Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard (Brassica juncea) and its relationship to heterosis

Genetic, phytochemical and morphological identification and genetic diversity of selected Moringa species

Moringa is the sole genus in the family Moringaceae used for medicinal and nutrient purposes. Morphological features, phytochemical attributes, and molecular characterization were used for the genetic association and classification among Moringa oleifera, M. peregrina, and M. stenopetala. Moringa peregrina recorded a similarity of 84% lonely and placed M. stenopetala with M. oleifera into a cluster score with a similarity of 95.3%. M. peregrina is characterized by phenolic content (243 mg/100 g), flavonoids (7 mg/100 g), and antioxidant activity (1226.85 mg/100 g). GC-MS analysis revealed that M. oleifera contained twenty compounds with 2-decenal (E) (39.14%), 2-undecenal (15.51%), nonanal (3.60%), and 2-octenal, (E) (2.48%), while M. peregrina identified eighteen compounds with 2-decenal (Z) (25.42%), 2-docecen-1-al (9.35%), and 13-Docosenoic acid, methyl ester, (Z) (4.16%). M. stenopetala identified fifteen compounds containing 2-decenal (E) (26.67%), 2-undecenal (24.10%), and nonanal (4.40%). A broad sense of similarity has been scored between M. oleifera and M. stenopetala by the phytochemical compositions, especially the similarity in the main compounds such as 2-decenal (E), 2-undecenal, and nonanal. It can be concluded that efforts need to be expanded to pay attention to study Moringa taxa, due to the rarity of Moringa peregrina, and the focus should be on sustainable utilization and conservation. The potential of these taxa would greatly benefit indigenous species in terms of their maintenance, and there is a need for more comprehensive bio-prospecting studies. Therefore, this study evaluates the variability among Moringa and highlights the significance of leaf and seed ultrastructure to provide more information and evaluate potential approaches.

Maximization through optimization? On the relationship between hybrid performance and parental genetic distance

Heterosis is the improved performance of hybrids compared with their parental components and is widely exploited in agriculture. According to quantitative genetic theory, genetic distance between parents at heterotic quantitative trait loci is required for heterosis, but how heterosis varies with genetic distance has remained elusive, despite intensive research on the topic. Experimental studies have often found a positive association between heterosis and genetic distance that, however, varied in strength. Most importantly, it has remained unclear whether heterosis increases continuously with genetic distance or whether there is an optimum genetic distance after which heterosis declines again. Here, we revisit the relationship between heterosis and genetic distance and provide perspectives on how to maximize heterosis and hybrid performance in breeding, as well as the consequences for the design of heterotic groups and the utilization of more exotic material and genetic resources.

Characterization of Some Cichorium Taxa Grown under Mediterranean Climate Using Morphological Traits and Molecular Markers

The verification of taxonomic identities is of the highest significance in the field of biological study and categorization. Morpho-molecular characterization can clarify uncertainties in distinguishing between taxonomic groups. In this study, we characterized five local taxa of the genus Cichorium using morphological and molecular markers for taxonomic authentication and probably future genetic improvement. The five Cichorium taxa grown under the Mediterranean climate using morphological traits and molecular markers showed variations. The examined taxa showed a widespread range of variations in leaf characteristics, i.e., shape, type, texture, margin, and apex and cypsela characteristics i.e., shape, color, and surface pattern. The phylogenetic tree categorized the Cichorium intybus var. intybus and C. intybus var. foliosum in a single group, whereas C. endivia var. endivia was grouped separately. However, C. endivia var. crispum and C. endivia subsp. pumilum were classified as a cluster. The recorded variance between classes using the molecular markers SCoT, ISSR, and RAPD was documented at 34.43%, 36.62%, and 40.34%, respectively. Authentication using molecular tools proved the usefulness of a dichotomous indented key, as revealed by morphological identification. The integrated methodology using morphological and molecular assessment could support improved verification and authentication of the various taxa of chicory. It seems likely that the Egyptian chicory belongs to C. endivia subsp. pumilum.

Physical mapping of introgressed chromosome fragment carrying the fertility restoring (Rfo) gene for Ogura CMS in Brassica juncea L. Czern & Coss

Rfo is located on a radish chromosome fragment (~ 108 Kb), which is seated in the middle of a pretty large C genome translocation at the distal region of chromosome A09 of B. juncea. Ogura cytoplasmic male sterility (CMS) is used to produce hybrids in Indian mustard (Brassica juncea L.). Fertility restorers for this CMS were developed by cross-hybridizing B. juncea (AABB; 2n = 36) with B. napus (AACC; 2n = 38) carrying radish Rfo gene. This hybrid production system is normally stable, but many commercial mustard hybrids show male sterile contaminants. We aimed to identify linkage drag associated with Rfo by comparing hybridity levels of 295 handmade CMS x Rfo crosses. Although Rfo was stably inherited, hybridity was < 85 percent in several combinations. Genome re-sequencing of five fertility restorers, mapping sequencing reads to B. juncea reference and synteny analysis with Raphanus sativus D81Rfo genomic region (AJ550021.2) helped to detect ~ 108 Kb of radish chromosome (R) fragment substitution in all fertility restorers. This radish segment substitution was itself located amidst a large C genome translocation on the terminal region of chromosome A09 of B. juncea. The size of alien segment substitution varied from 11.3 (NTCN-R9) to 22.0 Mb (NAJR-102B-R). We also developed an in silico SSR map for chromosome A09 and identified many homoeologous A to the C genome exchanges in the introgressed region. A to the R genome exchanges were rare. Annotation of the substituted fragment showed the gain of many novel genes from R and C genomes and the loss of B. juncea genes from the corresponding region. We have developed a KASPar marker for marker-aided transfer of Rfo and testing hybridity levels in seed production lots.

