Multivariate Analysis of Diversity of Tetraploid Wheat Germplasm from Ethiopia

The variability of 2420 plants of tetraploid (2n = 4x = 28, AABB genome) wheat germplasm representing 121 accessions from Ethiopia were evaluated for 23 agro-morphological traits at Debre Zeit Agricultural Research Center area, Akaki substation, during the 2003 main season using multivariate methods. This enabled to assess the extent and pattern of variation of the germplasm with respect to regions, altitude classes and species and to identify the major traits contributing to the diversity. The first three and two principal components explained about 83 and 80% of the total variance among regions and altitudinal class, respectively. In the first principal component plant height, days to heading, the length and density of the spike, and kernel color were the most important traits contributing to variation that explained about 50% of regional variance. Cluster analysis grouped the accessions into 15 clusters, with 9 accessions remaining ungrouped. Based on the observed patterns of variation, it is concluded that there exists great variation in the germplasm, which provides opportunities to be utilized for genetic improvement.     

Multivariate analysis of morphological variation in sorghum (Sorghum bicolor (L.) Moench) germplasm from Ethiopia and Eritrea

Multivariate methods, including principal component, cluster and discriminant analyses, were used to assess the patterns of morphological variation and to group 415 sorghum accessions for 15 quantitative characters. The first five principal components explained 79% of the total variation with plant height and days to 50% flowering being the most important characters in the first principal component. Cluster analysis grouped the accessions into ten clusters. A greater proportion of accessions of similar adaptation zones and accessions from regions of origin with similar agro-climatic conditions were grouped together. Moreover, discrimination of accessions was more pronounced when discriminant analysis was based on zone of adaptation rather than regions of origin. Based on the observed patterns of variation, it is concluded that the morphological variation in the material studied is structured by environmental factors. The implications of the results for plant breeding and germplasm conservation programmes arediscussed.     

Evaluation of phenotypic variation in a worldwide germplasm collection of safflower (<Emphasis Type="Italic">Carthamus tinctorius</Emphasis> L.) grown under organic farming conditions in Germany

An investigation was conducted to determine the extent of diversity and relationships among a worldwide safflower (Carthamus tinctorius L.) germplasm collection and to find out adapted accessions that can be used in an organic safflower breeding program in Germany. A total of 468 accessions was studied under organic farming conditions at Kleinhohenheim experimental station during the seasons of 2004 and 2005. All the accessions were evaluated for 12 phenotypic traits and three rated diseases. Multivariate analyses have been used to measure the diversity in a subset of 200 accessions and 11 geographical regions. Generally, the study showed that there was a large genetic variation within accessions. A coefficient of variation (CV%) for investigated traits and diseases ranged from 2.9 to 91.0% with the highest CV was recorded for yield/m2, yield/plant and seeds/plant. The most accessions that originated in Europe revealed relatively better performance compared to non-Europeans. High yielding, early maturing, and disease tolerant accessions were identified. However, the low oil content (8.7–22.8%) is the primary concern in this germplasm collection. The degree of heritability varied between 10% for lodging to 86% for plant height. Genotypic coefficient of correlation (r _g) was slightly higher for many traits than the respective phenotypic coefficient. Oil content and seed yield/m2 were highly significantly correlated (r _g = 0.78). The genotypic coefficient of correlation showed that selection for seeds/plant and thousand kernel weight was effective for improvement of seed yield and oil content. The results of the principal component analysis and the clustering pattern of accessions were consistent with the results of analysis of variance. About 78% of the total phenotypic diversity in the germplasm was explained on the basis of four principal components and 88% of the total variation among geographical regions was contributed by the first three principal components. The distribution of the accessions within clusters has no apparent relationship with the geographical origin. However, many of the European accessions have a tendency to stay together.     

