Genetic Diversity at Resistance Gene Clusters in Wild Populations of Lactuca

Genetic resistance is often the least expensive, most effective, and ecologically-sound method of disease control. It is becoming apparent that plant genomes contain large numbers of disease resistance genes. However, the numbers of different resistance specificities within a genepool and the genetic mechanisms generating diversity are poorly understood. Our objectives were to characterize diversity in clusters of resistance genes in wild progenitors of cultivated lettuce in Israel and California in comparison to diversity within cultivated lettuce, and to determine the extent of gene flow, recombination, and genetic instability in generating variation within clusters of resistance genes. Genetic diversity of resistance genes was analyzed in wild and cultivated germplasm using molecular markers derived from lettuce resistance gene sequences of the NBS-LRR type that mapped to the major cluster if resistance genes in lettuce (Sicard et al. 1999). Three molecular markers, one microsatellite marker and two SCAR markers that amplified LRR- encoding regions, were developed from sequences of resistance gene homologs at the Dm3 cluster (RGC2s) in lettuce. Variation for these markers was assessed in germplasm including 74 genotypes of cultivated lettuce, L. saliva and 71 accessions of the three wild Lactuca spp., L. serriola, L. saligna and L. virosa that represent the major species in the sexually accessible genepool for lettuce. Diversity was also studied within and between natural populations of L. serriola from Israel and California. Large numbers of haplotypes were detected indicating the presence of numerous resistance genes in wild species. We documented a variety of genetic events occurring at clusters of resistance genes for the second objective (Sicard et al., 1999; Woo el al., in prep; Kuang et al., in prepb). The diversity of resistance genes in haplotypes provided evidence for gene duplication and unequal crossing over during the evolution of this cluster of resistance genes. Comparison of nine resistance genes in cv. Diana identified 22 gene conversion and five intergenic recombinations. We cloned and sequenced a 700 bp region from the middle of RGC2 genes from six genotypes, two each from L. saliva, L. serriola, and L. saligna . We have identified over 60 unique RGC2 sequences. Phylogenetic analysis surprisingly demonstrated much greater similarity between than within genotypes. This led to the realization that resistance genes are evolving much slower than had previously been assumed and to a new model as to how resistance genes are evolving (Michelmore and Meyers, 1998). The genetic structure of L. serriola was studied using 319 AFLP markers (Kuang et al., in prepa). Forty-one populations from Turkey, Armenia, Israel, and California as well as seven European countries were examined. AFLP marker data showed that the Turkish and Armenian populations were the most polymorphic populations and the European populations were the least. The Davis, CA population, a recent post-Columbian colonization, showed medium genetic diversity and was genetically close to the Turkish populations. Our results suggest that Turkey - Armenia may be the center of origin and diversity of L. serriola and may therefore have the greatest diversity of resistance genes. Our characterization of the diversity of resistance genes and the genetic mechanisms generating it will allow informed exploration, in situ and ex situ conservation, and utilization of germplasm resources for disease control. The results of this project provide the basis for our future research work, which will lead to a detailed understanding of the evolution of resistance genes in plants.

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Unlocking Genetic Diversity in Selected Chickpea Genotypes Using Morphological and Molecular Markers

Current Agriculture Research Journal ◽

10.12944/carj.5.1.06 ◽

2017 ◽

Vol 5 (1) ◽

pp. 50-57

Author(s):

