4% genetic variance (p ≥ 0.003) was seen between the eight populations. MCW0123 marker had the highest genetic variance of 13% among populations (p ≥ 0.003) at 95% CI. Mean He ranged from 0.351 ± 0.031 (SIB) to 0.434 ± 0.022 (BM) with a grand mean He of 0.399 ± 0.011 across the populations using the microsatellite markers. Nei's genetic distance ranged from 0.016 (SIB and WP) to 0.126 (NR and SIB). DARwin6.501 analysis software was used to draw the population dendrogram and two major population clusters were observed, also seen with PCoA. This study found a lot of genetic variation and relatedness within and among populations. Based on the phylogenetic tree result, it is concluded that the clustering of the chicken populations in the present study is not based on geographical proximity. The microsatellite markers used in this study were suitable for the measurement of the genetic biodiversity and relationship of Kenyan chicken populations. These results can therefore serve as an initial step to plan the conservation of indigenous chickens in Kenya.
| S-EPMC6296579 | biostudies-other