Analysis of genetic diversity in Indian taro [Colocasia esculenta (L.) Schott] using random amplified polymorphic DNA (RAPD) markers

Taro [Colocasia esculenta (L.) Schott] germplasm accessions collected from different parts of India were subjected to RAPD (Random Amplified Polymorphic DNA) analysis to assess the genetic diversity prevalent and also to test the genetic basis of morphotypic classification. Thirteen random decamer primers out of the 22 tested were used to analyse 32 taro accessions belonging to 28 morphotypes. Three out of these thirteen primers analysed showed 100 per cent polymorphism. Per cent polymorphism varied from 60 to 100 among the polymorphic primers. High genetic diversity was revealed as the similarity coefficient values ranged from 0.50 to 0.98. No two accessions analysed in the present study showed a similarity coefficient value of one thereby indicating their distinctness and presence of high genetic diversity in Indian taro germplasm. Dendrogram obtained from UPGMA analysis grouped 32 accessions in four clusters and three accessions were placed as outliers. Clustering pattern did not show any strict relationship with geographical distribution, morphotype classification and genotypic diversity. Further, accessions classified, as belonging to the same morphotypic group did not always cluster together. Presence of a very close genepool of the wild, weedy and cultivated forms with extreme levels of phenotypic and genotypic variation is suggested as the reason for high genetic diversity reported. Usefulness of DNA markers such as RAPD in characterising and assessing the genetic diversity in Indian taro germplasm is hereby demonstrated.     

Nature of taro (Colocasia esculenta (L.) Schott) genetic diversity prevalent in a Pacific Ocean island, Vanua Lava, Vanuatu

Taro (Colocasia esculenta (L.) Schott), cultivated in Vêtuboso, a village of northern Vanuatu, Melanesia, was surveyed to: (1) assess the extent of morphological and molecular variation being maintained by growers at the village level and, (2) compare this diversity with the diversity found in the crops in Vanuatu. Ethnobotanical data were combined with AFLP analysis to elucidate possible sources of variation. Folk assessment of variation is based on: (a) morphological characteristics (11 characters), (b) names and (c) classification according to habitat, uses, origin and agronomic adaptation. This 3-fold approach allowed growers to differentiate 96 morphotypes, all of which are given distinct vernacular names. AFLP fingerprints successfully differentiated all these 96 morphotypes which do not present a significant intra-clonal variation. But genetic results showed no clear groupings according to geographic origin or habitat of morphotypes and stated that the diversity found within the village was comparable with the overall diversity found in Vanuatu. Local nomenclature and stories associated with each cultivar suggested three sources of diversity: introductions (38%), somatic mutations (15%) and sexual recombinations (48%). AFLP results confirm folk beliefs about origin at least for three pairs of mutants. The 11 so-called wild forms analysed by AFLP were suggested to be feral, escapes from domestication. A dynamic in situ conservation strategy (DISC), favouring a broadening of the national genetic base, was discussed for taro.     

Quantitative determination of NPK uptake requirements of taro (Colocasia esculenta (L.) Schott)

Taro yield in many parts of the world is stagnant mainly due to conventional blanket recommendation of fertilizers, lower nutrient use efficiency and imbalance in the use of nutrients. The Quantitative Evaluation of Fertility of Tropical Soils (QUEFTS) model was used for determining the region specific balanced NPK uptake requirements and recommendations for a target yield of taro. The constants for minimum and maximum accumulation (kg cormel kg^?1 nutrient) of N (33 and 177), P (212 and 606) and K (25 and 127) were derived as standard model parameters. The results showed that taro requires N, P and K accumulation of 12.97, 2.75 and 17.47?kg t^?1 of cormel yield, suggesting an average NPK ratio in the plant dry matter of about 4.7:1:6.4. The NPK fertilizer requirements for different potential yield situations were also calculated. The results need to be validated in major taro growing regions.     

Diversity of 21 taro (Colocasia esculenta (L.) Schott) accessions of Andaman Islands

The genetic diversity of taro (Colocasia esculenta (L.) Schott.) accessions growing naturally in Andaman Islands was analysed using morphological and DNA markers. Twenty one representative samples of C. esculenta from different parts of Islands in addition to three commercial varieties as reference genotypes were used in study. About 63% phenotypic variation was observed in C. esculenta A total number of 491 amplified fragments were obtained of which 347 showed polymorphic banding patterns. The accessions were grouped into two major clusters with both RAPD and ISSR markers with 56 and 57% diversity, respectively. The reference genotypes were grouped into one group and island population in other cluster. Both marker systems divided population into two sub clusters and showed correlation with morphological parameters. The diversity pattern observed in present study showed rich genetic diversity of C. esculenta in Andaman Islands provided simple strategy for reducing repeatability of taro germplasm in gene banks. The study also suggested pre-evaluation of germplasm using molecular and morphological markers to enhance efficiency of exploration trips.     

