Genetic diversity and structure of Ethiopian,Yemen and Brazilian C<Emphasis Type="Italic">offea arabica</Emphasis> L. accessions using microsatellites markers

Genetic diversity among 115 coffee accessions from the Coffea Germplasm Collection of IAC was assessed using SSR markers. The germplasm represents 73 accessions of Coffea arabica derived from spontaneous and subspontaneous plants in Ethiopia and Eritrea, species center of origin and diversity, 13 commercial cultivars of C. arabica developed by the Breeding Program of IAC, 1 accession of C. arabica cv. ‘Geisha’, 13 accessions of C. arabica from Yemen, 5 accessions of C. eugenioides, 4 accessions of C. racemosa and 6 accessions of C. canephora. Genetic analysis was performed using average number of alleles per locus (A), proportion of polymorphic loci (P), Shannon’s genetic index (H′ and G′_ST) and clustering analysis. All evaluated species were distinguished by a cluster analysis based on Jaccard’s coefficient. Differentiation between the cultivated plants of C. arabica and accessions derived from spontaneous and subspontaneous plants was observed. Spontaneous and subspontaneous accessions from Ethiopia were separated according to the geographical origin: east and west of the Great Rift Valley. Cultivated plants showed a low genetic diversity with a division in two groups: accessions from Yemen (H′=0,028) and Brazilian commercial cultivars (H′=0,030). The results agreed with previously reported narrow genetic basis of cultivated plants of C. arabica and supported the hypotheses about domestication of the species. This study also showed a significant genetic diversity among accessions from Ethiopia and Eritrea present in the Germplasm Collection of IAC. This diversity is specially observed in accessions from Sidamo (H′=0,143), Kaffa (H′=0,142) and Illubabor (H′=0,147) indicating their importance as source of genetic variability for coffee breeding programs.     

RAPD Polymorphism of the White-Flowered Gourd (Lagenaria siceraria (Molina) Standl. Landraces and its Wild Relatives in Kenya

The present study was performed to investigate genetic diversity of Kenyan landraces of the white-flowered gourd (Lagenaria siceraria), which exhibits tremendous morphological variation. RAPD analyses were performed on 53 landraces of the cultivated species L. siceraria and 42 accessions of three wild species (40 L. sphaerica, 1 L. abyssinica, and 1 L. breviflora). A total of 432 polymorphic bands were detected using 54 primers. The four species were clearly differentiated from one another. Intra-specific variations were investigated with L. siceraria and its wild relative L. sphaerica. Landraces of the cultivated species collected from different ethnic communities or regions were differentiated. Morphological variations were not associated with RAPD variations. Bitter landraces collected in Maasai communities showed two specific RAPD bands. In the wild species, accessions collected from the eastern and western sides of the Great Rift Valley were genetically differentiated from each other. In both species, genetic and geographical distance matrices computed among all pairs of accessions were significantly correlated, implying that the observed geographical variation can be explained by the 'Isolation by distance model'. Progeny plants derived from a common mother in L. siceraria showed a low level of segregation in RAPD pattern, suggesting that collected landraces are cultivated, maintaining their inherent traits although they are monoecious and insect-pollinated, whereas the wild relative L. sphaerica showed a higher level of segregation. The morphological diversity observed among landraces of L. siceraria is the result of human selection and their genetic identities are maintained by inbreeding probably resulting from frequent self-pollination.     

Genetic variability of Coffea arabica L. accessions from Ethiopia evaluated with RAPDs

The genetic diversity of 50 wild and semi-wild accessions of the Coffea arabica L. germplasm collection, gathered by the FAO and ORSTOM missions to Ethiopia, and maintained in Colombia by CENICAFE, was evaluated with RAPD markers. The evaluation was carried out in two phases: In phase one, the polymorphism of 8 Ethiopian accessions of different geographic origin, plus the cultivated variety 'Caturra' was assessed with the RAPD technique with forty-two 10-mer oligonucleotides. In phase two, 51 accessions were assessed with a set of 5 polymorphic primers that reproduced, with a correlation of 95%, the groups generated by the 24 polymorphic primers found in phase one. Principal Coordinate Analysis of molecular data revealed that a closely related group consisting of 86% of the Ethiopian C. arabica accessions evaluated are significantly different from the Caturra variety and could be used in a genetic breeding initiative to increase the variability of cultivated varieties. The results also indicate that a larger polymorphism is present in the Colombian replica of FAO Ethiopian coffee germplasm collection than previously reported.     

