Sripada Udupa - Academia.edu (original) (raw)

Papers by Sripada Udupa

regeneration protocol is necessary to facilitate genetic transformation of faba bean. However, le... more regeneration protocol is necessary to facilitate genetic transformation of faba bean. However, leaching of phenolics from the explants of most genotypes of faba bean to the culture medium causes browning, and eventually kills the explants, hindering in vitro regeneration. This study is aimed to minimize the effect of phenolics and to identify the most suitable types of explants for in vitro regeneration. We pre-treated faba bean seeds in polyvinylpyrrolidone (PVP), then cultured different types of explants on tissue culture media supplemented with an adsorbent (activated charcoal) and antioxidants (ascorbic acid, cysteine and silver nitrate). Our results showed that treating the over night soaked seed (after removing the seed coat) with PVP solution (1000 mg/l) for 1 h, followed by culturing in Murashige and Skoog medium (MS medium) with 3% (w/v) sucrose, 0.8% (w/v) agar, 2 mg/l 6-benzylaminopurine and 2 mg/l thidiazuron, supplemented with ascorbic acid (1 mg/l) or activated charcoal (10 g/l), greatly reduced lethal browning in explants and improved shoot regeneration. The shoots rooted on half-strength MS medium supplemented with 0.5 mg/l -naphthaleneacetic acid. The cotyledonary node is the most suitable type of explant for regeneration. Regenerated plantlets were successfully established in pots and set seeds in the green house.

The rhizobia, Sinorhizobium meliloti and Rhizobium sullae, which fix nitrogen in root nodules of ... more The rhizobia, Sinorhizobium meliloti and Rhizobium sullae, which fix nitrogen in root nodules of alfalfa (Medicago sativa L.) and sulla (Hedysarum sp.) forage legumes, respectively, were isolated from root nodules and soils from Morocco. We used three PCR-based techniques namely, rep-PCR, RAPD and ARDRA techniques for genotypic characterization of 10 isolates of S. meliloti and R. sullae, in order to identify rapid and reliable techniques for applications in population genetic analysis of these species. The analysis revealed characteristic banding patterns for S. meliloti and R. sullae isolates by all the three techniques, even though the isolates are from a narrow geographic region in Morocco. Furthermore, the results showed that the rep-PCR with REP and ERIC primers was more efficient than RAPD and ARDRA technique for genotyping S. meliloti isolates; and rep-PCR with REP primers and the ARDRA technique with restriction enzyme HinfI, were more efficient than the other rep-PCR and RAPD-PCR techniques for genotyping R. sullae isolates.

BMC Microbiology, 2010

Background: Sinorhizobium meliloti and S. medicae are symbiotic nitrogen fixing bacteria in root ... more Background: Sinorhizobium meliloti and S. medicae are symbiotic nitrogen fixing bacteria in root nodules of forage legume alfalfa (Medicago sativa L.). In Morocco, alfalfa is usually grown in marginal soils of arid and semi-arid regions frequently affected by drought, extremes of temperature and soil pH, soil salinity and heavy metals, which affect biological nitrogen fixing ability of rhizobia and productivity of the host. This study examines phenotypic diversity for tolerance to the above stresses and genotypic diversity at Repetitive Extragenic Pallindromic DNA regions of Sinorhizobium nodulating alfalfa, sampled from marginal soils of arid and semi-arid regions of Morocco.

BIOTECHNOLOGY RESEARCH IN MOROCCO

Physiological and Genetic Diversity in Rhizobium sullae from Morocco

Sulla is an important forage legume in the northern parts of Morocco and has a significant role i... more Sulla is an important forage legume in the northern parts of Morocco and has a significant role in minimizing soil erosion. Sulla consists of two species Hedysarum coronarium L. and H. flexuosum L and both are well adapted to marginal areas where drought, salinity and alkalinity are the major problems. With the aim to characterize the bacterial symbiotic partner, Rhizobium sullae isolates from the nodules were sampled from sulla growing regions of Morocco. A total of 62 isolates were characterized so far, for various physiological characters such as resistance to salinity stress, water stress, high temperature stress, antibiotics, heavy metals, and various pH levels. The results revealed a considerable diversity for various physiological traits. The 62 isolates were divided into 14 clusters which showed a wide range of diversity both within and between the clusters. Genetic diversity of the isolates was analyzed by Amplified Ribosomal DNA Restriction Analysis (ARDRA) using two enzymes HinfI and HaeIII and data was used for cluster analysis. The results revealed that the individual genetic clusters contain isolates with diverse phenotypic traits, indicating no relationship between physiological and genetic groupings.