Identification and characterization of SSR markers in taro [Colocasia esculenta (L.) Schott] by RAD sequencing

Genetic Resources and Crop Evolution - Taro [Colocasia esculenta (L.) Schott] is an old crop with high genetic diversity. However, the breeding of taro is limited by the lack of well-developed...     

Genetic diversity of taro (Colocasia esculenta (L.) Schott) in Vanuatu (Oceania): an appraisal of the distribution of allelic diversity (DAD) with SSR markers

In Vanuatu, an oceanic archipelago located in south-west Pacific, taro (Colocasia esculenta (L.) Schott) is one of the staple crops. An eco-geographical survey of its genetic resources was conducted in ten villages, each located on a different island. A sample of 344 landraces referred as the National Sample (NS) was collected. Its genetic diversity was assessed using nine microsatellites markers and then was compared with an International Core Sample (ICS) that was previously distributed in the ten villages of the study in order to test the geographical distribution of allelic diversity as an effective mean for the on-farm conservation of root crops. The ICS was composed of 41 accessions, including 23 originating from South-East Asia. The molecular dataset revealed in the NS (1) 324 distinct multilocus genotypes, (2) six genetic clusters mainly differentiated by rare alleles, (3) a geographical structure of the genetic resources of taro based, within each village, on the dominance of one or two of these clusters rather that their exclusivity, and (4) an analogy between the patterns of dominant clusters between villages and the past and present social networks. In addition, accessions from the ICS revealed 52 new alleles. Based on these findings, we formulate hypotheses regarding the processes involved in the genetic diversification of taro in Vanuatu. We also discuss the use of this set of microsatellite markers along with the molecular dataset obtained from this study as effective tools to monitor the diversity and evolution of taro in the future.     

Evaluation and selection of taro [Colocasia esculentra (L.) Schott] accessions under dryland conditions in South Africa

Taro [Colocasia esculenta (L.) Schott] is an important underutilised staple food crop in South Africa, with a lot of potential to address food insecurity among poor rural households. Development of high yielding stable taro cultivars is one of the most important goals of plant breeders. Twenty-nine taro accessions collected from major taro producing regions of the country were evaluated for growth performance, yield potential and stability under dryland conditions at two sites (Umbumbulu and Roodeplaat) in 2013, 2014 and 2015 cropping seasons. The experiment was laid in a randomised complete block design replicated three times. Growth and yield traits were measured. Analysis of variance and correlation analysis was done on all measured traits. The genotype by environment interaction was analysed using additive main effects and multiplicative interaction (AMMI). As a result, significant variation was observed for most of the traits except number of leaves and leaf width as well as number of suckers, while all the traits showed significant variation for location by year interaction. Number of corms showed significant variation for location by year by genotype interaction among all the traits evaluated. Genotype effect was highly significant (p?<?.01) on plant height, corm length, number of corms and significant (p?<?.05) on yield. The significant difference between genotypes for these traits proves that there was a genetic variability and there is a scope for selection. The correlation study also reveals that majority of the characters were positively correlated with each other. Total yield was positively and highly significantly (p?<?.01) correlated with all the measured traits. AMMI was effective in identifying stable genotypes. The top ranking cultivars per environment may be considered for cultivation under the specific environment, the stable cultivars may be considered for cultivation across all the taro growing regions.     

Evaluation of genetic diversity and relationships within an on-farm collection of Perilla frutescens (L.) Britt. using microsatellite markers

The present study demonstrates utilization of 11 microsatellite markers to explore genetic diversity held in Perilla frutescens (L.) Britt. landrace accessions growing on farms in different parts of Korea and Japan and to assess their genetic relationships. All microsatellite loci were polymorphic and produced a total of 96 alleles ranging from 4 to 20, with an average of 8.7 alleles per locus. Of the 96 alleles found, a total of 15 unique landrace-specific alleles were observed at 9 different loci. The locus GBPFM203 provided the highest number of alleles (20), of which five were unique and each specific to a particular landrace accession. The occurrence of unique, accession-specific alleles presented molecular evidence for the generation of new alleles within on-farm collection of Perilla. The mean values of observed (H _O) and expected heterozygosity (H _E) were 0.39 and 0.68, respectively, indicating a considerable amount of polymorphism within this collection. A genetic distance-based phylogeny grouped the two Perilla varieties, var. frutescens and var. crispa (Thunb.) Decne into two distinct groups. Accessions belonging to var. frutescens could also be divided into two subgroups at a close genetic distance (GD = 0.432). The overall clustering pattern did not strictly follow the grouping of accessions according to their geographic origins. These observations are indicative of extensive germplasm exchange among farms from different geographical regions. The genetic similarity observed among the Perilla landraces may be useful for future Perilla crop variety identification, conservation, and improvement programs.     