Estimation of seed yield in oilseed rape to identify the potential of semi-resynthesized parents for the development of new hybrid cultivars

Resynthesized (RS) Brassica napus can be used to increase the genetic diversity of this important crop plant and to develop the heterotic gene pool required for successful hybrid breeding programmes. The level of heterosis in F₁ hybrids depends on the individual performance of the parents and on the degree of genetic difference between them. However, RS forms obtained from crosses of B. rapa ssp. with B. oleracea ssp. possess many undesirable agronomic traits, such as low quality of seeds, low yield and seed oil content, high erucic acid level in the oil and high glucosinolate content in seed meal. Therefore, RS oilseed rape needs to be improved by crossing with natural double-low oilseed rape, leading to selected double-low quality semi-RS lines that can be used for breeding. In this study, we evaluated the seed yield potential of F₁ hybrids derived from crosses between Ogura cytoplasmic male-sterility (CMS) lines and doubled haploid (DH) semi-RS lines with restorer gene in three locations in Poland. The genotype by environment interaction (GE interaction) and general combining ability (GCA) of the restorer and CMS line effects, as well as the effects of heterosis, were also assessed. The results of the study provide the first insights into the use of semi-RS lines as components for the development of new hybrid cultivars. Even the introduction of 50% of the RS oilseed rape genotype to natural restorer lines resulted in a marked heterosis effect, with seed yield ranging from 4.56% to 90.17% more than that of the better parent. The yield of the best hybrid amounted to 108.6% of the seed yield of the open-pollinated cultivar Monolit and 94.4% of that of the hybrid cultivar Arsenal. The best DH semi-RS line S1, which had a significantly positive GCA for seed yield, can be recommended as a possible parent for inclusion in breeding programmes aimed at developing new hybrid cultivars.

Characterization of Brassica napus L. genotypes utilizing sequence-related amplified polymorphism and genotyping by sequencing in association with cluster analysis

Identifying parental combinations that exhibit high heterosis is a constant target for commercial Brassica napus L. hybrid development programs. Finding high heterotic parental combinations can require hundreds of test crosses and years of yield evaluation. Heterotic pool development could be used to divide breeding material into specific breeding pools and focus the number of parental combinations created. Here, we report the genotypic characterization of 79 B. napus genotypes by calculating genetic distance based on sequence-related amplified polymorphism (SRAP) and genotyping by sequencing (GBS) in association with a neighbour-joining clustering algorithm. Despite the different genotypic analyses, neighbour-joining cluster analysis based on genetic distance of SRAP and GBS produced similar clusters. Homology between SRAP and GBS clusters was approximately 77 % when manually comparing clusters and 68 % when comparing clusters using Compare2Trees. This research demonstrates that SRAP can have similar efficacy when compared to next-generation sequencing technology for heterotic pool classification. This information may provide an important breeding scaffold for the development of hybrid cultivars based upon genetic distance and cluster analysis.

Applications of molecular markers in the discrimination of Panax species and Korean ginseng cultivars (Panax ginseng)

The development of molecular markers is one of the most useful methods for molecular breeding and marker-based molecular associated selections. Even though there is less information on the reference genome, molecular markers are indispensable tools for determination of genetic variation and identification of species with high levels of accuracy and reproducibility. The demand for molecular approaches for marker-based breeding and genetic discriminations in Panax species has greatly increased in recent times and has been successfully applied for various purposes. However, owing to the existence of diverse molecular techniques and differences in their principles and applications, there should be careful consideration while selecting appropriate marker types. In this review, we outline the recent status of different molecular marker applications in ginseng research and industrial fields. In addition, we discuss the basic principles, requirements, and advantages and disadvantages of the most widely used molecular markers, including restriction fragment length polymorphism, random amplified polymorphic DNA, sequence tag sites, simple sequence repeats, and single nucleotide polymorphisms.

Population structure and breeding value of a new type of Brassica juncea created by combining A and B genomes from related allotetraploids

Derived amphiploidy helped to resynthesize agronomically superior B. juncea germplasm which showed high heterosis in crosses with natural B. juncea . This new procedure facilitates a seamless flow of variation across Brassica digenomics. Brassica digenomics, artificially resynthesized by hybridizing extant genome donor diploids, show poor breeding value due to the linkage drag associated with diploid donors. We recently developed a method that involves resynthesis through hybridization between related allotetraploids. Derived B. juncea was created by combining A and B genomes extant in B. napus and B. carinata, respectively. Large genomic and agronomic modifications resulted. Population structure analysis based on the DNA polymorphism generated using 108 locus-specific SSR primers helped to identify three pools of allelic diversity. Thirteen progenies with determinate plant growth habit were discovered, and these aligned closely with B genome of the donor species like B. nigra and B. carinata. The indeterminate group showed greater genetic affinity with extant B. juncea. Derived genotypes possessed high agronomic potential. Importantly, high heterosis was observed in crosses between derived and natural B. juncea. Some derived juncea progenies figured in heterotic combinations during both the years of F 1 hybrid evaluation. In essence, the hybrids between derived B. juncea and natural B. juncea can be considered as interspecific hybrids between B. juncea and B. napus for A genome and between B. juncea and B. carinata for B genome. This possibly explains their high heterosis-inducing potential. Integrating genetic diversity with the inherent breeding value allowed more efficient prediction of heterosis. Besides generation of new novel variability of huge economic importance and operational simplicity, the method of derived amphiploidy allows a seamless flow of heritable variation across Brassica digenomics.

