Mean Polymorphism Information Content Research Articles

Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank.

Finger millet [Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 – 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines (0.117 and 0.267, respectively). A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.

Screening for drought tolerance and molecular variability among some sugar beet cultivars

Drought is one of the significant abiotic stress factors that affect plant development and productivity. Screening and producing of more tolerant genotypes with higher yield capacity is the breeders' principal purpose. Therefore, this work was carried out to evaluate the performance of four sugar beet cultivars (Top, Hossam, Hercules and Kawamera) under water limitation. The drought stress experiment was applied based on three water regimes, 25%, 50% and 75% (severe, moderate and non-stress conditions, respectively) of relative water capacity (RWC). The study incorporated some productivity and quality traits. The results showed that drought stress has a significant effect on all studied traits. Whereas, increasing of water deficiency led to decrease of the productivity traits and increasing of quality parameters. Kawamera cultivar has superior performance in all the studied traits under all three different levels of water regime. Besides, the four cultivars were assessed by both SSR and ISSR molecular markers. SSR marker exhibited a higher polymorphism percentage (71.43%) than ISSR marker (44.26%). In addition, the mean polymorphism information content (PIC) value was higher for the SSR marker (0.25) than the ISSR marker (0.18) too. Moreover, the constructed dendrograms revealed that the SSR marker was able to separate the cultivars according to their drought-tolerance, where the highest drought-tolerant cultivar (Kawamera) was classified alone in the main cluster. However, the superiority of Kawamera cultivar under drought stress indicated that it could be utilized in breeding programs for developing more drought-tolerant sugar beet cultivars.

Exploring the genetic diversity and population structure of scarlet eggplant germplasm from Rwanda through iPBS-retrotransposon markers.

Scarlet eggplant (Solanum aethiopicum gr. gilo) is a part of African indigenous vegetables and acknowledged as a source of variations in the breeding of Brinjal. Since its genetic diversity is still largely unexplored, therefore genetic diversity and population structure of this plant were investigated in this study. Scarlet eggplant germplasm made of fifty-two accessions originated from two districts of Rwanda was assessed by employing the iPBS-retrotransposon markers system. Twelve most polymorphic primers were employed for molecular characterization and they yielded 329 total bands whereupon 85.03% were polymorphic. The recorded mean polymorphism information content was 0.363 and other diversity indices such as; mean the effective number of alleles, mean Shannon's information index and gene diversity with the following values; 1.298, 0.300 and 0.187 respectively. A superior level of diversity was noticed among accessions from Musanze district. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) gathered scarlet germplasm in a divergence manner to their collection district. Analysis of molecular variance (AMOVA) displayed that the utmost variations (81%) in scarlet eggplant germplasm are resulting in differences within populations. The extensive diversity of scarlet eggplant in Rwanda might be used to form the base and genetic resource of an exhaustive breeding program of this economically important African indigenous vegetable. For instance, accessions MZE53 and GKE11 might be proposed as parent candidates due to their high relative genetic distance (0.6781).

Genetic diversity and population structure assessment using molecular markers and SPAR approach in Illicium griffithii, a medicinally important endangered species of Northeast India