Rupsanatan Mandal ◽

Suprakash Pal ◽

Nonigopal Shit

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Coefficient Of Variation ◽

Block Design ◽

Crop Improvement ◽

Research Work ◽

Genetic Maps ◽

Quantitative Character ◽

Moderate Degree ◽

Improvement Program

Proficiency and organization of the genetic variability in cultivated and wild relatives are pivotal for a particular crop improvement program. In the present scenario there has been noteworthy improvement in the development of novel genetic tools such as DNA or molecular markers and genetic maps profiling techniques. In this study, seven chickpea (Cicer arietinum L.) genotypes including some cultivars were considered (Collection Id of the seven genotypes are TZCP-1, TZCP-2, TZCP-3, TZCP-4, TZCP-5, TZCP-6 and TZCP-7). The experiment was conducted out in Random Complete Block Design (RCBD) having three replications. All the quantitative characters were collected for assessing the diversity and to find key characters in chickpea cultivars. The statistical analysis was done for all the quantitative character (viz. plant height, number of branches per plant, number of pod per plant, number of seeds per pod, test weight, seed length, seed width, days to 50% flowering, days to 50% maturity and grain yield). Analysis of variance divulged significant differences among the genotypes for all the 10 characters. An extensive range of diversity was displayed by most of the characters under study. The magnitude of phenotypic coefficient of variation (1.23% - 33.71%) in the present study was slightly wider than genotypic coefficient of variation (1.13% - 33.02%) suggesting that environmental factors have high contribution to the observed variation among chickpea accessions. The first four PC axes from the principal component analysis accounted for 91.63% of the multivariate variation among entries indicating a moderate degree of correlation among characters for these entries. The genotypic data generated through RAPD profiling of seven chickpea genotypes were used to study genetic diversity or interrelationship. The pair wise Jaccard’s similarity coefficient ranged from 0.47 (TZCP-3 and TZCP-5) to 0.87 (TZCP-2 and TZCP-4). Finally, this research work helped with the analysis of genetic diversity in chickpea by using different approaches such as morphological and molecular marker system.

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Molecular screening of potato varieties bred by Falenki Breeding station for resistance to phytopathogens

Agricultural science Euro-North-East ◽

10.30766/2072-9081.2021.22.3.340-350 ◽

2021 ◽

Vol 22 (3) ◽

pp. 340-350

Author(s):

A. V. Bakulina ◽

L. S. Savintseva ◽

O. N. Bashlakova ◽

N. F. Sintsova

Keyword(s):

Molecular Markers ◽

Resistance Gene ◽

Potato Virus ◽

Resistance Genes ◽

Dna Marker ◽

Potato Virus X ◽

Pcr Analysis ◽

Gene Marker ◽

Breeding Station ◽

Short Period

The genotypes of potatoes bred by Falenki Breeding station were studied for the presence of resistance genes markers to the following pathogens: Globodera rostochiensis, Globodera pallidа, Synchytrium endobioticum, potato virus X (PVХ) and potato virus Y (PVY). The method of multiplex PCR analysis was used. The varieties Shurminsky 2, Alisa, Viza, Chayka, Ognivo, Darik, Gloriya, Golubka, Virazh and a promising variety sample 56-09 were studied. In most (8 out of 10) genotypes, marker linked to the Sen1 gene of resistance to S. endobioticum was identified. DNA marker of the G. rostochiensis resistance gene (H1) and the G. pallida resistance gene marker (Gpa2) were found in six genotypes. The marker of the PVX resistance gene (Rx1) was detected in the varieties Shurminsky 2, Alisa, Chayka, Golubka, and Virazh. It has been established that none of the studied potato genotypes carries markers RYSC3, Ry186, YES3-3A linked to the PVY resistance genes. Although in the field, resistance was detected in the samples Chayka, Darik, Virazh, Alisa. Molecular markers linked to the largest number of resistance genes studied (H1, Gpa2, Sen1, and Rx1) were identified in the varieties Shurminsky 2, Golubka, and Virazh. Among the DNA markers used in the work, the data of potato genotype assessment using markers of virus resistance genes (PVX, RYSC3, Ry186, YES3-3A) were less consistent with field observations. The use of molecular markers makes it possible to determine the presence of resistance genes and assess the prospects of a sample in a short period of time, but, at the same time, requires careful choice of a DNA marker that is highly correlated with the manifestation of the trait.

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Identification by genome scanning approach (GSA) of a microsatellite tightly associated with the apple scab resistance gene Vm

Genome ◽

10.1139/g05-036 ◽

2005 ◽

Vol 48 (4) ◽

pp. 630-636 ◽

Cited By ~ 49

Author(s):

A Patocchi ◽

M Walser ◽

S Tartarini ◽

G A.L Broggini ◽

F Gennari ◽

...

