Estimation of phenotypic divergence in a collection of <Emphasis Type="Italic">Capsicum</Emphasis> species for yield-related traits

Phenotypic divergence among the 24 accessions belonging to a collection of six species of Capsicum from different geoclimatic regions available in field gene bank of CIMAP, Lucknow, India, was quantified by multivariate analysis for 12 quantitative and qualitative traits. Based on their values, all 24 accessions were grouped into six clusters such that the genetic stocks within cluster had smaller D ² values among themselves than those belonging to different clusters. The accessions of Capsicum annuum were distributed in different clusters in morphotyping representing different species, suggesting that taxonomic characteristics are not always related to agronomic traits. No parallelism/association was found between geographical and phenotypic diversity. Accessions 15 and 23 (clusters V and VI, respectively) had distinct identity. The three characteristics that played the greatest role in differentiation were fruit diameter, number of fruits per plant, and leaf diameter, which can be utilized as conventional/morphological markers for the improvement of chilli yield and obtaining good segregants in chilli breeding programs.     

Phylogenetic relationships in the genus Arachis based on seed protein profiles

Summary Seed protein profiles of 19 accessions representing seven sections of the genus Arachis were studied using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The general profile showed appreciable homology between these taxa, supporting their classification based on morphology and cross-compatibility relationships. The accessions of section Arachis expressed a high variation confirming inferences from earlier studies. Variation between accessions of a species is limited. Accessions of the section Ambinervosae and Caulorhizae formed one cluster and accessions of sect. Erectoides and Procumbensae formed another. Whereas the representative accessions of sect. Triseminalae and Extranervosae formed two independent clusters. Using the percentage of dissimilarity in electrophoretic bands as a statistical genetic distance between accessions, sect. Arachis (containing the cultivated groundnut, A. hypogaea) is phylogenetically closest to sect. Erectoides followed by Procumbensae, Ambinervosae, Caulorhizae, Triseminalae and Extranervosae, respectively.Submitted as Journal Article No. 1485 by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru, A.P. 502 324, India.     

Molecular characterization of South and East Asian melon, Cucumis melo L., and the origin of Group Conomon var. makuwa and var. conomon revealed by RAPD analysis

The genetic diversity and relationship among South and East Asian melon Cucumis melo L. were studied by using RAPD analysis of 69 accessions of melon from India, Myanmar, China, Korea, and Japan. The genetic diversity was large in India, and quite small in Group Conomon var. makuwa and var. conomon from East Asia, clearly indicating a decrease in genetic variation from India toward the east. Cluster analysis based on genetic distance classified 17 groups of accessions into two major clusters: cluster I comprising 12 groups of accessions from India and Myanmar and cluster II that included five groups of accessions of Group Conomon var. makuwa and var. conomon from East Asia. Cluster I was further divided into three subclusters, of which subclusters Ib and Ic included small- and large-seed type populations, respectively. Therefore, this division was based on their seed size, not cultivation area. The large-seed type from east India was differently included in the subcluster of small-seed type (Ib). A total of 122 plants of 69 accessions were classified into three major clusters and subclusters: clusters I and II comprised melon accessions mostly from India and Myanmar, and cluster III comprised Group Conomon var. makuwa and var. conomon from East Asia. The frequency of large- and small-seed types was different between clusters I and II, also indicating genetic differentiation between large- and small-seed types. One plant of the small-seed type from east India was differently included in cluster III, and two plants from east India were classified into subcluster IV. These results clearly showed that South Asian melon is genetically differentiated by their seed size, and that small-seed type melon in east India is closely related to Group Conomon var. makuwa and var. conomon.     

Genetic diversity of Indian Jatropha species as revealed by morphological and ISSR markers

The selection of Jatropha based on morphological information and molecular markers is essential as it is more reliable and consistent. Hence, twelve Jatropha accessions from different geographical areas of India were screened for genetic diversity using 19 morphological traits and 21 ISSR primers. The analysis of morphological traits grouped the accessions into five clusters. The cluster I consisted of J. curcas (CJC 18), J. curcas (CJC 20), J. curcas (CJC 22), J. curcas (CJC21), and J. curcas (CJC 25), and contained the maximum number of accessions; clusters II and IV contained the minimum number of accessions. Among all the characters, the highest range was exhibited by plant height and the least value by the number of branches. The twenty-one ISSR primers generated 156 polymorphic alleles. The average number of ISSR alleles generated was 7.47 per primer. The ISSR primer UBC 884 was highly informative with the maximum of 12 alleles. The 12 genotypes were grouped into eight clusters. The cluster I contained the maximum number of accessions, namely J. curcas (CJC 18), J. curcas (CJC 20), J. curcas (CJC 22), J. curcas (CJC21), and J. curcas (CJC 25). The clusters II, III, IV, V, VI, VII, and VIII (J. tanjorensis, J. gossypiifolia, J. glandulifera, J. podagrica, J. ramanadensis J. villosa, and J. integerrima) contained the minimum number of accessions. Maximum diversity between J. villosa and J. integerrima was noticed and the least diversity between J. curcas (CJC21) and J. curcas (CJC 25) seen because the ISSR markers differentiated the Jatropha accession into a wide genetic diversity as compared to the morphological data. The species-specific diagnostic markers identified in the study such as 1000 bp alleles for J. glandulifera by the primer UBC 826 is suitable for discriminating species of Jatropha, and thus can be used for identifying a Jatropha species from any mixed population comprising other members of the Jatropha complex.     