SSR analysis of 38 genotypes of soybean (Glycine Max (L.) Merr.) genetic diversity in India

Sixteen polymorphic Simple sequence repeat (SSR) markers were used to determine the genetic diversity and varietal identification among 38 soybean (Glycine max (L.) Merr.) genotypes which are at present under seed multiplication chain in India. A total of 51 alleles with an average of 2.22 alleles per locus were detected. The polymorphic information content (PIC) among genotypes varied from 0.049 (Sat_243 and Satt337) to 0.526 (Satt431) with an average of 0.199. The pair wise genetic similarity between soybean varieties varied from 0.56 to 0.97 with an average of 0.761. These 16 SSR markers successfully distinguished 12 of the 38 soybean genotypes. These results suggest that used SSR markers are efficient for measuring genetic diversity and relatedness as well as identifying varieties of soybeans. Diverse genetic materials may be used for genetic improvements of soybean genotypes.

Cytoplasmic male sterility in Brassicaceae crops

Brassicaceae crops display strong hybrid vigor, and have long been subject to F1 hybrid breeding. Because the most reliable system of F1 seed production is based on cytoplasmic male sterility (CMS), various types of CMS have been developed and adopted in practice to breed Brassicaceae oil seed and vegetable crops. CMS is a maternally inherited trait encoded in the mitochondrial genome, and the male sterile phenotype arises as a result of interaction of a mitochondrial CMS gene and a nuclear fertility restoring (Rf) gene. Therefore, CMS has been intensively investigated for gaining basic insights into molecular aspects of nuclear-mitochondrial genome interactions and for practical applications in plant breeding. Several CMS genes have been identified by molecular genetic studies, including Ogura CMS from Japanese radish, which is the most extensively studied and most widely used. In this review, we discuss Ogura CMS, and other CMS systems, and the causal mitochondrial genes for CMS. Studies on nuclear Rf genes and the cytoplasmic effects of alien cytoplasm on general crop performance are also reviewed. Finally, some of the unresolved questions about CMS are highlighted.

Evidence from genome-wide simple sequence repeat markers for a polyphyletic origin and secondary centers of genetic diversity of Brassica juncea in China and India

The oilseed Brassica juncea is an important crop with a long history of cultivation in India and China. Previous studies have suggested a polyphyletic origin of B. juncea and more than one migration from the primary to secondary centers of diversity. We investigated molecular genetic diversity based on 99 simple sequence repeat markers in 119 oilseed B. juncea varieties from China, India, Europe, and Australia to test whether molecular differentiation follows Vavilov's proposal of secondary centers of diversity in India and China. Two distinct groups were identified by markers in the A genome, and the same two groups were confirmed by markers in the B genome. Group 1 included accessions from central and western India, in addition to those from eastern China. Group 2 included accessions from central and western China, as well as those from northern and eastern India. European and Australian accessions were found only in Group 2. Chinese accessions had higher allelic diversity per accession (Group 1) and more private alleles per accession (Groups 1 and 2) than those from India. The marker data and geographic distribution of Groups 1 and 2 were consistent with two independent migrations of B. juncea from its center of origin in the Middle East and neighboring regions along trade routes to western China and northern India, followed by regional adaptation. Group 1 migrated further south and west in India, and further east in China, than Group 2. Group 2 showed diverse agroecological adaptation, with yellow-seeded spring-sown types in central and western China and brown-seeded autumn-sown types in India.

QTL mapping of yield-associated traits in Brassica juncea: meta-analysis and epistatic interactions using two different crosses between east European and Indian gene pool lines

Genetic analysis of 12 yield-associated traits was undertaken by dissection of quantitative trait loci (QTL) through meta-analysis and epistatic interaction studies in Brassica juncea. A consensus (integrated) map in B. juncea was constructed using two maps. These were VH map, developed earlier in the laboratory by using a DH population from the cross between Varuna and Heera (Pradhan et al. in Theor Appl Genet 106:607-614, 2003; Ramchiary et al. in Theor Appl Genet. 115:807-817, 2007; Panjabi et al. in BMC Genomics 9:113, 2008), and the TD map, developed in the present study using a DH population of 100 lines from the cross between TM-4 and Donskaja-IV. The TD map was constructed with 911 markers consisting of 585 AFLP, 8 SSR and 318 IP markers covering a total genome length of 1,629.9 cM. The consensus map constructed by using the common markers between the two maps contained a total of 2,662 markers and covered a total genome length of 1,927.1 cM. Firstly, QTL analysis of 12 yield-associated traits was undertaken for the TD population based on three-environment phenotypic data. Secondly, the three-environment phenotypic data for the same 12 quantitative traits generated by Ramchiary et al. (2007) were re-analyzed for the QTL detection in the VH map. Comparative analysis identified both common and population-specific QTL. The study revealed the presence of QTL clusters on LG A7, A8 and A10 in both TD and VH maps. Meta-analyses resolved 187 QTL distributed over nine linkage groups of TD and VH maps into 20 meta-QTL. Maximum resolution was recorded for the LG A10 wherein all the 54 QTL were mapped to a single meta-QTL within a confidence interval of 3.0 cM. Digenic epistatic interactions of QTL in both TD and VH maps revealed substantial additive × additive interactions showing a higher frequency of Type 1 and Type 2 interactions than Type 3 interactions. Some of the loci interacted with more than one locus indicating the presence of higher order epistatic interactions. These findings provided some detailed insight into the genetic architecture of the yield-associated traits in B. juncea.