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.

Genetic and Phenotypic Diversity in Downy-mildew-resistant Sorghum (Sorghum bicolor (L.) Moench) Germplasm

Genetic and phenotypic diversity among randomly selected 36 downy-mildew-resistant sorghum accessions were assessed, the former using 10 simple sequence repeat (SSR) marker loci and the latter using 20 phenotypic traits. The number of alleles (a _j ) at individual loci varied from five to 14 with an average of 8.8 alleles per locus. Nei's gene diversity (H _j ) varied from 0.59 to 0.92 with an average of 0.81 per locus. High gene diversity and allelic richness were observed in races durra caudatum (H _j = 0.76, a _j = 4.3) and guinea caudatum (H _j = 0.76, a _j = 3.8) and in east Africa (H _j = 0.78, a _j = 7.2). The regions were genetically more differentiated than the races as indicated by Wright's F _st. The pattern of SSR-based clustering of accessions was more in accordance with their geographic proximity than with their racial likeness. This clustering pattern matched little with that obtained from phenotypic traits. The inter-accession genetic distance varied from 0.30 to 1.00 with an average of 0.78. Inter-accession phenotypic distance varied from 0.01 to 0.55 with an average of 0.33. Eleven accession-pairs had phenotypic distance of more than 0.50 and genetic distance of more than 0.70. These could be used as potential parents in a sorghum downy mildew resistance-breeding program.     

Genetic Diversity in Accessions of Wild Rice Oryza granulata from South and Southeast Asia

Oryza granulata, an upland wild rice species, represents an unique germplasm for possessing abilities of tolerance to shade and drought, immune to bacterial blight and resistance to brown planthopper. Although low degree of genetic variability has been revealed within its populations, little genetic information at the species level is available in determining rational conservation strategies. Here we used dominant DNA marker random amplified polymorphism DNA (RAPD) to assess the genetic variability among 23 accessions of O. granulata that collected from main distribution areas worldwide. Twenty decamer primers generated a total of 243 bands, with 83.5% of them (203 bands) being polymorphic. Calculation of Shannon index of diversity revealed an average value of 0.42 ± 0.25, indicating that O. granulata maintains a relatively high degree of genetic diversity on the species level. Analysis of genetic dissimilarity (GD) showed that genetic differentiation occurred among studied accessions, which supports the feasibility of current ex situ conservation strategies. We also suggested that information based on population studies, which could be achieved by international co-operation, is needed to conserve this widespread germplasm more effectively.     

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     

Level and Transmission of Genetic Heterozygosity in Apricot (Prunus armeniaca L.) Explored Using Simple Sequence Repeat Markers

In this study, 17 peach simple sequence repeat (SSR) sequences were used in the exploration of the genetic heterozygosity level of several apricot cultivars from Spain, France, Greece, and the USA, and 23 descendants. The genotypes can be classified in three groups as a function of their genetic heterozygosity (1) local cultivars from Murcia (Spain) (‘Gitanos’ and ‘Pepito del Rubio’) and several descendants from crosses among these cultivars, with very low genetic heterozygosities (less than 0.30); (2) cultivars from France and Spain (‘Moniquí’, ‘Currot’ and ‘Bergeron’) and several descendants, with intermediate levels of genetic heterozygosity (around 0.45); and (3) cultivars ‘Orange Red’ and ‘Goldrich’ from North America and ‘Lito’ from Greece, with the remaining descendants, having genetic heterozygosities higher than 0.50. The results showed the high increase of genetic heterozygosity in the case of descendants from complementary crosses. The use of cultivars from North America could increase greatly the genetic heterozygosity in the Spanish apricot breeding programs, enlarging the genetic variability of the local cultivars. On the other hand, in the case of transgressive crosses among local Spanish cultivars, the increase of genetic heterozygosity was much lower.     

Coconut (<Emphasis Type="Italic">Cocos nucifera</Emphasis> L.) DNA studies support the hypothesis of an ancient Austronesian migration from Southeast Asia to America

The centre of origin of coconut extends from Southwest Asia to Melanesia. Nevertheless, its pre-Columbian existence on the Pacific coast of America is attested. This raises questions about how, when and from where coconut reached America. Our molecular marker study relates the pre-Columbian coconuts to coconuts from the Philippines rather than to those of any other Pacific region, especially Polynesia. Such an origin rules out the possibility of natural dissemination by the sea currents. Our findings corroborate the interpretation of a complex of artefacts found in the Bahía de Caraquez (Ecuador) as related to South-East Asian cultures. Coconut thus appears to have been brought by Austronesian seafarers from the Philippines to Ecuador about 2,250 years BP. We discuss the implications of molecular evidence for assessing the possible contribution of early trans-pacific travels to and from America to the dissemination of domesticated plants and animals.     