Use of random amplified DNA markers to analyse genetic variability and relationships of Coffea species

Summary The use of random amplified DNA fragments as genetic markers in Coffea was investigated. Arbitrary oligonucleotides were used as primers to amplify genomic DNA of different coffee accessions representing major Coffea species by polymerase chain reaction. Intraspecific variation was easily detected in C. canephora and C. liberica whereas the primers assayed failed to reveal polymorphism between C. arabica accessions. Extensive interspecific variation was observed. Genetic relationships between Coffea species are deduced from the degrees of similarity in amplified product profiles. Random amplified DNA markers appeared to be of high value for characterization, analysis and utilization of coffee genetic resources.     

Inter Simple Sequence Repeat (ISSR) Analysis of Diploid Coffee Species and Cultivated Coffea arabica L. from Tanzania

Inter simple sequence repeat (ISSR) markers were used to evaluate levels of genetic similarity among Coffea arabica L. accessions from Tanzania and to estimate levels of genetic similarities in C. arabica and diploid coffee species. The six ISSR primers used generated a total of 82 fragments and the dissimilarity values ranged from 0.21 to 1. Mean dissimilarity values between provenances (0.56–0.85) were higher than within provenances (0.37–0.68). Cluster analysis based on Nei’s genetic distances showed C. arabica provenances grouping based on geographical origin. Two major clusters were formed that constituted of provenances from Kilimanjaro and Arusha in one sub-cluster; Tanga and Morogoro in the other; the second cluster had Mbeya provenances and diploid species, respectively. The implication is that Mbeya provenances are different from the rest of Tanzanian C. arabica. A principal coordinate analysis (PCA), whose first three coordinates explained 43% of the variation, showed similar groupings as in the cluster analysis. A separate cluster analysis of diploid species showed a distinct separation of the three species used. ISSR data gave results similar to previous findings from random amplified polymorphic DNA(RAPD) analysis. The results also confirm the limited diversity present in cultivated C. arabica in Tanzania     

Current status of coffee (Coffea arabica L.) genetic resources in Ethiopia: implications for conservation

The aim of this article is to provide an overview of the current situation of coffee genetic resources that are dwindling at an alarming rate in Ethiopia, the centre of diversity of Coffea arabica. Firstly, we describe the coffee growing systems (forest coffee, semi-forest coffee, garden coffee and plantation coffee) and recent research on the genetic diversity of the coffee planting material associated with those systems. Whilst the maximum genetic diversity revealed by DNA-based markers is found in the forest coffees of the south-western highlands, the natural habitat of C. arabica, the taxonomy of coffee landraces is particularly rich in garden coffee systems located in ancient growing zones such as Harerge in eastern Ethiopia. After reviewing the factors involved in the genetic erosion of the Ethiopian genepool, we give an update on the status of coffee genetic resources conserved ex situ in the field genebank of the Jimma Agricultural Research Centre, with 4,780 accessions spread over 10 research stations located in the main production areas, and in the main genebank of the Institute of Biodiversity Conservation located in Choche (Limu) with 5,196 accessions conserved. Lastly, we mention the in situ conservation operations currently being implemented in Ethiopia. Improving our knowledge of the genetic structure of Ethiopian forest and garden coffee tree populations as well as genetic resources conserved ex situ will help to plan the future conservation strategy for that country. To this end, modern tools as DNA-based markers should be used to increase our understanding of coffee genetic diversity and it is proposed, with the support of the international scientific community and donor organizations, to undertake a concerted effort to rescue highly threatened Arabica coffee genetic resources in Ethiopia.

