Assessment of natural and induced genetic variation in Alstroemeria using random amplified polymorphic DNA (RAPD) markers

Summary We have used random amplified polymorphic DNA (RAPD) markers to study genetic variation in Alstroemeria. The first objective was to examine the discriminatory power of RAPD markers in different genotypes of Alstroemeria obtained by traditional breeding. All genotypes examined, including commercial Alstroemeria varieties, could be distinguished on the basis of their RAPD profiles. Progeny plants could be distinguished from their parents. A second objective of this study was to investigate whether RAPD markers can be used as a routine tool to detect mutant plants, as an alternative to glasshouse testing. To address this objective, we analysed Alstroemeria plants that carried phenotypically visible mutations that either were induced by irradiation using X-rays or were the result of somaclonal variation. In eight out of a total of 13 mutant Alstroemeria plants obtained after irradiation or tissue culture we detected no polymorphisms when compared to control plants that were considered to be non-mutated. Only in five of the mutant plants analysed we detected one to two polymorphisms. These results suggest that frequent genome rearrangements had not occurred in the mutant plants analysed. These results also demonstrate that the RAPD technique is an inappropriate tool for the rapid screening of Alstroemeria for induced variation. It that the RAPD technique is an inappropriate tool for the rapid screening of Alstroemeria for induced variation. It seems probable that this conclusion would be equally applicable in other plant genera in which induced variation has occurred. However, the RAPD technique is a simple and effective tool for genetic fingerprinting of Alstroemeria varieties, provided their differences are due to sexual propagation.     

Occurrence and frequency of putatively Y chromosome linked DNA markers in Cannabis sativa L.

DNA from female and male hemp (Cannabis sativa L.) plants belonging to nine different varieties were screened with180 RAPD primers in a search for sex-associated DNA markers. About 1500bands were produced in total, nine primers were found yielding one or two DNA bands amplified in all nine male DNA bulks and absent in all female DNA bulks. These putatively male-associated markers were then scored in three different F1progenies, deriving from a cross between a common male parent and three different female plants. The sex of the progeny was accurately scored on the basis of the floral phenotype, and the presence of the nine male-associated markers was verified by RAPD analysis. In all three progenies examined, all the male plants showed the DNA markers previously identified by bulk segregant analysis (BSA) on the hemp varieties, while all the female plants lacked them. The fact that the association between these markers and the staminate phenotype is found when examining male plants of distantly related varieties, and that such linkage is never broken when different progenies are examined, strongly supports the hypothesis that the markers found are physically located on the Y chromosome, in a region excluded from recombination during meiosis. Another marker was shown to be present in the male parent, in all the male plants of each progeny, and in 50% of the female progenies, while it was absent in the female parent; the possible occurrence of markers deriving from multiple amplification sites of the genome is discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Analysis of genetic diversity in Agave tequilana var. Azul using RAPD markers

By federal law in Mexico, A. tequilana Weber var. Azul is the only variety of agave permitted for the production of any tequila. Our objective was to assay levels of genetic variation in field populations of A. tequilana var. Azul using randomly amplified polymorphic DNA (RAPD) markers. Ten plants were collected from each of four different fields, with two fields being located in each of two principal regions of Mexico for the cultivation of A. tequilana var. Azul. The two regions are separated geographically by approximately 100km. Genetic relationships between A. tequilana var. Azul and two other varieties of A. tequilana Weber, ‘Chato’ and ‘Siguin’, were also investigated using RAPDs. Among the three varieties, 19 decamer primers produced 130 markers, of which 20 (15.4%) were polymorphic betweenA. tequilana var. Chato and A. tequilana var. Siguin. The results of RAPD analysis suggest that A. tequilana var. Siguin is more closely related to A. tequilana var. Azul than is A. tequilana var. Chato. Among the 40 field selections of A. tequilana var. Azul, only 1 of124 RAPD products (0.8%) was polymorphic and 39 of 40 plants were completely isogenic. This is one of the lowest levels of polymorphism detected to date for the analysis of a crop species, and is proposed to be the result of the promotion of a single conserved genotype over many years due to an exclusive reliance on vegetative propagation for the production of new planting materials. The significance of these results is discussed in relation to breeding programs focused on the improvement of A. tequilana var. Azul. This revised version was published online in July 2006 with corrections to the Cover Date.     