Initial screening of chili and sweet pepper germplasm for resistance to chili thrips, Scirtothrips dorsalis Hood

Summary A preliminary evaluation for resistance to chili thrips, Scirtothrips dorsalis Hood of 41 and 194 pepper (Capsicum annuum L.) germplasms during 1987 and 1988, respectively, indicated chili accessions may be a promising source of resistance. In contrast, all sweet pepper accessions tested were highly susceptible. A number of chili accessions produced a moderate yield, in spite of a high thrips infestation indicating tolerance to S. dorsalis. Rating for thrips damage was more reliable and efficient than estimating thrips numbers in screening pepper accessions for resistance to thrips. Highly significant, positive correlation between ratings at the seedling stage and final rating for thrips damage indicated the feasibility of screening pepper accessions at the seedling stage. Comparing the similarities in rating among accessions resulted in 40 distinct groups. The variance-covariance matrix of the data from these 40 groups was subjected to principal component analysis. This accounted for 56 and 18 per cent of the variation across the two principal axes, respectively. Projection of chili and sweet pepper accessions along these two axes revealed three distinct clusters. About 80 per cent of chili accessions formed the first cluster, 58 per cent of the sweet pepper accessions formed the second cluster and a third cluster exhibited intermediate ratings for thrips damage. The significance of these findings in relation to geographical divergence and resistance to thrips among pepper accessions is discussed.     

Phylogenetic relationships as in Ocimum revealed by RAPD markers

Genetic relationships were examined among thirty germplasm accessions belonging to five Ocimum species using RAPD markers. A very high degree of polymorphism (98.20%) was observed. UPGMA cluster analysis of genetic similarity indices grouped all the accessions into two major clusters corresponding to previously reported botanical sections. Intra-clustering within the two clusters precisely grouped the accessions belonging to one species in one sub-cluster as expected from their genetic background. Our results show that RAPD technique is a sensitive, precise and efficient tool for genomic analysis in Ocimum species, that may be useful in future studies, by assigning new unclassified germplasm accessions to specific taxonomic groups and reclassifying previously classified accessions of other Ocimum species by traditional criteria on a more objective basis. This revised version was published online in August 2006 with corrections to the Cover Date.     

Multivariate Analysis in Relation to Genetic Improvement in Lavender,Lavandula officinalis Chaix*

Forty-three genotypes of lavender, Lavandula officinalis Chaix, comprising 20 parental stocks including variety ‘Karlovo’, and 23 promising clones were subjected to genetic divergence analysis by Mahalanobis D² statistics. All the clones were grouped in 12 clusters. Intracluster D² was highest for cluster × followed by cluster IX and I. Highest intercluster D² value was observed between cluster VII and IX. Major emphasis was given to including Sher-i-Kashmir, B 10, E 2, A3 and one from each cluster I, II, V, VII, VIII and × for polycross for maximum chance of transgressive segregants of practical utility.     

Inter and intra-population variability of <Emphasis Type="Italic">Jatropha curcas</Emphasis> (L.) characterized by RAPD and ISSR markers and development of population-specific SCAR markers

Jatropha curcas (Euphorbiaceae) is an oil-bearing species with multiple uses and considerable potential as a bioenergy crop. The present investigation has been undertaken to assess the extent of genetic diversity in a representative set of 42 accessions of J. curcas encompassing different crop growing regions in India along with a non-toxic genotype from Mexico as a prelude for utilization of promising and genetically divergent materials in the breeding programmes. Molecular polymorphism was 42.0% with 400 RAPD primers and 33.5% with 100 ISSR primers between accessions indicating modest levels of genetic variation in the Indian germplasm. The within-population variation based on RAPD polymorphism was 64.0% and was on par with the inter-population variation. Polymorphic ISSR markers have been identified that could differentiate the Indian accessions from the Mexican genotype and two of them were converted to SCAR markers. The SCAR primer pair ISPJ1 amplified a 543 bp fragment in all the Indian populations, while ISPJ2 with a specific amplicon of 1,096 bp was specific to the Mexican genotype. Population-specific bands have been identified for the accession from Kerala (2 RAPD markers), Neemuch-1 from Rajasthan (1 each of RAPD and ISSR markers) and the non-toxic genotype from Mexico (17 RAPD and 4 ISSR markers), which serve as diagnostic markers in genotyping. The study indicates an immediate need for widening the genetic base of J. curcas germplasm through introduction of accessions with broader geographical background.     

