Genetic diversity of anchote (Coccinia abyssinica (Lam.) Cogn.) from Ethiopia as revealed by ISSR markers

Anchote (Coccinia abyssinica) is plant endemic in Ethiopia with a high calcium content grown for its edible tuberous roots. In spite of its importance as food security crop, there is no information available on molecular genetic diversity of this crop. Therefore, the aim of this study was to assess genetic diversity within and among 12 populations of anchote using ISSR markers. Using nine ISSR primers, a total of 87 scorable bands was generated of which 74 were polymorphic. Within population diversity based on polymorphic bands ranged from 13.8 to 43.53 % with a mean of 33.05 %, Nei’s genetic diversity of 0.04–0.156 with a mean of 0.12, Shannon information index of 0.07–0.23 with a mean of 0.175 and analysis of molecular variation (AMOVA) of 51.4 % were detected. With all diversity parameters, the highest diversity was obtained from Gimbi, Bedele and Ale populations, whilst the lowest was from Manna. AMOVA showed a 48.56 % between populations variability and significantly lower than that of within population variation. Population differentiation with F_ST was 48.56 %. From Jaccard’s pairwise similarity coefficient, Decha and Nedjo were most related populations exhibiting 0.76 similarity and Manna and Nedjo were the most distantly related populations with similarity of 0.52. The only pentanucliotide primer used in the study, Primer 880 (GGAGA)3, showed a unique band in some individuals that appeared to be associated with morphological quantitative traits (lowest seed number, high protein content, largest fruit size and smallest vine length). Illubabor and Gimbi populations exhibited highest genetic diversity so that the populations should be considered as the primary sites in designing conservation areas for this crop.     

Analysis of genetic diversity and population structure of 135 dill (Anethum graveolens L.) accessions using RAPD markers

Dill (Anethum graveolens L.) leaf, seed and their essential oil are rich source of antioxidants. The plant is native in Southwest Asia and is cultivated in Europe, India and the United States. This study evaluated the genetic diversity structure of 135 accessions of A. graveolens from different continents, based on random amplified polymorphic DNA (RAPD) markers. The selected 10 RAPD primers generated a total of 142 highly reproducible bands, among which 89 were polymorphic. Percentage of polymorphism varied from 41.17 % (OPB20) to 92.85 % (OPB15) with an average of 77.74 %. A relatively high genetic diversity was detected among all the accessions with the Nei’s genetic diversity (H) values ranged from 0.346 (OPB07) to 0.444 (OPB18) with a mean of 0.401. When estimated for Shannon’s information index (I), it has ranged from 0.530 (OPB12) to 0.652 (OPB18), the mean was observed as 0.581. The respective values of H and I were found to be the highest value for primer OPB18. Cluster analysis of RAPD data using UPGMA algorithm based on Nei’s genetic similarity matrix placed the 135 accessions into two main clusters. Although a number of groups can be identified, the clusters show little to no association with the geographic origin of the material. The implication of the results of this study in developing a strategy for the conservation and breeding of dill germplasm are discussed.     

Revealing genetic diversity and population structure in Pistachio (Pistacia vera L.) by SSR markers

Genetic Resources and Crop Evolution - Pistachio (Pistacia vera L.) is the only cultivated species in Pistacia genus and it is one of the most important species of hard-shelled fruits. Pistachio...     

Genetic diversity and population structure of Leucaena leucocephala (Lam.) de Wit genotypes using molecular and morphological attributes

Genetic Resources and Crop Evolution - For the estimation of genetic diversity and population structure, 23 accessions of Leucaena leucocephala were characterized using morphological and molecular...     

