Microsatellite-based Genetic Diversity Research Articles

Microsatellite-Based Genetic Diversity, Population Structure and Bottleneck Analysis in Peanut: Conservation and Utilization Implications

Microsatellite-Based Genetic Diversity, Population Structure and Bottleneck Analysis in Peanut: Conservation and Utilization Implications

Microsatellite-based genetic diversity of Dermacentor reticulatus in Europe

Dermacentor reticulatus, also known as ornate dog tick, is an important vector of the causative agents of various tick-borne diseases in humans, livestock and wild animals. The geographical range of D. reticulatus in Europe is fragmented and divided into two main zones: The Western European and the Eastern European zone. To investigate D. reticulatus population structure through its distribution range we used microsatellite markers and compared the genetic diversity of D. reticulatus in 26 selected sites in the western and eastern European distribution areas. A total of 254 unfed adult D. reticulatus ticks were collected from vegetation and genotyped at 5 microsatellite loci, and altogether 26 alleles were detected. The overall FST value of pairwise comparisons among 26 sampling sites was 0.128 and revealed a moderate genetic differentiation. Bayesian-clustering analysis showed that D. reticulatus forms two genetically distinct groups across Europe. Division of D. reticulatus distribution range into Eastern European and Western European populations with a possible recent overlap in Poland has been supported by molecular data obtained in this study.

Microsatellite-Based Genetic Diversity among Egyptian Sheep Breeds

Sheep represent one of the most important domestic animals in Egypt, where meat and coarse wool production are the basic breeding objectives for Egyptian sheep. Therefore, evaluation of genetic diversity of sheep breeds is necessary for implementing the most suitable breed-region conservation programs. Animals from the three major Egyptian sheep breeds (Ossimi, Rahmani and Barki) were genotyped for 14 microsatellite markers. All loci tested were highly polymorphic. Various measures of genetic variation were calculated. The total observed number of alleles per microsatellite ranged from 6 to 12 for markers MAF65 and OarHH47, respectively. Estimates of effective number of alleles were between 3.11 for TGLA53 and 6.12 for OarHH47. The mean of polymorphism information content was 0.73. Overall gene diversity for all microsatellites analyzed was 0.66, 0.69 and 0.75 for Ossimi, Rahmani and Barki, respectively. For all breeds studied, estimates of observed heterozygosity were significantly lower than the expected heterozygosity. Average observed and expected heterozygosity estimates were 0.55 and 0.67, respectively. Significant departures from Hardy-Weinberg Equilibrium (HWE) due to heterozygote deficiency were observed for all the markers analyzed. The three breeds revealed significant deviation from HWE. The overall indicator of population subdivision (FST) was calculated to be 0.071; pointing out that about 7% of genetic diversity is due to genetic variation between breeds. Estimates of total inbreeding (FIT) and within-breed inbreeding (FIS) coefficients were 0.187 and 0.118, respectively. The estimates of pair-wise genetic differentiation were 0.039, 0.051 and 0.056 for Ossimi-Rahmani, Barki-Rahmani and Ossimi-Barki pairs, respectively. Measures of genetic distance between pairs of sheep breeds ranged from 0.423 to 0.615 for Rahmani-Ossimi and Barki-Ossimi sheep breed pairs. The results obtained in this study may be useful in sustainable breeding programs of Egyptian sheep breeds.

Microsatellite-based genetic diversity among accessions of Citrullus spp. collected from 36 countries

Microsatellite-based genetic diversity among accessions of Citrullus spp. collected from 36 countries

Microsatellite-based genetic diversity analyses of sugary1-, shrunken2- and double mutant- sweet corn inbreds for their utilization in breeding programme.