Keyword(s):

Molecular Markers ◽

Linkage Group ◽

Resistance Gene ◽

Resistance Genes ◽

Simple Sequence Repeat ◽

Apple Scab ◽

Scab Resistance ◽

Sequence Repeat ◽

Genome Scanning ◽

Simple Sequence

For all known major apple scab resistance genes except Vr, molecular markers have been published. However, the precise position of some of these genes, in the apple genome, remains to be identified. Knowledge about the relative position of apple scab resistance genes is necessary to preliminarily evaluate the probability of success of their pyramidization. Pyramidization of different resistance genes into the same genotype is a reliable way to create cultivars with durable apple scab resistance. Applying the genome scanning approach (GSA), we identified the linkage group of the scab resistance gene Vm, derived from Malus micromalus, and we found a new molecular marker tightly associated with the gene. The simple sequence repeat Hi07h02, previously mapped on linkage group 17, cosegregates with the Vm gene (no recombinants in the 95 plants tested). The already published sequence-characterized amplified region Vm marker OPB12687 was found to be linked at about 5 cM from the resistance gene and, therefore, this marker also maps on linkage group 17 of apple. This is the first report of the discovery of a major apple scab resistance gene on linkage group 17. The advantages of using GSA for the identification of molecular markers for qualitative traits are discussed.Key words: Malus, Venturia inaequalis, mapping, simple sequence repeat.

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Recombination and Spontaneous Mutation at the Major Cluster of Resistance Genes in Lettuce (Lactuca sativa)

Genetics ◽

10.1093/genetics/157.2.831 ◽

2001 ◽

Vol 157 (2) ◽

pp. 831-849

Author(s):

Doris B Chin ◽

Rosa Arroyo-Garcia ◽

Oswaldo E Ochoa ◽

Rick V Kesseli ◽

Dean O Lavelle ◽

...

Keyword(s):

Gene Conversion ◽

Resistance Genes ◽

Spontaneous Mutation ◽

Large Chromosome ◽

Crossing Over ◽

Unequal Crossing Over ◽

Chimeric Genes ◽

Recessive Mutations ◽

Major Cluster ◽

Genetic Mechanisms

Abstract Two sets of overlapping experiments were conducted to examine recombination and spontaneous mutation events within clusters of resistance genes in lettuce. Multiple generations were screened for recombinants using PCR-based markers flanking Dm3. The Dm3 region is not highly recombinagenic, exhibiting a recombination frequency 18-fold lower than the genome average. Recombinants were identified only rarely within the cluster of Dm3 homologs and no crossovers within genes were detected. Three populations were screened for spontaneous mutations in downy mildew resistance. Sixteen Dm mutants were identified corresponding to spontaneous mutation rates of 10–3 to 10–4 per generation for Dm1, Dm3, and Dm7. All mutants carried single locus, recessive mutations at the corresponding Dm locus. Eleven of the 12 Dm3 mutations were associated with large chromosome deletions. When recombination could be analyzed, deletion events were associated with exchange of flanking markers, consistent with unequal crossing over; however, although the number of Dm3 paralogs was changed, no novel chimeric genes were detected. One mutant was the result of a gene conversion event between Dm3 and a closely related homolog, generating a novel chimeric gene. In two families, spontaneous deletions were correlated with elevated levels of recombination. Therefore, the short-term evolution of the major cluster of resistance genes in lettuce involves several genetic mechanisms including unequal crossing over and gene conversion.

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A comprehensive analysis of drug resistance molecular markers and Plasmodium falciparum genetic diversity in two malaria endemic sites in Mali

Malaria Journal ◽

10.1186/s12936-019-2986-5 ◽

2019 ◽

Vol 18 (1) ◽

Cited By ~ 4

Author(s):

Seidina A. S. Diakité ◽

Karim Traoré ◽

Ibrahim Sanogo ◽

Taane G. Clark ◽

Susana Campino ◽

...