Insights from putatively neutral EST-SSR markers on the population genetic structure and genetic diversity of the Qinghai-Tibetan Plateau endemic Medicago archiducis-nicolai Sirjaev

Medicago archiducis-nicolai Sirjaev and M. ruthenica (L.) Ledebour are two phylogenetically closely related species in the section Platycarpae within Medicago. M. archiducis-nicolai is endemic to the Qinghai–Tibetan Plateau (QTP), shows more tolerance to abiotic stress than M. ruthenica, which inhabits relatively temperate areas, and has the potential to be domesticated and used as a legume forage germplasm in alpine meadows. Here, we analyzed the population genetic structure and genetic diversity of these species using 20 putatively neutral EST-SSR markers. Twenty-four wild populations, including 21 M. archiducis-nicolai and 3 M. ruthenica, were divided into two clusters that were consistent with current taxonomy. The 21 M. archiducis-nicolai populations were clustered into two geographically related groups. Positive relationships between population genetic distance and geographical factors, including geographical distance and altitudinal difference, revealed that the genetic differentiation of M. archiducis-nicolai populations was driven by both geographical distance and the complex topography of the QTP. Medicago archiducis-nocilai, a narrow-range endemic on the QTP, had lower genetic diversity than the more widespread M. ruthenica. Medicago archiducis-nicolai populations from the central platform of the QTP had relatively high genetic diversity, whereas those occupying the east platform and edge of the QTP showed variable levels of genetic diversity, implying the presence of refugia on the central platform. These results have implications for the genetic resource management and exploitation of M. archiducis-nicolai and provide novel insights into the mechanisms underlying the adaptation of this species to the harsh environment of the QTP.

     

Genetic diversity and population structure of masson pine (Pinus massoniana Lamb.) superior clones in South China as revealed by EST-SSR markers

Genetic Resources and Crop Evolution - Masson pine (Pinus massoniana Lamb.) is one of the most economically important and widely distributed forest species in China. Understanding the genetic...     

Assessing genetic diversity of sweet potato (Ipomoea batatas (L.) Lam.) cultivars from tropical America using AFLP

The sweet potato genebank at the International Potato Center (CIP) maintains 5,526 cultivated I. batatas accessions from 57 countries. Knowledge of the genetic structure in this collection is essential for rational germplasm conservation and utilization. Sixty-nine sweet potato cultivars from 4 geographical regions (including 13 countries) of Latin America were randomly sampled and fingerprinted using AFLP markers. A total of 210 polymorphic and clearly scorable fragments were generated. A geographic pattern of diversity distribution was revealed by mean similarity, multidimensional scaling (MDS), and analysis of molecular variance (AMOVA). The highest genetic diversity was found in Central America, whereas the lowest was in Peru-Ecuador. The within-region variation was the major source of molecular variance. The between-regions variation, although it only explains 10.0% of the total diversity, is statistically significant. Cultivars from Peru-Ecuador, with the lowest level of within region diversity, made the most significant contribution to the between region differentiation. These results support the hypothesis that Central America is the primary center of diversity and most likely the center of origin of sweet potato. Peru-Ecuador should be considered as a secondary center of sweet potato diversity.     

Genetic diversity,population structure and genetic relationships in apricot (Prunus armeniaca L.) germplasm of Jammu and Kashmir,India using ISSR markers

Genetic Resources and Crop Evolution - The collection and characterization of apricot germplasm is an important step for its utilization, conservation, and breeding programs. In the present study,...     

Single-locus EST-SSR markers for characterization of population genetic diversity and structure across ploidy levels in switchgrass (<Emphasis Type="Italic">Panicum virgatum</Emphasis> L.)

Polyploidy, ploidal variation between populations, and aneuploidy within some populations complicate population genetic analyses in switchgrass. We report 21 genic-simple sequence repeat marker loci with single-locus disomic segregation in tetraploids and apparently tetrasomic inheritance in octoploids, thus allowing population genetic analyses across ploidy levels. Based on 472 individuals sampled over four tetraploid and eight octoploid cultivars, six to 55 alleles were detected per locus with an average of 24.1. Genetic diversity was greater in octoploids than tetraploids, as expected from polysomic inheritance. One tetraploid cultivar displayed comparable diversity to the least diverse octoploid cultivars, suggesting breeding history or population history in the native stands of origin may have also affected within-cultivar diversity. Amplicon number at each locus and population relationships suggest autopolyploid origin of octoploids within upland tetraploids with significant cultivar differentiation. However, model-based Bayesian clustering of individuals indicated that closely related octoploid cultivars are difficult to identify, possibly due to slowed differentiation by polysomic inheritance. The analysis of the sampling effect indicated addition of loci is more effective for cultivar identification than more individuals sampled per cultivar. Discriminating power of loci tended to correlate with their variability. The eight loci with greatest discriminatory power within tetraploids were equally successful as 20 loci at identifying the four tetraploid cultivars. The set of markers reported in this study are useful for characterization of switchgrass germplasm and identifying population structure for association studies.     