Theoretical and Applied Genetics, 2004

In order to understand the dynamics of microsatellite evolution, we have studied allelic variatio... more In order to understand the dynamics of microsatellite evolution, we have studied allelic variation at a closely linked (TA)n and (TAA)n microsatellite loci in 114 land races of chickpea (Cicer arietinum L.), sampled worldwide. These two loci are separated by 27 bp. The two loci showed a very high degree of polymorphism and hence the combined length with the genetic diversity of 0.93, 0.90 and 0.98 for (TAA)n , (TA)n and the combined length, respectively. Using the variation data at the linked loci, a standardized index of linkage disequilibrium was also computed (I S A =0.092), which tests the null hypothesis of no linkage and was significant, indicating the presence of linkage disequilibrium. Furthermore, the dynamics of allelic variation showed that there is a threshold combined length, below which both (TAA)n and (TA)n loci evolve independently, and above which, if one locus increase in size, the other closely linked locus has a tendency to decrease its size and vice versa, without change in the overall ratio of (TAA)n and (TA)n allele sizes at the region. This result indicates that there are processes in the cell, which ‘read’ the combined size of the two loci both for proportion and length and determine the direction of tightly linked di- and tri-nucleotide repeat evolution.

Theoretical and Applied Genetics, 2003

Ascochyta blight is an economically important disease of chickpea caused by the fungus Ascochyta ... more Ascochyta blight is an economically important disease of chickpea caused by the fungus Ascochyta rabiei. The fungus shows considerable variation for pathogenicity in nature. However, studies on the genetics of pathotype-specific resistance are not available for this plant-pathosystem. The chickpea landrace ILC 3279 has resistance to pathotype I and II of the pathogen. In order to understand the inheritance of pathotype-specific resistance in this crop, both Mendelian and quantitative trait loci analyses were performed using a set of intraspecific, recombinant inbred lines derived from a cross between the susceptible accession ILC 1272 and the resistant ILC 3279, and microsatellite markers. We identified and mapped a major locus (ar1, mapped on linkage group 2), which confers resistance to pathotype I, and two independent recessive major loci (ar2a, mapped on linkage group 2 and ar2b, mapped on linkage group 4), with complementary gene action conferring resistance to pathotype II. Out of two pathotype II-specific resistance loci, one (ar2a) linked very closely with the pathotype I-specific resistance locus, indicating a clustering of resistance genes in that region of the chickpea genome.

Annals of Applied Biology, 2005

AFLP markers were used to measure the amount and distribution of genetic variation among Rhynchos... more AFLP markers were used to measure the amount and distribution of genetic variation among Rhynchosporium secalis isolates on a microgeographical scale in Syria. Forty isolates hierarchically sampled from a single barley field were assayed for AFLP variation using primer combinations not previously tested in populations of the pathogen from Syria. In contrast to a previous study, which showed high clonality within field populations of R. secalis in Syria, the present study revealed a much higher level of genetic diversity, stressing the important roles that sampling strategies and the choice of primers/primer combinations play in the evaluation of genetic variation in R. secalis populations at a microgeographical scale. A high level of genetic variation was found to occur on a fine scale throughout the pathogen population examined, with 40 different haplotypes being identified among the 40 isolates sampled. Data were consistent with the hypothesis that the primary inoculum originated from a genetically diverse founding population, which may have consisted of ascospores of an as yet undescribed teleomorph and/or asexual spores of a highly mutable local population.

Molecular Genetics and Genomics, 2001

Allelic variation at (TAA) n microsatellite loci in a world collection of chickpea ( Cicer arietinum L.) germplasm

Molecular and General Genetics, 1999

A set of 12 randomly selected (TAA)n microsatellite loci of the cultivated chickpea (Cicer arieti... more A set of 12 randomly selected (TAA)n microsatellite loci of the cultivated chickpea (Cicer arietinum L.) were screened in a worldwide sample comprising 72 landraces, four improved cultivars and two wild species of the primary gene pool (C. reticulatum and C. echinosperum) to determine the level and pattern of polymorphism in these populations. A single fragment was amplified from all the accessions with each of 12 sequence-tagged microsatellite site markers, except for one locus where no fragment was obtained from either of the two wild species. There was a high degree of intraspecific polymorphism at these microsatellite loci, although isozymes, conventional RFLPs and RAPDs show very little or no polymorphism. Overall, the repeat number at a locus (excluding null alleles) ranged from 7 to 42. The average number of alleles per locus was 14.1 and the average genetic diversity was 0.86. Based on the estimates obtained, 11 out of the 12 frequency distributions of alleles at the loci tested can be considered to be non-normal. A significant positive correlation between the average number of repeats (size of the locus) and the amount of variation was observed, indicating that replication slippage may be the molecular mechanism involved in generation of variability at the loci. A comparison between the infinite allele and stepwise mutation models revealed that for 11 out of the 12 loci the number of alleles observed fell in between the values predicted by the two models. Phylogenetic analysis of microsatellite polymorphism in C. arietinum showed no relationship between accession and geographic origin, which is compatible with the recent expansion of this crop throughout the world.