Genetic Analysis of Egyptian Date (<Emphasis Type="Italic">Phoenix dactylifera</Emphasis> L.) Accessions Using AFLP Markers

Forty-seven samples of date palm (Phoenix dactylifera L.) collected from eight locations in Egypt were studied using four sets of amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. These samples belonged to 21 named accessions and 9 of unknown pedigrees. A total of 350 bands were scored and 233 (66.6%) were polymorphic. Twenty-seven Egyptian accessions and ‘Medjool’and ‘Deglet Noor’accessions from California could beclassified into the major cluster. This major cluster may represent a major group of date palm germplasm in North Africa. There were four other clusters, each containing one or two accessions. The variety ‘Halawy’and one accession of unknown provenance were most likely from hybridization between two clusters. Six groups of accessions of which had the same names, revealed similar but not identical AFLP profiles suggesting these accessions might derive from seedlings rather thanthrough clonal offshoot propagation.     

Identifying and selecting for genetic diversity in Papua New Guinea sweetpotato Ipomoea batatas (L.) Lam. germplasm collected as botanical seed

A total of 141 Ipomoea batatas (L.) Lam. accessionsderived from botanical seed originally collected from 26 sites in 4 Provinces inPapua New Guinea, a secondary center of genetic diversity for sweetpotato, weregenetically analyzed. Two hundred Amplified Fragment Length Polymorphism (AFLP)markers were identified and utilized in the analysis. Relatedness amongaccessions was estimated by analyzing the AFLP data using the Dice coefficientof similarity and UPGMA methods. The molecular analysis revealed relativelylimited genetic diversity within and between sites. Genotypes collected in agiven region often displayed molecular marker variability similar to thatobserved over the entire sampled area. However, a subset of 14 genotypes derivedfrom seed collected from New Ireland island differed from genotypes collected onNew Guinea island. Estimates of genetic diversity-based similarity valuescalculated from the AFLP data indicated a moderate level of diversity (0.767mean coefficient of similarity) across all plant materials analyzed. Threemethods of selection were evaluated for their efficacy in capturing themolecular marker diversity within the plant materials in the form of a subset.They were random, stratified-random (geographic based), and marker-assistedselection (MAS). MAS was the most efficient. A Maximally Diverse Subset (MDS) of12 genotypes capturing 92% of the molecular marker diversity was identified.     

Relationships Among <Emphasis Type="Italic">Brassica napus</Emphasis> (L.) Germplasm from Spain and Great Britain as Determined by RAPD Markers

The genetic diversity and the relationships among a collection of Brassica napus L. European populations were evaluated using random amplified polymorphic DNA markers. The study included 33 accessions of B. napus collected from Galicia (northwestern Spain) and 18 British cultivars, 16 accessions of B. napus and two accessions of Brassica oleracea L. used as controls. DNA from 25 individuals per population was analyzed using 18 decamer primers. One hundred thirty-eight amplification products were scored of which 105 were polymorphic. These bands ranged in size from 350 to 2500 base pairs. Similarity coefficients and cluster analysis were computed and six groups were obtained. Cluster I was the largest and included all the landraces from northwestern Spain, except two accessions that grouped separately into Clusters III and IV, respectively. A low level of genetic variability was detected among the B. napus Spanish genotypes, while considerable diversity was present among the British ones, which grouped into three groups, two main clusters and one group formed by one accession. Cluster II included all commercial varieties grown in Great Britain whereas Cluster V grouped local varieties maintained by the growers for many years. Cluster VI was a singularity formed by one entry. British accessions of B. oleracea had the greatest dissimilarity with all the other populations and grouped separately in Clusters VII and VIII. As conclusion, B. napus landraces used in northwestern Spain as leafy-green vegetable probably have an independent origin from B. napus crops grown in other European regions. Besides, separate domestication in northwestern Spain and Great Britain for a different end use might have led to two distinct gene pools.     

Use of prolamine polymorphism in studying genetic resources of forage grasses

Summary Electrophoresis of single seed prolamines was used for the analysis ofLolium perenne L.,Festuca pratensis Huds., andDactylis glomerata L. populations. Identification and registration of populations was carried out according to the frequencies of occurrence of genotypes with corresponding types of prolamine banding patterns. The publication sums up the problems of applied use of molecular markers for identification and registration of world genetic resources of forage grasses, analysis of the dynamics of population composition and other problems of plant growing, genetics, breeding and seed control. The approaches mentioned in the article are promising for their use in genetic banks as well as at the institutions which store collections of genetic resources of given crops and at universities and breeding stations.