Genetic diversity in Lima bean (Phaseolus lunatus L.) as revealed by RAPD markers

The genetic variability of 46 accessions of the Lima bean (P. lunatus L.) including 16 wild forms and 30 landraces belonging to the three cultigroups Big lima, Sieva, Potato, and their intermediates, was evaluated using RAPD (Random amplified polymorphic DNA) markers. Twelve oligonucleotide primers produced 172 RAPD markers which allowed the differentiation of two main groups: the mesoamerican and the andean groups. This was confirmed by an AMOVA analysis which indicated that 37.7% of the variation was found between these two groups. For each botanical form (wild and cultivated), the molecular markers showed that small-seeded types (i.e. Sieva and Potato types and their related wild forms) had a wide distribution (from Mexico to Argentina) while the large-seeded types (Big lima type and its related wild forms) were circumscribed to the narrow west-coastal region from Ecuador to Bolivia. The results are in favour of an independent domestication process within the two groups, as the differentiation between mesoamerican and andean accessions was found to occur in both wild forms and landraces. Within each of the two main groups, wild forms and landraces were also found to be genetically differentiated and higher genetic diversity was observed among landraces than among wild forms. Within the mesoamerican landraces, low but significant differentiation between the Sieva and Potato cultigroups was observed. Some suggestions and hypotheses are discussed about evolution of the two small-seeded types. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular diversity and genome-wide linkage disequilibrium patterns in a worldwide collection of <Emphasis Type="Italic">Oryza sativa</Emphasis> and its wild relatives

Genetic diversity analysis within a species is vital for understanding evolutionary processes at the population and genomic levels. We report a detailed study of molecular diversity, polymorphism and linkage disequilibrium in three groups of rice (Oryza) germplasm accessions based on 176 SSR markers. The first group included 65 rice (O. sativa L.) accessions introduced from seven countries, including five regions of China. The second group included 58 US rice varieties released in the past 25 years. The third group consisted of 54 accessions of rice wild relatives represented by ten different species. The number of alleles per SSR marker ranged from 4 to 32 with a mean of 16 alleles and the polymorphism information content values ranged from 0.43 to 0.91 with a mean of 0.70. The variation in SSR alleles was a significant contribution to the genetic discrimination of the 177 accessions within the three Oryza groups. Analysis of molecular variance identified deviation from Hardy–Weinberg equilibrium. Principal coordinates analysis clearly separated the accessions into their respective three groups. Neighbor-joining phylogenetic cluster reflects the ordination of each accession. Linkage disequilibrium (D′) averaged 0.75 in wild Oryza spp., and about 0.5 in both US and international O. sativa accessions. Our results showed that LD among adjacent loci in both O. sativa and Oryza spp. accessions is strong enough to be detecting marker-trait association via genome-wide scans.     

Geographical differentiation of Asian taro, Colacasia esculenta (L.) Schott, detected by RAPD and isozyme analyses

Geographical differentiation and phylogenetic relationships of Asian taros, Colocasia esculenta (L.) Schott, and related species were analyzed by random amplified polymorphic DNA (RAPD) and isozymes of 13 enzyme systems with special interest in the accessions from the Yunnan area of China, which supposedly has served the secondary center of taro diversification and dispersal into the temperate Far East Asia. The RAPD analysis was found to be better suited for detecting genetic differences within taros and among its related species. However, both RAPD and isozyme analyses estimated quite similar genetic relationships within taros and between related species. Genetic differentiation was evident in the taro accessions of Nepal, Yunnan and other Asian areas; but, phylogenetic relationships between the differentiated taro groups were not clearly determined. When taro cultivation was introduced to a new area, only a small fraction of genetic variability in heterogeneous taro populations was transferred possibly causing random differentiation among locally adapted taro populations. Some of the Yunnan and Japanese accessions were found to be direct descendants of the common triploid population. Further analysis on taros from the eastern China and Korea is necessary to clarify the Yunnan's role in taro diversification and dispersal. The significant local differentiation in Asian taros was clearly demonstrated by RAPD and isozyme analyses in this study, and the results of this study will serve as a base to establish evolutionary and genetic relationships among Asian taros. This revised version was published online in August 2006 with corrections to the Cover Date.     

