Identification of two RAPD markers tightly linked with the Nicotiana debneyi gene for resistance to black root rot of tobacco

Understanding Root Rot Disease in Agricultural Crops

Root rot diseases remain a major global threat to the productivity of agricultural crops. They are usually caused by more than one type of pathogen and are thus often referred to as a root rot complex. Fungal and oomycete species are the predominant participants in the complex, while bacteria and viruses are also known to cause root rot. Incorporating genetic resistance in cultivated crops is considered the most efficient and sustainable solution to counter root rot, however, resistance is often quantitative in nature. Several genetics studies in various crops have identified the quantitative trait loci associated with resistance. With access to whole genome sequences, the identity of the genes within the reported loci is becoming available. Several of the identified genes have been implicated in pathogen responses. However, it is becoming apparent that at the molecular level, each pathogen engages a unique set of proteins to either infest the host successfully or be defeated or contained in attempting so. In this review, a comprehensive summary of the genes and the potential mechanisms underlying resistance or susceptibility against the most investigated root rots of important agricultural crops is presented.

Molecular breeding approaches for production of disease-resilient commercially important tobacco

Tobacco is one of the most widely cultivated nonfood cash crops, a source of income, model organism for plant molecular research, a natural pesticide and of pharmaceutical importance. First domesticated in South Americas, the modern-day tobacco (Nicotiana tabacum) is now cultivated in more than 125 countries to generate revenues worth billions of dollars each year. However, the production of this crop is highly threatened by the global presence of devastating infectious agents, which cause huge fiscal loss. These threats have been battled through breeding for acquiring disease resilience in tobacco plants, first, via conventional and now with the use of modern molecular breeding approaches. For efficacy and precision, the characterization of the genetic components underlying disease resistance is the key tool in tobacco for resistance breeding programs. The past few decades have witnessed significant progress in resilience breeding through advanced molecular techniques. The current review discusses history of tobacco breeding since its time of origin till date, highlighting the most widely used techniques and recent advances in molecular research and strategies for resistance breeding. In addition, we narrate the budding possibilities for the future. This review will provide a comprehensive and valuable information for the tobacco growers and researchers to deal with the destructive infectious diseases.

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.

Molecular Linkage Mapping and Marker-Trait Associations with NlRPT, a Downy Mildew Resistance Gene in Nicotiana langsdorffii

Nicotiana langsdorffii is one of two species of Nicotiana known to express an incompatible interaction with the oomycete Peronospora tabacina, the causal agent of tobacco blue mold disease. We previously showed that incompatibility is due to the hypersensitive response (HR), and plants expressing the HR are resistant to P. tabacina at all stages of growth. Resistance is due to a single dominant gene in N. langsdorffii accession S-4-4 that we have named NlRPT. In further characterizing this unique host-pathogen interaction, NlRPT has been placed on a preliminary genetic map of the N. langsdorffii genome. Allelic scores for five classes of DNA markers were determined for 90 progeny of a "modified backcross" involving two N. langsdorffii inbred lines and the related species N. forgetiana. All markers had an expected segregation ratio of 1:1, and were scored in a common format. The map was constructed with JoinMap 3.0, and loci showing excessive transmission distortion were removed. The linkage map consists of 266 molecular marker loci defined by 217 amplified fragment length polymorphisms (AFLPs), 26 simple-sequence repeats (SSRs), 10 conserved orthologous sequence markers, nine inter-simple sequence repeat markers, and four target region amplification polymorphism markers arranged in 12 linkage groups with a combined length of 1062 cM. NlRPT is located on linkage group three, flanked by four AFLP markers and one SSR. Regions of skewed segregation were detected on LGs 1, 5, and 9. Markers developed for N. langsdorffii are potentially useful genetic tools for other species in Nicotiana section Alatae, as well as in N. benthamiana. We also investigated whether AFLPs could be used to infer genetic relationships within N. langsdorffii and related species from section Alatae. A phenetic analysis of the AFLP data showed that there are two main lineages within N. langsdorffii, and that both contain populations expressing dominant resistance to P. tabacina.

Genes in S and T subgenomes are responsible for hybrid lethality in interspecific hybrids between Nicotiana tabacum and Nicotiana occidentalis

BACKGROUND

Many species of Nicotiana section Suaveolentes produce inviable F(1) hybrids after crossing with Nicotiana tabacum (genome constitution SSTT), a phenomenon that is often called hybrid lethality. Through crosses with monosomic lines of N. tabacum lacking a Q chromosome, we previously determined that hybrid lethality is caused by interaction between gene(s) on the Q chromosome belonging to the S subgenome of N. tabacum and gene(s) in Suaveolentes species. Here, we examined if hybrid seedlings from the cross N. occidentalis (section Suaveolentes)×N. tabacum are inviable despite a lack of the Q chromosome.