Genetic diversity and population structure in Jatropha (Jatropha curcas L.) based on molecular markers

Genetic Resources and Crop Evolution - Jatropha (Jatropha curcas L.) is an oleaginous potential, howetever, some studies report that there is low genetic diversity in Brazilian genotypes....     

Development and characterization of microsatellite markers,genetic diversity and population structure analysis in Sapota (Manilkara zapota (L.) P. Royen)

Genetic Resources and Crop Evolution - Manilkara zapota (L.) P. Royen, a widely adapted and popular tree meant for its appetizing fruits in tropics with no genomic resources like microsatellite...     

Genetic diversity and population structure analysis of Grass pea (Lathyrus sativus L.) accessions collected from North-Western Ethiopia using SSR markers

Genetic Resources and Crop Evolution - Grass pea (Lathyrus sativus L.) is a legume crop known to be an excellent source of protein, tolerant to drought, waterlogging, and salinity. The crop is used...     

Genetic diversity and population structure of vegetable soybean (Glycine max (L.) Merr.) in China as revealed by SSR markers

Vegetable soybean is a kind of value-added specialty soybean serving as vegetable or snacks. Understanding the genetic structure of vegetable soybean is a key point for further utilization in breeding programs. In the present study, the genetic structure and diversity of 100 vegetable soybean accessions planted in China was analyzed using 53 simple sequence repeat (SSR) markers. A total of 296 alleles were detected with an average of 5.6 alleles per SSR locus. The polymorphism information content (PIC) values of SSR markers ranged from 0.074 to 0.831, with an average of 0.573. Nei’s genetic distance between accessions ranged from 0 to 0.9434 with an average of 0.6286. These vegetable soybean germplasms could be divided into 8 subgroups based on STRUCTURE analysis, or 11 subgroups based on unweighted pair group method with arithmetic average (UPGMA) cluster. Further comparison showed that the UPGMA subgroups and STRUCTURE subgroups were in fact highly consistent. Germplasms in each classified groups showed great consistency with their origins, seed coat colors or pedigrees. Genetic relationships among germplasm panels that initially came from different geographical regions were also analyzed. Germplasm panels from China Mainland, Taiwan Island and Japan were highly similar to each other with the similarities of over 98 %. Molecular data and cluster analysis also showed that germplasms from China Mainland are more diverse than those from other areas. These results gave us a deep insight into the genetic structure of vegetable soybeans in China and will help us to improve the breeding strategies.     

Analysis of genetic diversity of Ruthenia Medic (Medicago ruthenica (L.) Trautv.) in Inner Mongolia using ISSR and SSR markers

Ruthenia Medic is tolerant to drought, cold, high salinity, resistance to trampling and high quality features. Inter-simple sequence repeat (ISSR) and simple sequence repeat (SSR) molecular markers were employed for the first time to access the genetic diversity and relationships of 30 wild Ruthenia Medic accessions obtained from Inner Mongolia in the present study. A total of 94 bands were amplified by ten ISSR primers, of which 83 (88.5 %) were polymorphic, and 57 polymorphic bands (80.4 %) were observed in 69 bands amplified by ten SSR primers. Shannon’s information index (I = 0.487), and average expected heterozygosis (He = 0.329) generated by ISSR primer were higher than that of SSR analysis (I = 0.372, He = 0.231). The study indicated that ISSR were more effective than SSR markers for assessing the degree of genetic variation of Ruthenia Medic. UPGMA cluster analysis revealed inconsistencies in the clustering patterns, as the Mantel’s test between the dendrograms for ISSR and SSR data indicated a poor fit for the ISSR and SSR data types (r = 0.0970). Whereas the pattern of clustering of the genotypes remained relatively the same in ISSR and combined data of ISSR and SSR. The results of principal components analysis also supports their UPGMA clustering. These results have an important implication for Ruthenia Medic germplasm characterization, improvement, and conservation.     