Geographic distribution of variation in quantitative traits in a world lentil collection

Summary In a world lentil collection the distribution of variation amongst accessions from 13 major lentil-producing countries was examined on the basis of nine quantitative morphological characters by discriminant analysis and canonical analysis. Stepwise discriminant analysis revealed major differences between accessions from different countries. Three major regional groups were apparent: 1) a levantine group (Egypt, Jordan, Lebanon and Syria, 2) a more northern group composed of Greece, Iran, Turkey, and USSR, and 3) accessions from India and Ethiopia with strikingly similar quantitative morphological characters. Misclassifications of individuals within groups were frequent. Characters useful in discriminating between accessions from different countries were in descending order of importance: time to maturity, lowest pod height and 100-seed weight. The regional grouping indicates the importance of local adaptation through clusters of associated characters with phenological adaptation to the ecological environment as the major evolutionary force in the species.     

Evaluation of genetic variation in Lachenalia bulbifera (Hyacinthaceae) using RAPDs

RAPD (randomly amplified polymorphic DNA) analyses were carried out on 21 accessions of Lachenalia bulbifera (Cyrillo) Engl. Five pre-selected primers produced an average of 88% polymorphisms. Fifteen of the 21 accessions could be identified using the five primers. In a pairwise comparison genetic distance values ranging from 0.11 to 1.08 were obtained. These values reveal a high amount of variation within the species. The genetic distance values within the tetraploid and hexaploid groups on the south coast were low, but values were high between the groups on the south coast and those on the west coast. A dendogram was constructed from the RAPD banding profiles, using UPGM cluster analysis. The dendogram clusters certain accessions together. These clusters are supported by their geographical locality and chromosome data. The hexaploid group, tetraploid group and octoploid group on the south coast are respectively clustered together. It is concluded that RAPDs can be used to assess the genetic variation at an intra-specific level in Lachenalia. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity of wild coffee (Coffea arabica L.) using molecular markers

Genetic diversity was studied using RAPD markers among119 coffee (Coffea arabica L.) individuals representing 88 accessions derived from spontaneous and subspontaneous trees in Ethiopia, the primary centre of species diversity, six cultivars grown locally in Ethiopia, and two accessions derived from the genetic populations Typica and Bourbon, spread in the 18^th century, which gave rise to the most currently grown cultivars. Twenty-nine polymorphic fragments were used to calculate a similarity index and construct dendrograms. The Ethiopian material was separated from the Typica- and Bourbon-derived accessions and classified in four groups: one with most of the collected material from southwestern Ethiopia and three from southern and southeastern Ethiopia. Almost all detected diversity was found in the southwestern group while the southern and southeastern groups presented only 59% of identified markers. The genetic distances were low between the southwestern group and the southern and southeastern groups, and between the southwestern group and the Typica- and Bourbon-derived accessions. The cultivated coffee derived from the genetic populations Typica and Bourbon appeared little differentiated from wild coffee growing in the southwest. The results supported the hypothesis that southwestern Ethiopian coffee trees could have been introduced recently in the south and southeast. A separate analysis of the 80accessions classified in the southwestern group allowed identifying particular spontaneous- and subspontaneous-derived accessions and redundancies in the collected material from southwestern Ethiopia. RAPD markers did not detect any within-collection polymorphism except for two trees that were identified as off-types in the CATIE field genebank. This revised version was published online in July 2006 with corrections to the Cover Date.     