METHODOLOGY/PRINCIPAL FINDINGS

Hybrid lethality in the cross of N. occidentalis×N. tabacum was characterized by shoots with fading color. This symptom differed from what has been previously observed in lethal crosses between many species in section Suaveolentes and N. tabacum. In crosses of monosomic N. tabacum plants lacking the Q chromosome with N. occidentalis, hybrid lethality was observed in hybrid seedlings either lacking or possessing the Q chromosome. N. occidentalis was then crossed with two progenitors of N. tabacum, N. sylvestris (SS) and N. tomentosiformis (TT), to reveal which subgenome of N. tabacum contains gene(s) responsible for hybrid lethality. Hybrid seedlings from the crosses N. occidentalis×N. tomentosiformis and N. occidentalis×N. sylvestris were inviable.

CONCLUSIONS/SIGNIFICANCE

Although the specific symptoms of hybrid lethality in the cross N. occidentalis×N. tabacum were similar to those appearing in hybrids from the cross N. occidentalis×N. tomentosiformis, genes in both the S and T subgenomes of N. tabacum appear responsible for hybrid lethality in crosses with N. occidentalis.

Somatic hybrid plants of Nicotiana x sanderae (+) N. debneyi with fungal resistance to Peronospora tabacina

BACKGROUND AND AIMS

The genus Nicotiana includes diploid and tetraploid species, with complementary ecological, agronomic and commercial characteristics. The species are of economic value for tobacco, as ornamentals, and for secondary plant-product biosynthesis. They show substantial differences in disease resistance because of their range of secondary products. In the last decade, sexual hybridization and transgenic technologies have tended to eclipse protoplast fusion for gene transfer. Somatic hybridization was exploited in the present investigation to generate a new hybrid combination involving two sexually incompatible tetraploid species. The somatic hybrid plants were characterized using molecular, molecular cytogenetic and phenotypic approaches.

METHODS

Mesophyll protoplasts of the wild fungus-resistant species N. debneyi (2n = 4x = 48) were electrofused with those of the ornamental interspecific sexual hybrid N. × sanderae (2n = 2x = 18). From 1570 protoplast-derived cell colonies selected manually in five experiments, 580 tissues were sub-cultured to shoot regeneration medium. Regenerated plants were transferred to the glasshouse and screened for their morphology, chromosomal composition and disease resistance.

KEY RESULTS

Eighty-nine regenerated plants flowered; five were confirmed as somatic hybrids by their intermediate morphology compared with parental plants, cytological constitution and DNA-marker analysis. Somatic hybrid plants had chromosome complements of 60 or 62. Chromosomes were identified to parental genomes by genomic in situ hybridization and included all 18 chromosomes from N. × sanderae, and 42 or 44 chromosomes from N. debneyi. Four or six chromosomes of one ancestral genome of N. debneyi were eliminated during culture of electrofusion-treated protoplasts and plant regeneration. Both chloroplasts and mitochondria of the somatic hybrid plants were probably derived from N. debneyi. All somatic hybrid plants were fertile. In contrast to parental plants of N. × sanderae, the seed progeny of somatic hybrid plants were resistant to infection by Peronospora tabacina, a trait introgressed from the wild parent, N. debneyi.

CONCLUSIONS

Sexual incompatibility between N. × sanderae and N. debneyi was circumvented by somatic hybridization involving protoplast fusion. Asymmetrical nuclear hybridity was seen in the hybrids with loss of chromosomes, although importantly, somatic hybrids were fertile and stable. Expression of fungal resistance makes these somatic hybrids extremely valuable germplasm in future breeding programmes in ornamental tobacco.

Tobacco blue mould disease caused by Peronospora hyoscyami f. sp. tabacina

Blue mould [Peronospora hyoscyami f. sp. tabacina (Adam) Skalicky 1964] is one of the most important foliar diseases of tobacco that causes significant losses in the Americas, south-eastern Europe and the Middle East. This review summarizes the current knowledge of the mechanisms employed by this oomycete pathogen to colonize its host, with emphasis on molecular aspects of pathogenicity. In addition, key biochemical and molecular mechanisms involved in tobacco resistance to blue mould are discussed.