BackgroundIllicium griffithii is an aromatic medicinal tree species that has been listed in the IUCN Red List as an endangered species. Dried seed pods of I. griffithii have a good market potential in the spices and pharmaceutical industries. Fruits are the potential source of shikimic acid and used for the production of oseltamivir (a drug against bird flu). However, in recent years, unscientific harvesting and rampant exploitation of the species has caused a negative and adverse effect on its natural population. Proper knowledge of genetic diversity and population structure is crucial to understand the population dynamics, adaptation, and evolutionary pattern of a particular species for conservation. It was from this view point that the present study was undertaken so as to compare the various types of DNA-based molecular markers namely RAPD, ISSR, DAMD, and SCoT by their efficiency and SPAR approach to evaluate the genetic diversity of I. griffithii as well as to analyze population genetic structure for conservation purpose. ResultA total of 250 discernible bands were generated with 246 bands (98.40 %) being polymorphic in nature. All the primers in combination gave a mean polymorphic information content (PIC) of 0.81 and Rp value (resolving power) of 4.32. Nei’s, Gst, and AMOVA analysis showed similar values of genetic differentiation among populations (Gst = 0.396, FST = 0.30, respectively), revealing a low level of genetic differentiation among the eight sampled populations. I. griffithii with an estimated gene flow value of Nm = 0.761 was significantly low among populations. Clustering pattern obtained with Bayesian structure and PCoA diagram revealed that intermixing of genetic material across populations is only possible when the populations lie close to each other. This is further validated with UPGMA clustering method where a positive correlation of genetic variability with geographical distance among closely related populations could be clearly seen. ConclusionThe result aids in the identification, collection, and preservation of diverse germplasm of I. griffithii from Arunachal Pradesh and Meghalaya of Northeast India. This would further help in understanding the population structure and genetic diversity among other Illicium species in order to formulate effective conservation strategies for the improvement of this endangered taxa.

Assessment of genetic diversity among wild populations of the striped catfish (Pangasianodon hypophthalmus) by 20 novel microsatellite markers

The striped catfish, Pangasianodon hypophthalmus, is one of the most economically important aquaculture species in Vietnam. This study developed 26 novel microsatellite markers from the draft genome of the striped catfish to assess the genetic diversity of three wild populations of the striped catfish (Bien Ho, Cuu Long, and Kratie) for establishing the breeding program. The study exhibited that 6 out of 26 loci had significantly high null allele frequency and deviated from Hardy - Weinberg equilibrium; thus, they were eliminated for further analysis. Across 20 loci without null alleles, a total of 255 different alleles was identified, ranging from 7 to 21 alleles per locus, with many unique alleles for each population. The results based on 20 loci revealed the mean polymorphic information content PIC=0.783; the mean observed heterozygosity Ho=0.809; the mean expected heterozygosity He=0.812; inbreeding coefficient Fis=-0.0147 (Fis<0). The results indicated that the striped catfish populations have high genetic diversity and are suitable for selective breeding. The Analysis of Molecular Variance (AMOVA) and comparison of genetic distances showed significant genetic differentiation among three populations while the Kratie population was distant from the others.

Genetic Diversity of Ancient Camellia sinensis (L.) O.Kuntze in Sandu County of Guizhou Province in China

The ancient tea plant germplasm is an important resource for breeding new tea plant varieties and has great economic value. However, due to man-made and natural disturbances, it has become endangered. In order to have a better management of the conserved tea plant germplasm, it is a requirement to understand the genetic and phenotypic diversity. The aim of this study was to evaluate the genetic and phenotypic diversity of 145 ancient tea plant germplasm resources from five populations in Sandu County of Guizhou province in China. To explore the population genetics of tea plant, we successfully identified 15 simple sequence repeat (SSR) markers, which were highly polymorphic. Additionally, we applied traditional phenotypic methods to evaluate the tea plant diversity. The results suggested that the genetic and phenotypic diversity were relatively high. A total of 96 alleles were identified, and the mean polymorphic information content (PIC) value was found to be 0.66. The analysis of molecular variance (AMOVA) showed that genetic variation within the populations was greater than among the populations. Overall, our results are the valuable baseline data in developing more efficient management and breeding plans for one of the most popular non-alcoholic beverage crops, the tea plant species.

Genetic Diversity among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

Deriving tropical gynoecious inbred backcross lines from exotic pickling cucumber using marker assisted backcross breeding

