Genetic Diversity in Natural Populations and Cultivated Stands of Walnut (Juglans regia L.) Using Microsatellite Marker

Abstract Information on genetic diversity is fundamental to developing in situ or ex situ conservation strategies. This study assessed the genetic differentiation between plantations and neighboring natural populations of Juglans regia. Genetic structures of three natural population and three neighboring plantations of J. regia in northwest of Iran were assessed using 10 nuclear microsatellite loci (SSR). Natural populations presented higher total number of alleles (119) and observed heterozygosity (Ho= 0.29) than planted stands (101 alleles, Ho= 0.21). The observed alleles of natural stands varied from 2 (WGA61 and WGA9) to 7 (WGA9) and from 2 (WGA321 and WGA276) to 5 (WGA202 and WGA9) in planted stands. One of the planted populations (B) indicated the largest level of genetic diversity. In conclusion, genetic diversity of all investigated plantation and natural stands are similar. This recommends that even plantations might qualify as gene conservation stands.

Genetic Similarity Among Accessions of Paspalum notatum Flügge (Poaceae): a Potential to Parental Selection

HIGHLIGHTS Low genetic similarity in Paspalum notatum accessions. High genetic distance among diploid accessions. The accessions have good potential to breeding program.

Abstract Paspalum notatum is an important forage grass contributing significantly to the coverage of the natural fields of Southern Brazil. Simple sequence repeat (SSR) markers were used to evaluate the genetic similarity of strains within a P. notatum collection. Genomic DNA was extracted in bulk from young leaves of five plants from each accession obtained from the USDA. In the molecular analysis, the eight SSR markers evaluated formed seven distinct groups, and two isolated genotypes, with an average similarity index of 0.29, ranging from zero to 0.83. All the loci were polymorphic and the polymorphism information content ranging from 0.41 to 0.69. The results evidenced a low genetic similarity, which can be explored via parental selection in a breeding program.

Genetic diversity and genetic structures of original plants of Viticis Fructus:an SSR markers-based analysis / 中国中药杂志

The present study aimed to provide the protection strategies for wild germplasm resources of original plants of Viticis Fructus and a theoretical basis for the sustainable use of Viticis Fructus. The genetic diversity and genetic structures of the 232 indivi-duals in 19 populations of Vitex rotundifolia and V. trifolia were analyzed by eight SSR markers with tools such as Popgene32, GenAlex 6.502, and STRUCTURE. Bottleneck effect was detected for the population with more than 10 individuals. The results indicated that 42 and 26 alleles were detected from the populations of V. rotundifolia and V. trifolia, respectively, with average expected heterozygo-sities of 0.448 6 and 0.583 9, which are indicative of low genetic diversity. AMOVA revealed the obvious genetic variation of V. rotundifolia and V. trifolia within population(84.43%, P<0.01; 60.37%, P<0.01). Furthermore, in eight SSR loci, six from V. rotundifolia populations and two from V. trifolia populations failed to meet Hardy-Weinberg equilibrium expectations(P<0.05), which confirmed that the populations experienced bottleneck effect. As assessed by Mantel test, geographical distance posed slight impacts on the genetic variation between the populations of V. rotundifolia and V. trifolia. Principal component analysis(PCA) and STRUCTURE analysis demonstrated evident introgression of genes among various populations. The original plants of Viticis Fructus were confirmed low in genetic diversity and genetic differentiation level. Therefore, the protection of wild resources of original plants of Viticis Fructus should be strengthened to ensure its sustainable use.

Genetic diversity among wild pomegranate (Punica granatum) in Azad Jammu and Kashmir region of Pakistan

BACKGROUND: Pomegranate (Punica granatum L.), one of the most important tropical fruits in Azad Jammu and Kashmir regions of Pakistan, is highly valued for its nutrition and medicinal purposes. Although pomegranate is native to this region, the genetic diversity among wild pomegranate accessions is currently unknown. Such information would be vital for germplasm conservation and breeding efforts. In the current study, genetic diversity among forty-eight wild pomegranate accessions collected from different agro-ecological zones of Azad Jammu and Kashmir was assessed using 41 simple sequence repeat (SSR) markers. RESULTS: The markers revealed 303 alleles averaging 7.39 alleles per marker. Polymorphic information content ranged from 0.12 (PGCT093B) to 0.88 (Pom006), with a mean of 0.54. The average genetic distance (GD) across all genotypes was 0.52, and was lowest between Chattar Class and Thorar genotypes (GD = 0.27), but highest between Khun Bandway and Akhor Ban (GD = 0.74). A neighbor-joining dendrogram separated the genotypes into three major clusters, with further sub-clustering within each cluster. CONCLUSIONS: Overall, the results presented here show significant genetic diversity among wild pomegranate accessions in Azad Jammu and Kashmir region of Pakistan. These accessions present a valuable genetic resource to breeding and cultivar improvement programs within the region.