A random amplified polymorphic DNA (RAPD) molecular marker for the Tm-2 a gene in tomato

Summary A RAPD marker, linked to the Tm-2 ^agene engendering TMV resistance in tomatoes, was identified. The validity of the RAPD marker was corroborated by screening several tomato varieties, and correctly identifying those which carried Tm-2 ^a, as well as by F₂ segregation analysis. All tested resistant varieties descending from a common Lycopersicon peruvianum/esculentum ancestor, LA1791, exhibited this marker.     

A comparison of genetic relationship measures in strawberry (Fragaria × ananassa Duch.) based on AFLPs, RAPDs, and pedigree data

Nineteen of the major strawberry (Fragaria × ananassa Duch.) cultivars grown in the UnitedStates and Canada were examined for AFLP markerpolymorphisms. For the AFLP reactions, the EcoRI-ACC primer was used in combination with fourMseI primers (MseI-CAC, MseI-CAG,MseI-CAT, or MseI-CTT). Each set ofprimers produced 46–66 scorable fragments ranging insize between 50 and 500 bp. The polymorphic fragmentsproduced from each set of primers were more thansufficient to distinguish among all the cultivars,demonstrating the usefulness of AFLP markers forcultivar identification. Similarity coefficients werecalculated based on data from 228 AFLP markers anddata from 15 previously characterized RAPD markers. The RAPD markers had been specifically selected forfingerprinting purposes because they succesfullydistinguish 41 strawberry cultivars, including the 19cultivars analyzed in this study. Separatedendrograms were constructed based on analysis of theAFLP and RAPD marker data using a neighbor-joiningalgorithm. The dendrograms were compared and found tobe very different. Correlations between similaritycoefficients calculated from AFLP marker data,similarity coefficients calculated from RAPD markerdata, and coefficients of coancestry calculated frompedigree information were evaluated. Interestingly,a better correlation with the coefficients ofcoancestry was observed with the RAPD marker data thanwith the AFLP marker data.     

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).     

Identification of RAPD markers closely linked to the mlo-locus in barley

Developing resistance to powdery mildew, Erysiphe graminis f.sp. hordei, is a major goal of many barley breeding programmes. Several resistance genes have been tagged or mapped with molecular markers. The mlo gene confers durable resistance towards all known isolates of the pathogen. In this study, RAPD markers and bulked segregant analysis were used to determine PCR-based markers linked to the mlo-locus. Sixty doubled haploid lines from a cross between an isogenic line of ‘Ingrid’ carrying the mlo11 allele and a susceptible cv. ‘Pokko’ were used as plant material. Seven linked RAPD markers were found, the closest lying 1.6 cM away from the resistance gene. When eight barley varieties were assayed for the presence of this band, F4-980, it was found in the resistant varieties but not in the susceptible ones. The linked marker bands could be amplified from DNA-samples prepared by using three different methods, including a quick squash technique. PCR-based markers linked to the resistance gene can be used as tools for selection in breeding programmes.     

Breeding forage grasses for organic conditions

Herbage yield trials are necessary to test if candidate varieties are well suited for organic conditions. In order to elucidate a particular suitability for organic conditions, we run such trials in parallel under both organic and conventional conditions. Here, we report on second and third year results of the sowings 2004 and 2005. These trials are part of a targeted breeding programme for organic conditions. Irregular colonisation of pure grass plots with adventitious plants, in particular white clover, was recognized as a major constraint to the quality of the results obtained under organic conditions. The coefficients of variance in dry matter yield almost doubled when compared to conventional trials, and significant differences in annual yield among varieties were rare. However, when herbage yield was corrected for the estimated fraction of adventitious plant colonization at each cut, the number of instances with statistically significant differences for annual yield among varieties increased more than fourfold. Dry matter yields under organic and conventional conditions were significantly and positively correlated. However, analysis of variance showed a significant culture type by variety interaction for annual dry matter yield in 12 out of 24 trials. When diploid and tetraploid varieties of the same Lolium species were tested in one common trial, only tetraploid varieties were identified as being particularly well suited for organic conditions, while in these trials, the great majority of apparently poorly suited varieties were diploid. This suggests that breeding tetraploid Lolium varieties is promising when aiming at a favourable response to organic agriculture.     

