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Papers by fida ALO

Genetic resources and crop evolution, Apr 21, 2024

Genetic Resources and Crop Evolution

Frontiers in Plant Science, Apr 25, 2022

Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar di... more Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar disease of chickpea (Cicer arietinum L.). The genotyping-by-sequencing (GBS)based approach was deployed for mapping QTLs associated with AB resistance in chickpea in two recombinant inbred line populations derived from two crosses (AB 3279 derived from ILC 1929 × ILC 3279 and AB 482 derived from ILC 1929 × ILC 482) and tested in six different environments. Twenty-one different genomic regions linked to AB resistance were identified in regions CalG02 and CalG04 in both populations AB 3279 and AB 482. These regions contain 1,118 SNPs significantly associated with AB resistance (p ≤ 0.001), which explained 11.2-39.3% of the phenotypic variation (PVE). Nine of the AB resistance-associated genomic regions were newly detected in this study, while twelve regions were known from previous AB studies. The proposed physical map narrows down AB resistance to consistent genomic regions identified across different environments. Gene ontology (GO) assigned these QTLs to 319 genes, many of which were associated with stress and disease resistance, and with most important genes belonging to resistance gene families such as leucine-rich repeat (LRR) and transcription factor families. Our results indicate that the flowering-associated gene GIGANTEA is a possible key factor in AB resistance in chickpea. The results have identified AB resistance-associated regions on the physical genetic map of chickpea and allowed for the identification of associated markers that will help in breeding of AB-resistant varieties.

Genetic diversity of 46 azerbaijani durum wheat (triticum durum l.) Genotypes were screened using... more Genetic diversity of 46 azerbaijani durum wheat (triticum durum l.) Genotypes were screened using simple sequence repeats (ssrs). These accessions were collected from various bioclimatic regions of azerbaijan. Out of the used twenty-two primers, 13 primers showed polymorphism and were selected for the analyses. Among the genotypes under study, 31 alleles were detected. Highest number of alleles was detected in locus gwm 335 (on chromosome 5b) and on locus gwm 445 (on chromosome 2a) with 5 and 4 alleles, respectively. The lowest number of alleles was determined in locus gwm 617 with only 1 allele. For a, b and d genomes, the total number of alleles detected were 14, 15 and 2, respectively. Pic value between studied ssr markers was 0.912 and this result shows high genetic diversity between azerbaijani durum wheat genotypes. Therefore, these primers can be recommended for studying genetic diversity of azerbaijani durum wheat accessions. The genetic structure of the genotypes was analyz...

Frontiers in Plant Science

Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar di... more Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar disease of chickpea (Cicer arietinum L.). The genotyping-by-sequencing (GBS)-based approach was deployed for mapping QTLs associated with AB resistance in chickpea in two recombinant inbred line populations derived from two crosses (AB3279 derived from ILC 1929 × ILC 3279 and AB482 derived from ILC 1929 × ILC 482) and tested in six different environments. Twenty-one different genomic regions linked to AB resistance were identified in regions CalG02 and CalG04 in both populations AB3279 and AB482. These regions contain 1,118 SNPs significantly associated with AB resistance (p ≤ 0.001), which explained 11.2–39.3% of the phenotypic variation (PVE). Nine of the AB resistance-associated genomic regions were newly detected in this study, while twelve regions were known from previous AB studies. The proposed physical map narrows down AB resistance to consistent genomic regions identified across d...

Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar di... more Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar disease of chickpea (Cicer arietinum L.). The genotyping-by-sequencing (GBS)-based approach was deployed for mapping QTLs associated with AB resistance in chickpea in two recombinant inbred line populations derived from two crosses (AB3279 derived from ILC 1929 × ILC 3279 and AB482 derived from ILC 1929 × ILC 482) and tested in six different environments. Twenty-one different genomic regions linked to AB resistance were identified in regions CalG02 and CalG04 in both populations AB3279 and AB482. These regions contain 1,118 SNPs significantly associated with AB resistance (p ≤ 0.001), which explained 11.2–39.3% of the phenotypic variation (PVE). Nine of the AB resistance-associated genomic regions were newly detected in this study, while twelve regions were known from previous AB studies. The proposed physical map narrows down AB resistance to consistent genomic regions identified across different environments. Gene ontology (GO) assigned these QTLs to 319 genes, many of which were associated with stress and disease resistance, and with most important genes belonging to resistance gene families such as leucine-rich repeat (LRR) and transcription factor families. Our results indicate that the flowering-associated gene GIGANTEA is a possible key factor in AB resistance in chickpea. The results have identified AB resistance-associated regions on the physical genetic map of chickpea and allowed for the identification of associated markers that will help in breeding of AB-resistant varieties.

Hamwieh, A., F. Alo, S. Ahmed. 2018. Molecular Tools Developed for Disease Resistant Genes in Whe... more Hamwieh, A., F. Alo, S. Ahmed. 2018. Molecular Tools Developed for Disease Resistant Genes in Wheat, Barley, Lentil and Chickpea: A Review. Arab Journal of Plant Protection, 36(1): 50-56. The major objective of using molecular tools by the plant pathologists is to identify markers linked to the resistant genes. The best markers are those located within the genes or tightly linlked to the resistant genes. This paper will review the most recent markers/QTL linked to resistant genes reported in wheat (strip rust, leaf rust, and stem rust), barley (stripe rust, leaf rust, and stem rust), lentil (Fusarium wilt, Ascochyta, Anthracnose and Stemphylium blight) and chickpea (Ascochyta blight and Fusarium wilt). The markers tightly linked to the resistant genes could be used as markers assisted selection in the breeding program to improve effectiveness and efficiency of variety

Arab Journal of Plant Protection, 2018

Alo, F., W. Al-Saaid, M. Baum, H. Alatwani and A. Amri. 2018. Slow rusting of bread wheat landrac... more Alo, F., W. Al-Saaid, M. Baum, H. Alatwani and A. Amri. 2018. Slow rusting of bread wheat landraces to Puccinia striiformis f.sp. tritici under artificial field inoculation. Arab Journal of Plant Protection, 36(2): 164-175. Yellow rust caused by Puccinia striiformis f. sp. tritici is the most devastating fungal disease of wheat, especially in the Central and West Asia and North Africa (CWANA) region. Most of the released cultivars in CWANA have become susceptible to the new virulence Yr27. Growing durable resistance cultivars is the most economical control measure. A field study was conducted to evaluate 500 bread wheat landraces along with the susceptible control 'Morocco' using artificial inoculation under field conditions at Tel Hadia, Syria during 2010/11 and 2011/12 growing seasons. The most prevailing and spreading yellow rust virulence (70E214) was used for artificial inoculation. Disease scoring started when disease severity was more than 50% on the leaves of cv. Morocco and continued for four readings at 7 days intervals. Slow rusting resistance was assessed based on development of the disease over time using the area under disease progress curve (AUDPC), coefficient of infection (CI), final rust severity (FRS), infection rate "r" and relative resistance index (RRI). None of the landraces showed immune reaction and 10% showed the lowest values for all parameters, suggesting that major genes control resistance in these landraces. Approximately 65% of the landraces were marked as having different levels of slow rusting and 25% were highly susceptible. Cluster analysis based on partial resistance parameters of the landraces along with cv. Morocco revealed two major clusters: susceptible and low level of slow rusting were grouped in the first cluster; resistant, high level and moderate level of partial resistance were grouped in the second cluster. These groups were also confirmed using principal coordinate analysis. By comparing the results of RRI and others parameters, it appeared that landraces with very low values exhibited high RRI value of 9, while those that showed high, moderate, and low levels of slow rusting, had RRI ranges of 8-9, 7-8 and 5-7, respectively. Landraces with maximum values from each parameter showed very low RRI values of less than 5. The results also suggest that AUDPC, CI, and FRS are the more appropriate parameters for assessing slow rusting than infection rate. Correlation coefficient and principle component analysis revealed a high and positive correlation between these parameters.

