Location of genes for high grain protein percentage and other quantitative traits in wild wheat Triticum turgidum var. dicoccoides

Summary The genetic control of grain protein percentage (GPP) in the wild tetraploid wheat, Triticum turgidum var. dicoccoides, was determined by crossing four accessions of this taxonomic variety with durum cultivar Inbar, and analyzing the parents, F₁ and F₂ populations. Reciprocal crosses indicated no cytoplasmic effect on GPP. The F₂ variation was continuous in all crosses, showing no transgressive segregation. However, crosses between different accessions of var. dicoccoides showed transgressive segregation indicating the presence of different genes for high GPP in these accessions. Grain protein percentage was mostly codominant with high GPP, showing either no dominance, or a weak dominance. Heritability coefficients (broad sense) ranged from 0.30 to 0.53. Correlation coefficients between GPP and yield components were usually significantly negative, with the exception of the number of spikelets per spike, and in some crosses, grain weight.The number and chromosomal location of genes coding for high GPP were determined by the association between GPP and 27 markers (23 morphological and 4 biochemical markers). For this purpose, the genetic control of these markers, their linkage groups and chromosomal location were studied. At least four loci for high GPP that segregated in the F₂ populations are suggested: one on chromosome arm 1AS, marked by the black glume gene (Bg); one on 1BS, marked by the HMW gliadin locus Gli-B1; one on group 5, marked by the genes for beaked glume (Bkg) and toothed palea (Tp); and one on group 7, marked by the kinky neck gene (Kn). The relationship between GPP and several yield components was studied in a similar manner. In general, loci of markers that correlated positively with high GPP were not correlated with a decrease in yield components. Moreover, several loci of var. dicoccoides were associated with an increase in yield components.The utilization of markers for chromosomal location of genes coding for quantitative traits is compared to the technique of aneuploid analysis, commonly used in wheat. The significance of the above findings for breeding is discussed.     

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.     

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.     

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.     

Genetic diversity of wheat wild relatives in the Near East detected by AFLP

In order to reveal the molecular genetic diversity of wheat wild relatives, an AFLP analysis was conducted with 16 accessions of five Triticum andAegilops species originating from the Near East. Variation within population was studied with at least seven individuals per accession. Four primer combinations were used for selective amplification. Based on the scored bands, we estimated percentage of polymorphic bands, 1 – proportion of shared bands (1-psb) and nucleotide diversity (π). Of the five species used in this study, Ae. speltoides had the highest level of `within population' variation. This species had also the highest value of the variation among populations. As for Triticum species, the level of variation within population was low in diploid species (T. urartu and T. boeoticum),whereas two tetraploid species (T. dicoccoides and T. araraticum) had relatively high levels of variation within population. While the two diploid Triticum indicated a clear interspecific divergence, the two tetraploid wild wheats were not clearly divergent in this study. The variance portioning analysis indicated that the variation detected for diploid Triticum species was mainly composed of `between species' variation, on the other hand that for tetraploid Triticum was mostly composed of `within population' variation. In conclusion, AFLP analysis reveals molecular variation in all accessions used in this study, suggesting a potential genetic diversity of the wheat wild relatives in natural populations. These results have implications for the design of strategies to maintain genetic diversity within genebank collections. This revised version was published online in August 2006 with corrections to the Cover Date.     

Intraspecific phenotypic variation associated with nuclear DNA content in Lolium perenne L.

The variation in nuclear DNA content and its association with phenotypic traits were examined in 15 cultivated populations of perennial ryegrass (Lolium perenne L.), including herbage and turf populations. Nuclear DNA contents of 15 populations were measured by a flow cytometric method using DAPI (4′-6-diamidino-2-phenylindole) as a fluorochrome. DNA contents were also measured using PI (propidium iodide) for six populations that showed large differences in DAPI values to confirm the difference. There were significant differences in nuclear DNA contents among the populations for both dyes. Of the total variation in nuclear DNA content measured with DAPI, 29% was ascribed to the inter-population variation, 46% was ascribed to the intra-population variation, 24% was ascribed to the random error variation. Herbage populations tended to have larger DNA content than did turf populations. 2C DNA content was positively correlated with cell size, seed size and single leaf size, although significant correlations were mainly due to a small number of populations with large and small DNA contents. These results suggest that intraspecific variation in nuclear DNA content plays important roles in determining phenotypic differences between cultivated populations of L. perenne. This revised version was published online in August 2006 with corrections to the Cover Date.     