Indian cucumber cultivars are basically monoecious and vigorous in nature with many lateral branches but they are poor in productivity. The present study was aimed to introgress gynoecious trait (F locus) from pickling cucumber line (Gy14) into elite Indian cultivar Pusa Uday using marker assisted backcross breeding. Based on allelic diversity analysis, the allele numbers per locus ranged from 2 to 3 in BC1F3 and the observed heterozygosity (Ho) was ranged from 0.01 to 0.55. The heterozygosity expected (He) mean was 0.28 (range 0.03 to 0.50) which was higher than mean Ho (0.18) and mean polymorphic information content (PIC) for 87 markers was 0.23. Whereas the allele numbers per locus was 2 in BC2F2 and the observed heterozygosity (Ho) was ranged from 0.01 to 0.56. The mean expected heterozygosity (He) was 0.24 which was higher than mean Ho (0.17) and the mean PIC value was 0.19. The gynoecism (F locus) was introgressed in the Indian slicing cucumber cv. Pusa Uday though backcross breeding accompanied by foreground and background selections. The foreground selection was performed with one dominant SCAR marker, and 3 SSR markers (SSR 00233, SSR 15516 and SSR13251). A total of 87 polymorphic markers spanning genetic distance of 1031 cM with an average distance of 12.9 cM between adjacent markers were used for background selection. The genome recovery of the individuals in BC1F3 population was ranged from 62.64% to 93.10% while among BC2F2 plants it was ranged from 89.66% to 95.40%. Four inbred backcross lines (IBL) were selected from backcross populations (BC1F4 and BC2F3) those were purely gynoecious even at 45°C with more than 5 lateral branches. Hence, marker assisted backcross breeding served as a potential approach for precise introgression of the gynoecy (F locus) from picking cucumber to Indian slicing cucumber.

The Development of the Genic SSR Markers for Analysis of Genetic Diversity in Gooseberry Cultivars

Gooseberry is one of the most promising and underrated small fruit crops. There is a need to improve and genotype the existing cultivars, and this work requires the use of new efficient DNA marking techniques. Marker-assisted selection (MAS) is a modern approach for work with genetic resources. However, the genetic determinants of key qualitative traits are poorly studied. Therefore, we developed SSR markers located in flavonoid biosynthesis genes that can affect the resistance of plants to biotic and abiotic stresses to study the genetic diversity of gooseberry cultivars grown in the Russian Federation and varying in genetic and geographical origin. We have genotyped 22 gooseberry cultivars using a set of 19 of our original microsatellite markers and two neutral previously published ones. A total of 53 alleles were found. Nine of the 21 analyzed loci were polymorphic. The most polymorphic loci of flavonoid biosynthesis were found in the DFR gene (RucDFR1-2, RucDFR1-3, RucDFR2-1), their mean PIC (polymorphism information content) being 0.65, comparable to the PIC values of neutral markers. Our set of gene-targeted SSR markers showed that most of all the studied gooseberry cultivars differed in origin, based on which they were divided into three groups: European cultivars, Russian cultivars, and interspecies hybrids. Thus, the polymorphic markers can be used for cultivar identification and certification as well as for the marker-assisted selection of gooseberry plants having different origins and phenotypic traits.

Association between microsatellite markers and rice response to the rice blast pathogen Magnaporthe oryzae in selected Zambian rice genotypes

Magnaporthe oryzae, the rice blast disease pathogen is estimated to cause losses of up to 30% in rice production worldwide, yet its impact on rice production in Zambia remains unknown. Symptomatic rice leaf tissue collected from rice fields in Mongu District of Zambia was cultured on oatmeal agar medium and fungal colonies were purified and identified through leaf lesions and conidia using published keys. An M. oryzae isolate from this study was used to challenge twenty-eight selected Zambian rice genotypes to determine their responses to infection with the pathogen estimated by lesion numbers and sizes. Twelve of the genotypes (42.8%) were highly resistant (HR) with 1 to 2 lesions per cm2, 6 (21.4%) were moderately resistant with mean lesion numbers of 3 to 4 per cm2 while 10 (35.7%) were susceptible with lesion numbers above 5 per cm2 of leaf tissue. Polymerase chain reaction (PCR)-amplification of rice genomic DNA extracted from the 28 genotypes using selected microsatellite marker primers revealed a moderate genetic diversity with three of them showing significant genetic diversity. Allelic diversity among the selected genotypes was also confirmed from a calculated mean polymorphic information content of 0.8. A correlation between 8 of the microsatellite markers in some of the rice genotypes and their resistance response to M. oryzae was also established. Results show that some of the analysed rice genotypes have a significant potential for use as a genetic resource in breeding for varieties that are resistant to the rice blast pathogen for Zambian farmers.