Genetic diversity in North American ginseng (Panax quinquefolius L.) grown in Ontario detected by RAPD analysis

Genetic diversity within North American ginseng (Panax quinquefolius L.) grown in Ontario was investigated at the DNA level using the randomly amplified polymorphic DNA (RAPD) method via the polymerase chain reaction (PCR). A total of 420 random decamers were initially screened against DNA from four ginseng plants and 78.8% of them generated RAPD fragments. Thirty-six of the decamers that generated highly repeatable polymorphic RAPD markers were selected for further RAPD analysis of the ginseng population. With these primers, 352 discernible DNA fragments were produced from DNA of 48 ginseng plants, corresponding to an average of 9.8 fragments per primer, of which over 45% were polymorphic. The similarity coefficients among the DNA of ginseng plants analyzed were low, ranging from 0.149 to 0.605 with a mean of 0.412, indicating that a high degree of genetic diversity exists in the ginseng population. Lower levels of genetic diversity were detected among 3-year-old ginseng plants selected on the basis of greater plant height than among the plants randomly selected from the same subpopulation or over the whole population, suggesting that genetic factors at least partly contribute to morphological variation within the ginseng population and that visual selection can be effective in identifying the genetic differences. The significance of a high degree of genetic variation in the ginseng population on its potential for improvement by breeding is also discussed.

Generation of B. nigra-B. rapa chromosome addition stocks: cytology and microsatellite markers (SSRs) based characterization

To improve Brassica nigra, the B-genome donor for Brassica juncea through selective introgression of useful variation from A-genome chromosomes, B. nigra-B. rapa chromosome addition stocks were successfully synthesized for the first time. Resynthesized B. juncea was used as B-genome donor species and A-genome addition stocks were developed by hybridizing sesquidiploid plant (ABB) as female and using B. nigra as the male parent. Various cycles of backcrossing and/or selfing were utilized to isolate plants carrying addition of three A-genome chromosomes in the background of B. nigra. These chromosome addition stocks were characterized by chromosome counts, pollen and seed fertility and chromosome specific microsatellite (SSRs) markers. The chromosome number in different backcross/self generations ranged between 2n=26 and 2n=19 with relatively high frequency of univalents (8-10I) at in meiotic configurations observed, suggesting the role of preferential transmission of A-genome chromosomes. SSRs analysis revealed that B. rapa chromosomes 3 and 4 were the first to get eliminated followed by chromosome 10. Remaining chromosomes were maintained till BC(1)F(4). However, second cycle of backcrossing (BC(2)) led to the elimination of chromosome numbers 1 and 2. BC(2)F(2) plants carried the chromosome numbers 6, 7, 8 and 9. Generation BC(3) having plants with 2n=19 carried chromosome numbers 6, 7 and 8. It is possible that chromosomes 6, 7 and 8 had higher transmission frequency and these were better tolerated by the B. nigra genome.

Genetic diversity in natural populations of Jacaranda decurrens Cham. determined using RAPD and AFLP markers

Jacaranda decurrens (Bignoniaceae) is an endemic species of the Cerrado with validated antitumoral activity. The genetic diversity of six populations of J. decurrens located in the State of São Paulo was determined in this study by using molecular markers for randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP). Following optimization of the amplification reaction, 10 selected primers generated 78 reproducible RAPD fragments that were mostly (69.2%) polymorphic. Two hundred and five reproducible AFLP fragments were generated by using four selected primer combinations; 46.3% of these fragments were polymorphic, indicating a considerable level of genetic diversity. Analysis of molecular variance (AMOVA) using these two groups of markers indicated that variability was strongly structured amongst populations. The unweighted pair group method with arithmatic mean (UPGMA) and Pearson's correlation coefficient (RAPD -0.16, p = 0.2082; AFLP 0.37, p = 0.1006) between genetic matrices and geographic distances suggested that the population structure followed an island model in which a single population of infinite size gave rise to the current populations of J. decurrens, independently of their spatial position. The results of this study indicate that RAPD and AFLP markers were similarly efficient in measuring the genetic variability amongst natural populations of J. decurrens. These data may be useful for developing strategies for the preservation of this medicinal species in the Cerrado.

Genetic relationships within and between Capsicum species

Genetic relationships were estimated among 24 accessions belonging to 11 species of Capsicum, using 2,760 RAPD markers based on touch-down polymerase chain reactions (Td-RAPD-PCR). These markers were implemented in analyses of principal coordinates, unweighted pair group mean average, and 2,000 bootstrap replications. The accessions were divided into four groups, corresponding to previously described Capsicum complexes: C. annuum complex (CA), C. baccatum complex (CB), C. pubescens complex (CP), and C. chacoense accessions (CA/B). Their overall mean genetic similarity index was 0.487 +/- 0.082, ranging from 0.88 to 0.32, based on Jaccard's coefficient. The highest genetic variation was observed among the accessions in CP; the accessions in CB had a low level of variation as judged from the standard deviations of the genetic similarity indices. Based on the Td-RAPD-PCR markers, the 24 accessions were divided into four major groups, three of which corresponded to the three distinct Capsicum complexes. Accessions of C. chacoense were found to be equally related to complexes CA, CB, and CP.