Keyword(s):

Genetic Diversity ◽

Drug Resistance ◽

Plasmodium Falciparum ◽

Molecular Markers ◽

Malaria Transmission ◽

Resistance Gene ◽

Artemisinin Resistance ◽

Chloroquine Resistance ◽

Malaria Control Programme ◽

Codon Substitution

Abstract Background Drug resistance is one of the greatest challenges of malaria control programme in Mali. Recent advances in next-generation sequencing (NGS) technologies provide new and effective ways of tracking drug-resistant malaria parasites in Africa. The diversity and the prevalence of Plasmodium falciparum drug-resistance molecular markers were assessed in Dangassa and Nioro-du-Sahel in Mali, two sites with distinct malaria transmission patterns. Dangassa has an intense seasonal malaria transmission, whereas Nioro-du-Sahel has an unstable and short seasonal malaria transmission. Methods Up to 270 dried blood spot samples (214 in Dangassa and 56 in Nioro-du-Sahel) were collected from P. falciparum positive patients in 2016. Samples were analysed on the Agena MassARRAY® iPLEX platform. Specific codons were targeted in Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps, Pfarps10, Pfferredoxin, Pfexonuclease and Pfmdr2 genes. The Sanger’s 101-SNPs-barcode method was used to assess the genetic diversity of P. falciparum and to determine the parasite species. Results The Pfcrt_76T chloroquine-resistance genotype was found at a rate of 64.4% in Dangassa and 45.2% in Nioro-du-Sahel (p = 0.025). The Pfdhfr_51I-59R-108N pyrimethamine-resistance genotype was 14.1% and 19.6%, respectively in Dangassa and Nioro-du-Sahel. Mutations in the Pfdhps_S436-A437-K540-A581-613A sulfadoxine-resistance gene was significantly more prevalent in Dangassa as compared to Nioro-du-Sahel (p = 0.035). Up to 17.8% of the isolates from Dangassa vs 7% from Nioro-du-Sahel harboured at least two codon substitutions in this haplotype. The amodiaquine-resistance Pfmdr1_N86Y mutation was identified in only three samples (two in Dangassa and one in Nioro-du-Sahel). The lumefantrine-reduced susceptibility Pfmdr1_Y184F mutation was found in 39.9% and 48.2% of samples in Dangassa and Nioro-du-Sahel, respectively. One piperaquine-resistance Exo_E415G mutation was found in Dangassa, while no artemisinin resistance genetic-background were identified. A high P. falciparum diversity was observed, but no clear genetic aggregation was found at either study sites. Higher multiplicity of infection was observed in Dangassa with both COIL (p = 0.04) and Real McCOIL (p = 0.02) methods relative to Nioro-du-Sahel. Conclusions This study reveals high prevalence of chloroquine and pyrimethamine-resistance markers as well as high codon substitution rate in the sulfadoxine-resistance gene. High genetic diversity of P. falciparum was observed. These observations suggest that the use of artemisinins is relevant in both Dangassa and Nioro-du-Sahel.

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Genetic variation of populations of Pinus oocarpa revealed by resistance gene analog polymorphism (RGAP)

Genome ◽

10.1139/g03-023 ◽

2003 ◽

Vol 46 (3) ◽

pp. 404-410 ◽

Cited By ~ 7

Author(s):

V Díaz ◽

E Ferrer

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Resistance Gene ◽

Population Diversity ◽

Resistance Gene Analog ◽

Resistance Gene Analogs ◽

Analysis Of Molecular Variance ◽

Molecular Variance ◽

Pinus Oocarpa

Primers based on conserved motifs of plant resistance genes were used to generate multilocus molecular markers referred to as resistance gene analog polymorphisms (RGAPs) in Pinus oocarpa subsp. oocarpa. Ten populations from three regions of Nicaragua were analyzed with 53 RGAPs. The aim of this study was to determine the levels of within- and between-population diversity with this kind of marker, and to compare estimates with previously obtained results based on RAPD and AFLP. All populations showed high levels of diversity. GST values and the analysis of molecular variance (AMOVA) revealed most variation to be within populations, although significant differences between populations and regions were also detected. This pattern of genetic diversity was similar to that obtained for RAPD and AFLP, which suggests that variation at RGAP loci as detected in this work is mostly influence by non-selective forces.Key words: resistance gene analogs, molecular markers, genetic diversity, population structure, Pinus oocarpa.