Chloroplast DNA Variation in the Most Primitive Cultivated Diploid Potato Species Solanum stenotomum Juz. et Buk. and its Putative Wild Ancestral Species using High-Resolution Markers

Solanum stenotomum Juz. et Buk. (2n = 2x = 24) is considered to be the most primitive diploid cultivated species from which all the other Andean cultivated potatoes were originated (Hawkes 1990). To disclose chloroplast DNA (ctDNA) variability and the maternal origin of S. stenotomum, 36 accessions of S. stenotomum and 86 accessions of putative wild ancestral species were determined for ctDNA types and analyzed by high-resolution markers (seven ctDNA microsatellites and an H3 marker). High-resolution markers discriminated 57 different ctDNAs (haplotypes), which were classified into the W-type ctDNA group and C-, S- and A-type ctDNA group, and within the latter group S- and A-type ctDNAs were distinct from each other among many different haplotypes mostly having C-type ctDNA. This ctDNA relationship supported our previous findings obtained for mostly Andean cultivated species (Sukhotu et al. 2004). Compared with other putative ancestral wild species, S. stenotomum showed somewhat limited ctDNA diversity, having two major haplotypes 1 and 2 also found in different wild species in different places. Therefore, the ctDNA in S. stenotomum was of at least dual origins either by successive domestication from different species or else by introgression after initial S. stenotomum arose.     

Evaluation of perennial wild <Emphasis Type="Italic">Cicer</Emphasis> species for drought resistance

About 90% of chickpea (Cicer arietinum L.) in the world is grown under rainfed conditions where drought is one of the major constraints limiting its productivity. Unlike the cultivated chickpea, wild Cicer species possesses sources of resistance to multiple stresses; we therefore evaluated perennial wild Cicer species for resistance to drought. C. anatolicum, C. microphyllum, C. montbretii, C. oxydon and C. songaricum were compared with special checks; C. echinospermum, C. pinnatifidum and C. reticulatum and five cultivated chickpeas. After the cultivated chickpeas were killed, accessions were evaluated using a 1–5 scale, where 1 = highly drought resistant (no visible drought effect and full recovery after three successive wiltings) and 5 = highly drought susceptible (leaves and branches dried out, no recovery at all). All accessions of perennial wild Cicer species were significantly superior to those annual wild species and the cultivated chickpeas including the best drought tolerant chickpea, ICC 4958 under drought conditions. Perennial wild Cicer species did not only recover after wilting and drying out above ground level, they also tolerated high temperatures up to 41.8°C. But, they do not cross with the cultivated chickpeas. C. anatolicum should be taken account in long term breeding programs because it has closer affinities to the first crossability group than the others.     

Perennial Wild Relatives of Chickpea as Potential Sources of Resistance to Helicoverpa armigera

The legume pod borer, Helicoverpa armigera (Hübn.), is one of the major constraints to chickpea production, and host plant resistance is an important component for the management of this pest. The levels of resistance in the cultivated chickpea are low to moderate, and therefore, we evaluated 17 accessions of perennial Cicer along with three cultivated chickpea genotypes for resistance to H. armigera. There was a significant reduction in both leaf feeding and larval weights when the larvae were fed on the leaves of Cicer microphyllum Benth. accessions ICC 17146, ICC 17236, ICC 17240, and ICC 17248. Relative resistance index based on leaf feeding, larval survival, and larval weight indicated that C. microphyllum accessions ICC 17146, ICC 17236, ICC 17234, ICC 17240, ICC 17243, and ICC 17248 were highly resistant to H. armigera. Under natural infestation, accessions belonging to C. microphyllum, C. canariense Santos Guerra et Lewis, and C. macracanthum M. Pop suffered a damage rating of <2.0 compared to 4.0 in C. judaicum Boiss. accession ICC 17148 (annual species) and 8.5–9.0 in the cultivated chickpeas (1 = <10% leaf area damaged, and, 9 = >80% leaf area damaged). There was considerable diversity in the accessions belonging to perennial wild species of chickpea, and these can be exploited to increase the levels and diversify the basis of resistance to H. armigera in the cultivated chickpea.     