Assessment of genetic variation within Indian mustard (Brassica juncea) germplasm using random amplified polymorphic DNA markers

Genetic diversity among 45 Indian mustard (Brassica juncea L.) genotypes comprising 37 germplasm collections, five advance breeding lines and three improved cultivars was investigated at the DNA level using the random amplified polymorphic DNA (RAPD) technique. Fifteen primers used generated a total of 92 RAPD fragments, of which 81 (88%) were polymorphic. Of these, 13 were unique to accession 'Pak85559'. Each primer produced four to nine amplified products with an average of 6.13 bands per primer. Based on pairwise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were calculated to evaluate the relationships among the accessions. Pairwise similarity indices were higher among the oilseed accessions and cultivars showing narrow ranges of 0.77-0.99. An unweighted pair-group method with arithmetic averages cluster analysis based on these genetic similarities placed most of the collections and oilseed cultivars close to each other, showing a low level of polymorphism between the accessions used. However, the clusters formed by oilseed collections and cultivars were comparatively distinct from that of advanced breeding lines. Genetically, all of the accessions were classified into a few major groups and a number of individual accessions. Advanced breeding lines were relatively divergent from the rest of the accessions and formed independent clusters. Clustering of the accessions did not show any pattern of association between the RAPD markers and the collection sites. A low level of genetic variability of oilseed mustard was attributed to the selection for similar traits and horticultural uses. Perhaps close parentage of these accessions further contributed towards their little diversity. The study demonstrated that RAPD is a simple and fast technique to compare the genetic relationship and pattern of variation among the gene pool of this crop.

Use of random amplified polymorphic DNA markers to estimate heterosis and combining ability in tomato hybrids

Random Amplified Polymorphic DNAs (RAPD) were used to estimate genetic distances and determine the correlation between genetic distance and hybrid performance of 29 tomato lines that were the parents in a diallel mating design. Among 97 observed bands, 69 showed polymorphism and were used for establishing genetic distances based on the Nei coefficient between parents. A UPGMA dendrogram and Multi-Dimensional Scaling (MDS) analysis based on Nei genetic distances clearly clustered each group, confirming the variation at a molecular level. Correlations between genetic distances of the parents and performances of hybrids were established for various quantitative traits. Significant correlations were found between RAPD markers estimated genetic distances and MPH, HPH, SCA for some traits. The low correlation between parental genetic distances and hybrid performances for some quantitative traits suggested that RAPD markers have low linkage to Quantitative Trait Loci (QTLs) or have inadequate genome coverage for these traits. The results indicated that RAPD markers can be used as a tool for determining the extent of genetic diversity among tomato lines, for allocating genotypes into different groups and also to aid in the choice of the superior crosses to be made among tomato lines, so reducing the number of crosses required under field evaluation.

Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology

Understanding the distribution of genetic diversity among individuals, populations and gene pools is crucial for the efficient management of germplasm collections and breeding programs. Diversity analysis is routinely carried out using sequencing of selected gene(s) or molecular marker technologies. Here we report on the development of Diversity Arrays Technology (DArT) for pigeonpea (Cajanus cajan) and its wild relatives. DArT tests thousands of genomic loci for polymorphism and provides the binary scores for hundreds of markers in a single hybridization-based assay. We tested eight complexity reduction methods using various combinations of restriction enzymes and selected PstI/HaeIII genomic representation with the largest frequency of polymorphic clones (19.8%) to produce genotyping arrays. The performance of the PstI/HaeIII array was evaluated by typing 96 accessions representing nearly 20 species of Cajanus. A total of nearly 700 markers were identified with the average call rate of 96.0% and the scoring reproducibility of 99.7%. DArT markers revealed genetic relationships among the accessions consistent with the available information and systematic classification. Most of the diversity was among the wild relatives of pigeonpea or between the wild species and the cultivated C. cajan. Only 64 markers were polymorphic among the cultivated accessions. Such narrow genetic base is likely to represent a serious impediment to breeding progress in pigeonpea. Our study shows that DArT can be effectively applied in molecular systematics and biodiversity studies.

Comparison of phenotypic and molecular distances to predict heterosis and F1 performance in Ethiopian mustard (Brassica carinata A. Braun)