Genetic Characterization of a Sheep Population in Oaxaca, Mexico: The Chocholteca Creole.

Simple SummaryCreole animals are an important genetic resource due to their adaptation to adverse conditions, however, many of them have disappeared or have been reduced in number; therefore, their identification and preservation should be promoted. In the Mixteca zone of Oaxaca, México, there is a group of creole sheep with physical differences with respect to the other known breeds. The objective of the present study was to determine the degree of differentiation among the individuals of the population of creole sheep and the similarities with other breeds, as well as to measure their level of conservation and consanguinity. It was found that there is a group of sheep which is different from the presently known breeds and that they do not present high degree of consanguinity, and thus may be considered a new breed. Therefore, it is proposed that they are identified as the Chocholteca Creole breed, in honor of the ethnic group which inhabits this region. The present study is very important because it discovers a new genotype of sheep, which amplifies the genetic diversity. Therefore, further studies are needed, given that they are a potential alternative of meat and wool.Creole sheep in México have undergone crossbreeding, provoking the loss of genetic variability. The objective of the present study is to determine the intra-racial genetic diversity, the genetic relationship with other genotypes, and the populational substructure of the Oaxacan Creole sheep. Twenty-nine blood samples were obtained of Creole sheep of the Oaxaca Mixteca region in México. A genetic analysis was made with 41 microsatellites recommended for studies of genetic diversity in sheep. An analysis was made of genetic diversity, populational structure, and genetic distance with 27 other sheep populations. The study found 205 alleles with a range of 2 to 9 by locus and an effective number of 3.33. The intra-racial analysis showed a moderate genetic diversity with values of expected heterozygosity of 0.686 and observed of 0.756, a mean polymorphic information content of 0.609, and a mean coefficient of consanguinity of −0.002. In interracial genetic diversity for the coefficients of consanguinity, the values were FIS = 0.0774, FIT = 0.16993, and FST = 0.10028, showing an elevated genetic distance with other creole breeds, but close to Argentine Creole, to another Creole of México and the Spanish Merino. Its genetic structure showed that it does not have any populational subdivision nor mixes with the others analyzed. It is concluded that it is a distinct and isolated population and is proposed as the creole breed “Chocholteca” for its conservation.

Genetic Diversity and Relationships of Terebinth (Pistacia terebinthus L.) Genotypes Growing Wild in Turkey

Genetic diversity and relationships of 54 wild-grown terebinths (Pistacia terebinthus L.) were determined using 40 SSR (simple sequence repeat) markers (38 in silico polymorphic SSR markers and 2 SSR markers). In silico polymorphic SSR analysis, 430 alleles were identified. The number of alleles per locus ranged from 3 to 25 with a mean value of 11 alleles per locus. The values of polymorphism information content (PIC) ranged from 0.34 (CUPOhBa4344) to 0.91 (CUPSiBa4072) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), the Structure, and Principal Coordinates (PCoA) based clustering. The structure analysis and UPGMA clustering of the genotypes depicted two major clusters. PCoA results supported cluster analysis results. The dendrogram revealed two major clusters. Forty-two samples were obtained from the Kazankaya canyon and 12 samples from the Karanlıkdere region. The two regions are 130 km apart from each other but in a dendrogram, we did not find geographical isolation. The results proved the efficiency of SSRs for genetic diversity analysis in the terebinth. Based on the results, SSRs can be applied as a trustworthy tool for the evaluation of genetic diversity in terebinth genotypes. Molecular analysis on the terebinth genotypes in this study will promote the germplasm collection and the selection of the populations in future studies on terebinths for genetic mapping, genetic diversity, germplasm characterization, and rootstock breeding.