Arab Journal Of Plant Protection, 2018

American Journal of Plant Sciences, 2013

Wheat leaf rust caused by Puccinia triticina, is the most common and widely distributed wheat rus... more Wheat leaf rust caused by Puccinia triticina, is the most common and widely distributed wheat rust in the world. In order to study the genetic structure of leaf rust population 14 pairs of AFLP and 6 pairs of FAFLP primers evaluated on 86 isolates samples collected in Iran during spring of 2009. Results showed that almost all investigated isolates were genetically different and special pattern of AFLP allele's that confirm high genetic diversity within leaf rust population was observed. Analyses showed, all provinces were classified into three major groups particularly similar clusters were found between then neighboring provinces. Rust spore can follow the migration pattern in short and long distances to neighbor in provinces. Results indicated that the greatest variability was revealed by 97% of genetic differentiation within leaf rust populations and the lesser variation of 3% was observed between the rust populations. These results suggested that each population was not completely identical and high gene flow has occurred among the leaf rust population of different provinces. The highest differentiation and genetic distance among the Iranian leaf rust populations was detected between leaf rust population in Sistan and Baluchistan and highest similarity was observed between in Ardabil provinces. The high pathogenic variability of leaf rust races in Ardabil and Northern Khorasan may be an indication that these two regions are the center of origin of pathogenic arability. Present study shows that leaf rust population in Iran is highly dynamic and variable.

The Journal of Agricultural Science, 2014

SUMMARYStripe rust, caused byPuccinia striiformisf. sp.tritici(Pst), is a major wheat disease tha... more SUMMARYStripe rust, caused byPuccinia striiformisf. sp.tritici(Pst), is a major wheat disease that can inflict yield losses of up to 70% on susceptible varieties under favourable environmental conditions. The timely identification of plant genetic resources likely to possess novel resistance to this disease would facilitate the rapid development of resistant wheat varieties. The focused identification of germplasm strategy (FIGS) approach was used to predict stripe rust resistance in a collection of wheat landraces conserved at ICARDA genebank. Long-term climate data for the collection sites, from which these accessions originated and stripe rust evaluation scores for one group of accessions were presented to three different non-linear models to explore the trait×collection site environment interactions. Patterns in the data detected by the models were used to predict stripe rust resistance in a second and different set of accessions. The results of the prediction were then tested a...

Journal of Heredity, 2011

Advances in comparative genomics have provided significant opportunities for analysis of genetic ... more Advances in comparative genomics have provided significant opportunities for analysis of genetic diversity in species with limited genomic resources, such as the genus Lens. Medicago truncatula expressed sequence tags (ESTs) were aligned with the Arabidopsis thaliana genome sequence to identify conserved exon sequences and splice sites in the ESTs. Conserved primers (CPs) based on M. truncatula EST sequences flanking one or more introns were then designed. A total of 22% of the CPs produced polymerase chain reaction amplicons in lentil and were used to sequence amplicons in 175 wild and 133 domesticated lentil accessions. Analysis of the sequences confirmed that L. nigricans and L. ervoides are well-defined species at the DNA sequence level. Lens culinaris subsp. odemensis, L. culinaris subsp. tomentosus, and L. lamottei may constitute a single taxon pending verification with crossability experiments. Lens culinaris subsp. orientalis is the progenitor of domesticated lentil, L. culinaris subsp. culinaris (as proposed before), but a more specific area of origin can be suggested in southern Turkey. We were also able to detect the divergence, following domestication, of the domesticated gene pool into overlapping largeseeded (megasperma) and small-seeded (microsperma) groups. Lentil domestication led to a loss of genetic diversity of approximately 40%. The approach followed in this research has allowed us to rapidly exploit sequence information from model plant species for the study of genetic diversity of a crop such as lentil with limited genomic resources.