Predicting heterosis and F1 performance from the parental generation could largely enhance the efficiency of breeding hybrid or synthetic cultivars. This study was undertaken to determine the relationship between parental distances estimated from phenotypic traits or molecular markers with heterosis, F1 performance and general combining ability (GCA) in Ethiopian mustard (Brassica carinata). Nine inbred lines representing seven different geographic regions of Ethiopia were crossed in half-diallel. The nine parents along with their 36 F1s were evaluated in a replicated field trail at three locations in Ethiopia. Distances among the parents were calculated from 14 phenotypic traits (Euclidean distance, ED) and 182 random amplified polymorphic DNA (RAPD) markers (Jaccard's distances, JD), and correlated with heterosis, F1 performance and GCA sum of parents (GCAsum). The correlation between phenotypic and molecular distances was low (r=0.34, P< or =0.05). Parents with low molecular distance also had low phenotypic distance, but parents with high molecular distance had either high, intermediate or low phenotypic distance. Phenotypic distance was highly significantly correlated with mid-parent heterosis (r=0.53), F1 performance (r=0.61) and GCA (r=0.79) for seed yield. Phenotypic distance was also positively correlated with (1) heterosis, F1 performance and GCA for plant height and seeds plant(-1), (2) heterosis for number of pods plant(-1), and (3) F1 performance for 1,000 seed weight. Molecular distance was correlated with GCAsum (r=0.36, P< or =0.05) but not significantly with heterosis and F1 performance for seed yield. For each parent a mean distance was calculated by averaging the distances to the eight other parents. Likewise, mean heterosis was estimated by averaging the heterosis obtained when each parent is crossed with the other eight. For seed yield, both mean ED and JD were significantly correlated with GCA (r=0.90, P< or =0.01 for ED and r=0.68, P< or =0.05 for JD) and mean heterosis (r=0.79, P< or =0.05 for ED and r=0.77, P< or =0.05 for JD). In conclusion, parental distances estimated from phenotypic traits better predicted heterosis, F1 performance and GCA than distances estimated from RAPD markers.

Genetic relationships within Brassica rapa as inferred from AFLP fingerprints

Amplified fragment length polymorphism (AFLP) markers were employed to assess the genetic diversity amongst two large collections of Brassica rapa accessions. Collection A consisted of 161 B. rapa accessions representing different morphotypes among the cultivated B. rapa, including traditional and modern cultivars and breeding materials from geographical locations from all over the world and two Brassica napus accessions. Collection B consisted of 96 accessions, representing mainly leafy vegetable types cultivated in China. On the basis of the AFLP data obtained, we constructed phenetic trees using MEGA 2.1: software. The level of polymorphism was very high, and it was evident that the amount of genetic variation present within the groups was often comparable to the variation between the different cultivar groups. Cluster analysis revealed groups, often with low bootstrap values, which coincided with cultivar groups. The most interesting information revealed by the phenetic trees was that different morphotypes are often more related to other morphotypes from the same region (East Asia vs. Europe) than to similar morphotypes from different regions, suggesting either an independent origin and or a long and separate domestication and breeding history in both regions.

Molecular Discrimination of Medicinal Astragali Radix by RAPD Analysis

The randomly amplified polymorphic DNA (RAPD) analysis has been applied for estimating genetic diversity in plant populations or cultivars. To discriminate geographical origin among Astragali radix populations, RAPD analysis was carried out using 20 mer-random primers. The similarity coefficient between the DNA of Astragali radix plants analyzed was 0.527. Although the coefficients of similarity were high, primer 7, 8 and 10 gave distinguishable bands between Korean and Chinese Astragali radix. We obtained the specific RAPD markers to discriminate between Korean and Chinese Astragali radix at a DNA level. These results suggest that this method is able to discriminate the concerned Astragali radix geographical origin species. Also, this is the first report on the genetic diversity in geographical origin among Astragali radix populations using RAPD analysis. Broader application of this approach to authenticate other morphologically similar medicinal materials is rationalized.

Plant molecular biology and biotechnology research in the post-recombinant DNA era

After the beginning of the recombinant DNA era in the mid-1970s, researchers in India started to make use of the new technology to understand the structure of plant genes and regulation of their expression. The outcome started to appear in print in early the 1980s and genes for histones, tubulin, photosynthetic membrane proteins, phototransduction components, organelles and those regulated differentially by developmental and extrinsic signals were sequenced and characterized. Some genes of biotechnological importance like those encoding an interesting seed protein and the enzyme glyoxalase were also isolated. While work on the characterization of genome structure and organization was started quite early, it remained largely focused on the identification of DNA markers and genetic variability. In this context, the work on mustard, rice and wheat is worth mentioning. In the year 2000, India became a member of the international consortium to sequence entire rice genome. Several laboratories have also given attention to regulated expression of plastid and nuclear genes as well as to isolate target-specific promoters or design promoters with improved potential. Simultaneously, transgenic systems for crops like mustard, rice, wheat, cotton, legumes and several vegetables have been established. More recently, genes of agronomic importance like those for insect resistance, abiotic stress tolerance, nutritional improvement and male sterility, isolated in India or abroad, have been utilized for raising transgenics for crop improvement. Some of these transgenics have already shown their potential in containment facility or limited field trials conducted under the stipulated guidelines. Plant molecular biology and biotechnology are thus clearly poised to make an impact on research in basic biology and agriculture in the near future.

Development of an AFLP-based linkage map and localization of QTLs for seed fatty acid content in condiment mustard (Brassica juncea)

A genetic linkage map of Brassica juncea based on AFLP and RAPD markers was constructed using 131 F1-derived doubled-haploid (DH) plants from a cross between two mustard lines. The map included 273 markers (264 AFLP, 9 RAPD) arranged on 18 linkage groups, and covered a total genetic distance of 1641 cM; 18.3% of the AFLP markers showed a segregation distortion (P < 0.01). The markers with biased segregation were clustered on seven linkage groups. QTLs for oil contents, palmitic acid (16:0), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), linolenic acid (18:3), eicosenoic acid (20:1), and erucic acid (22:1), were mapped on the AFLP linkage map. Correlation studies among fatty acids in the DH population and the localization of QTLs involved in their control indicated that a major gene located on linkage group (LG) 2 controlled the elongation step of erucic acid.