Sweet corn has recently experienced sharp rise in demand worldwide. Recessive sugary1 (su1) and shrunken2 (sh2) that enhances kernel sweetness have been abundantly used in sweet corn breeding. Analyses of genetic diversity among sweet corn inbreds assume great significance for their effective utilization in hybrid breeding. A set of 48 diverse sweet corn genotypes encompassing su1su1, sh2sh2 and su1su1/sh2sh2 types were analyzed using 56 microsatellite markers. A total of 213 alleles with mean of 3.8 alleles per locus were generated. Two unique- and 12 rare- alleles were identified. The average PIC and genetic dissimilarity was 0.50 and 0.73, respectively. Cluster analysis grouped the inbreds into three major clusters, with each of the su1su1-, sh2sh2- and su1su1/sh2sh2-types were broadlyclustered together. Principal coordinate analyses also depicted the diverse origin of the genotypes. The study identified inbreds for synthesis of pools and pedigree populations to develop novel inbreds. The study led to the identification of prospective heterotic combinations in various genetic backgrounds (sh2sh2×sh2sh2, su1su1×su1su1, su1su1/sh2sh2×su1su1/sh2sh2, sh2sh2×su1su1/sh2sh2 and su1su1×su1su1/sh2sh2).

Heterologous microsatellite-based genetic diversity in blue mussel (Mytilus chilensis) and differentiation among localities in southern Chile

Mussels (Mytilus spp.) are one of the most cultivated and commercialized bivalves in southern Chile; culture is currently supplied almost entirely from wild-caught seed obtained from relatively few collection centers. The genetic diversity and differentiation of the blue mussel in southern Chile was investigated by sampling six locations: one natural bank and five seed collection centers. Nine polymorphic microsatellite (SSR) loci were genotyped (Mgu1, Mgu3, MT203, MT282, Mg15, Mg56, Med737, MIT02 and MGE005). We found 75 different alleles, six of which were private alleles. Of the analyzed loci, 45 of 54 tests performed deviated from Hardy-Weinberg equilibrium after sequential Bonferroni correction (P < 0.05), revealing significant heterozygote deficiencies. The polymorphic information content (PIC) ranged from 0.322 (MGE005) to 0.893 (Mgu1). Despite the long distance between some sampling sites (up to 1360 km), genetic differentiation among the sites was low (FST = 0.043, P < 0.0001). The Bayesian cluster analysis (STRUCTURE) indicated two probable clusters, while the non-parametric cluster analysis (AWclust) identified two to four clusters. Both analyses showed a high level of admixture within clusters. Our results indicate that blue mussels in southern Chile show lower genetic diversity than in other countries, low inbreeding levels, and limited genetic differentiation among locations.

Microsatellite-based genetic diversity patterns in disjunct populations of a rare orchid.

We investigated the patterns of genetic diversity and structure in seven disjunct populations of a rare North American orchid, Cypripedium kentuckiense by including populations that represented the periphery and the center of the its range. Eight nuclear and two chloroplast microsatellites were used. Genetic diversity was low across the sampled populations of C. kentuckiense based on both nuclear (average An=4.0, Ho=0.436, He=0.448) and cpDNA microsatellites (average An=1.57, Nh=1.57 and H=0.133). The number of private alleles ranged from one to four per population with a total of 17 private alleles detected at five nuclear microsatellites. One private allele at one cpDNA microsatellite was also observed. Although the absolute values for nuclear microsatellite based population differentiation were low (Fst=0.075; ϕPT=0.24), they were statistically significant. Pairwise Fst values ranged from 0.038 to 0.123 and each comparison was significant. We also detected isolation by distance with nDNA microsatellites based on the Mantel test (r(2)=0.209, P=0.05). STRUCTURE analysis and the neighbor joining trees grouped the populations similarly whereby the geographically proximal populations were genetically similar. Our data indicate that the species is genetically depauperate but the diversity is distributed more or less equally across its range. Population differentiation and isolation by distance were detectable, which indicates that genetic isolation is beginning to manifest itself across the range in this rare species.

Evaluation of microsatellite-based genetic diversity, protein and mineral content in chickpea accessions grown in Kyrgyzstan.