The response of Pisum sativum L. germplasm to high concentrations of soil boron

Summary Tolerance to high levels of boron in the soil is an important aspect of the adaptation of crop varieties to southern Australian conditions. This paper reports investigations aimed at exploring the extent of genetic variation in Pisum sativum and at defining appropriate selection criteria for selection for boron tolerance in breeding programs.A collection of 617 accessions of Pisum was screened in controlled conditions and visually assessed for symptoms of boron toxicity. A high proportion of accessions were sensitive with only 3.5% being more tolerant than any of the Australian varieties. Relatively high proportions of tolerant and moderately tolerant accessions originated from Asia and South America.In a second experiment the responses of selected tolerant accessions were evaluated with respect to different parameters. The objectives were to confirm the performance of the putative boron tolerant accessions and identify appropriate parameters for selecting boron tolerant genotypes. In addition to the visual assessment of boron toxicity, measurements at the time of harvest included dry matter yield and concentration of boron in tissues. Symptom expression was highly correlated with dry matter yield and concentration of boron in tissues under high boron conditions and so could be used as a non-destructive selection criteria. A low degree of symptom expression by tolerant accessions could usually be attributed to low levels of boron in the vegetative tissues. The results of this study indicate that considerable genetic variation exists among exotic accessions of Pisum sativum and tolerance to boron could be transferred to sensitive varieties.     

Species relationships in the subgenus Ceratotropis (genus Vigna) as revealed by RAPD analysis

Summary The genetic variation among 23 accessions of 5 species in the subgenus Ceratotropis, genus Vigna, were investigated by random amplified polymorphic DNA (RAPD) analysis. A total of 404 fragments amplified with 24 primers were scored and analyzed by cluster analysis. The accessions used were separated into two main groups with an average of 70% differences. Within the main groups, five subgroups were recognized, which are in complete agreement with taxonomic species. Wild forms were always grouped with their most closely related cultivated forms and they showed variation in each species. The largest intraspecific variation was found in V. radiata (mungbean), in which wild forms (V. radiata var. sublobata) were highly different from each other and from cultivated forms. V. angularis (adzuki bean) showed the least variation and thus, was probably differentiated in relatively recent times.     

Geographical differentiation and diallel analysis of seed dormancy in barley

Seed dormancy is one of the most important parameters affecting the malting process and pre-harvest sprouting in barley (Hordeum vulgare L.). Variation of seed dormancy in 4365 cultivated and 177 wild barley (ssp. spontaneum) accessions derived from different regions of the world was investigated in Okayama University, Kurashiki, Japan. Seed dormancy of each accession was estimated from their germination percentages at 0, 5, 10 and 15 weeks post-harvest after-ripening periods. All of the wild barley accessions showed less than 10% germination at 0 week after-ripening period. Level of seed dormancy in 4365 cultivated barley accessions showed a clear geographical differentiation. Seventy seven percent of Ethiopian accessions showed high germination percentages, while 86% of Japanese, Turkish and North African accessions showed low germination percentages at 0 week after-ripening period. A half diallel cross using eleven barley accessions with different level of dormancy revealed that seed dormancy was predominately controlled by additive gene effects. These results suggest that large genetic diversity for seed dormancy in barley is explained as different levels of additive accumulation of genetic factors. Barley varieties showing appropriate dormancy could be developed by crossing among barley germplasm accessions used in the present study.     

Symbiotic variability in Vicia faba. 3. Genetic effects of host plant,rhizobium strain and of host × strain interaction

Summary Six Vicia faba populations were grown in all possible combinations with six Rhizobium leguminosarum strains in order to estimate the relative importance of the three genetic components of symbiotic variability. Additive genetic effects of host genotype and rhizobium genotype accounted for only 8.9% and 11.8% of the total phenotypic variation. Non-additive variation attriabutable to specific host genotype × rhizobium genotype interactions was by far the largest component of variation and accounted for 73.8% of phenotypic differences. Therefore the greatest improvement in symbiotic nitrogen fixation is likely to arise from simultaneous selection of both symbionts.     