Analysis of genetic diversity in Turkish sesame (Sesamum indicum L.) populations using RAPD markers⋆

The genetic diversity of 38 cultivated populations of Sesamum indicum L. from four different regions of Turkey was estimated at the DNA level with the random amplified polymorphic DNA (RAPD) technique. Sixty-one bands were obtained for all populations 78% of which were polymorphic. Analysis of molecular variance (AMOVA) was used to investigate the genetic diversity of the populations which yielded highly significant differences among populations within regions (91.9% of the total genetic diversity). According to AMOVA and Shannon's index that were performed separately for each region, the highest value of genetic variation was observed among Northwest region populations (CV = 7.7; H₀ = 0.304) and lowest in the Southeast regions' populations (CV = 2.6; H₀ = 0.068). Nei and Li's similarity index was calculated and phylogenetic tree was established using the neighbor-joining algorithm. This phenetic analysis grouped 35 of 38 accessions in six groups leaving three highly diverse accessions outside. Wagner phylogenetic method was used to assess the phylogenetic relationships among the populations. In the majority-rule consensus tree, only 7 of the 32 forks showed above 60% occurrence. Using Principal Coordinate Analysis (PCO) of the RAPD data set, the groups were clearly separated along the first three axis. These results indicate that RAPD technique is useful for sesame systematics, and should be valuable for the maintenance of germplasm banks and the efficient choice of parents in breeding programs.     

Evaluation of genetic diversity in a Camelina sativa (L.) Crantz collection using microsatellite markers and biochemical traits

A genomic DNA library enriched with GA/TC repeats from Camelina sativa variety Calena has been analysed. After sequencing of about 200 randomly selected clones, approximately 60 % of them showed to contain simple or compound microsatellites with a high number of repeats. Among all microsatellite markers analysed 15 primer pairs amplified polymorphic fragments. Forty C. sativa accessions of different origin were genotyped with 15 microsatellite markers that generated 134 alleles with an average of 8.93 alleles per locus. The observed heterozygosity (Ho) among the accessions ranged from 0.0 to 0.15 with an average of 0.0370, whereas the average of expected heterozygosity (He) among accessions was 0.2769. The analysis of the average total heterozygosity (H_T = 0.651), the intrapopulation genetic diversity (H_S = 0.260), the interpopulation genetic diversity (D_ST = 0.391) and the coefficient of genetic differentiation among populations (G_ST = 0.574) demonstrated that 57.4 % of the genetic diversity is among the accessions, while 42.6 % resides within them. Phylogenetic tree of the 40 C. sativa accessions was constructed based on Nei’s genetic distance. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram shows, except for CAM108 and CAM170, a clear discrimination among C. sativa accessions grouping them in five subgroups. ANOVA analysis indicates significant differences in some biochemical and agronomic parameters among the C. sativa accessions grouped according to Nei’s genetic distance. The result of the Tukey HSD test demonstrated that the A4 subgroup showed a significant higher TWS and linoleic acid (LA) content, while the subgroup A1 showed a significant higher linolenic and lower LA content compared to the remaining groups.     

Population genetic diversity and genetic affinity analyses of sweet orange cultivars (Citrus sinensis (L.) Osbeck) by using IRAP molecular markers

Genetic Resources and Crop Evolution - Citrus plants are one of the most important fruit plants which are consumed all over the world. The breeding of these valuable fruit plants is based on...