云南省小粒咖啡种植生态适宜性区划

小粒咖啡产业是云南省发展高原特色农业和精准扶贫的重点内容,开展生态适宜性研究有助于优化布局和扩大规模。基于ArcGIS建立了云南省气候、土壤理化、地形地貌因子精细化空间分布模型,利用层次分析法确定3个层次、11个生态适宜性指标权重,在重点区域进行小粒咖啡种植区生态适宜性分析及区划研究。结果表明:1)气候因子是小粒咖啡种植生态适宜性的关键性因子,地形地貌因子影响其次,土壤理化性质因子的影响最小;最冷月平均气温、2—3月降水量和海拔3项因子对小粒咖啡生态适宜性影响较大,各地在开展种植规划时要重点关注。2)小粒咖啡最适宜、适宜种植区主要分布在云南西南部和东南部,分别占国土面积的18.8%和15.0%,次适宜区占国土面积的21.0%。3)普洱市小粒咖啡适宜性最好,在中部和南部可开展大规模种植;临沧、德宏和保山等地应结合横断山脉的影响,在适宜性高的区域加强规划;西双版纳、文山、红河适宜性条件好,需加强规划和提高投入,充分发挥生态资源优势潜力;大理、怒江以及河谷热区也可以开展小粒咖啡种植,但需注意防范低温和干旱等灾害的影响。4)经采样点调查验证,生态适宜性分析及区划结果准确。云南省仍有较大范围的小粒咖啡种植适宜区,加强适宜种植区的规划布局有助于提高产量和品质,进而提升云南省小粒咖啡产业的国际竞争力。研究方法可以推广至其他高原特色农业品种,为优化选址规划和科学生态布局提供科学依据。     

Sources of winter hardiness in wild lentil

Summary In high altitude areas (> c. 850 m elevation) in west Asia and north Africa, lentil (Lens culinaris) is grown as a spring crop to avoid severe winter cold. But late fall-sown lentil with winter hardiness has higher yield potential in these areas. In this study a total of 245 accessions of wild lentil, 10 of cultivated lentil and three accessions of Vicia montbretii (syn. L. montbretii) were evaluated for winter hardiness in Syria and Turkey during the 1991/92 season. The absolute minimum temperatures were-16°C in Syria and-18.9°C in Turkey and the susceptible indicators were killed at both locations showing that the cold was sufficient for screening. Although winter hardiness was assessed as percentage of survived plants in Syria and as a visual damage rating on a 1–9 scale in Turkey, there was agreement between the winter hardiness ratings with a correlation of r=–0.56, P<0.001. Accessions of L. culinaris ssp. orientalis exhibited the highest level of winter hardiness, on average; whereas accessions of L. nigricans ssp. ervoides were the most susceptible. Correlations revealed that winter hardiness was concentrated among accessions originating from high elevation areas.     

Processes affecting genetic structure and conservation: a case study of wild and cultivated <Emphasis Type="Italic">Brassica rapa</Emphasis>

When planning optimal conservation strategies for wild and cultivated types of a plant species, a number of influencing biological and environmental factors should be considered from the outset. In the present study Brassica rapa was used to illustrate this: to develop Scandinavian conservation strategies for wild and cultivated B. rapa, DNA-marker analysis was performed on 15 cultivated and 17 wild accessions of B. rapa plus 8 accessions of the cross compatible B. napus. The B. rapa cultivars were bred in Sweden and Finland in 1944–1997 and the wild B. rapa material was collected from Denmark, Sweden and United Kingdom. The B. napus accessions were bred within the last 20 years in the Scandinavian countries. Results were based on scoring of 131 polymorphic ISSR markers in the total plant material. A Bayesian Markov chain Monte Carlo (MCMC) approach implemented in NewHybrids demonstrated a clear distinction of B. rapa and B. napus individuals except for three individuals that seemed to be backcrosses. The backcrossed hybrids descended from two Swedish populations, one wild and one escaped. The overall pattern of genetic variation and structure in B. rapa showed that cultivated and wild B. rapa accessions formed two almost separated clusters. Geographical origin and breeding history of cultivars were reflected in these genetic relationships. In addition, wild populations from Denmark and Sweden seemed to be closely related, except for a Swedish population, which seemingly was an escaped cultivar. The study point to that many processes, e.g. spontaneous introgression, naturalisation, breeding and agricultural practise affected the genetic structure of wild and cultivated B. rapa populations.     