Germplasm diversity and estimate of genetic advance of four morpho-physiological traits in a world collection of jute

Summary To improve jute productivity, locating of sources of suitable quantitative-trait genes in the recently acquired world jute collection was needed. Two hundred sixteen accessions of Corchorus capsularis and 192 accessions of C. olitorius were evaluated at a jute seed research station (87°60\s'E, 23°80\s'N) for four yield and quality linked morpho-physiological traits. The objectives were to estimate the germplasm diversity, phenotypic (PCV) and genetic (GCV) coefficients of variation, broad sense heritability (h²) and genetic advance (GA) with respect to origins and traits. Irrespective of origins all the traits showed more than 60–80% diversity in both species. Trait means of diversity were significant but not the origin means. Generally, only slightly higher PCV values than GCV were obtained for all the traits in both the species. High h² values ranging from 50% to more than 98% were also found. All the traits can be simultaneously utilized for genetic gain. Most of the C. olitorius accessions with two times higher GA estimates than those of the C. capsularis are likely to be more successful for that matter. Maximum genetic gain is expected from Mutants > China > Brazil > India > Thailand > Nepal > Burma in C. capsularis while from Thailand > Tanzania > Mutants > Kenya > Other countries in C. olitorius. C. capsularis mutants with high heterogenity for most of the traits should be useful for finding many rare alleles.     

Genetic variability measures among Bromus catharticus Vahl. populations and cultivars with RAPD and AFLP markers

The objectives of this study were to optimize RAPD and AFLP techniques in B. catharticus, and to determine the genetic variability of populations and commercial prairie grass cultivars with the aforementioned molecular markers. Two populations with contrasting morphological characteristics were evaluated from individual and bulked DNA samples using RAPD markers. Both analyses showed a similar information about inter population variability. Each accession was sampled by a single leaf bulk of 10 plants. Accession similarities were established with 276 RAPD and 714 AFLP bands using Jaccard similarity coefficient. The dendrogram of the accessions using RAPD markers showed that they shared high similarity values (>94%). A similar result was obtained with AFLP markers (similarity values >98%), revealing a narrow genetic basis in the analyzed accessions. Consequently, molecular characterization of germplasm should be considered in addition to morphological criteria, to choose the parental genotypes for breeding programs of this forage crop. The AFLP technique was more efficient to detect DNA polymorphism in our experiments and unique fingerprints were detected for all the accessions. RAPD is a simple and non expensive technique, suitable to estimate genetic similarity. This revised version was published online in August 2006 with corrections to the Cover Date.     

Evaluation and verification of resistance to Meloidogyne hapla Chitwood in a Cannabis germplasm collection

A collection of Cannabis accessions was evaluated for resistance to the root-knot nematode Meloidogyne hapla Chitwood in a seedling test. After inoculation with a larval suspension, significant variation was found for the number of galls and egg masses on the seedling roots. These parameters were considered as estimates for nematode infection and larval multiplication, respectively. A subset of the tested accessions was grown on a naturally infested arable field to study the relation between the test results and host characteristics in the field. The ranking order of accessions for the number of galls in the seedling test agreed well with that for the number of root galls on juvenile plants in the field. Therefore the test provides a useful indication for nematode infection. The number of egg masses in the seedling test and the population density of Meloidogyne measured in post-treatment soil samples of the field trial, showed a comparable ranking of accessions. Differences between accessions in the field were however smaller and not statistically significant.     

Genetic relationship of Mediterranean mandarins (Citrus deliciosa Tenore) using RAPD markers

Summary Random amplified polymorphic DNA (RAPD) analysis was carried out to evaluate polymorphism and genetic similarity between 39 Mediterranean mandarin genotypes. One hundred eleven amplification products were identified using 21 random primers. An average of 2.2 RAPD markers was obtained for each primer, corresponding to 42% of the amplification products. Genotype-specific RAPD markers were also found, mainly in known hybrids. UPGMA cluster analysis revealed the low level of genetic variation between accessions of Mediterranean mandarins, whereas their hybrids with other Citrus species showed greater genetic dissimilarity. Twenty accessions yielded very similar patterns, suggesting either that they could be a single clone, or that the technique was not able to detect genomic variation. However, for the other specimens genetic polymorphism can easily be detected by RAPD, although the genetic variation between accessions was quite low. The large number of hybrids and the low polymorphism between accessions support the hypothesis that Mediterranean mandarins are all true hybrid of Common mandarins (Citrus reticulata Blanco).     