The genetic diversity of 23 chickpea accessions representing Kyrgyz landraces and cultivars, ICARDA breeding lines, Spanish and Turkish cultivars was characterized using nine microsatellite (SSR) markers which generated a total of 122 alleles. The number of alleles (Na) per locus varied from 9 to 20. The observed heterozygosity (Ho) ranged between 0.05 and 0.43 (average 0.13) whereas both the expected heterozygosity (He) and polymorphic information content (PIC) ranged from 0.71 to 0.90 (average 0.83). Analysis of molecular variance (AMOVA) showed that 62% of the total genetic variation was found within accessions while the remaining 38% was found among accessions. Principal coordinate analysis (PCoA) indicated the presence of two groups. The two Kyrgyz cultivars were found apart from these groups. Cluster analysis generally confirmed the results of PCoA and also separated the Kyrgyz cultivars from the subcluster formed by Kyrgyz landraces and the subclusters formed by breeding lines from ICARDA along with landraces from Turkey and Spain. In addition, protein content and mineral concentration were determined. Protein content and mineral concentrations for Ca, S, Mg, P, K, Fe, Mn, Cu and Zn varied significantly among accessions. The results show that Kyrgyz germplasm provides a source of diversity for improvement of chickpea.

Microsatellite-based genetic diversity in selected exotic and indigenous maize (Zea maysL.) inbred lines differing in total kernel carotenoids

A set of 24 diverse maize inbred lines, selected on the basis of their total kernel carotenoid concentration, were characterized using 36 microsatellite/simple sequence repeat markers distributed throughout the genome. A total of 140 polymorphic SSR alleles was detected, with a mean of four allelesper locus.The study led to the identification of eight informative SSR loci detecting 10 unique alleles. The average polymorphism information content was 0.55, with a range of 0.18 to 0.78. Genetic dissimilarity calculated using Jaccard's coefficient varied from 0.41 to 0.94 with a mean of 0.77. Cluster analysis using the unweighted pair group method with arithmetic mean showed four major clusters among the inbred lines. High degree of congruence was observed between clustering pattern and the pedigree data. Principal Coordinate Analysis (PCoA) also depicted the genetic diversity amongthe selected inbred lines.The study led to identification of genetically diverse and phenotypically contrasting inbred lines.These inbred lines can be potentially used in developing suitable mapping populations for QTL analysis, besides generating hybrid combinations with desirable kernel carotenoids.

Microsatellite-based genetic diversity among accessions of maize landraces from Sinaloa in México

In the state of Sinaloa México, traditional farmers still cultivate maize accessions with a wide diversity of morphological characteristics, but the gene reservoir maintained in these populations has been poorly studied and it is being lost due to changes in land use and the adoption of hybrid commercial varieties. The aim of this study was to evaluate the genetic diversity of some of these maize populations to contribute to their preservation. Twenty eight accessions were used for the analysis. DNA was extracted from 396 individuals and probed with 20 microsatellites distributed across the maize genome. A total of 121 alleles were obtained (average of 6.1 alleles per locus) and a total genetic diversity of 0.72. The UPGMA-cluster analysis, model-based population structure and principal component analysis revealed three major groups, one formed mainly by accessions of races typical of the Northwestern lowlands (Chapalote, Dulcillo del Noroeste, Tabloncillo Perla, Blando de Sonora and Elotero de Sinaloa) and the other two with accessions mainly from Tabloncillo and Tuxpeño. The high number of alleles per locus and total genetic diversity found in this study demonstrate a broad genetic basis of the accessions of maize landraces from Sinaloa, representing a gene reservoir useful in breeding programs.

Microsatellite-based genetic diversity of 2×2 full diallel cross of Jian carp and Huanghe carp and related bodyweight correlation

The objective of this study was to investigate the relationship between diversity of microsatellite loci with common carp cross F1.25 microsatellite loci were used to analyze the genetic diversity of 2×2 full diallel cross of common carp(Cyprinus carpio) population and body weight variation among different genotypes.The result showed that the number of alleles ranged from 5.08 to 6.08.Effective numbers of alleles ranged from 1.4 to 6.8,PIC were from 0.42 to 0.49.The average expected heterozygosity value was ranged from 0.47 to 0.55.The highest genetic similarity index that came from the populations of Hh and Hj was 0.9795.The UPG MA trees based on genetic distance demonstrated that Huanghe carp was genetically near to Huanghe carp ♂×Jian carp♀.The association between these microsatellite loci and body weight was analyzed by least square linear model.The results showed that significant differences were detected between different genotypes of purebred carps on the HLJ13 locus.Compared to this,this difference was only found in Jian purebred group of Koi42.AA genotype of Koi42 was the most favorable one,while the Hj and JH combinations had higher body weight than that of their parents' pure breds.The study provis the foundation for molecular assistant selection of common carp in the fu-ture.