Determination of the site of origin of Pinellia ternata roots based on RAPD analysis and PCR-RFLP

Analyses of randomly amplified polymorphic DNA (RAPD) and PCR-restriction fragment length polymorphism (PCR-RFLP) were performed in an effort to distinguish between two different origins of Pinellia ternata. To determine whether the origin of Pinellia ternata is in China or Korea. RAPD analysis was carried out using ten 20-mer random primers. Although the coefficients of similarity between the DNA of Chinese and Korean accessions of Pinellia ternata were high, distinguishable band patterns were observed in the reaction performed using primer numbers 3, 6 and 10. Primer 3 produced one (410 bp) and primer 6 produced four (410 bp, 350 bp, 300 bp, 250 bp) Chinese Pinellia-specific fragments. Primer 10 produced one (900 bp) Korean Pinellia rhizome-specific fragment. In addition, using PCR-RFLP analysis, different fingerprints were obtained from Korean and Chinese Pinellia ternata respectively. These results suggest that the analyses with RAPD and PCR-RFLP can be used to authenticate the relevant Chinese and Korean herbal medicines.

Construction of an RAPD linkage map and localization of QTLs for oleic acid level using recombinant inbreds in mustard (Brassica juncea)

RAPD markers were employed for construction of a linkage map and localization of QTLs for oleic acid level using a set of 94 recombinant inbred lines (RILs) of mustard (Brassica juncea L.) as a mapping population. Only 30% of the 235 random primers used were useful in terms of polymorphism detected and the reproducibility of those patterns. Normal Mendelian segregation was observed for the majority of the 130 markers obtained with 71 informative primers; only 13.1% deviated (P < 0.01) from the expected 1:1 ratio. One-hundred and fourteen markers were assigned to 21 linkage groups (LGs) covering a total length of 790.4 cM with an average distance of 6.93 cM between markers. Two quantitative trait loci (QTL) for oleic acid level were mapped to 14- and 10.6-cM marker intervals on two different LGs. Both loci together explained 32.2% of phenotypic variance. One major QTL explained 28.5% of the trait variance observed in this species.

Molecular authentication of Panax ginseng species by RAPD analysis and PCR-RFLP

In order to develop convenient and reproducible methods for the identification of ginseng drugs at a DNA level, randomly amplified polymorphic DNA (RAPD) and PCR-restriction fragment length polymorphism (PCR-RFLP) analyses were applied within Panax species. To authenticate Panax ginseng among ginseng populations, RAPD analysis was carried out using a 20 mer-random primer. The similarity coefficients among the DNA of ginseng plants analyzed were low, ranging from 0.197 to 0.491. In addition, by using PCR-RFLP analysis, very different fingerprints were obtained within Korean ginseng plants. These results suggest that these methods are able to authenticate the concerned Panax species. Broader application of this approach to authenticate other morphologically similar medicinal materials is rationalized.

Molecular phylogeny of mangroves. VI. Intraspecific genetic variation in mangrove species Excoecaria agallocha L. (Euphorbiaceae)

Genomic DNA from 84 individuals of Excoecaria agallocha from seven mangrove populations were analysed for random amplified polymorphic DNAs (RAPDs) using 16 random 10-mer primers. Polymorphism within populations varied from 20% to 31%. At the interpopulation level, 111/149 (74%) of RAPDs were polymorphic. Restriction fragment length polymorphism (RFLP) analysis of 21 individuals (3 individuals randomly selected from the 7 populations) using 30 probe-enzyme combinations revealed a high level of interpopulation polymorphism (62.2%) indicating interpopulation genetic divergence. The polymorphic RAPDs and RFLPs were pooled, and clustering was carried out based on mean similarity for individual populations. The dendrogram showed groupings of populations from the West and East Coasts of India into separate clusters, at 60% similarity level. Further, RAPD and RFLP analysis of male and female plants showed approximately the same level of variation in both sexes, and no sex-linked markers were found. These results demonstrate that considerable intrapopulation and interpopulation genetic variations exist in E. agallocha, and that lack of genetic variation is not the reason for the morphological uniformity observed across the range of the species.

Evaluation of genetic diversity and genome fingerprinting ofPandorea(Bignoniaceae) by RAPD and inter-SSR PCR

Evaluation of the genetic relationship between five Pandorea jasminoides and eight Pandorea pandorana cultivars was investigated using random amplification of polymorphic DNA and inter-SSR (simple sequence repeat) PCR. Twenty-five random primers generated 375 polymorphic products with a mean number of 15 polymorphic bands per primer. The mean number of polymorphic products obtained by inter-SSR PCR was 18.7 per primer. Random amplification of polymorphic DNA and inter-SSR amplification of genomic DNA revealed higher genetic variability among the cultivars of P. pandorana than among those of P. jasminoides. Two random primers each produced species-specific amplification products in both the Pandorea species, while four random primers and two SSRs produced species-specific amplification products in only one of the species. A distinct cultivar-specific DNA fingerprint for each of the 13 cultivars was obtained by 2 random primers and 1 SSR primer. A dendrogram constructed on the basis of 513 amplification products generated by random amplification of polymorphic DNA and inter-SSR PCR showed the separation of 13 cultivars into two major groups that corresponded to P. jasminoides and P. pandorana. The data resulting from random amplification of polymorphic DNA and inter-SSR PCR were congruent. Our study showed that it should be possible to take advantage of existing genetic variability of P. pandorana to enhance the narrow genetic base of P. jasminoides by interspecific crosses. Such crosses would have the potential to generate novel commercially important elite cultivars of Pandorea.Key words: Pandorea, RAPD, inter-SSR, DNA fingerprint, genetic variability.