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Development of isogenic lines for resistance to Septoria tritici blotch in wheat

Czech Journal of Genetics and Plant Breeding ◽

10.17221/3262-cjgpb ◽

2011 ◽

Vol 47 (Special Issue) ◽

pp. S98-S101 ◽

Cited By ~ 5

Author(s):

S.B. Goodwin ◽

I. Thompson

Keyword(s):

Molecular Markers ◽

Resistance Gene ◽

Resistance Genes ◽

Backcross Progeny ◽

Septoria Tritici Blotch ◽

Septoria Tritici ◽

The Past ◽

Wheat Improvement ◽

Improvement Programs ◽

Elite Germplasm

Septoria tritici blotch (STB), caused by the fungus Mycosphaerella graminicola (asexual stage: Septoria tritici), is one of the most economically important diseases of wheat worldwide. During the past decade 13 genes for resistance to STB have been identified and several molecular markers have been developed. However, analysis of resistance gene expression and utility for plant improvement programs would be increased if the resistance genes were isolated in a common susceptible background. To address this problem, a program was begun to backcross resistance genes Stb1–8 into two susceptible wheat cultivars. Work with genes Stb2, Stb3, Stb6 and Stb8 has proceeded the farthest. Resistance gene Stb3 is dominant, while Stb2 may be recessive. This will be the first report of recessive resistance to STB if confirmed. Molecular markers linked to the resistance genes are being validated in the backcross progeny and should provide the materials for efficient introgression of these genes into elite germplasm for future wheat improvement.

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Resistance gene analogues are clustered on chromosome 3 of sugar beet and cosegregate with QTL for rhizomania resistance

Genome ◽

10.1139/g06-131 ◽

2007 ◽

Vol 50 (1) ◽

pp. 61-71 ◽

Cited By ~ 26

Author(s):

Jens Christoph Lein ◽

Katrin Asbach ◽

Yanyan Tian ◽

Daniela Schulte ◽

Chunyan Li ◽

...

Keyword(s):

Molecular Markers ◽

Sugar Beet ◽

Resistance Gene ◽

Resistance Genes ◽

Bac Library ◽

Artificial Chromosome ◽

Chromosome 3 ◽

Resistance Locus ◽

Resistant Varieties ◽

Rhizomania Resistance

Worldwide, rhizomania is the most important disease of sugar beet. The only way to control this disease is to use resistant varieties. Four full-length resistance gene analogues (RGAs) from sugar beet (cZR-1, cZR-3, cZR-7, and cZR-9) were used in this study. Their predicted polypeptides carry typical nucleotide-binding sites (NBSs) and leucin-rich repeat (LRR) regions, and share high homology to various plant virus resistance genes. Their corresponding alleles were cloned and sequenced from a rhizomania resistant genotype. The 4 RGAs were mapped as molecular markers, using sequence-specific primers to determine their linkage to the rhizomania resistance locus Rz1 in a population segregating for rhizomania resistance. One cZR-3 allele, named Rz-C, together with 5 other molecular markers, mapped to the Rz1 locus on chromosome 3 and cosegregated with quantitative trait loci for rhizomania resistance. After screening a bacterial artificial chromosome (BAC) library, 25 cZR-3-positive BACs were identified. Of these, 15 mapped within an interval of approximately 14 cM on chromosome 3, in clusters close to the Rz1 locus. Rz-C differentiates between susceptible and resistant beet varieties, and its transcripts could be detected in all rhizomania resistant varieties investigated. The potential of this RGA marker for cloning of rhizomania resistance genes is discussed.