Genetic Diversity of Six Duck Populations in India

Background: The variety of indigenous duck germplasm contribute maximum to the poultry industry in India, besides chicken population. In southern part of India, the available duck genetic resource, particularly Arni ducks (comprises of Sanyasi and Keeri ducks) of Tamil Nadu, has its own characteristics with innate potentiality of higher productivity without any input system of management. Genetic characterization and diversity of indigenous duck genetic resources has not been properly studied. In the present study, the genetic diversity of Arni ducks with other indigenous and exotic duck germplasm were analysed with microsatellite markers. Method: Genomic DNA was isolated from the blood samples of six duck populations. Molecular characterization was carried out with duck specific FAO recommended microsatellite markers. The genotyping of ducks was done based on the size of 4324 PCR amplicons of 23 microsatellite loci, which were subjected to capillary electrophoresis using automatic sequencer.Result: A total of 222 alleles in six duck populations across 23 microsatellite loci with a mean of 9.65 ± 0.95 alleles were found. Kuttanad duck variety had the highest number of alleles (139) followed by Sanyasi (136), Keeri (129), Muscovy (118), Assam (91) and White Pekin (78) ducks. The mean observed number of alleles was 6.04 ± 0.59, 5.91 ± 0.76, 5.61 ± 3.17, 5.13 ± 0.44, 3.96 ± 0.76 and 3.39 ± 0.40 in Kuttanad, Sanyasi, Keeri, Muscovy, Assam and White Pekin ducks respectively. The overall mean polymorphism information content (PIC) values among the six duck populations was 0.6269. In most of the duck populations, the mean PIC value was more than 0.5 except in Assam (0.4815) and White Pekin (0.3725) ducks. The observed heterozygosity was the highest in Keeri ducks (0.5217) and lowest in White Pekin ducks (0.2766), while, the mean expected heterozygosity was the highest in Sanyasi (0.5628) and lowest in White Pekin (0.4038) ducks. The variations in the observed and expected number of alleles, differences in PIC of various microsatellite loci might be attributed to the genetic variability of the duck populations, number and type of microsatellite primers utilised for analysis and the genetic diversity of the duck breeds under study. Higher FST value indicates the substantial degree of breed differentiation among the studied duck populations.

New hyper-variable SSRs for diversity analysis in mango (Mangifera indica L.)

Whole genome sequence in mango offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, simple sequence repeats (SSRs) were predicted from genome sequence of mango. Based on the SSR length (? 50 bp), highly-variable mango SSRs (MSSRs) were sorted. A sub-set of 129 MSSRs was validated on a set of 24 diverse mango genotypes yielding marker validation and polymorphism of 88.96 and 85.27 per cent, respectively. One hundred and ten polymorphic markers were identified for the present set of mango genotypes. Polymorphic information content (PIC) ranged from 0.10 to 0.78 and the highest value was observed with MSSR133. The mean PIC value was 0.40 but 33 MSSR markers showed PIC values ? 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs) in mango. MSSRs data was further used for diversity analysis of mango genotypes belonging to different agro-ecological conditions including chance seedlings, landraces, exotic and indigenous germplasm and hybrids. Cluster analysis using UPGMA of 24 mango genotypes revealed that these MSSRs were informative in diversity analysis and distinguished mango genotypes based on their origin, parentage and embryo types. A novel set of 110 hyper-variable SSR markers have been added to the mango repository depicting usefulness in discriminating closely related mango germplasm and their use in mango improvement programme.

Genome-wide diversity and structure variation among lablab [Lablab purpureus (L.) Sweet] accessions and their implication in a Forage breeding program