Mycopathologia, 2007

Genetic variability among 122 Rhynchosporium secalis isolates collected from barley in three regi... more Genetic variability among 122 Rhynchosporium secalis isolates collected from barley in three regions of Tunisia was investigated using host differentials, amplified fragment length polymorphism (AFLP), and microsatellite markers. The isolates were collected from a widely grown scald-susceptible barley cultivar Rihane and a range of local landrace cultivars in geographically distinct regions with different agroclimatic conditions. Pathotypic diversity (the proportion of unique pathotypes) was high in R. secalis populations from the high (100% diversity), moderate (95%), and low (100%) rainfall areas of Tunisia, and from both Rihane (which is the sole variety grown in the high rainfall region) and local landraces (which predominate in the low rainfall area). This may reflect a general adaptability for aggressiveness and suggests that the widely grown cultivar Rihane has exerted little or no selection pressure on the pathogen population since its release in 1983. Genotypic diversity (GD), defined as the probability that two individuals taken at random had different genotypes, was high for populations from Rihane, local landraces, and different agro-ecological zones (GD = 0.96–0.99). There was low genetic differentiation among pathogen populations from different host populations (G ST ≤ 0.08, θ ≤ 0.12) and agro-ecological zones (G ST ≤ 0.05, θ ≤ 0.04), which may be partly explained by gene flow due to the movement of infected stubble around the country. There was no correlation (r = 0.06, P = 0.39) between virulence phenotype and AFLP haplotype. A phenetic tree revealed groups with low bootstrap values that did not reflect the grouping of isolates based on host, pathotype, or agro-ecological region. The implications of these findings for R. secalis evolutionary potential and scald-resistance breeding in Tunisia are discussed.

Genetic variation among populations of the Hessian fly Mayetiola destructor (Diptera: Cecidomyiidae) in Morocco and Syria

Bulletin of Entomological Research, 2000

The RAPD-PCR technique was used to study genetic variation within and among geographical populati... more The RAPD-PCR technique was used to study genetic variation within and among geographical populations of the Hessian fly, Mayetiola destructor (Say), from Morocco and Syria, associated with the fly's ability to overcome resistance in three wheat cultivars containing H5, H13 and H22 resistance genes. Variation was detected both for the level of susceptibility of the cultivars and RAPD profiles of M. destructor populations. By the use of RAPD-PCR, high genetic variability was detected among individuals and populations of M. destructor within and between areas separated geographically. The DNA fingerprints of populations of M. destructor were area-specific with Nei's measures of genetic distance ranging from 0.156 (between Abda and Beni Mellal, Morocco) to 1.977 (between Marchouch, Morocco and Lattakia, Syria). Cluster analysis of the genetic distances among the populations, identified the Syrian population as an outlier. A highly significant correlation (r = 0.81) observed between the genetic and geographic distances among the populations, provided genetic support for dispersal of the fly from its presumed origin in West Asia to Morocco.

Theoretical and Applied Genetics, 1998

The poor definition of variation in the ascochyta blight fungus (Ascochyta rabiei) has historica... more The poor definition of variation in the ascochyta blight fungus (Ascochyta rabiei) has historically hindered breeding for resistance to the chickpea (Cicer arietinum L.) blight disease in West Asia and North Africa. We have employed 14 RAPD markers and an oligonucleotide probe complementary to the microsatellite sequence (GATA)4 to construct a genotype-specific DNA fragment profile from periodically sampled Syrian field isolates of this fungus. By using conventional pathogenicity tests and genome analysis with RAPD and microsatellite markers, we demonstrated that the DNA markers distinguish variability within and among the major pathotypes of A. rabiei and resolved each pathotypes into several genotypes. The genetic diversity estimate based on DNA marker analysis within pathotypes was highest for the least-aggressive pathotype (pathotype I), followed by the aggressive (pathotype II) and the most-aggressive pathotype (pathotype III). The pair-wise genetic distance estimated for all the isolates varied from 0.00 to 0.39, indicating a range from a clonal to a diverse relationship. On the basis of genome analysis, and information on the spatial and temporal distribution of the pathogen, a general picture of A. rabiei evolution in Syria is proposed.

Assessment of genetic diversity of cultivated chickpea using microsatellite-derived RFLP markers: Implications for origin

Plant Breeding, 1997

Restriction fragment length polymorphism (RFLP) analysis was performed on 30 accessions of cultiv... more Restriction fragment length polymorphism (RFLP) analysis was performed on 30 accessions of cultivated chickpea (Cicer arietinum L.) collected from 11 different countries representing the Near East, Central Asian and Hindustani regions. A synthetic digoxygenated oligonucleotide (GATA)4 complementary to a microsatellite DNA sequence was used as a probe. The results revealed that simple repetitive sequences are abundant and polymorphic in the chickpea genome. The fragments detected were used lo estimate the genetic diversity within accessions and a similarity index between the genotypes of the accessions. The genetic distance data were used to construct a dendrogram depicting genetic relationships among the different accessions. The results indicate that the greatest genetic diversity occurs in Pakistan, Iraq, Afghanistan, south-east Russia, Turkey and Lebanon. Lower genetic diversity was found in Iran, India, Syria, Jordan and Palestine, Based on DNA markers, it is concluded that there are three centres of diversity for chickpea: Pakistan-Afghanistan. Iraq Turkey and Lebanon. India, which was previously considered as a secondary center of diversity for chickpea, showed lower diversity than the above regions.