TAXONOMY

Kingdom: Chromista (Straminipila); Phylum: Heterokontophyta; Class: Oomycete; Order: Peronosporales; Family: Peronosporaceae; Genus: Peronospora; Species: Peronospora hyoscyami f. sp. tabacina.

DISEASE SYMPTOMS

The pathogen typically causes localized lesions on tobacco leaves that appear as single, or groups of, yellow spots that often coalesce to form light-brown necrotic areas. Some of the leaves exhibit grey to bluish downy mould on their lower surfaces. Diseased leaves can become twisted, such that the lower surfaces turn upwards. In such cases, the bluish colour of the diseased plants becomes quite conspicuous, especially under moist conditions when sporulation is abundant. Hence the name of the disease: tobacco blue mould.

INFECTION PROCESS

The pathogen develops haustoria within plant cells that are thought to establish the transfer of nutrients from the host cell, and may also act in the delivery of effector proteins during infection.

RESISTANCE

Several defence responses have been reported to occur in the Nicotiana tabacum-P. hyoscyami f. sp. tabacina interaction. These include the induction of pathogenesis-related genes, and a correlated increase in the activities of typical pathogenesis-related proteins, such as peroxidases, chitinases, beta-1,3-glucanases and lipoxygenases. Systemic acquired resistance is one of the best characterized tobacco defence responses activated on pathogen infection.

Molecular diversity in the genus Nicotiana as revealed by randomly amplified polymorphic DNA

The genus Nicotiana consists of 64 recognized species of which, only two species, tabacum and rustica are cultivated extensively. Wild Nicotiana species are storehouses of genes for several diseases and pests, besides genes for several important phytochemicals and quality traits, which are not present in cultivated varieties. Randomly amplified polymorphic DNA (RAPD) analysis was used to determine the degree of genetic variation in the genus Nicotiana and to develop species specific markers. Twenty two species and two interspecific hybrids were analyzed by using 18 random decamer primers. Genetic polymorphism abounds among the wild species of genus Nicotiana (99.5 %) as evidenced by the high degree of polymorphism in RAPD profiles. The pairwise similarity measures in the species of subgenus Rustica was 0.252 whereas in the subgenus Tabacum was 0.189, suggesting that there was significant diversity among the species of these subgenera. In the species of subgenus Petunioides, the range of pairwise similarity measures was 0.128 to 0.941. The clustering pattern coincided with the traditional classification of Nicotiana species. All the primers generated specific bands in the various species. Thirty six species-specific markers identified in the present study will be useful in interspecific breeding programs.

Use of transferable Nicotiana tabacum L. microsatellite markers for investigating genetic diversity in the genus Nicotiana

The recent development of microsatellite markers for tobacco, Nicotiana tabacum L., may be valuable for genetic studies within the genus Nicotiana. The first objective was to evaluate transferability of 100 N. tabacum microsatellite primer combinations to 5 diploid species closely related to tobacco. The number of primer combinations that amplified scorable bands in these species ranged from 42 to 56. Additional objectives were to assess levels of genetic diversity amongst available accessions of diploid relatives closely related to tobacco (species of sections Sylvestres and Tomentosae), and to evaluate the efficacy of microsatellite markers for establishing species relationships in comparison with existing phylogenetic reconstructions. A subset of 46 primer combinations was therefore used to genotype 3 synthetic tobaccos and an expanded collection of 51 Nicotiana accessions representing 15 species. The average genetic similarity for 7 diverse accessions of tobacco was greater than the average similarity for N. otophora accessions, but lower than the average genetic similarities for N. sylvestris, N. tomentosa, N. kawakamii, and N. tomentosiformis accessions. A microsatellite-based phylogenetic tree was largely congruent with taxonomic representations based on morphological, cytological, and molecular observations. Results will be useful for selection of parents for creation of diploid mapping populations and for germplasm introgression activities.