Genotype-Environment Interactions and Stability Analysis for Herbage and Seed Yields of Forage Peas Under Rainfed Conditions

Twenty-five genotypes of forage peas (Pisum sativum L.) were evaluated under rainfed conditions for two years at four locations in Syria and one in Lebanon. Since local climatic variation is significant, each location in each year was treated as a separate environment, to give ten environments. Genotype-environment interactions (GXE) were analysed using linear regression techniques. There was considerable variation in herbage and seed yields within both genotypes and environments. Genotype-environment interactions were present for both herbage and seed yields; a large proportion of these interactions was accounted for by the linear regression. Although the non-linear component was also significant, its magnitude was smaller than that of the linear component. The highest and most stable herbage yields were obtained from accessions 46/61, 135/175, 3211/323, 99/103 and 88/335. The highest and most stable seed yields were produced by accessions 4/166, 2428/240, 424/242 and 88/335. Accession 88/335 from Germany, F.R. was the only genotype to combine high herbage and seed yields with wide adaptation and stability and could thus be considered the most widely adapted genotype. Other stable genotypes were identified as suitable for poor environments. Yield of the locally collected genotype, though often high, was found to be unstable. The importance of genotype-environment interactions in future breeding strategies is discussed.     

Adaptation and yield stability of selected lines of Lathyrus spp. under rainfed conditions in West Asia

Summary Sixteen promising lines (selections) of Lathyrus spp. (chicklings), comprising 11 L. sativus, four L. ochrus, and one L. cicera, were evaluated under rainfed conditions in Syria. Two locations in each of four years were treated as separate environments, to give eight environments altogether. Genotype x environment (G×E) interactions were analysed using linear regression.There was considerable variation in herbage and seed yields within both lines and environments. Genotype x environment interactions were present for both herbage and seed yields; a little over half was accounted for by the linear regression. The non-linear component was also significant, although it was smaller than that of the linear component.The most stable herbage and seed yields were obtained from L. sativus. Two selections, 347 and 311, origmating from Syria and Turkey respectively, combined both high herbage and seed yields with wide adaptation and stability, and could be considered the most widely adapted lines. Other lines were identified as suitable for favourable and unfavourable environments; in particular, all four lines of L. ochrus have great potential in frost-free climates. The importance of genotype x environment interactions in future breeding strategies is discussed.     

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.     

Random amplified polymorphic DNA (RAPD) variation in Fagopyrum tataricum Gaertn. accessions from China and the Himalayan region

The diversity among 52 landraces and cultivars of tartary buckwheat (Fagopyrum tataricum Gaertn.) and one accession of its wild ancestor, F. tataricum ssp. potanini Batalin, from diverse geographic origins was examined using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) markers. Eighteen primers produced a total of 240 fragments, of which 153 (63.75%) were monomorphic and 87 (36.25%) polymorphic bands. UPGMA-based pairwise Jaccard’s coefficient of similarity was used to deduce the relationships among 53 genetically diverse accessions. The similarity between cultivated tartary buckwheat accessions ranged from 0.61 to 1.00. Four distinct clusters were formed which corresponded well with the geographic distribution of the tartary buckwheat. Nepalese accessions showed maximum diversity followed by Chinese accessions. Tartary buckwheat accessions from the Himalayan region of northwestern India revealed a narrow gene pool. The wild buckwheat accession did not group with any of the three cultivated tartary buckwheat groups, and formed its own single-entry group. Genetic similarity (0.59) of Chinese buckwheat accessions with the wild ancestor reaffirmed that cultivated tartary buckwheat originated in the Yunnan province of northwestern China. Consistent with some earlier reports, our study demonstrated the usefulness of the RAPD technique for the characterization of plant genetic resources and assessment of diversity between species. This revised version was published online in August 2006 with corrections to the Cover Date.     