Preliminary analysis of microsatellite-based genetic diversity of goats in southern Nigeria – Erratum

Preliminary analysis of microsatellite-based genetic diversity of goats in southern Nigeria – Erratum

Preliminary analysis of microsatellite-based genetic diversity of goats in southern Nigeria

To better understand natural genetic variation in indigenous livestock resources, as well as formulate conservation policies, better genetic characterization is required to balance the competing needs of genetic improvement and conservation of native germplasm, primarily in rural agricultural systems in developing countries. Genetic diversity of goats in southern Nigeria was assessed using 295 indigenous goats with ten microsatellite DNA markers. The breeds are West African Dwarf (WAD), Red Sokoto (RS) and Sahel (SA) sampled from farms, market places and rural homesteads. The mean expected heterozygosity (HE) ranged from 0.608 to 0.784 in two sub-populations of WAD goats. Deviations from Hardy�Weinberg equilibrium (HWE) were statistically significant ( p < 0.05) indicating that these populations are under various forces stemming from the management choices of rural dwellers. Polymorphic information content of these markers averaged 0.803 and mean GST index was 0.176. The measure of genetic distance between pairs of breeds indicated that the lowest distance was between WAD and RS (0.268) and the highest distance was between WAD and SA (0.662) goats, respectively. The estimated dendogram clustered these Nigerian goats into nine sub-populations and two major genetic groups. The study suggests that indigenous goat populations in southern Nigeria may be collapsed from three breeds into two distinct genetic groups, possibly due to extensive cross-breeding and gene flow between them, which are symptomatic of uncontrolled crossing across much of the country.

Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia

BackgroundIdentification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation.ResultsBayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity.ConclusionsDuring initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.

Microsatellite-based genetic diversity and differentiation of foreign common carp ( Cyprinus carpio) strains farmed in the Czech Republic

This study set out to improve our understanding of the molecular genetic characteristics of imported strains of common carp reared in the Czech Republic. To do this we characterized the genetic diversity and population structure of 11 carp strains including two farmed strains from Germany (Scheuerman and Glinzig mirror carp) and France (Forez and Dombez scaly carp), one farmed population from Amur river basins, and one feral population from the Ebro River (Spain), by microsatellite analysis of 10 loci. Mean heterozygosity within populations ranged from 0.584 to 0.700, and the mean number of alleles per population ranged from 5.0 to 9.8. Of the analysed loci, 92 out of 130 possible tests were found to deviate significantly ( P < 0.05) from the Hardy–Weinberg equilibrium revealing significant heterozygote deficit after Bonferroni correction. Global analysis of hierarchical gene diversity (AMOVA) further revealed that the total genetic variation among populations was 21%, whilst variation within populations was estimated to be 79%. After grouping, the majority of total microsatellite loci variation appeared to be due to variation within populations. A relationship tree based on Nei's D A genetic distance and the UPGMA algorithm grouped the strains and populations into two major clusters, reflecting their affiliation to the European/Central Asian or East-Asian subspecies of common carp, rather than their country of origin. An individual assignment test (self-classification) using a Bayesian method demonstrated 89.6% accuracy in assigning individuals into their correct strains/population of origin at P < 0.05. Thus, the set of 10 highly polymorphic microsatellite markers used in the present study demonstrated significant worth in monitoring the genetic diversity of cultured common carp. Additionally, our results proved the efficiency of the conservation programme and highlighted the need for better control of genetic variability in common carp strains. This could also be useful for the conservation of carp strains in the Czech Republic.