Association of SSR based genetic distances with heterosis in sunflower

Aim: Development of commercial hybrid of sunflower on basis of best inbred combination remains a key challenge to sunflower breeders. In the current investigation, heterosis of F1 hybrids, parental genetic diversity and correlation between genetic distance and level of heterosis were estimated. Methodology: Thirty five parental genotypes (3 CMS A lines and 32 R lines) and their hybrids were assessed for physio-morphological, yield and quality traits. Heterosis was measured as mid-parent and better parent heterosis. Among parents, SSR marker based genetic distances were calculated using DARwin software. Correlation between heterosis and genetic distances was carried out by Karl Pearson’s simple correlation method. Results: Range of genetic distances, based on SSR marker analysis, varied from 0.32-0.73. Genetic distance had significant positive correlation with the heterosis for oil content (r = 0.22 p<0.05) and linoleic acid (r = 0.32 p<0.05), but negative correlation was observed for days to maturity, test weight, volume weight, stearic acid and oleic acid. There was no significant correlation between genetic distance and heterosis for seed yield and other agronomic traits. Interpretation: Although, genetic distance is poor predictor of heterosis, dependence of oil content on genetic distance among parental lines may be used for designing an effective breeding program for sunflower.

SSR based Characterization of Indigenous Harnai Sheep Breed of Balochistan

This study was on the molecular characterization of Harnai sheep breed in Balochistan. A set of (n=16) ovine specific SSR markers, recommended by FAO, was used on (n=50) blood samples from unrelated animals of Harnai sheep breed from their breeding tract. Various genetic parameters were observed using Pop gene software. A total of 74 alleles were found on 13 loci. The finding values for observed number of alleles (Na), effective number of alleles (Ne) and Shannon’s Information index (I) the average values were found along with standard deviation to be 2.448±0.869, 1.7050.604 and 0.5890.357 respectively, further more, the mean values of observed heterozygosity (Obs_Het) expected homozygosity (Exp._Hom), expected heterozygosity (Exp_Het), effective number of allele (Ne) average Heterozygosity (Ave Het) were found to be 0.598±0.299, 0.366±0.284, 0.602±0.238, 0.363±0.219, 0.347±0.209 and 0.347±0.209, respectively. The value of F-statistic ranged from 0.2851 to 0.9132 for different microsatellite markers with an average of 0.515±0.021. Majority of the markers showed higher than average expected reduction in heterozygosity. The standard errors were generally low, which indicated that homozygosity prevails in the population under study. This might be due to intense inbreeding in this flock of Harnai sheep.

Population Structure and Genetic Diversity of Sweet Cassava Accessions from the Midwestern, Southeastern and Southern Regions of Brazil

Abstract The objective of this work was to screen sweet cassava accessions collected in smallholding areas in the Midwestern, Southeastern and Southern regions of Brazil, using 15 SSR molecular markers, to determine population structure and genetic diversity. Polymorphism was detected in every loci analyzed, with mean of 6.33 alleles per locus, and mean polymorphism information content (PIC) of 0.6057, pointing out that the primers were highly informative. The observed heterozygosity ranged from 0.0709 (SSRY 101) to 0.9398 (GA 12), with a mean of 0.6511, and mean genetic diversity of 0.6578, ranging from 0.3592 (GA 136) to 0.8116 (SSRY 21). The most dissimilar combinations observed were BGM526PR-BGM596MS, BGM526PR-BGM622MS and BGM526PR-BGM629MS. The traditional cassava cultivars assessed were divided into four distinct groups: two with cultivars from the South, one from the Southeast and one from the Midwestern region of Brazil. The variances among and within groups determined by the analysis of molecular variance were 44 and 56%, respectively. The PhiPT parameter (analogue to Fst) of 0.44 indicates high differentiation among groups. Broad genetic diversity was found among the traditional sweet cassava cultivars assessed, and the most divergent groups were formed by cultivars from the South and the Midwestern regions of Brazil.