Genetic variation between several species of sections Extranervosae, Caulorrhizae, Heteranthae, and Triseminatae (genus Arachis) estimated by DNA polymorphism

Genetic variation within and among accessions of the genusArachis representing sections Extranervosae, Caulorrhizae, Heteranthae, and Triseminatae was evaluated using RFLP and RAPD markers. RAPD markers revealed a higher level of genetic diversity than did RFLP markers, both within and among the species evaluated. Phenograms based on various band-matching algorithms revealed three major clusters of similarity among the sections evaluated. The first group included the species from section Extranervosae, the second group consisted of sections Triseminatae, Caulorrhizae, and Heteranthae, and the third group consisted of one accession of Arachis hypogaea, which had been included as a representative of section Arachis. The phenogramsobtained from the RAPD and RFLP data were similar but not identical. Arachis pietrarellii, assayed only by RAPD, showed a high degree of genetic similarity with Arachis villosulicarpa. This observation supported the hypothesis that these two species are closely related. It was also shown that accession V 7786, previously considered to be Arachis sp. aff.pietrarellii, and assayed using both RFLPs and RAPDs, was possibly a new species from section Extranervosae, but very distinct from A. pietrarellii.Keywords: Arachis, RFLP, RAPD, genetic similarity, genetic distance.

Genetic diversity evaluation of some elite cotton varieties by RAPD analysis

Random amplified polymorphic DNA (RAPD) analysis was used to evaluate the genetic diversity of elite commercial cotton varieties. Twenty two varieties belonging to Gossypium hirsutum L. and one to G. arboreum L. were analyzed with 50 random decamer primers using the polymerase chain reaction (PCR). Forty nine primers detected polymorphism in all 23 cotton varieties, while one produced monomorphic amplification profiles. A total of 349 bands were amplified, 89.1% of which were polymorphic. Cluster analysis by the unweighted pair group method of arithmetic means (UPGMA) showed that 17 varieties can be placed in two groups with a similarity ranging from 81.51% to 93.41%. G. hirsutum L. varieties S-12, V3 and MNH-93 showed a similarity of 78.12, 74.46 and 69.56% respectively with rest of the varieties. One variety, CIM-1100, showed 57.02% similarity and was quite distinct. The diploid cotton G. arboreum L. var. Ravi was also very distinct from rest of its tetraploid counterparts and showed only 55.7% similarity. The analysis revealed that the intervarietal genetic relationships of several varieties is related to their center of origin. As expected, most of the varieties have a narrow genetic base. The results obtained can be used for the selection of possible parents to generate a mapping population. The results also reveal the genetic relationship of elite commercial cotton varieties with some standard "Coker" varieties and the diploid G. arboreum L. var. Ravi (old world cotton).

Population genetics of cultivated common buckwheat, Fagopyrum esculentum Moench. X. Diffusion routes revealed by RAPD markers

Diffusion routes of common buckwheat were investigated by constructing phylogenetic trees based on variability of RAPD markers among 46 land races and two natural populations of the ancestor. Thirty two primers out of 40 generated reliable RAPD bands, 295 in total. The percentage of polymorphic bands was the highest (45.9%) in southern China, the region in which buckwheat originated, and it declined sharply from southern China to the peripheral range of buckwheat cultivation. Phylogenetic trees for land races were constructed from RAPD variability by the unweighted pair group (UPG) and neighbors joining (NJ) methods. They suggest two major routes of diffusion of buckwheat cultivation; one from southern China-->northern China-->Korea-->Japan, the other from southern China-->Bhutan-->Nepal-->Kashmir-->Karakoram and the Hindukush.

The use of RAPD markers inHordeumphylogeny

The phylogenetic relationships among 39 wild Hordeum species, subspecies, and cultivated barley were investigated using RAPD markers as discriminating characters. Seventy-six RAPD fragments were generated using 12 single decameric primers of arbitrary nucleotide sequences. Amplification reactions resulted in fragments ranging in length between 200 and 2000 bp. Clearly resolved bands were scored for their presence or absence in a binary matrix. Amplified products were treated as independent characters to generate a phenogram using the NTSYS-PC package. Tree topology was generally found to be consistent with those based on morphological treatments. However, a few species like H. erectifolium, H. jubatum and, to a lesser extent, H. bulbosum occupied a position different from previous classifications. The results demonstrated that RAPD technology represents a useful and reliable tool for detecting polymorphism for phylogenetic studies. Key words : RAPD analysis, molecular markers, phylogenetic studies, Hordeum species, barley.

Molecular mapping and tagging of genes in crop plants

In India, molecular mapping and tagging of agronomically important genes using RFLP and RAPD markers have been carried out in three different crops: rice, mustard and chickpea. In rice, tagging of genes for resistance to gall midge and blast has been accomplished. Molecular mapping of cooking quality traits in rice is in progress. For fingerprinting rice cultivars, suitable probe enzyme combinations have been identified. In mustard, a partial RFLP linkage map has been constructed and one of the yellow seed-coat colour loci has been mapped. Significant associations of RFLP markers with quantitative traits have also been established. Potential use of RAPD markers to identify heterotic groups among mustard accessions has been demonstrated. In chickpea, the occurrence of considerable interspecific DNA polymorphism as revealed by RAPD analysis has facilitated construction of a partial linkage map.