Intra- and inter-population variations in grain protein percentage in wild tetraploid wheat,Triticum turgidum var. dicoccoides

Summary Grain protein percentage (GPP) was studied in 910 accessions of the wild tetraploid wheat, Triticum turgidum var. dicoccoides, collected from 22 populations representing different ecogeographical conditions in Israel. High values of GPP were found, ranging from 19.7% to 28.0% for population means, and from 14.1% to 35.1% for single accessions. Marginal populations had usually lower GPP and smaller intra-population variation than central ones. Repeated sampling of some central populations for four consecutive years revealed relatively large intra-population fluctuations. A high and significant genetic component of variation was found within and between populations by a nested analysis of variance in two nurseries. However, the regression coefficients of parents vs. offsprings were relatively low, indicating a smaller genetic component of variation which may be accounted for by a significant genotype × environment interaction. No correlation was found between GPP and ecological factors, except for soil type: accessions growing on terra-rossa had higher GPP than those growing on basaltic soil. Accessions with black glumes, or with glabrous auricles, or with large grains exhibited high GPP values. A strategy for collecting accessions with high GPP is presented, and the potential use of high GPP genotypes in breeding programs is discussed.     

Pathogenic variation in, sources of, and breeding for resistance to Phaeoisariopsis griseola causing angular leaf spot in common bean

If we are to breed common bean (Phaseolus vulgaris L.) for durable resistance to diseases, we must understand pathogenic variation and find sources of resistance. Our first objective was to determine the patterns of pathogenic variation found among isolates of Phaeoisariopsis griseola (PG), the fungus that causes angular leaf spot (ALS) in common bean. We characterized 433 PG isolates from 11 Latin American and 10 African countries, using differential cultivars, isozymes, and/or random amplified polymorphic DNA (RAPD) markers. We also systematically screened, for ALS resistance, common bean accessions from the world collection held at CIAT, and assessed the progress so far made in breeding for resistance to ALS. Despite their great diversity within and between countries on both continents, the PG isolates were classified into two major groups: Andean, and Middle American. Although each group had internal differences for virulence, and biochemical and molecular characteristics, the ‘Andean’ PG isolates were more virulent on common beans of Andean origin, than on those of Middle American origin, thus, suggesting a host-pathogen co-evolution. The ‘Middle American’ PG isolates, although more virulent on common beans from Middle America, also attacked Andean beans, thus, exhibiting a much broader virulence spectrum. To find sources of resistance, we tested 22,832 common bean accessions against naturally occurring PG isolates in the field at CIAT's Experiment Station, Quilichao, Colombia, between 1985 and 1992. The resulting 123 intermediate (scores of 4 to 6) and resistant (scores of 1 to 3) accessions were then tested in the greenhouse against selected 14 PG isolates of diverse origins. Nineteen accessions were intermediate or resistant to at least 13 of 14 PG isolates. Similarly, of 13,219 bred lines tested in the field between 1978 and 1996, 89 were intermediate or resistant. Of these, 33 bred lines proved intermediate or resistant to at least eight of nine PG isolates to which they were challenged in the greenhouse. We suggest that, to breed for durable resistance to ALS, common bean populations should be developed from crosses between Andean and Middle American gene pools. The populations should then be systematically evaluated and selected against the broadest range of the most virulent PG isolates of diverse evolutionary origins. This revised version was published online in August 2006 with corrections to the Cover Date.     

Variation among maize (Zea mays L.) accessions of Bendel State,Nigeria. Multivariate analysis of agronomic data

Summary Two multivariate techniques were used to characterize 30 maize accessions collected from three ecological zones of Bendel State, Nigeria. Differentiation of the 30 accessions into five distinct groups was achieved with the unweighted variable group method of the average linkage cluster analysis of 34 agronomic characters. Four of the taxonomic groups contained at least three accessions each, while a fifth group contained only one. The single accession contained in the fifth group was characterised by very early maturity, deeply pigmented leaves and ear husks and short statured plants. Clustering of the accessions into different phenetic groups followed substantially along geographical and traditionally trading routes. A few cases of overlapping of accessions from different geographical locations were obtained.Principal component analysis revealed that days to 50% tasseling and silking, number of nodes/plant, ear length, ear weight, leaf width, and kernel colour were the principal discriminatory characters that differentiated the accessions. Sixty-four percent of the total variation among the 34 characters were accounted for by the first five principal components while the first and second components accounted for 26 and 14 respectively.     