Genetic resources and crop evolution, Apr 21, 2024

Genetic Resources and Crop Evolution

Frontiers in Plant Science, Apr 25, 2022

Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar di... more Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar disease of chickpea (Cicer arietinum L.). The genotyping-by-sequencing (GBS)based approach was deployed for mapping QTLs associated with AB resistance in chickpea in two recombinant inbred line populations derived from two crosses (AB 3279 derived from ILC 1929 × ILC 3279 and AB 482 derived from ILC 1929 × ILC 482) and tested in six different environments. Twenty-one different genomic regions linked to AB resistance were identified in regions CalG02 and CalG04 in both populations AB 3279 and AB 482. These regions contain 1,118 SNPs significantly associated with AB resistance (p ≤ 0.001), which explained 11.2-39.3% of the phenotypic variation (PVE). Nine of the AB resistance-associated genomic regions were newly detected in this study, while twelve regions were known from previous AB studies. The proposed physical map narrows down AB resistance to consistent genomic regions identified across different environments. Gene ontology (GO) assigned these QTLs to 319 genes, many of which were associated with stress and disease resistance, and with most important genes belonging to resistance gene families such as leucine-rich repeat (LRR) and transcription factor families. Our results indicate that the flowering-associated gene GIGANTEA is a possible key factor in AB resistance in chickpea. The results have identified AB resistance-associated regions on the physical genetic map of chickpea and allowed for the identification of associated markers that will help in breeding of AB-resistant varieties.

Genetic diversity of 46 azerbaijani durum wheat (triticum durum l.) Genotypes were screened using... more Genetic diversity of 46 azerbaijani durum wheat (triticum durum l.) Genotypes were screened using simple sequence repeats (ssrs). These accessions were collected from various bioclimatic regions of azerbaijan. Out of the used twenty-two primers, 13 primers showed polymorphism and were selected for the analyses. Among the genotypes under study, 31 alleles were detected. Highest number of alleles was detected in locus gwm 335 (on chromosome 5b) and on locus gwm 445 (on chromosome 2a) with 5 and 4 alleles, respectively. The lowest number of alleles was determined in locus gwm 617 with only 1 allele. For a, b and d genomes, the total number of alleles detected were 14, 15 and 2, respectively. Pic value between studied ssr markers was 0.912 and this result shows high genetic diversity between azerbaijani durum wheat genotypes. Therefore, these primers can be recommended for studying genetic diversity of azerbaijani durum wheat accessions. The genetic structure of the genotypes was analyz...

Frontiers in Plant Science

Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar di... more Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar disease of chickpea (Cicer arietinum L.). The genotyping-by-sequencing (GBS)-based approach was deployed for mapping QTLs associated with AB resistance in chickpea in two recombinant inbred line populations derived from two crosses (AB3279 derived from ILC 1929 × ILC 3279 and AB482 derived from ILC 1929 × ILC 482) and tested in six different environments. Twenty-one different genomic regions linked to AB resistance were identified in regions CalG02 and CalG04 in both populations AB3279 and AB482. These regions contain 1,118 SNPs significantly associated with AB resistance (p ≤ 0.001), which explained 11.2–39.3% of the phenotypic variation (PVE). Nine of the AB resistance-associated genomic regions were newly detected in this study, while twelve regions were known from previous AB studies. The proposed physical map narrows down AB resistance to consistent genomic regions identified across d...

Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar di... more Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar disease of chickpea (Cicer arietinum L.). The genotyping-by-sequencing (GBS)-based approach was deployed for mapping QTLs associated with AB resistance in chickpea in two recombinant inbred line populations derived from two crosses (AB3279 derived from ILC 1929 × ILC 3279 and AB482 derived from ILC 1929 × ILC 482) and tested in six different environments. Twenty-one different genomic regions linked to AB resistance were identified in regions CalG02 and CalG04 in both populations AB3279 and AB482. These regions contain 1,118 SNPs significantly associated with AB resistance (p ≤ 0.001), which explained 11.2–39.3% of the phenotypic variation (PVE). Nine of the AB resistance-associated genomic regions were newly detected in this study, while twelve regions were known from previous AB studies. The proposed physical map narrows down AB resistance to consistent genomic regions identified across different environments. Gene ontology (GO) assigned these QTLs to 319 genes, many of which were associated with stress and disease resistance, and with most important genes belonging to resistance gene families such as leucine-rich repeat (LRR) and transcription factor families. Our results indicate that the flowering-associated gene GIGANTEA is a possible key factor in AB resistance in chickpea. The results have identified AB resistance-associated regions on the physical genetic map of chickpea and allowed for the identification of associated markers that will help in breeding of AB-resistant varieties.

Hamwieh, A., F. Alo, S. Ahmed. 2018. Molecular Tools Developed for Disease Resistant Genes in Whe... more Hamwieh, A., F. Alo, S. Ahmed. 2018. Molecular Tools Developed for Disease Resistant Genes in Wheat, Barley, Lentil and Chickpea: A Review. Arab Journal of Plant Protection, 36(1): 50-56. The major objective of using molecular tools by the plant pathologists is to identify markers linked to the resistant genes. The best markers are those located within the genes or tightly linlked to the resistant genes. This paper will review the most recent markers/QTL linked to resistant genes reported in wheat (strip rust, leaf rust, and stem rust), barley (stripe rust, leaf rust, and stem rust), lentil (Fusarium wilt, Ascochyta, Anthracnose and Stemphylium blight) and chickpea (Ascochyta blight and Fusarium wilt). The markers tightly linked to the resistant genes could be used as markers assisted selection in the breeding program to improve effectiveness and efficiency of variety

Arab Journal of Plant Protection, 2018

Alo, F., W. Al-Saaid, M. Baum, H. Alatwani and A. Amri. 2018. Slow rusting of bread wheat landrac... more Alo, F., W. Al-Saaid, M. Baum, H. Alatwani and A. Amri. 2018. Slow rusting of bread wheat landraces to Puccinia striiformis f.sp. tritici under artificial field inoculation. Arab Journal of Plant Protection, 36(2): 164-175. Yellow rust caused by Puccinia striiformis f. sp. tritici is the most devastating fungal disease of wheat, especially in the Central and West Asia and North Africa (CWANA) region. Most of the released cultivars in CWANA have become susceptible to the new virulence Yr27. Growing durable resistance cultivars is the most economical control measure. A field study was conducted to evaluate 500 bread wheat landraces along with the susceptible control 'Morocco' using artificial inoculation under field conditions at Tel Hadia, Syria during 2010/11 and 2011/12 growing seasons. The most prevailing and spreading yellow rust virulence (70E214) was used for artificial inoculation. Disease scoring started when disease severity was more than 50% on the leaves of cv. Morocco and continued for four readings at 7 days intervals. Slow rusting resistance was assessed based on development of the disease over time using the area under disease progress curve (AUDPC), coefficient of infection (CI), final rust severity (FRS), infection rate "r" and relative resistance index (RRI). None of the landraces showed immune reaction and 10% showed the lowest values for all parameters, suggesting that major genes control resistance in these landraces. Approximately 65% of the landraces were marked as having different levels of slow rusting and 25% were highly susceptible. Cluster analysis based on partial resistance parameters of the landraces along with cv. Morocco revealed two major clusters: susceptible and low level of slow rusting were grouped in the first cluster; resistant, high level and moderate level of partial resistance were grouped in the second cluster. These groups were also confirmed using principal coordinate analysis. By comparing the results of RRI and others parameters, it appeared that landraces with very low values exhibited high RRI value of 9, while those that showed high, moderate, and low levels of slow rusting, had RRI ranges of 8-9, 7-8 and 5-7, respectively. Landraces with maximum values from each parameter showed very low RRI values of less than 5. The results also suggest that AUDPC, CI, and FRS are the more appropriate parameters for assessing slow rusting than infection rate. Correlation coefficient and principle component analysis revealed a high and positive correlation between these parameters.