Most orphan crops have not been fully sequenced, hence we rely on genome sequences of related species to align markers to different chromosomes. This hinders their utilisation in plant population improvement programs. Utilising the advances in the science of sequencing technologies, the population structure, relatedness, and genetic diversity among accessions can be assessed quickly for better exploitation in forage breeding programs. Using DArTseq technology, we studied the genetic and structural variation in 65 Lablab purpureus (L.) Sweet conserved gene-bank accessions using 9320 DArTseq-based SNPs and 15,719 SilicoDart markers. These markers had a low discriminating ability with mean polymorphic information content (P.I.C.) of 0.14 with DArTseq-based SNPs and 0.13 with SilicoDart markers. However, the markers had a high mean call rate of 73% with DArTseq-based SNPs and 97% with SilicoDart markers. Analysis of molecular variance revealed a high within populations variance (99.4%), indicating a high gene exchange or low genetic differentiation (PhiPT = 0.0057) among the populations. Structure analysis showed three allelic pools in variable clusters of ΔK = 3 and 6. Phylogenetic tree of lablab accessions showed three main groups with variable membership coefficients. Most pairs of accessions (40.3%) had genetic distances between 0.10 and 0.15 for SilicoDart markers, while for DArTseq-based SNPs, (46.5%) had genetic distances between 0.20 and 0.25. Phylogenetic clustering and minimum spanning analysis divided the 65 accessions into three groups, irrespective of their origin. For the first time, this study produced high-density markers with good genom coverage. The utilisation of these accessions in a forage program will base on the information from molecular-based grouping. The outcomes uncovered the presence of noteworthy measure of variety in Uganda, CIAT and ILRI accessions, thus demonstrating an opportunity for further marker-trait-association studies.

Molecular characterization and diversity analysis of selected maize inbred lines using single-nucleotide polymorphism markers

The level of genetic diversity among the available breeding materials determines the potential success of a breeding program. In this study, 92 maize inbred lines were genotyped with 3047 single-nucleotide polymorphism (SNP) markers using a Kompetitive allele-specific polymerase chain reaction (KASP™) genotyping protocol. The objectives were to determine the level and pattern of genetic diversity and define potential heterotic groups of maize inbred lines developed by the Agricultural Research Council maize program of South Africa. More than 91% of the SNPs used were polymorphic with a mean polymorphic information content of 0.36. Gene diversity ranged from 0.35 to 0.37, with a mean of 0.36. Cluster analysis revealed the presence of three distinct subpopulations. Analysis of molecular variance revealed low but highly significant (P < 0.0001) variations among populations and high within and among individual variations. Variation among individuals contributed 83% of the total variation, whereas variation within individuals and among populations contributed 14% and 3%, respectively. Low mean population differentiation observed in this study suggested that the inbred lines might be developed from parental genotypes with similar genetic backgrounds. The mean percentage of genetic purity among the inbred lines was 4.8, with more than 79% of the inbred lines exhibiting less than 5% heterozygosity, indicating the inbred lines are fixed. Genotypes in different clusters may be earmarked as belonging to distinct heterotic groups, and their crosses may result in better heterosis. Thus, the findings of this study set the basis for earmarking heterotic groups and parental selection.

English

Cape gooseberry (Physalis peruviana L.) is a neglected high potential crop, knowledge of the genetic diversity of the genotypes domesticated in Kenya is limited. To understand the genetic diversity and structure within and between Cape gooseberry germplasm, 70 accessions from six selected counties were analyzed using 15 pairs of highly polymorphic SSR primers. In this study, a total of 61 polymorphic SSR alleles were identified with mean polymorphic information content (PIC) of 0.43. Analysis of Molecular Variance (AMOVA) revealed that 92.8% of the total genetic variation was within accessions whereas variation among accessions accounted for 7.2% of the total genetic variation. Genetic diversity parameters among the 70 accessions revealed that Cape gooseberry was more diverse than previously recorded. Based on the SSR data, the 70 accessions were classified into five main phylogenetic groups, which corresponded to the county of origin through factorial analysis, principal component analysis (PCA), and phylogenetic analysis. Seven core SSR primer pairs, namely SSR1, SSR2, SSR10, SSR11, SSR123, SSR138, and SSR146 were found to have a wide applicability in genotype identification of cape gooseberry, and thus they are recommended for use in genetic characterization of germplasm collected from other counties not covered by the present study. This study demonstrated the existence of considerable genetic diversity in Cape gooseberry accessions growing in selected counties in Kenya and can therefore be used as a basis for future breeding programs in the development of hybrids with desirable traits. This wider genetic diversity is vital for posterity as it will help cope with unpredictable climatic changes and human needs.   Key words: Simple sequence repeats (SSRs), genetic diversity, germplasm, Physalis peruviana L., polymorphic information content (PIC).