The in vitro phytotoxicity of culture filtrates of Fusarium oxysporum to five genotypes of Amaranthus hybridus

Stem decay and root rot of Amaranthus hybridus, caused by Fusarium oxysporum is a serious threat to the commercial production of this crop in South Africa. Five Amaranthus hybridus varieties were examined in vitro for sensitivity to a culture filtrate of Fusarium oxysporum. The phytotoxicity of the culture filtrate was assessed for its inhibitory effect on callus and seeding root growth, as well as on the viability of callus cells. The five varieties exhibited a significant amount of variation in response to the culture filtrate of the pathogen. Variety 17 was the most sensitive variety in each bioassay, whereas variety 20 displayed least sensitivity to the culture filtrate. Callus of variety 20 grew well in the presence of concentrations of culture filtrate that were toxic to another four varieties and the percentage mortality of callus cells after exposure to the filtrate was also the lowest of the five varieties. Root growth of variety 20 was also least affected by exposure to the culture filtrate for up to 6 days. To our knowledge, the presence of resistance in germplasm of A. hybridus to culture filtrates of F. oxysporum has not been demonstrated before. The present study is therefore of significant value to breeding programs aimed at speedily finding amaranth cultivars that are resistant to this important pathogen. This revised version was published online in August 2006 with corrections to the Cover Date.     

Resistance to Verticillium albo-atrum in lucerne (Medicago sativa L.) to distinguish between varieties

France is responsible for DUS (Distinction–Uniformity–Stability) testing of new varieties of lucerne (Medicago sativa L.) for several European countries. Many varieties fail to be registered because of a lack of distinctness from the already registered varieties. The addition of the other traits such as disease or pest resistance could help in distinction. The aim of the present study was to optimize measurement of the resistance of lucerne to Verticillium albo-atrum. Although the resistance to V. albo-atrum is a qualitative trait for each plant, varietal resistance is a continuous variable because each variety contains a variable percentage of resistant plants. Fifty cultivars were tested for V. albo-atrum in two laboratories at random from among five private and public laboratories. Five check varieties were tested in the five laboratories in two tests. A score of resistance, corrected from the effect of the test, was given for each cultivar. A method to validate any new test is proposed. This data set can now be incremented by the resistance scores to V. albo-atrum of new varieties. It will help in distinguishing between lucerne varieties.     

Pedigree, RAPD and simplified AFLP-based assessment of genetic relationships among Avena sativa L. cultivars

Two molecular marker techniques: RAPD and simplified ^PstIAFLP have been compared in order to decide on, which technique is better suited to genetic characterization of oat (Avena sativa L.) cultivars. It was investigated, if the same pattern of variability is revealed by two approaches and whether the observed molecular variability reflects pedigree-based relationships. Polymorphic RAPD and ^PstIAFLP markers were sufficient to distinguish all analysed cultivars, demonstrating the usefulness of both methods for cultivar identification. Genetic similarity estimates derived from RAPD, simplified ^PstIAFLP and combined RAPD and ^PstIAFLP data were compared with coefficients of parentage (COP). Molecular markers-based mean genetic similarities were considerably greater than mean COP value. Correlation coefficients between COP and genetic similarities calculated from RAPD, ^PstIAFLP and combined molecular data were very low and not significant. A better correlation (0.50) was found between similarity estimates derived from RAPD and ^PstIAFLP markers. Four separate dendrograms were constructed based on pedigree and molecular analyses using a neighbor-joining algorithm (NJ). The dendrograms were compared and found to be topologically different. The results of this study showed, that both molecular techniques can be conveniently used for genetic characterization of oat cultivars, however ^PstIAFLP would be the method of choice due to the higher efficiency and reproducibility. This revised version was published online in August 2006 with corrections to the Cover Date.     

Analysis of genetic variability in various tissue culture-derived lemon plant populations using RAPD and flow cytometry

Five populations of lemon plants [Citrus limon (L.) Burm] obtained from undeveloped ovules through different tissue culture procedures were examined for the presence of somaclonal and irradiation-induced genetic variation. Tested groups were: (1) nucellar seedlings; (2) organogenic, regenerated via adventitious buds from nucellar seedling internodes; (3) embryogenic population, regenerated from non-irradiated nucellar callus via somatic embryogenesis; (4) embryogenic population, regenerated from irradiated nucellar callus via somatic embryogenesis; and (5) protoplast-derived, regenerated via somatic embryogenesis. Genomic DNA samples from 360 plants (72 from each group) were screened for polymorphism among RAPD fingerprints amplified by 10 decamer primers. Among all tested plants, genetic variation was detected only within the group of plants recovered from irradiated embryogenic calli. Out of 72 plants from that group, three had RAPD fingerprints different from the rest of the population, and fourth plant was found to be cytochimeric, consisting of diploid and tetraploid cells as revealed by flow cytometry. In all other populations of regenerated plants, we did not come across any plants with changed ploidy level.     