Genetic diversity in algerian durum wheat varieties (Triticum turgidum L var. durum) using microsatellite markers / Diversidade genética em variedades de trigo duro argelino (Triticum turgidum L var. durum) usando marcadores microssatélites

Characterization of germplasm by DNA-markers provides powerful tool to precise germplasm identification. This study aimed to quantify the genetic diversity and to estimate the phylogenetic relationship among genotypes in many crop species. The results of the present study realized between Nov and Dec 2016 in biotechnologie unit (ICARDA, Morocco) which aimed to characterize a subset of 14 Algerian selected durum wheat cultivars (Triticum turgidum L. var. durum), using 13 SSR (Single Sequence Repeat) indicated the presence of a total of 39 alleles. The genetic diversity at the 13 microsatellites loci varied from 0,142 for Xgwm337 to 0.735 for Xgwm213 with a mean of 0.444. Polymorphic information content (PIC) values ranged from 0.13 to 0.70 and the genetic distance among the cultivars from 0.15 to 0.77. Clustering analysis showed that the studied varieties were grouped according to their population of origin, suggesting a provenance effect in their ordination. In fact the most similar varieties were those introduced from CIMMYT-ICARDA breeding program, which may have common parents in their pedigree. Selections from local landraces were more similar to each other and dissimilar to CIMMYT-ICARDA material, showing an agro-ecological adaptation.

A caracterização de germoplasma por marcadores de DNA fornece uma ferramenta poderosa para a identificação precisa de germoplasma, quantificar a diversidade genética e estimar a relação filogenética entre genótipos em muitas espécies de culturas. Os resultados do presente estudo foram realizados entre novembro e dezembro de 2016 na unidade de biotecnologia (ICARDA, Marrocos) que objetivou caracterizar um subconjunto de 14 cultivares de trigo duro argelinos selecionados (Triticum turgidum L. var. durum), utilizando 13 SSR (Single Sequence Repeat ) indicou a presença de um total de 39 alelos. A diversidade genética nos 13 locos de microssatélites variou de 0,142 para Xgwm337 a 0,735 para Xgwm213 com uma média de 0,444. Os valores do conteúdo de informação polimórfica (PIC) variaram de 0,13 a 0,70 e a distância genética entre as cultivares de 0,15 a 0,77. A análise de agrupamento mostrou que as variedades estudadas foram agrupadas de acordo com sua população de origem, sugerindo um efeito de proveniência em sua ordenação. De fato, as variedades mais similares foram aquelas introduzidas no programa de criação CIMMYT-ICARDA, que podem ter pais comuns em seu pedigree. Seleções de variedades locais foram mais similares entre si e diferentes do material CIMMYT-ICARDA, mostrando uma adaptação agroecológica.

Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)

Background Genetic diversity of finger millet (Eleusine coracana), a nutritious neglected staple cereal in Africa and South Asia is largely uncharacterized. This study analysed 82 published SSR markers for finger millet across 10 diverse accessions to compile an informative set for genetic characterisation. Extensive optimization compared single samples with bulked leaf or bulked DNA samples for capturing within accession genetic diversity. The markers were evaluated to determine (1) how efficiently they amplified target loci during high-throughput genotyping with a generic PCR protocol, (2) ease of scoring PCR products and (3) polymorphism and ability to discern genetic diversity within the tested finger millet germplasm. Results Across 88 samples, the 52 markers that worked well amplified 274 alleles, ranging from 2 to 14 per locus with a mean of 4.89. Major allele frequency ranged from 0.18 to 0.93 with a mean of 0.57. Polymorphic Information Content (PIC) ranged from 0.13 to 0.88 with a mean of 0.5 and availability varied between 64 and 100% with a mean of 92.8%. Heterozygosity ranged from 0 to 1.0, with a mean of 0.26. Discussion Five individual samples from an accession captured the largest number of alleles per locus compared to the four different bulked sampling strategies but this difference was not significant. The identified set comprised 20 markers: UGEP24, UGEP53, UGEP84, UGEP27, UGEP98, UGEP95, UGEP64, UGEP33, UGEP67, UGEP106, UGEP110, UGEP57, UGEP96, UGEP66, UGEP46, UGEP79, UGEP20, UGEP12, UGEP73 and UGEP5 and was since used to assess East African finger millet genetic diversity in two separate studies.