利用SSR标记分析野生小豆及其近缘野生植物的遗传多样性

利用28对SSR引物对96份野生小豆资源、小豆近缘野生植物及栽培小豆品种进行遗传多样性分析,共检测到255个等位变异,平均每对SSR引物9.10个,多态信息含量的变异范围从0.374到0.865,平均为0.722。野生小豆材料和近缘植物Vigna minima遗传变异丰富。来自不同地域的野生小豆材料具有大量特异等位变异,基于非加权成组配对算术平均法的聚类分析可将不同地理来源的野生小豆单独分群,且与主坐标分析的结果相一致。4份栽培小豆材料与日本野生小豆遗传距离较近,表明目前国内小豆育种中较多使用了含有日本血缘的小豆材料,以及国内野生小豆资源的搜集和利用工作落后于日本。本研究对国内野生小豆资源的搜集和保存具有指导意义,并可以为这些资源的评价、利用和优异基因的发掘提供参考。     

应用SSR标记对小豆种质资源的遗传多样性分析

利用24对SSR引物对158份栽培小豆及18份野生小豆资源进行遗传多样性分析。结果表明,栽培小豆的遗传变异水平显著低于野生小豆,其中18对引物在栽培小豆中能检测到多态性,平均等位变异数为3.0个,21对引物在野生小豆中能检测到多态性,平均等位变异数为2.6个。栽培小豆种质间平均遗传相似性系数为0.724,野生小豆间为0.605。基于类平均法的聚类分析可以将栽培小豆和野生小豆区分开,这与主坐标分析的结果基本吻合。不同来源的栽培小豆群体间也有一定的遗传分化。SSR分析不仅验证了小豆品种间的遗传背景与其系谱来源相吻合,而且揭示了同名种质天津红小豆之间的遗传差异。本研究为我国小豆种质资源育种及SSR标记在小豆多样性分析、基因标记、品种鉴定等工作提供了信息。     

Diversity in selected wild and cultivated species of pigeonpea using RFLP of mtDNA

Diversity in 28 accessions representing 12 species of the genus, Cajanus arranged in 6 sections including 5 accessions of the cultivated species, C. cajan, and 4 species of the genus Rhyncosia available in the germplasm collection at ICRISAT was assessed using RFLP with maize mtDNA probes. Cluster analysis of the Southern blot hybridization data with 3 restriction enzymes – 3 probe combinations placed the genus Rhyncosia in a major group well separated from all the species belonging to the genus Cajanus. Within the genus Cajanus, the 4 accessions of C. platycarpus belonging to section Rhynchosoides formed a separate group in contrast to those in other sections of pigeonpea. In the section, Cajanus all the 5 accessions of C. cajan were grouped together and C. cajanifolius belonging to the same section was in a subgroup by itself closer to the main group. The four accessions of C. scarabaeoides, were together and the other species belonging to section Cantharospermum were in different subgroups. The intra-specific variation was seen even within accessions of certain pigeonpea wild species such as C. scarabaeoides, C. platycarpus, C. acutifolius, and even the cultivated species of C. cajan. This study suggests that RFLP of mtDNA can be used for the diversity analysis of pigeonpea and it gives some indications on the maternal lineage among the species. The variations in the mitochondrial DNA hybridization patterns also suggest the extensive rearrangement of the organelle genome among the Cajanus species. This revised version was published online in July 2006 with corrections to the Cover Date.     