Characterization of a landrace collection for Tomàtiga de Ramellet (Solanum lycopersicum L.) from the Balearic Islands

Tomàtiga de Ramellet (Ramellet) is a traditional long-storage tomato from the Mediterranean Islands of Mallorca, Menorca, Eivissa (Ibiza), and Formentera (Balearic Islands). To investigate the observed phenotypic and shelf life variability within local varieties, we studied 142 accessions characterized as Ramellet varieties, and 29 accessions representing other local varieties. The 171 accessions constitute a new germplasm collection at the University of Balearic Islands (UIB). The evaluation of the collection demonstrated wide variability in most agronomic, morphological and quality traits of Ramellet accessions and clearly differentiates them from other local varieties with respect to fruit shape, size, fruit composition, and fruit storage. All accessions of Ramellet evaluated have the ripening mutation alcobaça (alc), suggesting an important role for this variant in controlling shelf life. Results of evaluation also showed wide variability between the Ramellet accessions for storage time, suggesting that other traits like fruit size and composition may play a role in fruit conservation. Observed variation within the Ramellet accessions is consistent with a genetically variable population or landrace group. The establishment of this collection will help prevent genetic erosion of this local landrace group and constitute a resource for future investigation and breeding.     

Genetic Diversity in Tef [<Emphasis Type="Italic">Eragrostis tef</Emphasis> (Zucc.) Trotter] Germplasm

One hundred and forty-four heterogeneous tef germplasm accessions collected from 10 major tef growing areas in Ethiopia were evaluated for 18 quantitative traits in a simple lattice design, at Holetta and Ginchi, in 2001 main growing season to study the genetic diversity in tef. The combined analysis of variance revealed the presence of significant variation among germplasm accessions for all traits studied. Cluster analysis revealed the overlapping of the germplasm accessions from different origin and the accessions were grouped into eight distinct clusters of 1–78. Generalized distance square confirmed the presence of significant genetic distance between clusters. In principal component (Prin) analysis, the first four principal components with latent root values above one accounted for about 80.6% of the variability existing among the germplasm accessions. Prin1 constituted about 55% of the variability mainly from almost equal contribution of 10 quantitative traits, indicating that most of the traits are equally important in tef diversity. In this study, the regions and altitudes of origin were not found to have a substantial effect on the genetic diversity in tef germplasm. Diversity within the regions was found to be significant and, hence, an opportunity for exploitation in tef improvement.     

Extent and Pattern of Genetic Diversity for Morpho-agronomic Traits in Ethiopian Highland Pulse Landraces: I. Field Pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.)

An experiment was conducted in 2001 at Holetta and Kulumsa, Ethiopia, to study the extent and pattern of genetic diversity in Ethiopian field pea (Pisum sativum L.) landraces. One hundred forty-eight germplasm accessions were grown in an alpha lattice design with 2 replications. Data on 12 traits were collected and analyzed. Differences among the accessions were significant for most of the traits (except number of seeds/ pod) at each location even though differences pooled over location were mostly non-significant. The accessions were grouped into five clusters of different sizes. Accessions from the southern part of the country (Arsi) distributed overall clusters while those from the northern half (North and South Wello, North Gonder and North Shewa) fell into clusters C₁ to C₃. Cumulative effects of a number of characters dictated differentiation of the accessions into clusters. There was no definite relationship between geographic diversity and genetic diversity as overlapping was encountered in clustering pattern among accessions from different parts of the country. Accessions from different regions might have similar genetic background and those from the same origin might also have different genetic background. Therefore, geographic diversity should not necessarily be used as an index of genetic diversity and parental selection should be based on a systematic study of genetic diversity in a specific population. Genetic distances among most of the clusters were significant that crosses between parents selected out of them are expected to generate desirable genetic recombination. Selection should also consider the special advantages of each cluster and each accession within a cluster. Future germplasm collection, conservation and breeding efforts should focus not only on inter-regional diversity but also on intra-regional diversity.     