Characterization and mapping of sequence-tagged microsatellite sites in the chickpea ( Cicer arietinum L.) genome

Molecular and General Genetics, 1999

A size-selected genomic library comprising 280,000 colonies and representing ≈18% of the chickpea... more A size-selected genomic library comprising 280,000 colonies and representing ≈18% of the chickpea genome, was screened for (GA)n, (GAA)n and (TAA)n microsatellite-containing clones, of which 389 were sequenced. The majority (∼75%) contained perfect repeats; interrupted, interrupted compound and compound repeats were only present in 6%–9% of cases. (TAA)-microsatellites contained the longest repeats, with unit numbers from 9 to 131. For 218 loci primers could be designed and used for the detection of microsatellite length polymorphisms in six chickpea breeding cultivars, as well as in C. reticulatum and C. echinospermum, wild, intercrossable relatives of chickpea. A total of 174 primer pairs gave interpretable banding patterns, 137 (79%) of which revealed at least two alleles on native polyacrylamide gels. A total of 120 sequence-tagged microsatellite site (STMS) markers were genetically mapped in 90 recombinant inbred lines from an inter-species cross between C. reticulatum and the chickpea cultivar ICC 4958. Markers could be arranged in 11 linkage groups (at a LOD score of 4) covering 613 cM. Clustering as well as random distribution of loci was observed. Segregation of 46 markers (39%) deviated significantly (P ≥ 0.05) from the expected 1:1 ratio. The majority of these loci (73%) were located in three distinct regions of the genome. The present STMS marker map represents the most advanced co-dominant DNA marker map of the chickpea genome.

Journal of Phytopathology, 2004

In order to study genetic variation among populations of Rhynchosporium secalis, 65 isolates were... more In order to study genetic variation among populations of Rhynchosporium secalis, 65 isolates were sampled from the West Asian and North African regions and used for polymerase chain reaction (PCR)-based DNA marker analyses [namely random amplified polymorphism DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs)]. The study revealed that genetic diversity among and within populations accounted for 80 and 20%, respectively, of the total genetic diversity, indicating that the local field populations of R. secalis in West Asia and North Africa originated from genetically diverse source populations. Furthermore, high genetic similarity among isolates from the same location suggests that scald populations originated from a local founder population, possibly through rain-splash-dispersed conidia.

Barley genotypes, in particular landraces and wild species, represent an important source of vari... more Barley genotypes, in particular landraces and wild species, represent an important source of variation for adaptive traits that may contribute to increase yield and yield stability under drought conditions, and that could be introgressed into improved varieties. Traits that have been investigated include physiological/biochemical and developmental/ morphological traits. Yield performance under drought is particularly a complex phenomenon, and plants exhibit a diverse range of genetically complex mechanisms for drought resistance. Quantitative trait loci (QTL) studies with and without H. spontaneum have shown that developmental genes, notably those involved in flowering time and plant stature show pleiotropic effects on abiotic stress tolerance and ultimately determine yield. Problems associated with the hybridization of H. spontaneum such as alleles with deleterious effects on field performance could be best addressed in the advanced backcross (AB-) QTL analysis. It was interesting to see that in AB-QTL populations like in balanced populations major QTL overshadowed minor QTL-alleles. Nevertheless, crosses with H. spontaneum, AB-QTL populations and association studies with H. spontaneum have also identified new alleles and genes that are related to abiotic stress tolerance. In order to identify genes that are related to drought tolerance microarrays analysis to monitor gene expression profiles for plants exposed to limited water environment is performed. Several studies with rapid dehydration treatment have shown that osmotic-stress-inducible genes could explain the response to drought stress in plants. Another development is the identification and use of nucleotide polymorphisms (SNP) in genes related to abiotic stress tolerance. An understanding of the combined function and expression of genes involved in various abiotic stresses, could help identify candidate genes underlying QTL of interest.

BMC Plant Biology, 2008

Background: Plant genetic resources (PGR) are the basic raw materials for future genetic progress... more Background: Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions.

Development of new microsatellite markers and their application in the analysis of genetic diversity in lentils

Breeding Science, 2009

This paper reports the development of new microsatellite markers for lentil (Lens culinaris subsp... more This paper reports the development of new microsatellite markers for lentil (Lens culinaris subsp. culinaris) and their use for genetic diversity analysis of a lentil core collection developed at ICARDA (Aleppo-Syria). Fourteen new markers were developed from microsatellite ...