Variation for agronomic characteristics in Crambe hispanica, a wild relative of Crambe abyssinica

Summary In order to assess the potential of Crambe hispanica, either in breeding programmes of C. abyssinica or as an oilseed crop in itself, 36 accessions of C. hispanica (29 of var. hispanica and 7 of var. glabrata) were grown in a greenhouse and evaluated for morphological characteristics, earliness, plant habit, seed characteristics and fatty acid composition. Four lines of C. abyssinica were included for reference. The 29 accessions of var. hispanica showed significant variation for all observed characteristics. Besides morphological characteristics, large variation was found for earliness, number of primary branches, seed yield, 1000 seed weight and volume, and linoleic, linolenic and erucic acid content. Morphological characteristics, earliness and plant habit did not show any high correlations with seed characteristics or fatty acid composition, except for seed hull (pericarp) mottling, which was related to a high oil and erucic acid content. The seven accessions of var. glabrata showed little variation. The large genetic variation in combination with promising figures for several characteristics, found in C. hispanica, may be useful in breeding programmes of the oilseed crop C. abyssinica, for which the available genetic variation is limited. Prospects of selection for high-erucic acid genotypes are discussed. Compared to C. abyssinica, both botanical varieties of C. hispanica are characterized by a cordate shape of the basal leaves, lack of seed retention and a lower DNA content. Plants of var. glabrata differed from var. hispanica in a sparsely hispid upper leaf surface and round stems and branches covered with a waxy layer. These clear differences and lack of success in intercrossing both varieties of C. hispanica strongly suggest that their taxonomic classification should be reconsidered.     

Inter and intra-species Inter Simple Sequence Repeat (ISSR) variations in the genus Cicer

Intra and inter-species ISSR variation and use of ISSR markers in determination of genetic relationship were investigated in an accession collection representing twoperennial and six annual Cicerspecies. Screening of Ciceraccessions with SSR primers revealed highly reproducible amplicon profiles with relatively high multiplex ratios. Many of the primers generated amplicon profiles with which not only the differences among species can readily be identified, but also polymorphisms within species could be detected more efficiently. PCR products at 150 gel positions detected using six SSR primers in Cicer accessions were treated as dominant DNA markers and utilized to compute the distances among accessions and species. Cluster analysis of accessions and species revealed groupings that corroborate our previous studies of relationships based on allozyme and AFLP analysis. Consistent with the AFLP analysis carried out in the same accession collection, ISSR-based groupings indicated that perennial C. incisumis genetically close to the annuals of the second crossability group (C. pinnatifidum,C. bijugum, C. judaicum) while C. reticulatum is the closest wild species to the cultivated chickpea. ISSR-based variation estimates were relatively higher when compared to previous estimates computed from RAPD and AFLP data. Technically, ISSR analysis combines the PCR-based targeting of microsatellite-associated polymorphisms with no prior sequence requirement and stringent PCR conditions. Similarly, when compared to AFLP analysis, it is less technically demanding allowing to survey polymorphic loci in the genome. Thus, ISSR-PCR technology is a reliable, fast, and cost-effective marker system that can be used to study genetic variation and genetic relationships in the genusCicer. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity in tef [Eragrostis tef (Zucc) Trotter] and its relatives as revealed by Random Amplified Polymorphic DNAs

Tef is one of the staple cereal crops in Ethiopia. To evaluate genetic diversity of tef and its relatives, 47 accessions of tef, three accessions of E. pilosa, and six accessions of E. curvulawere analyzed using random amplified polymorphic DNA (RAPD) markers. The level of polymorphism among the wild species was extremely high, while low polymorphism was detected among tef accessions. All cultivars and wild species under study could be distinguished with the help of different primers, thereby indicating the potential of RAPD in the genetic fingerprinting of tef. Accessions from E. curvula and E. pilosa can be differentiated by a single selected primer. In spite of low polymorphism within tef, accessions under study could be distinguished by a combination of selected primers. Cluster analysis indicated that tef is a very closely related species to E. pilosa with 45%similarity, supporting the hypothesis that tef originated from E. pilosa based on morphological data. Given that RAPD are relatively quick, simple to use, and are not subjected to environmental influences, they provide a valuable new approach for the genetic fingerprinting and study of genetic diversity in tef. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic variation in F<Subscript>2</Subscript> populations and their potential in the improvement of grain yield in tef (<Emphasis Type="Italic">Eragrostis tef</Emphasis>)