Microsatellite-based Genetic Diversity and Evolutionary Relationships of Six Dog Breeds

The Tibetan Mastiff is one of the most archaic, ferocious and the largest dogs in the world. The Kunming dog is the chief working-dog breed in China. In this study, ten microsatellite loci were used to assess the genetic diversity and evolutionary relationships in six dog breeds, including Tibetan Mastiff, Kunming dog, Belgian Malinois, Labrador Retriever, English Springer Spaniel, and German Shepherd. The highest genetic diversity was exhibited by the Tibetan Mastiff, indicating useful protection and little inbreeding in the modern Tibetan Mastiff. Higher genetic diversity was observed in European breeds, supporting the hypotheses that breeders outcross their pure breed dogs occasionally to avoid deleterious effects in Europe. Evolutionary relationships showed that English Springer Spaniel and Labrador Retriever were clustered together, then with the Tibetan Mastiff, consistent with previous cluster results. German Shepherd and Kunming dog were grouped together, coinciding with the breeding history of Kunming dog. It is the first time that Tibetan Mastiff and Kunming dog have been analyzed with microsatellites.

Microsatellite-Based Genetic Diversity Assessment in Grape (Vitis vinifera L) Germplasm and its Relationship with Agronomic Traits

The population of grape (Vitis vinifera L), commonly cultivated in India, shows a wide range of ripening periods and fruit quality and is an unexploited resource for breeding programs. The main purpose of this study was to fingerprint these accessions and to construct a molecular database including the cultivars commonly grown in India. A total of 42 genotypes were analyzed using seven microsatellite simple sequence repeat (SSR) markers and their main morphological and agronomic characteristics were compared. A total of 45 alleles in all 42 genotypes were obtained with 7 primers with an average number of 6.4 alleles per locus. The dissimilarity matrix showed that a maximum of 110 units was obtained between the genotypes “Convent Large Black” and “Arka Hans,” while a minimum dissimilarity if 37 units were obtained between the genotypes “Anab-e-Shahi” and “Dilkhush.” In the dendrogram the microsatellite segregated the genotypes into two clusters (A and B) at 476 units with two subclusters each. The subclusters grouped genotypes predominantly as A1 with seeded fruits, A2 with seedless fruits, B1 with pigmented and seedless fruits, and B2 with colorless and seeded fruits. The use of seven polymorphic microsatellite markers and the level of genetic variability detected within Indian grapevine germplasm suggested that this is a reliable, efficient, and effective marker system that can be used for diversity analysis and subsequently in crop improvement programs.

Aphid feeding response and microsatellite-based genetic diversity among diploidBrachypodium distachyon(L.) Beauv accessions

False brome grass,Brachypodium distachyon(L.) Beauv, has been proposed as a new model species to bridge rice and temperate cereal crops for genomics research. However, much basic information for this species is still lacking. In this study, six diploidB. distachyon(2n = 2x = 10) accessions (Bd1-1, Bd2-3, Bd3-1, Bd18-1, Bd21 and BD29) were evaluated for their response to infestation by two cereal aphid pests of common wheat (Triticum aestivumL.): the greenbug,Schizaphis graminumRondani, and the Russian wheat aphid (RWA),Diuraphis noxiaMordvilko. Through database mining ofB. distachyonexpressed sequence tag (EST) and genomic DNA sequences, 160 EST- and 21 genomic microsatellite markers were developed and used to evaluate genetic diversity among theB. distachyonaccessions. All six accessions were resistant to RWA biotype RWA1 but showed distinct responses to feeding by greenbug biotypes C and E, as well as RWA2 RWAs. Although microsatellite-based genetic diversity among different accessions was generally low, Bd1-1 and BD29 were the most diverged from the other four lines. The genetic divergence was correlated with geographical distances between theBrachypodiumaccessions. Comparison of simple sequence repeat polymorphisms in three inbred lines (Bd2-3, Bd3-1 and Bd18-1) with their respective original parental lines revealed no effect of inbreeding on genetic diversity. Phylogenetic analysis suggested thatAegilops tauschii(Coss.) Schmal., the D genome donor of common wheat, was closer toB. distachyonthan to rice. The greenbug - B. distachyonsystem seems to be a model of choice for plant–aphid interaction studies in the grass genome.