Proposal Title: Allele Mining Based on Non-Coding Regulatory SNPs in barley germplasm. Targeted Subprogramme: Subprogramme 1: Genetic diversity of global genetic resources

regeneration protocol is necessary to facilitate genetic transformation of faba bean. However, le... more regeneration protocol is necessary to facilitate genetic transformation of faba bean. However, leaching of phenolics from the explants of most genotypes of faba bean to the culture medium causes browning, and eventually kills the explants, hindering in vitro regeneration. This study is aimed to minimize the effect of phenolics and to identify the most suitable types of explants for in vitro regeneration. We pre-treated faba bean seeds in polyvinylpyrrolidone (PVP), then cultured different types of explants on tissue culture media supplemented with an adsorbent (activated charcoal) and antioxidants (ascorbic acid, cysteine and silver nitrate). Our results showed that treating the over night soaked seed (after removing the seed coat) with PVP solution (1000 mg/l) for 1 h, followed by culturing in Murashige and Skoog medium (MS medium) with 3% (w/v) sucrose, 0.8% (w/v) agar, 2 mg/l 6-benzylaminopurine and 2 mg/l thidiazuron, supplemented with ascorbic acid (1 mg/l) or activated charcoal (10 g/l), greatly reduced lethal browning in explants and improved shoot regeneration. The shoots rooted on half-strength MS medium supplemented with 0.5 mg/l -naphthaleneacetic acid. The cotyledonary node is the most suitable type of explant for regeneration. Regenerated plantlets were successfully established in pots and set seeds in the green house.

The rhizobia, Sinorhizobium meliloti and Rhizobium sullae, which fix nitrogen in root nodules of ... more The rhizobia, Sinorhizobium meliloti and Rhizobium sullae, which fix nitrogen in root nodules of alfalfa (Medicago sativa L.) and sulla (Hedysarum sp.) forage legumes, respectively, were isolated from root nodules and soils from Morocco. We used three PCR-based techniques namely, rep-PCR, RAPD and ARDRA techniques for genotypic characterization of 10 isolates of S. meliloti and R. sullae, in order to identify rapid and reliable techniques for applications in population genetic analysis of these species. The analysis revealed characteristic banding patterns for S. meliloti and R. sullae isolates by all the three techniques, even though the isolates are from a narrow geographic region in Morocco. Furthermore, the results showed that the rep-PCR with REP and ERIC primers was more efficient than RAPD and ARDRA technique for genotyping S. meliloti isolates; and rep-PCR with REP primers and the ARDRA technique with restriction enzyme HinfI, were more efficient than the other rep-PCR and RAPD-PCR techniques for genotyping R. sullae isolates.

BMC Microbiology, 2010

Background: Sinorhizobium meliloti and S. medicae are symbiotic nitrogen fixing bacteria in root ... more Background: Sinorhizobium meliloti and S. medicae are symbiotic nitrogen fixing bacteria in root nodules of forage legume alfalfa (Medicago sativa L.). In Morocco, alfalfa is usually grown in marginal soils of arid and semi-arid regions frequently affected by drought, extremes of temperature and soil pH, soil salinity and heavy metals, which affect biological nitrogen fixing ability of rhizobia and productivity of the host. This study examines phenotypic diversity for tolerance to the above stresses and genotypic diversity at Repetitive Extragenic Pallindromic DNA regions of Sinorhizobium nodulating alfalfa, sampled from marginal soils of arid and semi-arid regions of Morocco.

BIOTECHNOLOGY RESEARCH IN MOROCCO

Physiological and Genetic Diversity in Rhizobium sullae from Morocco

Sulla is an important forage legume in the northern parts of Morocco and has a significant role i... more Sulla is an important forage legume in the northern parts of Morocco and has a significant role in minimizing soil erosion. Sulla consists of two species Hedysarum coronarium L. and H. flexuosum L and both are well adapted to marginal areas where drought, salinity and alkalinity are the major problems. With the aim to characterize the bacterial symbiotic partner, Rhizobium sullae isolates from the nodules were sampled from sulla growing regions of Morocco. A total of 62 isolates were characterized so far, for various physiological characters such as resistance to salinity stress, water stress, high temperature stress, antibiotics, heavy metals, and various pH levels. The results revealed a considerable diversity for various physiological traits. The 62 isolates were divided into 14 clusters which showed a wide range of diversity both within and between the clusters. Genetic diversity of the isolates was analyzed by Amplified Ribosomal DNA Restriction Analysis (ARDRA) using two enzymes HinfI and HaeIII and data was used for cluster analysis. The results revealed that the individual genetic clusters contain isolates with diverse phenotypic traits, indicating no relationship between physiological and genetic groupings.