Analysis of an introgressed Nicotiana tomentosa genomic region affecting leaf number and correlated traits in Nicotiana tabacum

Germplasm from closely related diploid relatives of tobacco (Nicotiana tabacum L.) could be of value for continued genetic modification of this species and for mapping quantitative trait loci (QTLs). We examined near isogenic tobacco lines and hybrids differing for an introgressed genomic region from N. tomentosa Ruiz and Pavon designated as Many Leaves that exhibits a large influence on leaf number and correlated traits. Within a 'Red Russian' genetic background, the region acted in an additive to partially dominant fashion to delay flowering time, and increase leaf number, plant height, and green leaf yield. Evidence of epistasis was observed as the region affected these traits to varying degrees in diverse near isogenic hybrids. Fifteen amplified fragment length polymorphism (AFLP) markers of N. tomentosa origin were mapped within a single linkage group of 34.5 cM using a population of 207 BC(1)F(1) individuals segregating for Many Leaves. Composite interval mapping produced 2-LOD confidence intervals for likely QTL positions influencing leaf number (3.1 cM region), plant height (2.9 cM region), and days to flowering (3.3 cM region). These intervals were overlapping. Results demonstrate that genomic regions with large genetic effects can be transferred to tobacco from closely related diploid relatives, and that sufficient recombination within these regions may permit mapping of genes controlling quantitative traits. Materials and results described here may be useful in future research to gain insight on the genetic control of the transition from vegetative to reproductive development in Nicotiana.

Development of SCAR markers linked to three disease resistances based on AFLP within Nicotiana tabacum L

Amplified fragment length polymorphism (AFLP) was conducted on a set of 92 Nicotiana tabacum L. accessions from diverse types (flue-cured, dark air-cured, burley, oriental, and cigar wrapper) and breeding origins to identify markers associated with disease resistances. Eleven primer combinations were required to identify 33 polymorphic fragments. This allowed the identification of 92% of these accessions, and yielded sufficient information for building a neighbor joining tree. Clusters of accessions with common traits or breeding origins were observed. An important part of this polymorphism could be related to interspecific introgressions from other Nicotiana species, performed during the breeding history of N. tabacum to confer resistance to pathogens. Seven fragments were associated with three different resistances: two for the blue-mold (Peronospora tabacina Adam) resistance derived from Nicotiana debneyi Domin, two for the Va gene (Potato Virus Y susceptibility), and three for the black root rot (Chalara elegans) resistance of N. debneyi origin. Some of these markers were converted into sequence characterized amplified region markers, and validated on recombinant inbred lines or doubled-haploid lines.

Genomic relationships among Nicotiana species with different ploidy levels revealed by 5S rDNA spacer sequences and FISH/GISH

We used the intergenic spacer sequences of the 5S ribosomal RNA genes (5S rDNA) to obtain insights into the genomic origin of putative amphidiploid/tetraploid species with 2n = 48 and their descendants in Nicotiana. Amplification of the spacer sequences and subsequent multiple alignment using the consensus sequences from each species, showed that two Australian species shared common large deletions, suggesting that the origin of the 5S rDNA is closely related in these species. Comparison of the spacer sequences with those from diploid (2n = 24) Nicotiana species made it possible to detect some groups consisting of the sequences from the 2n = 24 and 2n = 48 level species. Chromosomal localizations of the 5S rDNA arrays were similar in most groups. The relationships suggested by the 5S rDNA were also assessed at the genome level by using genomic in situ hybridization. We showed that the grouping based on the 5S rDNA spacer sequence reflects high genomic homology between 2n = 24 and 2n = 48 level species. As a result, the putative polyploid species such as N. debneyi, N. quadrivalvis, and N. africana were suggested to involve the close relatives of the diploid species such as N. glauca, N. obtusifolia and N. sylvestris, and N. langsdorffii, respectively, in their speciation. Our results are generally in agreement with the relationships previously suggested by morphological and cytogenetic observations, and some novel relationships were also revealed.

Marker-Assisted Selection for Resistance to Black Shank Disease in Tobacco

Bulked segregant (BSA) and random amplified polymorphic DNA (RAPD) analyses were used to identify markers linked to the dominant black shank resistance gene, Ph, from flue-cured tobacco (Nicotiana tabacum) cv. Coker 371-Gold. Sixty RAPD markers, 54 in coupling and 6 in repulsion phase linkage to Ph, were identified in a K 326-derived BC₁F₁ (K 326-BC₁F₁) doubled haploid (DH) population. Thirty RAPD markers, 26 in coupling and 4 in repulsion phase linkage to Ph, were used to screen 149 K 326-BC₂F₁ haploid plants. Complete linkage between the 26 coupling phase markers and Ph was confirmed by screening 149 K 326-BC₂F₁ DH lines produced from the haploid plants in black shank nurseries. RAPD markers OPZ-5₇₇₀ in coupling and OPZ-7₃₇₀ in repulsion phase linkage were used to select plants homozygous for the Ph gene for further backcrossing to the widely grown flue-cured cultivar K 326. Black shank disease nursery evaluation of 11 K 326-BC₄S₁ lines and their testcross hybrids to a susceptible tester confirmed linkage between Ph and OPZ-5₇₇₀. The results demonstrated the efficiency of marker-assisted selection for Ph using a RAPD marker linked in coupling and repulsion. Complete linkage between 26 RAPD markers and the Ph gene was confirmed in the K 326-BC₅ generation, and RAPD phenotypes were stable across generations and ploidy levels. These RAPD markers are useful in marker-assisted selection for Ph, an important black shank resistance gene in tobacco.