High frequency spontaneous production of doubled haploid plants in microspore cultures of Brassica rapa ssp. chinensis

Brassica rapa (syn. Brassica campestris) ssp. chinensis is an important vegetable crop, but it is relatively recalcitrant to microspore culture. One genotype each of B. rapa ssp. chinensis var. communisand var. utilis were used formicrospore culture. Embryo production of3.8–42.4 embryos/bud was obtained. A high rate of plant regeneration directly from microspore-derived embryos without subculture was achieved by an improved protocol involving replacement of culture media and reduction of sucrose concentrations after 48 h of induction,among other modifications. More than 70%of regenerated plants were spontaneous diploids. Some spontaneous tetraploid plants were also obtained from isolated microspores of both genotypes tested. These tetraploids may be directly exploited a snew varieties in a Brassica rapabreeding programme. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular tagging of a gene for resistance to brown planthopper in rice (Oryza sativa L.)

An introgression line derived from an interspecific cross between Oryzasativa and Oryza officinalis, IR54741-3-21-22 was found to beresistant to an Indian biotype of brown planthopper (BPH). Genetic analysisof 95 F₃ progeny rows of a cross between the resistant lineIR54741-3-21-22 and a BPH susceptible line revealed that resistance wascontrolled by a single dominant gene. A comprehensive RAPD analysisusing 275 decamer primers revealed a low level of (7.1%) polymorphismbetween the parents.RAPD polymorphisms were either co-dominant (6.9%), dominant forresistant parental fragments (9.1%) or dominant for susceptible parentalfragments (11.6%). Of the 19 co-dominant markers, one primer,OPA16, amplified a resistant parental band in the resistant bulk and asusceptible parental band in the susceptible bulk by bulked segregantanalysis. RAPD analysis of individual F₂ plants with the primerOPA16 showed marker-phenotype co-segregation for all, with only onerecombinant being identified. The linkage between the RAPD markerOPA16₉₃₈ and the BPH resistance gene was 0.52 cM in couplingphase. The 938 bp RAPD amplicon was cloned and used as a probe on122 Cla I digested doubled haploid (DH) plants from aIR64xAzucena mapping population for RFLP inheritance analysis and wasmapped onto rice chromosome 11. The OPA16₉₃₈ RAPD markercould be used in a cost effective way for marker-assisted selection of BPHresistant rice genotypes in rice breeding programs.     

An assessment of morphogenic and transformation efficiency in a range of varieties of potato (Solanum tuberosum L.)

Summary To provide a truly genotype-independent transformation system, it is necessary to be able to transform a wide range of potato genotypes. The ability to regenerate shoots in vitro was determined for 34 potato varieties using tuber disc explants. Following a culture regime used extensively in previous studies with the variety Desiree, half of the varieties could be regenerated from tuber discs and half could not. From a sample of varieties that could be regenerated from tuber discs, all but one variety gave transgenic plants. Twelve varieties were evaluated for the capacity to regenerate shoots from leaf and internode explants excised from in vitro grown plants. All of the varieties tested regenerated adventitious shoots. Leaf and internode explants from 5 varieties were subsequently used for transformation, and transgenic plants were produced from two potato varieties that did not give transgenic plants from tuber disc explants. Some varieties could not be transformed by either method, and will require modification of the in vitro regeneration and transformation system to be successful.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - GA₃ gibberellic acid - IAA indole-3-acetic acid     

In vitro techniques for selecting wheat (Triticum aestivum L.) for Fusarium-resistance. II. Culture filtrate technique and inheritance of Fusarium-resistance in the somaclones

Summary Calli of resistant, intermediary and susceptible wheat (Triticum aestivum L.) varieties were selected using culture filtrates of Fusarium graminearum and F. culmorum and the regenerants were evaluated for resistance up to R₃. Czapek-Dox broth medium was inoculated with mycelia of Fusarium isolates and incubated for 2–6 weeks. Filtrates were added to MS callus growing medium, then 5 weeks-old calli were transferred onto this medium (MST) for 4–5 weeks. MST containing 30% filtrate was found to be suitable for selection. Resistant calli were transferred again to fresh MST for further two selection cycles. The surviving calli produced less fertile regenerated lines (R₀) than the non-selected ones. Among 18 R₁ lines tested for Fusarium-resistance in the seedling stage by artificial inoculation in the greenhouse, two (11.1%) were significantly more resistant, one (5.6%) was more susceptible than the original cultivar and the rest (83.3%) behaved similarly to the donor plants. Among unselected R₃ lines of three varieties, practically the same number of resistant plants were found as among the related selected ones. When the R₃ selfed generations obtained through double-layer and culture filtrate selection techniques were tested for Fusarium-resistance, 35.7% of the lines were found to be more resistant than the original cultivars, none was more susceptible and 64.3% had a reaction similar to that of the source materials. Thus, inheritance of the disease reaction was not stable in all cases. Success of in vitro selection for Fusarium-resistance depended also on the genotype, and toxin analysis showed that although being effective, the selective media contained deoxynivalenol only exceptionally. In selecting wheat for Fusarium-resistance in vitro, the culture filtrate technique proved better than the double-layer procedure.     