The power of 28 microsatellite markers for parentage testing in sheep

Background In sheep breeding, there are situations where relationships recorded at the farm among pedigrees such as parent-offspring, full-sibs or half-sibs need to be tested. A panel of 28 microsatellite (MST) markers was tested to provide accurate pedigree information and resolve the common problem of significant error in pedigree records in Merino sheep. Three different flocks of Australian Merino sheep were investigated. A private farm flock represents a flock with no record availability. Two other flocks were maintained under good managements of full keeping records and being selected for high and low parasite resistances. Results In the studied panel, eight MSTs provided an average of Polymorphic Information content (PIC) equal to 0.65 or more in order to be sufficient to make an accurate and successful DNA-based parentage analysis. The panel of twenty-eight MST loci was obviously sufficient for providing 100% accurate pedigree and genotyping data. DNA-based pedigree records were constructed and all significant pedigree record errors were eliminated. Conclusions These results were used for further study of population genetic parameters such as recombination and haplotyping which heavily based on pedigree information. Nevertheless MST based parentage testing is still available and affordable in most countries and for each farmer with reasonable cost in comparison with fast growing SNP based parentage technologies.

Morphological and SSR Assessment of Putative Drought Tolerant M3 and F3 Families of Wheat (Triticum aestivum L.).

In an attempt to develop drought tolerant genotypes of bread wheat, two procedures, i.e., mutation and hybridization were used to induce new genetic variation. Selection for high grain yield/plant (GYPP) and other desirable traits was practiced in the M2 populations of 7 gamma irradiated genotypes and F2 populations of 15 diallel crosses among 6 genotypes of wheat under well watering (WW) and water stress (WS) conditions. Progenies of these selections (53 M3 and 109 F3 families) and their seven parents were evaluated in the field under WW and WS. Significant yield superiority of twelve families (7 M3 ’s and 5 F2 ’s) over their original and better parents, respectively under WS reached 74.71% (SF9). These putative drought tolerant families were assessed on the DNA level using SSR analysis. Fifteen SSR primers were used for PCR amplification of the genomic DNA of these 12 selections and their parents. The SSR analysis proved that the 12 families are genetically different from their 7 parents, with an average polymorphism of 86.67%. The genetic similarities (Gs) ranged from 30% to 88%. Both mutants SF3 and SF4 exhibited very low Gs (42 and 40%, respectively) with their common parent (Giza-168), indicating that gamma rays were very effective in changing the genetic background of Giza-168 towards high GYPP under WS conditions. SSR assay permitted the identification of seven unique bands (5 positive and 2 negative) for three drought tolerant wheat genotypes (SF3, SF4 and Aseel-5). These bands might be considered useful as markers associated with drought tolerance in bread wheat breeding programs.

Pleiotropic effects of the sdw1 locus in barley populations representing different rounds of recombination

Background In the present study populations, representing different rounds of recombination were used for the analysis of phenotypic effects associated with the sdw1/denso locus. Other studies have mostly focused only on one type of population. Many different QTLs mapped at the same position as the sdw1/denso locus may indicate a pleiotropy of this gene or a tight linkage between genes conditioning quantitative traits. To date, results of studies have not unequivocally proven either of these two phenomena. Results Both breeding and molecular mapping experiments were undertaken to examine 200 single seed descent (SSD) and 60 doubled haploid (DH) lines obtained from the Maresi (with a semi-dwarfing gene) and Pomo cross combination. They were evaluated for the type of juvenile growth habit and certain agronomic traits were measured after harvesting. The estimates of mean values, standard errors and significance of effects were analyzed. In terms of the analyzed characteristics, the greatest variability was obtained for genotypes with the prostrate growth habit. Microsatellite markers (SSR) were also used to identify co-segregation with the sdw1/denso locus and Bmag0013, Bmag0877, Bmag0306b markers were linked the closest. A partial linkage map of chromosome 3H with the sdw1/denso semi-dwarfing gene was constructed and QTLs were identified. Conclusions Our experiments confirmed the impact of the semi-dwarfing gene on plant height, heading and flowering date both in SSD and DH populations, which may indicate pleiotropy. Moreover, a partial linkage between sdw1/denso locus and grain weight per spike and 1000-grain weight was found in the SSD population.