Origin of the Black Shank Resistance Gene, Ph, in Tobacco Cultivar Coker 371-Gold

Flue-cured tobacco (Nicotiana tabacum) cultivar Coker 371-Gold (C 371-G) possesses a dominant gene, Ph, that confers high resistance to black shank disease, caused by race 0 of the soil-borne pathogen Phytophthora parasitica var. nicotianae. The origin of this gene is unknown. Breeding lines homozygous for the Ph gene were hybridized with NC 1071 and L8, flue-cured and burley genotypes known to possess qualitative resistance genes from Nicotiana plumbaginifolia and N. longiflora, respectively. The F₁ hybrids were out-crossed to susceptible testers and the progenies evaluated in field black shank nurseries and in greenhouse disease tests with P. parasitica var. nicotianae race 0. Results showed that Ph was allelic to Php from N. plumbaginifolia in NC 1071. Testcross populations of hybrids between burley lines homozygous for Ph and L8, possessing Phl from N. longiflora, showed that Ph and Phl integrated into the same tobacco chromosome during interspecific transfer. Nevertheless, the two loci were estimated to be 3 cM apart. Random amplified polymorphic DNA (RAPD) analyses of the testcross progenies confirmed that recombination between the two loci was occurring. Forty-eight RAPD markers linked to Ph in doubled haploid lines were used in cluster analyses with multiple accessions of N. longiflora and N. plumbaginifolia, breeding lines L8, NC 1071, and DH92-2770-40, and cultivars K 326, Hicks, and C 371-G. A cladogram or region tree confirmed the data obtained from field and greenhouse trials, that Ph, transferred from C 371-G to DH92-2770-40, and Php in NC 1071 were allelic and originated from N. plumbaginifolia.

Development of resistance gene analog polymorphism markers for the Yr9 gene resistance to wheat stripe rust

The Yr9 gene, which confers resistance to stripe rust caused by Puccinia striiformis f.sp. tritici (P. s. tritici) and originated from rye, is present in many wheat cultivars. To develop molecular markers for Yr9, a Yr9 near-isogenic line, near-isogenic lines with nine other Yr genes, and the recurrent wheat parent 'Avocet Susceptible' were evaluated for resistance in the seedling stage to North American P. s. tritici races under controlled temperature in the greenhouse. The resistance gene analog polymorphism (RGAP) technique was used to identify molecular markers for Yr9. The BC7:F2 and BC7:F3 progeny, which were developed by backcrossing the Yr9 donor wheat cultivar Clement with 'Avocet Susceptible', were evaluated for resistance to stripe rust races. Genomic DNA was extracted from 203 BC7:F2 plants and used for cosegregation analysis. Of 16 RGAP markers confirmed by cosegregation analysis, 4 were coincident with Yr9 and 12 were closely linked to Yr9 with a genetic distance ranging from 1 to 18 cM. Analyses of nulli-tetrasomic 'Chinese Spring' lines with the codominant RGAP marker Xwgp13 confirmed that the markers and Yr9 were located on chromosome 1B. Six wheat cultivars reported to have 1B/1R wheat-rye translocations and, presumably, Yr9, and two rye cultivars were inoculated with four races of P. s. tritici and tested with 9 of the 16 RGAP markers. Results of these tests indicate that 'Clement', 'Aurora', 'Lovrin 10', 'Lovrin 13', and 'Riebesel 47/51' have Yr9 and that 'Weique' does not have Yr9. The genetic information and molecular markers obtained from this study should be useful in cloning Yr9, in identifying germplasm that may have Yr9, and in using marker-assisted selection for combining Yr9 with other stripe rust resistance genes.Key words: molecular markers, Puccinia striiformis f.sp. tritici, resistance gene analog polymorphism, Triticum aestivum.