Assessment of somaclonal variability in hop (Humulus lupulus L.) in vitro meristem cultures and clones by molecular methods

In vitro meristem tissue cultures are used for production of virus-free rootstocks of hop (Humulus lupulus L.). Because use of plant tissue cultures is associated with occurrence of somaclonal variability, we assessed somaclonal variability in hop meristem in vitro cultures before and after thermotherapy by different molecular methods (RFLP, RAPD, STS, ISSR and AFLP) and compared it with existing clonal variability of Osvald's clones 31, 72 and 114. No molecular differences were observed between mother plants and in vitro mericlones by RFLP and STS analyses. Amplified molecular differences were found in RAPD and ISSR products of one from five in vitromericlones cvs. Eroica (E5) and Southern Brewer (SB2), respectively. Similarities with mother plants were 0.965 and 0.913 (JSC), respectively. Specific amplified polymorphic products were found for every mericlone and mother plant in AFLP reactions and variability of DNA sequence ranged from 0.824 to 0.993 (JSC). This variability was very similar to determined intra-clonal variability within Osvald's clones 31, 72 and 114 by AFLP analysis. Inter-clonal variability of DNA sequence was exactly higher than intra-clonal variability of DNA sequence in these clones. The molecular differences between Osvald's clone 72 normal and meristem derived were not verifiable. Thermotherapy increased frequency of molecular changes, since amplified differences were found in 14 from 20 in vitro mericlones of cv. Eroica, in 6 from 11 in vitro mericlones of cv. Yeoman and in 15 from 23 in vitro mericlones of cv. Southern Brewer by RAPD and ISSR analyses.     

DNA polymorphisms in Oryza sativa L. and Lactuca sativa L. amplified by arbitrary primed PCR

Summary Thirty-five rice (Oryza sativa L.) varieties, including 18 japonica, 5 javanica and 12 indica subspecies and 12 lettuce (Lactuca sativa L.) varieties were identified taxonomically, using PCR with originally designed 21 RAPD (Random Amplified Polymorphic DNA) primers and 8 sequence-specific primers, used for amplifying four specific DNA fragments. Use of these primers revealed polymorphisms among varieties in rice and lettuce and facilitates DNA fingerprinting. Dendrograms of both species based on polymorphisms were constructed and genetical relationships were established. In rice, half the number of amplified bands were polymorphic and almost all varieties differentiated. However, differentiation of minor genetic alterations among somaclonal variants or mutants and their mother varieties was not feasible. In L. sativa, 47% of the amplified fragments were polymorphic and all 12 varieties were differentiated. Some of the PCR fragments were variety or type specific, which could be used for indicators for type-selection. The dendrogram obtained showed differentiated clusters of crisphead, leaf and butterhead type, findings in good accord with the classification based on the genetic background.     

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.     

Use of PCR-based methodologies for the determination of DNA diversity between Saccharum varieties

Summary In this study, two PCR-based methodologies were evaluated for potential use in the determination of DNA diversity between 20 commercial sugarcane hybrids and 6 outgroup varieties of S. spontaneum, S. officinarum and hybrids from early in the genealogy. The first method involved PCR amplification of sugarcane DNA in the presence of random, decamer primers (RAPDs), while the second protocol utilized specific microsatellite and telomere sequences as primers. A total of 41 RAPD primers (356 loci) were screened across the varieties of which 15 (160 loci) were used in the calculation of DNA diversity (expressed% similarity). This varied from 61 to 95%, with most of the commercial varieties showing more than 80% similarity in their DNA. The RAPD data indicated that there had been a gradual decline in DNA diversity (84% reduction) from the early inter-specific crosses to the commercial hybrids, probably as a result of backcrossing and in-breeding strategies used in the previous 5 to 6 generations of sugarcane breeding. The microsatellite and telomere data produced a much greater range in DNA similarity values (25–91%), probably due to the fact that these primers detect highly variable regions of the genome. It is suggested that these specific primers would not be suitable for determination of DNA diversity, but could be used more effectively in the development of a methodology for routine, rapid identification of sugarcane varieties.