Assessing Genetic Diversity of Chinese Cultivated Barley by STS Markers

To assess the genetic diversity among China’s cultivated barley, sequence tagged site (STS) marker analysis was carried out to characterize 109 morphologically distinctive accessions originating from five Chinese eco-geographical zones. Fourteen polymorphic STS markers representing at least one in each chromosome were chosen for the analysis. The 14 STS markers revealed a total of 47 alleles, with an average of 3.36 alleles per locus (range 2–8). The proportion of polymorphic loci per population averaged 0.84 (range 0.71–1.00); the mean gene diversity averaged 0.39 (range 0.28–0.49). The means of P and H_e were highest in the Yangtze reaches and Southern zone (P = 1.00; H_e = 0.46) and lowest (P = 0.71 He = 0.28) in the Yellow river reaches zone. The STS diversity in different zones is quite different from the morphology diversity. The STS variation was partitioned into 17% among the zone and 83% within the zone. Both cluster and principal coordinate analyses clearly separated the accessions into a dispersed group (mostly two-rowed barley with a lower mean GS value) and a concentrated group (mostly six-rowed barley with a higher mean GS value) according to the spike characteristic with only a few exceptions. The accessions from the Qinghai-Tibet plateau formed a distinctive subgroup and can be distinguished from the concentrated group. The role of Tibet in the origin and evolution of cultivated barley has been discussed.     

Preliminary screening and selection for cold tolerance in annual wild <Emphasis Type="Italic">Cicer</Emphasis> species

The study was aimed to select cold tolerant accessions of annual wild Cicer species in the highlands in the west Mediterranean area of Turkey. A total of 43 accessions of eight annual wild Cicer species was screened for cold tolerance and compared with the best cold tolerant cultivars, ILC 8262 and FLIP 93-53C. After the sensitive check, ILC 533, was killed, accessions were evaluated using a 1–9 scale. Three accessions of Cicer bijugum, 2 accessions of Cicer reticulatum and 2 accessions of Cicer echinospermum were highly cold tolerant, while 3 accessions of C. bijugum, 9 accessions of C. reticulatum, 2 accessions of C. echinospermum and 1 accession of Cicer pinnatifidum were cold tolerant. All accessions of Cicer judaicum were sensitive to cold. Whereas Cicer chorassanicum and Cicer cuneatum were killed, Cicer yamashitae was recorded as highly sensitive to cold. The cold tolerant accessions of annual wild Cicer species were superior to the best cultivar as far as hardiness is concerned.     

Distribution of arbuscular mycorrhizal fungi spores in soils of smallholder agroforestry and monocultural coffee systems in southwestern Ethiopia

Arbuscular mycorrhizal fungi (AMF) are associated with the root system of coffee (Coffea arabica L.) plants, but their distribution in smallholder agroforestry and monocultural coffee systems is not well known. This study investigates the spatial distribution of AMF spores in a field study in southwestern Ethiopia. Soil samples from different depths (0–50 cm) were collected under the tree canopies of Acacia abyssinica, Albizia gummifera, Ficus sur, Ficus vasta and randomly selected unshaded coffee plants at different sampling points (canopy base, radius, edge and outside canopy). Significantly higher AMF spore densities were recorded at canopy bases and at 0–30 cm soil depth. Spore populations were found to belong to five genera: Acaulospora, Entrophospora, Glomus, Gigaspora and Scutellospora, with Glomus and Acaulospora dominating. Sampling points, sites and depths, shade tree species and shade tree/coffee plant age affected AMF spore density. Agroforestry practices including the use of leguminous shade trees effectively maintained AMF numbers in soils even at depth compared with unshaded coffee plants (monocultures).     

Inverse Sequence-tagged Repeat (ISTR) Analysis of Genetic Variability in Forest Coffee (Coffea arabica L.) from Ethiopia

Genetic diversity in forest coffee (Coffea arabica L.) was estimated using inverse sequence-tagged repeat (ISTR) markers. One hundred ninety two samples representing 16 populations of C. arabica from four regions of Ethiopia were analyzed with 12 pairs of forward and backward ISTR primer combinations. A total of 144 reproducible bands were generated out of which 37 (25%) were polymorphic and scored as present (1) or absent (0) data matrix. This data was used to compute Jaccard coefficient to estimate genetic variability among all possible pairs of samples. The proportion of polymorphic bands within populations ranged from 19% for Bale-3, to 54% for Walega-2 populations. Un-weighted pair group method with arithmetic mean (UPGMA) based cluster analysis generated two clusters at 56% similarity value. The samples were clustered on the basis of their geographical origin, which could be attributed to a few region specific banding patterns detected. However, within regions most of the samples failed to cluster on the basis of their respective populations, which may be due to the presence of substantial gene flow between local populations in the form of seedlings carried out by farmers. The results may provide information to develop strategies for in situ conservation.     