Genetic diversity of cowpea [<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp.] in four West African and USA breeding programs as determined by AFLP analysis

Cowpea is an important grain legume and hay crop of many tropical and subtropical regions, especially in the dry savanna region of West Africa. The cowpea gene pool may be narrow because of a genetic bottleneck during domestication. Genetic variation within specific breeding programs may be further restricted due to breeding methods, ‘founder effects’ and limited exchange of germplasm between breeding programs. Genetic relationships among 60 advanced breeding lines from six breeding programs in West Africa and USA, and 27 landrace accessions from Africa, Asia, and South America were examined using amplified fragment length polymorphism (AFLP) markers with six near infrared fluorescence labeled EcoRI + 3/1bases/MseI + 3/1bases primer sets. A total of 382 bands were scored among the accessions with 207 polymorphic bands (54.2%). Despite a diverse origin, the 87 cowpea accessions shared a minimum 86% genetic similarity. Principal coordinates analysis showed clustering of breeding lines by program origin, indicating lack of genetic diversity compared to potential diversity. Accessions from Asia and the Americas overlapped and were distinct from West African breeding lines, indicating that germplasm from Asia and the Americas have common origins outside West Africa. US and Asian breeding programs could increase genetic variability in their programs substantially by incorporating germplasm from West Africa, while national programs in West Africa should consider introgression of Asian germplasm and germplasm from other parts of Africa into their programs to ensure long-term gains from selection.     

Variation in melon (<Emphasis Type="Italic">Cucumis melo</Emphasis>) landraces adapted to the humid tropics of southern India

We present here the first comprehensive genetic characterization of melon landraces from the humid tropics of southern India. The genetic diversity among 50 melon landraces collected from 3 agro-ecological regions of southern India (6 agro-ecological sub-regions) was assessed by variation at 17 SSR loci, morphological traits of plant habit and fruit, 2 yield-associated traits, pest and disease resistance, biochemical composition (ascorbic acid, carotenoids, titrable acidity) and mineral content (P, K, Fe, Zn). Differences among accessions were observed in plant and fruit traits. Melon germplasm with high titrable acidity, higher than average amounts of mineral content and resistance to Cucumber mosaic virus, Zucchini yellow mosaic virus, powdery mildew (races 1, 2, 3, 5), Fusarium wilt (races 1, 2), Aphis gossypii and leafminer was recorded in the collection. A high level of genetic variability in melon germplasm was suggested by the SSR analysis. Comparative analysis using SSRs of the genetic variability between Indian melons from north, south, and east regions and reference accessions of melon from Spain, France, Japan, Korea, Iraq, Zambia showed regional differentiation between Indian melon accessions and that Indian germplasm was weakly related to the melon accessions from other parts of the world, suggesting that an important portion of the genetic variability found within this melon collection has not been used yet for the development of new cultivars. Additional collections of acidulus melon germplasm should be made in southern India and adequate management of this important genetic resource is clearly a necessity.     

Wild melon diversity in India (Punjab State)

We present here the first comprehensive genetic characterization of wild melon accessions from northern India. The genetic diversity among 43 wild melon accessions collected from the six agro-ecological regions of the Punjab State of India was assessed by measuring variation at 16 Simple Sequence Repeat (SSR) loci, morphological traits of plant habit and fruit morphological traits, two yield-associated traits, root nematode resistance and biochemical composition (ascorbic acid, carotenoids, titrable acidity). Variation among accessions was observed in plant habit and fruit traits and wild melon germplasm with high acidity and elevated carotenoid content and possessing resistance to Meloidogyne incognita was identified in the collection. A high level of genetic variability in wild melon germplasm was suggested by SSR analysis. Comparative analysis using SSRs of the genetic variability between wild melons from the north and other melons from the south and east regions of India and also reference accessions of cultivated melon from Spain, Japan, Korea, Maldives, Iraq and Israel, showed regional differentiation among Indian melon accessions and that Indian germplasm was not closely related to melon accessions from other parts of the world. A highly drought tolerant accession belonging to var. agrestis Naud. was also identified.     