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Genetic variations among passion fruit species using rapd markers

Revista Brasileira de Fruticultura ◽

10.1590/s0100-29452002000300044 ◽

2002 ◽

Vol 24 (3) ◽

pp. 738-740 ◽

Cited By ~ 14

Author(s):

Ana Paula de Andrade Aukar ◽

Eliana Gertrudes de Macedo Lemos ◽

João Carlos Oliveira

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Research Work ◽

Botanical Variety ◽

Passiflora Edulis ◽

Large Variability ◽

Fruit Species ◽

Passiflora Edulis Sims

It has been evaluated the genetic variability through the use of RAPD molecular markers on the following passionflower species: Passiflora amethystina, P. caerulea, P. cincinnata, P. coccinea, P. serrato digitata, P. foetida, P. maliformis, P. alata, P. giberti, P. laurifolia, P. macrocarpa, P. nitida, P. setacea, P. suberosa, P. ligularis, P. capsularis, P. edulis Sims and its botanical variety P. edulis Sims f. flavicarpa Deg. In this research work, the analyses of the random amplified polymorphic DNA products (RAPD) were employed to estimate the genetic diversity and the taxonomic linkage within the species above. The total of 21 primers were used in this study which generated 270 different polymorphic products. It was possible to detect that the Passiflora species had shown a similarity of 17,3%, and between Passiflora edulis Sims and Passiflora edulis Sims f. flavicarpa a similarity of 34,35% has been found. The rate of similarity within edulis specie is low, making it clear that a large variability between the yellow and the purple forms exists.

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Evaluation of Genetic Diversity by Molecular Markers ISSR of Algodoeiro (Gossypium mustelinum) in Native Populations of Pernambuco, Brazil

Journal of Experimental Agriculture International ◽

10.9734/jeai/2019/v33i530154 ◽

2019 ◽

pp. 1-10

Author(s):

Luiz Sergio Costa Duarte Filho ◽

Edson Ferreira Da Silva ◽

Danielson Ramos Ribeiro ◽

Allison Vieira Da Silva ◽

Iêda Ferreira De Oliveira

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Variability ◽

Urban Areas ◽

Issr Markers ◽

Ex Situ ◽

Native Populations ◽

Gossypium Mustelinum ◽

New Germplasm ◽

Diversity Studies

In order to assure and evaluate the genetic diversity, wild populations of Cotton (Gossypium mustelinum) were collected and evaluated from the coastal plain north of Pernambuco, Brazil. Such populations occur in urban areas in a state of real expansion and with imminent risks of extinction. As a result of these risks and the state of real expansion, aiming at the ex situ conservation of these genetic resources, branches of 66 plants were collected in three populations of G. mustelinum that are located in restinga vegetation in the localities of Ponta de Pedras and Bara of Catuama, both in the municipality of Goiana and in the locality Sossego Beach in the municipality Island of Itamaracá. The collected genotypes were inserted in a new Germplasm Bank (BAG) at the Federal Rural University of Pernambuco, after which a sample composed of 24 genotypes contained in the BAG was collected to perform genetic diversity studies using molecular markers of ISSR type. For the molecular analysis, 24 accesses with 4 ISSR primers were analyzed, which produced a total of 36 bands, with a mean of 1,52 alleles per amplified locus. The genetic dissimilarity values, calculated according to the complement of the Jaccard index, ranged from 0.000 to 0.080. The UPGMA method grouped the accesses into three groups. The UFRPE30, UFRPE42 and UFRPE45 accessions were more dissimilar and UFRPE-48, UFRPE-50, UFRPE-52, UFRPE-55, UFRPE60, UFRPE06, UFRPE28, UFRPE29, UFRPE1, UFRPE2, UFRPE17 the least dissimilar. The ISSR markers used in this study demonstrated efficiency in the detection of molecular polymorphisms, revealing genetic variability among the 24 accessions. Considering the results obtained in this work, it is possible to infer that there is considerable genetic variability among the accessions of cotton, demonstrating the importance of the markers in the analysis of variability of species not studied, such as (G. mustelinum).

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