Pod and seed traits in candidate plus trees of Pongamia pinnata (L.) Pierre from southern peninsular India in relation to provenance variation and genetic variability

Provenance variation and genetic variability in pod and seed traits were carried out with 232 candidate plus trees of Pongamia pinnata collected from selected agro-ecological zones of southern peninsular India during February–March 2008 to 2010. Significant variation (P < 0.01) for pod and seed traits across zones and provenances within zones was recorded. The southern dry and transition zone of Karnataka showed the highest mean value for all the pod and seed traits. A significant negative (P < 0.05) correlation and positive correlation was recorded for latitude with 100-seed weight and seed germination, respectively. Altitude positively correlated with 100-pod weight and negatively correlated with oil content. Phenotypic co-efficient of variation was higher than the genotypic co-efficient of variation indicating the influence of environment. Central dry zone and eastern dry zone of Karnataka showed high heritability and genetic advance for 100-pod weight, 100-seed weight, and seed germination. Positive significant (P < 0.05) genotypic correlation of co-efficient was recorded between seed thickness and oil content (0.211). Germination percentage showed significant positive correlation with seed weight and oil content. Path analysis revealed that seed thickness contributed directly to oil content (0.272). Based on D² analysis, pongamia accessions could be grouped into seven clusters. Maximum diverse Clusters I and VII were identified based on inter-cluster distance (40.19). Thus on the basis of the present findings, it might be suggested that accessions from these clusters could be most suitably used for hybridization and in situ germplasm conservation.     

Molecular Analysis of Local Potato Cultivars from Tenerife Island Using Microsatellite Markers

We have used 19 SSR markers to fingerprint 41 local potato cultivars from 10 locations of Tenerife Island. These varieties represent relicts of the early introductions originating from South America and have been characterised previously morphologically and ecophysiologically. The SSR primers generated a varying degree of polymorphisms. A total of 67 alleles were observed, 12 of them were present in all cultivars. Several accession and group specific alleles were detected. Similarity coefficients were computed from the molecular data and cluster analyses were performed. Generally, cultivar groups with identical or related common names showed the same SSR patterns or clustered closely together. According to the molecular patterns misleading or confounded names were evident for four accessions. The dendrogram clusters were generally in good agreement with previous classifications of the accessions as Solanum tuberosum subsp. andigena, S. tuberosum subsp. tuberosum and Solanum chaucha genotypes. However in four cases the molecular patterns showed discrepancies with previous species assignments suggesting the need for a more detailed and comparative study of these accessions.     

Genetic distance between Triticum timopheevi Zhuk., T. aramticum Jakubz. and T. aestivum L.

The genetic distances between two cultivated wheat (Triticum aestivum L.) varieties (Martonvásári 9, Martonvásári 15), a Martonvásári 9 line possessing the crossability gene krl, and 21 accessions of T. timopheevi Zhuk. and T. araraticum Jakubz. were estimated, based on agro-morphological, physiological and biochemical analysis of data. Cluster analysis based on Mahalanobis' D² values was applied. All 21 accessions of T. timopheevi and T. araraticum could be classified into eight clusters. Clusters I and II consisted of all the T. timopheevi, while T. araraticum was located in six clusters. Discriminant analysis was applied to test significant differences between cluster pairs. The genetic distance (GD) based on the electrophoretic data of gliadins indicated two types of electrophoregrams in T. timopheevvi, distinguished as groups A and B. T. araraticum accessions were variable as regards the spectra. Mean, minimum and maximum GD were estimated within and between different wheat groups based on acid polyacrylamide gel electrophoresis.     

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.     

Population genetic structure of the clonal plant Zingiber zerumbet (L.) Smith (Zingiberaceae), a wild relative of cultivated ginger, and its response to Pythium aphanidermatum

Zingiber zerumbet (L) Smith, a wild clonal species related to the cultivated ginger (Zingiber officinale Roscoe), is a potential resistance donor for soft rot disease in ginger caused by Pythium aphanidermatum (Edson) Fitzp. In this study we evaluated the genetic diversity and P. aphanidermatum resistance of 74 Z. zerumbet accessions belonging to 15 populations from eight districts in Kerala state, India. The disease index (DI) of the accessions varied from 0% to 72.24% and the accessions could be separated into six frequency classes according to their DI values. More than 65% of the accessions had a DI < 20%. Eight accessions were found to be immune to the infection. The relative frequency of resistant accessions was higher in the central and northern regions of Kerala. Amplified fragment length polymorphism (AFLP) analysis of Z. zerumbet accessions using five primer combinations yielded 215 bands in total, of which 175 (81.4%) were polymorphic. Nei’s genetic diversity (h) of 0.2738 and Shannon information index (I) of 0.4012 revealed a high genetic diversity in Z. zerumbet unexpected for a clonal species. In the UPGMA dendrogram, accessions were clustered mostly according to their geographical origin and no clear correspondence was observed between the clustering pattern of accessions and their responses to Pythium aphanidermatum. The study revealed high genetic diversity and variability for pathogen resistance among Z. zerumbet accessions and confirmed the value of Z. zerumbet as a potential donor for soft rot resistance for the genetic improvement of ginger.