Diversity among landraces of Indian snapmelon (<Emphasis Type="Italic">Cucumis melo</Emphasis> var. <Emphasis Type="Italic">momordica</Emphasis>)

Diversity among 36 snapmelon landraces, collected from 2 agro-ecological regions of India (9 agro-climatic sub-regions), was assayed using RAPD primers, morphological traits of plant habit and fruit, 2 yield-associated traits, pest and disease resistance and biochemical composition (TSS, ascorbic acid, titrable acidity). Typical differences among accessions were observed in plant and fruit characteristics and snapmelon germplasm with high titrable acidity and possessing resistance to downy mildew, Cucumber mosaic virus, Zucchini yellow mosaic virus, Papaya ringspot virus, Aphis gossypii and Meloidogyne incognita was noticed in the collection. RAPD based grouping analysis revealed that Indian snapmelon was rich in genetic variation and region and sub-region approach should be followed across India for acquisition of additional melon landraces. Accessions of var. agrestis and var. momordica clustered together and there was a separate cluster of the accessions of var. reticulatus. Comparative analysis of the genetic variability among Indian snapmelons and an array of previously characterized reference accessions of melon from Spain, Israel, Korea, Japan, Maldives, Iraq, Pakistan and India using SSRs showed that Indian snapmelon germplasm contained a high degree of unique genetic variability which was needed to be preserved to broaden the genetic base of melon germplasm available with the scientific community. N. P. S. Dhillon and Ranjana contributed equally to this work and are considered the first authors.     

Microsatellite based analysis of the genetic structure and diversity of Capsicum chinense in the Neotropics

Capsicum chinense Jacq., one of the five domesticated species of pepper grown in the New World, is a major contributor to both local and international markets and the economy of the Caribbean islands. The planning and implementation of germplasm conservation and breeding programs for the sustainable use of C. chinense genetic resources are hampered by the poor understanding of the genetic structure and diversity of C. chinense in the region. In the present study, the genetic structure, diversity and relatedness of C. chinense germplasm collections within the Caribbean basin and South America were assessed using nuclear microsatellite markers. C. chinense accessions (102) representing seven geographical regions were genotyped using nine polymorphic nuclear microsatellite markers along with 16 accessions representing four other species of Capsicum. The results revealed that the highest genetic diversity (He = 0.58) was found in the Amazon region supporting the postulated center of diversity of C. chinense as the Amazon basin. The cluster analysis resulted in two distinct genetic clusters corresponding to Upper Amazon and Lower Amazon regions, suggesting two independent domestication events or two putative centers of diversity in these regions respectively. The cluster analysis further revealed that populations in Central America and the Caribbean may have been primarily derived from progenitors from Upper Amazon region and later diverged through geographical isolation. Conservation and germplasm collection programs should therefore target these genetically distinct clusters and satellite populations, towards supporting breeding programs to harness heterosis.     

Genetic variation among populations of wild safflower, <Emphasis Type="Italic">Carthamus oxyacanthus</Emphasis> analyzed by agro-morphological traits and ISSR markers

Wild species of safflower, Carthamus oxyacanthus Bieb., is highly crossable with cultivated species, C. tinctorius L. and could be directly exploited in broadening safflower gene pool and improving the crop for biotic and abiotic stress environments. In this study, genetic diversity among accessions of C. oxyacanthus and their relationships with cultivated safflower were evaluated using agro-morphological traits and polymorphic inter-simple sequence repeats (ISSR) markers. Significant variation was observed among accessions particularly for seeds per capitulum, seed yield per plant, harvest index and capitula per plant. Cluster analysis based on agro-morphological traits classified the wild accessions in two groups according to their geographical regions, and separated them from the cultivated genotypes. ISSR marker also revealed a high genetic variation among the accessions, and cluster analysis based on this marker divided genotypes into four groups, with cultivated ones in a separate clade. Genetic variation observed among the wild safflower germplasm at the DNA level was higher than the agro-morphological traits, indicating that ISSR is an effective marker system for detecting diversity among safflower genotypes and their genetic relationships. Accessions of C. oxyacanthus with high genetic relationship to cultivated species could be used for interspecific hybridization in breeding programs of safflower.     