Characterization, diversity, and relationships of the Spanish striped (Listada) eggplants: a model for the enhancement and protection of local heirlooms

Spanish striped eggplants (Solanum melongena L.) are generally known as Listada. Among them, the most internationally renowned is the Listada de Gandía heirloom. Enhancement and legal protection of these local materials requires the analysis of their characteristics, diversity and relationships with similar accessions. We performed a morphological, agronomic and molecular (amplified fragment length polymorphism; AFLP) characterization of 33 eggplant accessions, which included 20 Striped accessions, of which nine were Spanish (five Listada de Gandía and four of Other Spanish Listada), 11 non-Spanish (six of Non-Spanish Listada and five of Other Non-Spanish Striped) and 13 Non-Striped accessions. The Striped accessions presented a range of morphological, agronomic and genetic diversity comparable to the one observed in the Non-Striped accessions. Multivariate PCA (morphological) and PCoA (molecular) analyzes group together the Listada accessions, and clearly separate the three Listada subgroups (Listada de Gandía, Other Spanish Listada and Non-Spanish Listada). On the other hand, the Other Non-Spanish Striped accessions are closer to Non-Striped than to Listada accessions. Listada eggplants, as well as each of their subgroups, are characterized by a syndrome of morphological traits that allows distinguishing them from other accessions. Furthermore, AFLP markers which allow distinguishing Listada accessions and the Listada de Gandía heirloom have been found. The agronomic characterization shows that despite the low diversity within Listada de Gandía group, it is possible to select accessions with improved agronomic performance. The results obtained have important implications for the conservation, improvement and legal protection of Spanish striped eggplants, and in particular of the Listada de Gandía heirloom. The methodology and approaches used may provide a model for the enhancement and protection of other vegetable crops heirlooms.     

Comparison of yield based drought tolerance indices in improved varieties, genetic stocks and landraces of potato (Solanum tuberosum L.)

Drought strongly influences potato (Solanum tuberosum) production and quality. Potato being a drought susceptible crop, the development of varieties with enhanced tolerance to water stress could highly improve productivity in drought prone areas. The objective of this study was to evaluate the ability of several yield based indices to be used in large scale screening for drought tolerance. The experiment included improved varieties, genetic stocks and landraces potatoes grown under drought and irrigated conditions. A group of accessions with high yield under both conditions was identified. Mean productivity (MP), geometric mean productivity (GMP), tolerance (TOL), drought tolerance index (DTI), drought susceptible index (DSI) and yield stability index (YSI) were calculated from tuber yield under drought and irrigated conditions. The relationships between these indices and yield were analyzed. The Fleiss’ Kappa concordance test was used to analyze the correspondence between accessions previously identified as highly productive under both drought and irrigated conditions and accessions with optimal values for the different indices. MP, GMP and DTI allowed identifying genotypes combining high yield potential and high yield under drought within the three subsets of genotypes. Conversely, DSI, YSI and TOL showed low and variable concordance values across subsets, suggesting that their efficiency in screening genotypes highly depends on the nature of the tested genetic material.     

Evaluation of the genetic diversity among elite tea (Camellia sinensis var. sinensis) accessions using RAPD markers

The diversity of 27 superior tea (Camellia sinensis var. sinensis) accessions from Korea, Japan and Taiwan was examined with RAPD-PCR (Random Amplified Polymorphic DNA Polymerase Chain Reaction) markers. Out of the 50 primers screened, 17 primers generated 58 polymorphic and reproducible bands. A minimum of 3 primers was sufficient to distinguish all the 27 accessions studied. The Shannon's index used to partition diversity into inter- and intra-group, revealed that 71 percent of variability resided within groups and 29 percent between groups. Diversity was greatest within the Korean group followed by Taiwan and Japan. The relatively high diversity observed in Korea might reflect the larger genetic base of its plantations while the low diversity in Japan could be explained by the long and intensive tea selection programme in this country. A dendrogram based on the UPGMA-link method using Jaccard's distances and multivariate Factorial correspondence analysis clustered the tea accessions into two main groups, regrouping the Taiwan cultivars on the one side and the Korean and Japanese accessions on the other side. This suggests that the Taiwan tea studied here may have a different origin from that of Korea and Japan. This revised version was published online in July 2006 with corrections to the Cover Date.     