Theoretical and Applied Genetics, 2004

In order to understand the dynamics of microsatellite evolution, we have studied allelic variatio... more In order to understand the dynamics of microsatellite evolution, we have studied allelic variation at a closely linked (TA)n and (TAA)n microsatellite loci in 114 land races of chickpea (Cicer arietinum L.), sampled worldwide. These two loci are separated by 27 bp. The two loci showed a very high degree of polymorphism and hence the combined length with the genetic diversity of 0.93, 0.90 and 0.98 for (TAA)n , (TA)n and the combined length, respectively. Using the variation data at the linked loci, a standardized index of linkage disequilibrium was also computed (I S A =0.092), which tests the null hypothesis of no linkage and was significant, indicating the presence of linkage disequilibrium. Furthermore, the dynamics of allelic variation showed that there is a threshold combined length, below which both (TAA)n and (TA)n loci evolve independently, and above which, if one locus increase in size, the other closely linked locus has a tendency to decrease its size and vice versa, without change in the overall ratio of (TAA)n and (TA)n allele sizes at the region. This result indicates that there are processes in the cell, which ‘read’ the combined size of the two loci both for proportion and length and determine the direction of tightly linked di- and tri-nucleotide repeat evolution.

Theoretical and Applied Genetics, 2003

Ascochyta blight is an economically important disease of chickpea caused by the fungus Ascochyta ... more Ascochyta blight is an economically important disease of chickpea caused by the fungus Ascochyta rabiei. The fungus shows considerable variation for pathogenicity in nature. However, studies on the genetics of pathotype-specific resistance are not available for this plant-pathosystem. The chickpea landrace ILC 3279 has resistance to pathotype I and II of the pathogen. In order to understand the inheritance of pathotype-specific resistance in this crop, both Mendelian and quantitative trait loci analyses were performed using a set of intraspecific, recombinant inbred lines derived from a cross between the susceptible accession ILC 1272 and the resistant ILC 3279, and microsatellite markers. We identified and mapped a major locus (ar1, mapped on linkage group 2), which confers resistance to pathotype I, and two independent recessive major loci (ar2a, mapped on linkage group 2 and ar2b, mapped on linkage group 4), with complementary gene action conferring resistance to pathotype II. Out of two pathotype II-specific resistance loci, one (ar2a) linked very closely with the pathotype I-specific resistance locus, indicating a clustering of resistance genes in that region of the chickpea genome.

Annals of Applied Biology, 2005

AFLP markers were used to measure the amount and distribution of genetic variation among Rhynchos... more AFLP markers were used to measure the amount and distribution of genetic variation among Rhynchosporium secalis isolates on a microgeographical scale in Syria. Forty isolates hierarchically sampled from a single barley field were assayed for AFLP variation using primer combinations not previously tested in populations of the pathogen from Syria. In contrast to a previous study, which showed high clonality within field populations of R. secalis in Syria, the present study revealed a much higher level of genetic diversity, stressing the important roles that sampling strategies and the choice of primers/primer combinations play in the evaluation of genetic variation in R. secalis populations at a microgeographical scale. A high level of genetic variation was found to occur on a fine scale throughout the pathogen population examined, with 40 different haplotypes being identified among the 40 isolates sampled. Data were consistent with the hypothesis that the primary inoculum originated from a genetically diverse founding population, which may have consisted of ascospores of an as yet undescribed teleomorph and/or asexual spores of a highly mutable local population.

Molecular Genetics and Genomics, 2001

Allelic variation at (TAA) n microsatellite loci in a world collection of chickpea ( Cicer arietinum L.) germplasm

Molecular and General Genetics, 1999

A set of 12 randomly selected (TAA)n microsatellite loci of the cultivated chickpea (Cicer arieti... more A set of 12 randomly selected (TAA)n microsatellite loci of the cultivated chickpea (Cicer arietinum L.) were screened in a worldwide sample comprising 72 landraces, four improved cultivars and two wild species of the primary gene pool (C. reticulatum and C. echinosperum) to determine the level and pattern of polymorphism in these populations. A single fragment was amplified from all the accessions with each of 12 sequence-tagged microsatellite site markers, except for one locus where no fragment was obtained from either of the two wild species. There was a high degree of intraspecific polymorphism at these microsatellite loci, although isozymes, conventional RFLPs and RAPDs show very little or no polymorphism. Overall, the repeat number at a locus (excluding null alleles) ranged from 7 to 42. The average number of alleles per locus was 14.1 and the average genetic diversity was 0.86. Based on the estimates obtained, 11 out of the 12 frequency distributions of alleles at the loci tested can be considered to be non-normal. A significant positive correlation between the average number of repeats (size of the locus) and the amount of variation was observed, indicating that replication slippage may be the molecular mechanism involved in generation of variability at the loci. A comparison between the infinite allele and stepwise mutation models revealed that for 11 out of the 12 loci the number of alleles observed fell in between the values predicted by the two models. Phylogenetic analysis of microsatellite polymorphism in C. arietinum showed no relationship between accession and geographic origin, which is compatible with the recent expansion of this crop throughout the world.