Pattern of genetic variability of <Emphasis Type="Italic">Solanum habrochaites</Emphasis> in its natural area of distribution

The tomato wild relative species Solanum habrochaites (previously known as Lycopersicon hirsutum) is a potential source of novel genes for tomato breeding. It shows resistance to many diseases and pests, cold tolerance and fruit quality traits. This species inhabits the western Andean slopes at high elevations from central Ecuador to central Peru. In this study the genetic variation of S. habrochaites was studied using 91 accessions from the whole range of distribution of this species. To this end, we employed two kinds of markers: 9 SSRs and 6 AFLP combinations. The Principal Coordinate Analysis based on AFLP data showed the existence of clinal genetic variation from north to south. The accessions of the different geographic groups were sequentially arranged in the first axis from north to south and a clear separation between them was found. The groups from the centre of the area of distribution showed the highest variation and heterozygosis. The ones from the margins showed lower variability and presented higher homozygosis. The morphotypes typicum and glabratum considered by Müller constituted the extreme forms of the continuous variation in the pubescence grade. These differences in pubescence were not associated with the homozygosis grade.     

Spatial and temporal genetic analyses of Ethiopian barley (Hordeum vulgare L.) landraces reveal the absence of a distinct population structure

Ethiopia is known for its wide topographically induced variation that favours a large amount of plant genetic diversity, and determination of the genetic structure of the germplasm is a crucial step towards exploiting this variation. Accordingly, a study was initiated to determine population structure patterns based on spatial and temporal factors and thereby establish group accessions depending on genetic similarity. To achieve this goal, 15 simple sequence repeats (SSRs) were used for 199 barley landraces collected from ten administrative regions of Ethiopia. The analysis of the spatial genetic structure was performed on the entire data set and on two groups created based on the year of collection. The results obtained from the model-based Bayesian clustering revealed 16 unstructured groups. Furthermore, the grouping of the accessions based on SSR markers resulted in hierarchical chain-type clusters with most of the accessions in the first cluster. The spatial correlations between the genetic and geographical distances revealed a weak population structure for the entire data set, and a weak temporal population structure was also observed for the barley populations from the recent collection. In general, the results indicated the absence of a distinct and consistent population structure among the regions, which could be presumed because of high gene flow. These findings will facilitate parent selection in order to broaden the genetic base of modern cultivars via breeding efforts and also provide information for the planning of an efficient germplasm collection strategy.     

Simple sequence repeats marker polymorphism in emmer wheat (<Emphasis Type="Italic">Triticum dicoccon</Emphasis> Schrank): Analysis of genetic diversity and differentiation

Genetic diversity was investigated in 73 accessions of emmer wheat (Triticum dicoccon Schrank) from 11 geographical regions using a set of 29 simple-sequence repeat (SSR or microsatellite) markers, representing at least two markers for each chromosome. The SSR primers amplified a total of 357 different alleles with an average of 12.31 alleles per locus. The number of fragments detected by each primer ranged between 6 (Xgwm1066) and 21 (Xgwm268). Null alleles were detected in nine of the 29 primers used. A high level of gene diversity index was observed. Across the 29 primers, gene diversity ranged from 0.60 (Xgwm46) to 0.94 (Xgwm655), with a mean of 0.82. There was a highly significant correlation (r=0.882; p<0.01) between gene diversity index and the number of loci, showing the number of loci per se is a strong indicator of diversity. Analysis of genetic diversity within and among eleven geographical regions revealed most of the genetic diversity of the total sample resided within regions. The coefficient of gene differentiation (Gst = 0.27) showed that the genetic variation within and among the 11 geographical regions was 73 and 27%, respectively. High value of mean number of alleles per locus was found in Iran (4.86) followed by Morocco (4.10) and Armenia (4.03). On the contrary, lower mean number of alleles per locus was detected in Yemen (2.83). The average gene diversity index across regions ranged from 0.52 (Slovakia) to 0.67 (Morocco) with an average of 0.60. Multivariate techniques of principal component analysis and clustering were employed to examine genetic relationship among the 73 emmer wheat accessions vis-à-vis geographical regions of collections. The genetic distance coefficients for all possible 55 pairs of regional comparisons ranged from 0.63 (between Iran and Armenia, Georgia and Azerbaijan, Georgia and Slovakia) to 0.97 (between Morocco and Yemen, Spain and Georgia, and Turkey and Iran) with a mean of 0.82. From the PCA results, a two dimensional plot of PC1 versus PC2 was constructed. The scatter plot of the first two principal components which explained altogether 27% of the total variation depicted the presence of a clear pattern of geographical differentiation except in few cases like accessions from Caucasian region. Similar pattern of genetic relationships among accessions was observed in cluster analysis. The study provided genetic information of emmer wheat in relation to geographical regions of origin. The information could be utilized in crop improvement, germplasm conservation programs, and in further investigation.     