Tef is a staple cereal of Ethiopia in high demand by consumers. In order to cope up with this high consumer demand, productivity per unit of land must increase through the development and use of high-yielding varieties. To this effect, the National Tef Research Project has long been striving towards the development of high yielding varieties through direct selection from germplasm and concentrating favourable alleles through hybridization and selection, despite the tedious crossing technique. The objective of this study was to assess the degree of genetic variation in F₂ populations of tef as a basis for improving grain yield. F₂ populations from 12 crosses and their parents were grown at the Debre Zeit Agricultural Research Center, Ethiopia, and assessment was made on eight traits on individual plant basis. Eleven of the 12 crosses showed substantial genetic variation for grain yield and its components, indicating the potential for improvement through selection. Moreover, grain yield, plant weight and yield related traits showed moderate to high heritability values (17–80%). In all the crosses, tiller number, panicle weight, yield per panicle and panicle length showed significant (P ≤ 0.05) and positive association with grain yield. Considering the degree of genetic variation and heritability values, emphasis should be given to selected crosses in an effort to developing high-yielding tef varieties.     

Estimation of between and within accession variation in selected Spanish melon germplasm using RAPD and SSR markers to assess strategies for large collection evaluation

The population structure of 15 Spanish melon (C. melo L.)accessions, mostly of Group Inodorus, was assessed by the analysis of 16individuals of each accession using 100 random amplified polymorphic DNA (RAPD) bands produced by 36 primers, and allelic variation at 12microsatellite (SSR) loci (23 alleles). A relatively high level of polymorphism (25.6%) was detected using RAPD markers, and eight SSR loci (66.7%) were useful in discriminating accessions. Cluster analysis using RAPD- and SSR-based genetic distance estimates resulted in similar and consistent groupings of most of the accessions studied. The mean genetic distance and standard error among accessions estimated by RAPD variation was 0.421 ± 0.099, and mean SSR-based genetic distance estimate was 0.285 ± 0.141. Albeit many dominant markers examined were fitted to a 3:1 test ratio, deviation from this ratio and from Hardy-Weinberg expectations for many SSR loci suggests that some populations were in genotypic disequilibrium. Moreover, a higher level of genetic variation was observed between Cassaba market classes than within accessions, suggesting that, depending upon the accession, allelic fixation has occurred in these populations. The relatively high level of heterogeneity observed (different band morphotypes and cluster grouping within a particular market class), however, indicates that the Spanish melons examined possess a relatively broad genetic background. An appraisal of accession population structure such as the one reported herein indicates that bulk sampling techniques coupled with molecular analysis techniques that employ a unique array of discriminating markers can provide information leading to effective strategies for diversity analyses of large collections. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic characterization of Malawian cowpea (Vigna unguiculata (L.) Walp) landraces: diversity and gene flow among accessions

Cowpea has been cultured from ancient timesin Africa and Asia and is now widespreadthroughout the tropics and subtropics.Cowpea accessions can be distinguishedphenotypically from one another by theirgrowth habit, time to maturity, yield, andseed size and colour. Data on geneticdiversity of farmer-developed accessionsare lacking. The main objective of thisstudy was to determine the pattern andextend of RAPD marker variation within andamong cowpea populations from differentagroecological zones and to determine thedegree of genetic relationships and geneflow among different landraces used bylocal farmers. Twenty of the 30 RAPDprimers tested allowed amplifications ofrandom polymorphic (RAPD) loci. Overall,80% of the scored loci were polymorphic. The degree of band sharing was used toevaluate genetic distance betweenaccessions and to construct a phylogenetictree. The genetic distance values amongaccessions varied between 0.09 to 0.57.Although some small clusters groupedaccessions of the same growth habits, ageneral lack of agreement betweenclustering and morphological features wasobserved. The analysis of molecularvariance revealed that within-region ortypes (among accessions) variationaccounted for 96% of the total molecularvariance. This high within-accessionvariability is being sustained by anuncontrolled gene flow among populations.