Mycopathologia, 2007

Genetic variability among 122 Rhynchosporium secalis isolates collected from barley in three regi... more Genetic variability among 122 Rhynchosporium secalis isolates collected from barley in three regions of Tunisia was investigated using host differentials, amplified fragment length polymorphism (AFLP), and microsatellite markers. The isolates were collected from a widely grown scald-susceptible barley cultivar Rihane and a range of local landrace cultivars in geographically distinct regions with different agroclimatic conditions. Pathotypic diversity (the proportion of unique pathotypes) was high in R. secalis populations from the high (100% diversity), moderate (95%), and low (100%) rainfall areas of Tunisia, and from both Rihane (which is the sole variety grown in the high rainfall region) and local landraces (which predominate in the low rainfall area). This may reflect a general adaptability for aggressiveness and suggests that the widely grown cultivar Rihane has exerted little or no selection pressure on the pathogen population since its release in 1983. Genotypic diversity (GD), defined as the probability that two individuals taken at random had different genotypes, was high for populations from Rihane, local landraces, and different agro-ecological zones (GD = 0.96–0.99). There was low genetic differentiation among pathogen populations from different host populations (G ST ≤ 0.08, θ ≤ 0.12) and agro-ecological zones (G ST ≤ 0.05, θ ≤ 0.04), which may be partly explained by gene flow due to the movement of infected stubble around the country. There was no correlation (r = 0.06, P = 0.39) between virulence phenotype and AFLP haplotype. A phenetic tree revealed groups with low bootstrap values that did not reflect the grouping of isolates based on host, pathotype, or agro-ecological region. The implications of these findings for R. secalis evolutionary potential and scald-resistance breeding in Tunisia are discussed.

Genetic variation among populations of the Hessian fly Mayetiola destructor (Diptera: Cecidomyiidae) in Morocco and Syria

Bulletin of Entomological Research, 2000

The RAPD-PCR technique was used to study genetic variation within and among geographical populati... more The RAPD-PCR technique was used to study genetic variation within and among geographical populations of the Hessian fly, Mayetiola destructor (Say), from Morocco and Syria, associated with the fly's ability to overcome resistance in three wheat cultivars containing H5, H13 and H22 resistance genes. Variation was detected both for the level of susceptibility of the cultivars and RAPD profiles of M. destructor populations. By the use of RAPD-PCR, high genetic variability was detected among individuals and populations of M. destructor within and between areas separated geographically. The DNA fingerprints of populations of M. destructor were area-specific with Nei's measures of genetic distance ranging from 0.156 (between Abda and Beni Mellal, Morocco) to 1.977 (between Marchouch, Morocco and Lattakia, Syria). Cluster analysis of the genetic distances among the populations, identified the Syrian population as an outlier. A highly significant correlation (r = 0.81) observed between the genetic and geographic distances among the populations, provided genetic support for dispersal of the fly from its presumed origin in West Asia to Morocco.

Theoretical and Applied Genetics, 1998

The poor definition of variation in the ascochyta blight fungus (Ascochyta rabiei) has historica... more The poor definition of variation in the ascochyta blight fungus (Ascochyta rabiei) has historically hindered breeding for resistance to the chickpea (Cicer arietinum L.) blight disease in West Asia and North Africa. We have employed 14 RAPD markers and an oligonucleotide probe complementary to the microsatellite sequence (GATA)4 to construct a genotype-specific DNA fragment profile from periodically sampled Syrian field isolates of this fungus. By using conventional pathogenicity tests and genome analysis with RAPD and microsatellite markers, we demonstrated that the DNA markers distinguish variability within and among the major pathotypes of A. rabiei and resolved each pathotypes into several genotypes. The genetic diversity estimate based on DNA marker analysis within pathotypes was highest for the least-aggressive pathotype (pathotype I), followed by the aggressive (pathotype II) and the most-aggressive pathotype (pathotype III). The pair-wise genetic distance estimated for all the isolates varied from 0.00 to 0.39, indicating a range from a clonal to a diverse relationship. On the basis of genome analysis, and information on the spatial and temporal distribution of the pathogen, a general picture of A. rabiei evolution in Syria is proposed.

Assessment of genetic diversity of cultivated chickpea using microsatellite-derived RFLP markers: Implications for origin

Plant Breeding, 1997

Restriction fragment length polymorphism (RFLP) analysis was performed on 30 accessions of cultiv... more Restriction fragment length polymorphism (RFLP) analysis was performed on 30 accessions of cultivated chickpea (Cicer arietinum L.) collected from 11 different countries representing the Near East, Central Asian and Hindustani regions. A synthetic digoxygenated oligonucleotide (GATA)4 complementary to a microsatellite DNA sequence was used as a probe. The results revealed that simple repetitive sequences are abundant and polymorphic in the chickpea genome. The fragments detected were used lo estimate the genetic diversity within accessions and a similarity index between the genotypes of the accessions. The genetic distance data were used to construct a dendrogram depicting genetic relationships among the different accessions. The results indicate that the greatest genetic diversity occurs in Pakistan, Iraq, Afghanistan, south-east Russia, Turkey and Lebanon. Lower genetic diversity was found in Iran, India, Syria, Jordan and Palestine, Based on DNA markers, it is concluded that there are three centres of diversity for chickpea: Pakistan-Afghanistan. Iraq Turkey and Lebanon. India, which was previously considered as a secondary center of diversity for chickpea, showed lower diversity than the above regions.