Assessment of genetic diversity in Brassica juncea Brassicaceae genotypes using phenotypic differences and SSR markers / Evaluación de la diversidad genética en genotipos de Brassica juncea Brassicaceae utilizando diferencias fenotípicas y marcadores SSR

Brassica mustard species represent one of the most important oilseed crops in India, nevertheless, their genetic diversity is barely known. A better understanding on this topic is essential for the proper utilization of genotypes in breeding programmes. We evaluated the genetic diversity among 44 Indian mustard Brassica juncea genotypes including varieties/purelines from different agro-climatic zones of India and few exotic genotypes Australia, Poland and China. For this, we used A and B genome specific SSR markers and phenotypic data on 12 yield and yield contributing traits. Out of the 143 primers tested, 134 reported polymorphism and a total of 355 alleles were amplified. Dendrograms based on Jaccards similarity coefficients and Manhattan dissimilarity coefficients were generated based on an average linkage algorithm UPGMA using marker data and phenotypic data. Genotypes were grouped into four clusters based on genetic distances. Both the clustering patterns based on Jaccards similarity and Manhattan dissimilarity coefficients, independently, discriminated the genotypes effectively as per their pedigree and origin. PCoA revealed that, the grouping of genotypes based on SSR marker data is more convincing than phenotypic data, however, the correlation between phenotypic and genetic distance matrices was observed to be very low r=0.11. Hence, for diversity studies reliability on molecular markers is worth proving and SSR markers are the stronger tools than quantitative traits in discriminating B. juncea genotypes.

Las especies de mostaza del género Brassica representan uno de los cultivos de semillas oleaginosas más importantes en India, sin embargo, su diversidad genética es poco conocida. Para la utilización de genotipos en programas de cultivos resulta esencial un mayor conocimiento sobre este tema. Debido a ello, se evaluó la diversidad genética entre 44 genotipos de mostaza de la India Brassica juncea incluyendo variedades y líneas puras de diferentes zonas agro-climáticas de la India y algunos genotipos exóticos Australia, Polonia y China. Para ello, se utilizaron marcadores SSR específicos del genoma A y B y datos fenotípicos del rendimiento de 12 cosechas y sus características. De los 143 primers evaluados, 134 reportaron polimorfismo y un total de 355 alelos fueron amplificados. Se generaron dendrogramas a partir de los coeficientes de similitud de Jaccard y de disimilitud Manhattan, basados en un algoritmo de vinculación promedio UPGMA. Se utilizaron datos de marcadores genéticos y datos fenotípicos. Los genotipos se agruparon en cuatro grupos basados en las distancias genéticas. Ambos patrones de agrupamiento, tanto los basados en los coeficientes de similitud de Jaccard como los basados en los de disimilitud Manhattan, separaron independientemente los genotipos por su genealogía y origen, de una manera efectiva. El PCoA reveló que la agrupación de genotipos basada en datos de marcadores SSR, es más convincente que los datos fenotípicos, sin embargo, se observó que la correlación entre las matrices de distancia fenotípica y genética resultó muy baja r=0.11. Por lo tanto, para estudios de diversidad basados en marcadores moleculares es necesario realizar más pruebas. Los marcadores SSR constituyen herramientas más eficientes para discriminar entre genotipos de B. juncea, que las características cuantitativas.

Genetic diversity among native varieties and commercial cultivars of Solanum tuberosum ssp. tuberosum L. present in Chile

Background: The object of this work was to determine the genetic and allelic diversity of Solanum species present in Chile, assessing allelic distribution among native varieties and commercial cultivars of Solanum tuberosum ssp. tuberosum L., using microsatellite markers. Results: A high level of allelic richness was found in the potatoes studied. The seven microsatellite markers used presented a total of 64 allelic variants among native varieties and commercial cultivars of Solanum tuberosum ssp. tuberosum. The SSR loci generated an average of 9.16 alleles/locus. The group with the highest PIC was that of native varieties collected in the Chiloe archipelago. The high PIC values found indicate that the native varieties from Chiloe have a low level of interrelation, representing wide genetic diversity. Conclusions: The markers with the highest number of alleles in native varieties corresponded to loci STG 0016 and LEMALX. Commercial cultivars do not present the same genetic variability as native varieties, and the allelic richness of commercial cultivars is lower than that of native varieties of S. tuberosum ssp. tuberosum. Most of the native varieties were clustered in accordance with their geographical location, while commercial cultivars, were clustered in accordance with their breeding programs in Chile and Europe, with the exception of Shepody.