Nuclear RFLP between pepper cultivars (Capsicum annuum L.)

Summary Forty one nuclear probes, distributed across the different linkage groups of the previously published map, were used to examine restrition fragment length polymorphism between cultivated peppers. Total DNA from thirteen accessions of Capsicum annuum var. annuum and one accession of C. baccatum var. pendulum was separately cut with ten restriction enzymes. The analyses were restricted to only one enzyme per probe to reduce the polymorphism redundancy. Nei & Li's genetic distances between accessions were calculated from the 141 resultant nuclear DNA restriction fragments. The genetic variation was larger between C. annuum and C. baccatum than between C. annuum cultivars. Large fruited related accessions closely clustered together. Distances between the small fruited cultivars were larger than within the bell pepper group. A correspondence analysis performed on differences between the global RFLP patterns of each accessions of C. annuum revealed the particular genomic structure of four small fruited cultivars: Criollo de Morelos 334, H3, Perennial and Doux Long des Landes. The percentage of probes revealing at least one RFLP with at least one enzyme ranged from zero to fifty percent for all the pairwise comparisons of C. annuum accessions. 82 presumptive loci were detected with a mean number of 1.46 alleles per locus within C. annuum and 1.83 within all the accessions. This result indicates that molecular markers will be more usable in intraspecific study of C. annuum than isozyme markers.     

Reactions of Hordeum spontaneum to infection with two cultures of Puccinia hordei from Israel and United States

Summary The reactions to infection with two cultures of Puccinia hordei were determined for 292 Hordeum spontaneum (syn. H. vulgare ssp. spontaneum) accessions, collected at 16 sites which encompassed the ecological range of H. spontaneum in Israel. Culture Tel-Aviv was from Israel and culture 57.19 was from the United States. Fifty-two percent of the accessions were resistant to culture Tel-Aviv and 67% were resistant to culture 57.19. Forty-three percent of the accessions were resistant to both cultures. The average infection type (IT) of accessions within sites ranged from 2.7 to 7.5 on a 0–9 rating scale. The results showed that the presence of Ornithogalum species, the alternate hosts of P. hordei, may increase the percentage of H. spontaneoum accessions resistant to P. hordei. More accessions were resistant at sites where humidity at 1400 was higher, the annual evaporation was lower, and where the glumes were shorter. Kernel weight and annual rainfall was not correlated with resistance. A lower percentage of H. spontaneum accessions were resistant to P. hordei culture Tel-Aviv from Israel than to culture 57.19 from the United States. In a previous study a lower percentage of H. spontaneum accessions also was found to be resistant to a culture of Erysiphe graminis hordei from Israel than to cultures from other countries. Previous studies also have shown that cultures of P. hordei and E. graminis hordei from Israel have many genes for virulence on barley, and that H. spontaneum accessions from Israel have many genes for resistance to these two pathogens. Previous results and the results reported in this paper support the hypothesis of coevolution of resistant host genes and virulent pathogen genes where hosts and pathogens have coexisted for many thousand years.     

The nature of Solanum × chaucha Juz. et Buk., a triploid cultivated potato of the South American Andes

Summary The variation in Solanum × chaucha Juz. et Buk. (2n=3x=36) was studied using 114 accessions from the Potato Collection maintained by the International Potato Center. These accession represented less than 5% of the collection originally screened for ploidy. Twenty morphological characters of the tubers, inflorescences and leaves were scored. The accessions were grouped into 20 morphotypes on the basis of the tuber characters. Two-qualitative characters, red-anther tip and sky-blue flowers were diagnostic of 4 morphotypes, but the variation of the quantitative characters overlapped among morphotypes, and were of limited value. Electrophoretic separation of tuber proteins in 7.5% polyacrylamide gels generally confirmed the morphotype groupings. It is concluded that each of the morphotypes represents a single genotype, and these are named according to the International Code of Nomenclature for Cultivated Plants. The variation within S. × chaucha apparently has been restricted by its hybrid origin.