Morphological and Molecular Assessment of Genetic Diversity of Seven Species of the Genus Artemisia L. (Asteraceae)

Species belonging to the genus Artemisia have high economic value and are used in folk and modern medicine. Analysis and identification of their genetic relationships can help in efficient conservation and further utilization of Artemisia genetic resources. This study was conducted to evaluate the genetic diversity among seven species of the genus Artemisia using their morphological characteristics and inter-simple sequence repeat (ISSR)-based molecular markers. The morphology of leaf and achene was examined by light microscopy and scanning electron microscopy. Morphological and molecular data were analyzed using the multivariate statistical package program. There were obvious variations in the morphology of leaf and achene among the Artemisia species. The ISSR results showed a total of 173 amplified loci, consisting of 132 polymorphic loci and 41 unique loci. Polymorphism percentage ranged from 62.5 to 88.8% for nine primers. Mean polymorphism information content for ISSR markers was 0.88, which suggested the efficacy of the ISSR marker system in determining polymorphisms. Significant correlation (r = 0.56, P = 0.004) was observed between similarity coefficients of morphological parameters and ISSR data based on the Mantel test. A wide range of diversity was observed at both morphological and molecular levels among the species. Genetic analyses using ISSR allowed for the detection of relationships between various Artemisia species than was apparent by the analyses of morphological characteristics of these species. Moreover, a mixed pattern of grouping in cluster analysis was found, indicating the close affinities of species with each other and also that the section Artemisia is polyphyletic.

Genetic Diversity of Indigenous Chicken (Gallus Gallus domesticus) from Ecozones of Egypt and Kingdom of Saudi Arabia

Genetic diversity of two chicken ecotypes from Ismailia-Egypt (ISM) and Taif-Saudi Arabia (TA) was evaluated using 39 microsatellites. DNA was extracted from blood of 25 chickens/ecotype. The number of alleles was 157 and 138, the number of alleles/locus averaged 4.2±2.2 and 3.6±1.6, and the highest number of private alleles was 9 and 5 for ISM and TA, respectively. Percentage of shared alleles between the two ecotypes was 45%. This panel of markers is reasonably informative as the mean polymorphic information content for ISM and TA was 0.47±0.21, and 0.41±0.2. Similar average of observed heterozygosity was attained for both ecotypes. Conversely, averages of expected heterozygosity differed between two ecotypes, 0.52±0.23 vs. 0.45±0.21 for ISM and TA. 8 and 12 loci have significantly deviated from HWE of ISM and TA. Estimate of genetic distance was 0.2 and FST index was 0.29. Results showed only 6% of genetic diversity is shared between these two ecotypes.

The traceability of Eucalyptus clones using molecular markers

Abstract The improvement of Eucalyptus clones plays a crucial role in modern silviculture. This study used a set of 17 microsatellite loci to analyze the genetic diversity and structure of 107 elite clones (80 E. grandis and 27 E. globulus). All clones were cultivated in Uruguay and were sourced from three different providers. Using the fingerprinting technique, an exclusive molecular profile was assigned for each clone, and the genotyping reaction showed differences between the two species. The cumulative probability of identifying two random individuals that share the same genotype (PI) with all 17 loci, was estimated as low for E. grandis (1.18×10-15) and E. globulus (4.03×10-14). The combined PIsibs was (1.05×10-5) and (2.17×10-5) for E. grandis and E. globulus, respectively. A total of 180 alleles were detected for E. grandis and 100 for E. globulus. We found a high mean number of alleles per locus (10 for E. grandis and 6 for E. globulus), and the results for mean polymorphic information content (PIC ) were (0.648) and (0.548), respectively. The observed heterozygosity (Ho ) ranged from 0.216 to 0.838 (mean = 0.509) for E. grandis and 0 to 1 (mean = 0.566) for E. globulus. Two core sets of seven EST-SSR loci were identified for each species. These markers revealed unambiguous fragment amplification, providing a minimum number of SSRs for effective clonal identification. The genetic structure analysis suggests that the germplasm of the E. grandis population is structured in four clusters, while the E. globulus population consists of two clusters.