SSR- Based Genetic Diversity Assessment in Tetraploid and Hexaploid Wheat Populations.

Molecular analysis for a set of hexaploid (Triticum aestvium) and tetraploid (Triticum durum) wheat cultivars was investigated by applying 11 SSR primers set. The plant materials consisted of 45 genotypes 15 of which were Triticum aestivum and 30 of T. durum obtained from four different regions Egypt, Greece, Cyprus and Italy. PCR products were separated on a 6% denaturing polyacrylamide gel electrophoresis and produced a total of 3840 DNA fragments which were used for the molecular analysis. The estimated parameters computed by POPGENE (Version 1.32) within the two population indicated that the Nei’s genetic diversity (H) was 0.2827, and the Shannon's Information index (I) was 0.4533 with standard deviation ± 0.0699 and ± 0.0852 respectively. The analysis of population structure revealed that genetic diversity within populations (Hs=0.2761) represented 97.7% of the total genetic diversity (HT=0.2827). The proportion of the total genetic diversity that was attributed to the population differentiation was low (Gst=0.0233) within population. ANOSIM (ANalysis Of Similarities), results showed that R was equal to 0.9048 (P<0.0001) indicated that all the most similar samples of genotypes are within the same population. The wheat varieties from the four distinct regions were clustered according to SSR data into two main clusters, durum wheat varieties and bread wheat varieties, the principal coordinate analysis (PCOORDA) validated the results of the dendrogram. This study showed that the two populations still had moderate considerable level of genetic diversity and show little genetic differentiation among them. Understanding genetic variation within and between populations is essential for the establishment of an effective breeding program concerning the intraspecific and interspecific hybridization.

Natural selection for efficiency in the use of nitrogen in common bean identified by analysis of microsatellites and grain yield

This study was carried out in order to verify whether natural selection acts on segregating common bean populations grown in the presence and absence of N, and to verify that natural selection affects the frequency of microsatellite alleles specifically, and in order to identify those that can assist in selection. Four populations from the crosses Ouro Negro x CI-107 and VC-5 x IAPAR-81 were carried forward in bulk to F8 at both levels of N. Ouro Negro and VC-5 are considered stress tolerant to nitrogen and IAPAR-81 and CI-107 responsive. One hundred progenies were obtained from each cross and grown in the presence and absence of N. DNA was extracted from 400 progenies, of which 194 were evaluated in the rainy season and 79 in the winter crop for grain yield. These progenies were evaluated in two separate experiments with and without N, in a 14 x 14 lattice design during rainy season and 9 x 9 in the winter season. We selected 35 pairs of polymorphic primers from the parents, with 20 being common from the two crosses. Using DNA of the 400 progenies, it was found that natural selection acted in 33 loci, in at least one environment and cross, and that alleles of the four parents were favoured by natural selection. QTLs were identified for the response rate of N and for grain yield and the linked markers are potential for assisted selection, especially the two most stable; BMD-20, in response to the use of N and PVBR-93 for grain yield.

Genetic diversity and population structure analysis of strawberry ( fragaria x ananassa duch. ) using ssr markers

In total, 18 simple sequence repeat (SSR) markers were used to analyze the genetic diversity and population structure of 59 accessions of cultivated strawberry (Fragaria x ananassa Duch.) from Korea, Germany, United States, United Kingdom, and Japan. In total, 101 alleles were detected with an average of 5.6 per locus and 21 specific alleles were identified. Notably, one genotype (Blonoli from Germany) possessed a maximum of 10 different unique alleles specific to each genotype. The gene diversity varied from 0.027 (EMPaEKO1B) to 0.791 (CFACT110), with an average value of 0.509. PIC values ranged from 0.026 to 0.762 (average 0.454). A model-based structure analysis revealed the presence of two populations. The accessions that were clearly assigned to a single population in which > 70 percent of their inferred ancestry was derived from one of the model-based populations. However, two accessions (3.4 percent) in the sample were categorized as having admixed ancestry. Here, we report detailed information on commercially grown strawberry accessions from five different origins using SSR markers. These results couldbe used for broadening the genetic base of commercially grown varieties.