Arab Journal Of Plant Protection, 2018

American Journal of Plant Sciences, 2013

Wheat leaf rust caused by Puccinia triticina, is the most common and widely distributed wheat rus... more Wheat leaf rust caused by Puccinia triticina, is the most common and widely distributed wheat rust in the world. In order to study the genetic structure of leaf rust population 14 pairs of AFLP and 6 pairs of FAFLP primers evaluated on 86 isolates samples collected in Iran during spring of 2009. Results showed that almost all investigated isolates were genetically different and special pattern of AFLP allele's that confirm high genetic diversity within leaf rust population was observed. Analyses showed, all provinces were classified into three major groups particularly similar clusters were found between then neighboring provinces. Rust spore can follow the migration pattern in short and long distances to neighbor in provinces. Results indicated that the greatest variability was revealed by 97% of genetic differentiation within leaf rust populations and the lesser variation of 3% was observed between the rust populations. These results suggested that each population was not completely identical and high gene flow has occurred among the leaf rust population of different provinces. The highest differentiation and genetic distance among the Iranian leaf rust populations was detected between leaf rust population in Sistan and Baluchistan and highest similarity was observed between in Ardabil provinces. The high pathogenic variability of leaf rust races in Ardabil and Northern Khorasan may be an indication that these two regions are the center of origin of pathogenic arability. Present study shows that leaf rust population in Iran is highly dynamic and variable.

The Journal of Agricultural Science, 2014

SUMMARYStripe rust, caused byPuccinia striiformisf. sp.tritici(Pst), is a major wheat disease tha... more SUMMARYStripe rust, caused byPuccinia striiformisf. sp.tritici(Pst), is a major wheat disease that can inflict yield losses of up to 70% on susceptible varieties under favourable environmental conditions. The timely identification of plant genetic resources likely to possess novel resistance to this disease would facilitate the rapid development of resistant wheat varieties. The focused identification of germplasm strategy (FIGS) approach was used to predict stripe rust resistance in a collection of wheat landraces conserved at ICARDA genebank. Long-term climate data for the collection sites, from which these accessions originated and stripe rust evaluation scores for one group of accessions were presented to three different non-linear models to explore the trait×collection site environment interactions. Patterns in the data detected by the models were used to predict stripe rust resistance in a second and different set of accessions. The results of the prediction were then tested a...

Journal of Heredity, 2011

Advances in comparative genomics have provided significant opportunities for analysis of genetic ... more Advances in comparative genomics have provided significant opportunities for analysis of genetic diversity in species with limited genomic resources, such as the genus Lens. Medicago truncatula expressed sequence tags (ESTs) were aligned with the Arabidopsis thaliana genome sequence to identify conserved exon sequences and splice sites in the ESTs. Conserved primers (CPs) based on M. truncatula EST sequences flanking one or more introns were then designed. A total of 22% of the CPs produced polymerase chain reaction amplicons in lentil and were used to sequence amplicons in 175 wild and 133 domesticated lentil accessions. Analysis of the sequences confirmed that L. nigricans and L. ervoides are well-defined species at the DNA sequence level. Lens culinaris subsp. odemensis, L. culinaris subsp. tomentosus, and L. lamottei may constitute a single taxon pending verification with crossability experiments. Lens culinaris subsp. orientalis is the progenitor of domesticated lentil, L. culinaris subsp. culinaris (as proposed before), but a more specific area of origin can be suggested in southern Turkey. We were also able to detect the divergence, following domestication, of the domesticated gene pool into overlapping largeseeded (megasperma) and small-seeded (microsperma) groups. Lentil domestication led to a loss of genetic diversity of approximately 40%. The approach followed in this research has allowed us to rapidly exploit sequence information from model plant species for the study of genetic diversity of a crop such as lentil with limited genomic resources.