Characterization and mapping of sequence-tagged microsatellite sites in the chickpea ( Cicer arietinum L.) genome

Molecular and General Genetics, 1999

A size-selected genomic library comprising 280,000 colonies and representing ≈18% of the chickpea... more A size-selected genomic library comprising 280,000 colonies and representing ≈18% of the chickpea genome, was screened for (GA)n, (GAA)n and (TAA)n microsatellite-containing clones, of which 389 were sequenced. The majority (∼75%) contained perfect repeats; interrupted, interrupted compound and compound repeats were only present in 6%–9% of cases. (TAA)-microsatellites contained the longest repeats, with unit numbers from 9 to 131. For 218 loci primers could be designed and used for the detection of microsatellite length polymorphisms in six chickpea breeding cultivars, as well as in C. reticulatum and C. echinospermum, wild, intercrossable relatives of chickpea. A total of 174 primer pairs gave interpretable banding patterns, 137 (79%) of which revealed at least two alleles on native polyacrylamide gels. A total of 120 sequence-tagged microsatellite site (STMS) markers were genetically mapped in 90 recombinant inbred lines from an inter-species cross between C. reticulatum and the chickpea cultivar ICC 4958. Markers could be arranged in 11 linkage groups (at a LOD score of 4) covering 613 cM. Clustering as well as random distribution of loci was observed. Segregation of 46 markers (39%) deviated significantly (P ≥ 0.05) from the expected 1:1 ratio. The majority of these loci (73%) were located in three distinct regions of the genome. The present STMS marker map represents the most advanced co-dominant DNA marker map of the chickpea genome.

Journal of Phytopathology, 2004

In order to study genetic variation among populations of Rhynchosporium secalis, 65 isolates were... more In order to study genetic variation among populations of Rhynchosporium secalis, 65 isolates were sampled from the West Asian and North African regions and used for polymerase chain reaction (PCR)-based DNA marker analyses [namely random amplified polymorphism DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs)]. The study revealed that genetic diversity among and within populations accounted for 80 and 20%, respectively, of the total genetic diversity, indicating that the local field populations of R. secalis in West Asia and North Africa originated from genetically diverse source populations. Furthermore, high genetic similarity among isolates from the same location suggests that scald populations originated from a local founder population, possibly through rain-splash-dispersed conidia.

Barley genotypes, in particular landraces and wild species, represent an important source of vari... more Barley genotypes, in particular landraces and wild species, represent an important source of variation for adaptive traits that may contribute to increase yield and yield stability under drought conditions, and that could be introgressed into improved varieties. Traits that have been investigated include physiological/biochemical and developmental/ morphological traits. Yield performance under drought is particularly a complex phenomenon, and plants exhibit a diverse range of genetically complex mechanisms for drought resistance. Quantitative trait loci (QTL) studies with and without H. spontaneum have shown that developmental genes, notably those involved in flowering time and plant stature show pleiotropic effects on abiotic stress tolerance and ultimately determine yield. Problems associated with the hybridization of H. spontaneum such as alleles with deleterious effects on field performance could be best addressed in the advanced backcross (AB-) QTL analysis. It was interesting to see that in AB-QTL populations like in balanced populations major QTL overshadowed minor QTL-alleles. Nevertheless, crosses with H. spontaneum, AB-QTL populations and association studies with H. spontaneum have also identified new alleles and genes that are related to abiotic stress tolerance. In order to identify genes that are related to drought tolerance microarrays analysis to monitor gene expression profiles for plants exposed to limited water environment is performed. Several studies with rapid dehydration treatment have shown that osmotic-stress-inducible genes could explain the response to drought stress in plants. Another development is the identification and use of nucleotide polymorphisms (SNP) in genes related to abiotic stress tolerance. An understanding of the combined function and expression of genes involved in various abiotic stresses, could help identify candidate genes underlying QTL of interest.

BMC Plant Biology, 2008

Background: Plant genetic resources (PGR) are the basic raw materials for future genetic progress... more Background: Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions.

Development of new microsatellite markers and their application in the analysis of genetic diversity in lentils

Breeding Science, 2009

This paper reports the development of new microsatellite markers for lentil (Lens culinaris subsp... more This paper reports the development of new microsatellite markers for lentil (Lens culinaris subsp. culinaris) and their use for genetic diversity analysis of a lentil core collection developed at ICARDA (Aleppo-Syria). Fourteen new markers were developed from microsatellite ...

Proposal Title: Allele Mining Based on Non-Coding Regulatory SNPs in barley germplasm. Targeted Subprogramme: Subprogramme 1: Genetic diversity of global genetic resources