Genetic diversity analysis of rice cultivars (Oryza sativa L. ) differing in salinity tolerance based on RAPD and SSR markers

Thirty rice cultivars were evaluated for salinity tolerance during the seedling stage and were divided into five tolerance groups including tolerant (T), moderately tolerant (MT), moderately susceptible (MS), susceptible (S) and highly susceptible (HS) which comprised 5, 10, 9, 4 and 2 cultivars respectively. Genetic diversity of all rice cultivars was evaluated using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) markers. The cultivars were evaluated for polymorphisms after amplification with 20 random decamer primers and 20 SSR primer pairs. A total of 161 RAPD markers and 190 SSR alleles were produced which revealed 68.94 percent and 89.47 percent polymorphism respectively. Mean genetic similarity coefficient was 0.82 for RAPD and 0.70 for SSR. Cluster analysis based on RAPD markers was effective in grouping cultivars based on their salt tolerance ability. Group IA1, IB and IV contained three T, three S and two HS rice cultivars respectively. The MT and MS cultivars which showed similar physiological responses to salinity were resolved into two groups: Group IA2 and Group II comprising ten and eight MT/MS cultivars respectively. Cluster analysis based on SSR markers separated rice cultivars into groups based on genetic relatedness which did not correspond to salinity tolerance level. The results from this study provided some useful implications for salt tolerance breeding programs. The evaluation of genetic similarity and cluster analysis together with salt tolerance ability provides some useful guides for assisting plant breeders in selecting suitable genetically diverse parents for the crossing program.

Natural selection in common bean microsatellite alleles and identification of QTLs for grain yield

Natural selection acts to select better adapted individuals or alleles in segregating population and help plant breeding. The objective of this work was to verify the effect of natural selection on microsatellite alleles as indicators of better adaptation and identification of quantitative trait loci (QTLs) for grain yield. This study evaluated 107 progenies from the F8 and 107 from the F24 generation derived from crossing Carioca MG and ESAL 686 lines, carried out by the bulk method, and evaluated in three different seasons: winter 2001; rainy 2001 and dry 2002. It was utilized 22 polymorphic markers and the natural selection acted in all of them. The frequency of the alleles of the parent Carioca MG, the most adapted, was increased in all of the 22 loci in F8 and 19 loci in F24. Selection affected each locus with different intensities in different generations. All of the selected alleles can be important for breeding program. QTLs were identified in generation F8 and F24 at varied magnitudes. The best marker PVttc002 explained 11.76 percent of variation in grain yield. However, an elevated interaction between QTLs and the environments was observed, showing the great difficulty in assisted selection.

Molecular diversity in rice genotypes differing in physiological mechanisms of salt tolerance through SSR and ISSR markers.

Two different DNA-based techniques viz, simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers were used to estimate genetic diversity among 20 rice genotypes possessing different physiological mechanisms contributing to salt tolerance. A total of 11 clear and repeatable bands were amplified from ten selected SSR primers pairs and 43 fragments were detected from nine ISSR primers. The level of polymorphism was 1.1% with SSR compared to 90.7% with ISSRs. Mean genetic similarity of 0.88 based on SSRs and 0.85 using ISSRs was observed. A total of 43 (39 polymorphic) and 11 bands were detected using 9 ISSR primers and 10 well distributed mapped SSR markers, respectively. Estimates of genetic similarity of ISSRs based on the 39 polymorphic markers between 20 rice cultivars ranged from 0.55 for PR108/CSR19 to 0.94 for Pokkali/CSR20 with an average of 0.81. The estimates revealed by the 11 polymorphic SSR bands showed the average value (0.94) and also the range of genetic similarity (from 0.86 to 1.00 for CSR22/CSR18 and CSR24/CSR20, respectively) reflecting their hyper variability and their high resolution power. The findings are likely to expedite breeding new salt tolerant cultivars by involving parents from diverse molecular clusters.