Following the track of “Híbrido de Timor” origin by cytogenetic and flow cytometry approaches

The supposedly first plant of the coffee cultivar “Híbrido de Timor” (HT) was found in 1927, being denoted as HT CIFC 4106. According to different researchers, this plant originated from a natural interspecific hybridation between Coffea arabica (4x = 44) and Coffea canephora (2x = 22). From HT CIFC 4106, other HT accessions were obtained and employed to establish germplasm banks in some countries. As HT has been widely used in Coffea breeding programs, this study aimed to characterize different HT accessions with regard to ploidy, nuclear DNA content and base composition. Based on these data, the ploidy of HT CIFC 4106 was determined, suggesting that this accession is an allotriploid formed from reduced reproductive cell of C. canephora and of C. arabica. All HT CIFC 4106 plants exhibited the same 2C-value, AT% and chromosome number, showing that vegetative propagation has enabled the multiplication and germplasm conservation of this cytotype since 1927. Further five analyzed HT accessions showed distinct nuclear 2C-value and AT%. Since HT CIFC 4106 has been considered the first HT, it is suggested that aneuploid reproductive cells of this HT originated the other plants. Considering that HT accessions are used in the development of C. arabica cultivars, the findings of this study are important for the design of strategies to obtain new cultivars for breeding programs. Moreover, these data represent the first step to understand the origin and genome evolution of the HT.     

Phylogenetic relationships of Cajanus cajan (L.) Millsp. (pigeonpea) and its wild relatives based on seed protein profiles

Total seed storage protein of 9 accessions of cultivated C. cajan and 10 wild Cajanus species was reported and compared by sodium dodecyl sulphate polyacrylamide gel electrophoresis. A considerable variation was detected among the protein profiles of different accessions of C. cajan while those of wild species were very specific and distinctly different from each other. Relative similarities between various taxa were estimated by Jaccard's similarity index and cluster analysis was performed to produce a UPGMA dendrogram. The clustering of 10 wild species and C. cajan more or less agrees with their sectional classification and available data based on morphological characteristics, crossability, genome pairing in hybrids and nuclear RFLPs. The species closest to C. cajan is C. cajanifolia although the accessions of C. cajan also share some bands present in the profiles of C. scarabaeoides, C. goensis, C. lineatus, C. acutifolius and C. volubilis. This points towards polyphyletic origin of the cultigen which has been discussed in this paper.     

Genetic Diversity of the Vigna Germplasm from Thailand and Neighboring Regions Revealed by AFLP Analysis

Thailand is a center of diversity for section Angulares of the Asian Vigna (genus Vigna subgenus Ceratotropis) and 4 Vigna species are cultivated in Thailand. Using newly collected wild and cultivated germplasm of Vigna from Thailand and outgroup accessions AFLP analysis was conducted to clarify genetic diversity and relationships. The results suggest that cultivated V. umbellata and V. mungo evolved from wild relatives in a single domestication event. Vigna umbellata is poorly differentiated from its wild and weedy relatives compared to V. mungo. Results suggest northern Thailand and the neighboring Shan state, Myanmar, is the probable center of domestication for V. umbellata as wild accessions from this area and cultivated rice bean from a wide area in Asia are not greatly diverged. Vigna minima, V. tenuicaulis and V. exilis accessions in Thailand are well differentiated with considerable intra-specific variation. Vigna hirtella consists of two well differentiated subgroups, suggesting taxonomic revision may be necessary. Close genetic relationships between V. radiata and V. grandiflora, and between V. mungo and V. trinervia are confirmed. Naturally growing V. mungo populations in northern Thailand appear to be true wild species as they are well differentiated from Indian wild and Thai cultivated populations. The origin of naturally growing cowpea in Thailand needs to be further studied using a more comprehensive set of materials. This study clarifies inter and intra-specific genetic diversity and inter species relationships of Thai Vigna species.