Genetic basis of long shelf life and variability into Penjar tomato

Penjar tomato is a varietal type cultivated in northeast Spain that characteristically has a long shelf life, small fruit, and wide morphological variability among cultivars. To determine the genetic basis for the long shelf life in the Penjar varietal type and to describe the genetic background and agromorphologic characteristics of the group, we studied 27 Penjar accessions representative of the entire range of variation in traits related to agronomic behavior, fruit morphology, and sensory quality. We found that the long shelf life of Penjar (mean: 126.8 days) is due to the ripening mutant alcobaça (alc), and the molecular basis of this mutation is the replacement of thymine by adenine in position 317 of the coding sequence of the NAC.NOR gene; thus, alcobaça (alc) is an allele of non-ripening (nor). The amplified fragment length polymorphism (AFLP) study found 18.07% polymorphic loci within the Penjar varietal type, which is higher than usual in landraces. The variation in agronomic and morphologic traits between accessions was also very high; thus, the heterogeneity of the Penjar group probably results from the introduction of the allele alc in distinct landraces. Our results also show that in germplasm containing the alc mutation shelf life is negatively correlated with fruit size (weight, width, length, and number of locules); thus, the predominance of small fruit within the varietal type is probably the result of this trait being dragged along in the selection for long shelf life.     

Analysis of genetic variability in <Emphasis Type="Italic">Couepia</Emphasis> accessions using AFLP markers

Couepia is a genus distributed in tropical regions of America. The nut of some Couepia species is used as fresh fruit and oil source for local communities. Despite its critical situation of conservation and its economic potential, there is a lack of information on the genetic variability of Couepia species. This study examines AFLP variation among 40 accessions of Couepia collected in the Colombian Amazonian region, representing two species: Couepia dolichopoda and Couepia subcordata. The individuals were examined for 96 markers generated from four EcoRI/MseI primer pairs, with 80% polymorphism across all accessions studied. According to cluster analysis, 40 accessions were grouped into two major clusters, corresponding to the two species analyzed, except one case whose situation is discussed. In C. dolichopoda accessions, significant correlation between the clustering pattern and the geographical origin was detected; the extent of variation within and among its collect sites was examined by AMOVA. The knowledge about the genetic variability of the accessions examined contributes to development of Couepia conservational efforts.     

Morphological and molecular diversity of an underutilized fruit crop - <Emphasis Type="Italic">Cordia myxa</Emphasis> L. germplasm from the arid region of Rajasthan,India

Twenty two germplasm accessions of Cordia myxa were collected from Rajasthan and established at the field gene bank for conservation and evaluation. Morphological characterization of 10 year-old trees for 17 traits indicated wide variations among the accessions tested. Higher number of flowers per cyme was found in accession ACHM11 and higher pulp:stone ratio in AHCM25. Overall, AHCM22 was found to be a superior germplasm line for most of the horticulturally useful traits among the accessions tested as it had higher percent of fruit set, pulp:stone ratio and fruit weight. High significant positive correlation was obtained between leaf, fruit characters and pulp:stone ratio. However, these characters were found to be negatively correlated with number of flowers per cyme. Out of 50 random decamer primers used for random amplification (RAPD), 25 were polymorphic. Average polymorphism resolved by these markers among these accessions was 69.8% with an average polymorphic information content of 0.43. Genetic diversity revealed by Jaccard’s co-efficient was between 0.44 and 0.94, and three major clusters were identified among these accessions by phylogenetic analysis using NTSYSpc-2.02e software. RAPD markers associated with leaf size and pulp:stone ratio were also identified. This study shows the existence of high genetic diversity among these accessions.