Dr. Mohamed Atia Omar is an Associate Professor of Genomics and Bioinformatics at Biotechnology Program, Faculty of Science, Cairo University (CU). Currently, he is the Senior Research (Associate Professor) of Molecular Genetics and Genome Mapping Laboratory at Genome Mapping Department, Agricultural Biotechnology and Genetic Engineering Research Institute (AGERI), Egypt. Additionally, he is a member of the board of directors of Bioinformatics Center at Faculty of Science, Helwan University, Egypt. Dr. Atia received his Ph.D. Degree in Genetics in 2013 from Cairo University (CU) in Egypt. Prior of receiving his Ph.D., he worked as faculty staff in Wisconsin-Madison University at United States of America (USA) from 2010 to 2011. During his work in the USA, he focuses on Next-Generation Sequencing technologies and its applications and he gained a great experience in high-throughput data analysis. He also got another opportunity to join King Abdullah University for Science and Technology (KAUST) at KSA as a postdoctoral fellow (2013-2014) with focusing on the development of new CRISPR/Cas9 Phone: +2-01000164922 Address: 9 Gamaa st. , Giza, Egypt. 12619
In this study, we undertook a survey to analyze the distribution and frequency of microsatellites... more In this study, we undertook a survey to analyze the distribution and frequency of microsatellites or Simple Sequence Repeats (SSRs) in Spodoptera littoralis multiple nucleopolyhedrovirus (SpliMNPV) genome (isolate AN–1956). Out of the 55 microsatellite motifs, identified in the SpliMNPV-AN1956 genome using in silico analysis (inclusive of mono-, di-, tri- and hexa-nucleotide repeats), 39 were found to be distributed within coding regions (cSSRs), whereas 16 were observed to lie within intergenic or noncoding regions. Among the 39 motifs located in coding regions, 21 were located in annotated functional genes whilst 18 were identified in unknown functional genes (hypothetical proteins). Among the identified motifs, trinucleotide (80%) repeats were found to be the most abundant followed by dinucleotide (13%), mononucleotide (5%) and hexanucleotide (2%) repeats. The 39 motifs located within coding regions were further validated in vitro by using PCR analysis, while the 21 motifs located within known functional genes (15 genes) were characterized using nucleotide sequencing. A comparison of the sequence analysis data of the 21 sequenced cSSRs with the published sequences is presented. Finally, the developed SSR markers of the 39 motifs were further mapped/localized onto the SpliMNPV-AN1956 genome. In conclusion, the SSR markers specific to SpliMNPV, developed in this study, could be a useful tool for the identification of isolates and analysis of genetic diversity and viral evolutionary status.
Cotton is the world’s leading natural fiber and second most important oilseed crop and has been a... more Cotton is the world’s leading natural fiber and second most important oilseed crop and has been a focus of genetic, systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. “Giza 83” and “Deltapine” was used in this study. Different molecular markers including SS R, ES T, ES T-SS R, AFLP and RAPD were employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with 140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11 and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19 and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton cultivars with improved agronomic traits
Cotton is the world's leading fiber crop and the second most important oil seed crop. In Egypt, p... more Cotton is the world's leading fiber crop and the second most important oil seed crop. In Egypt, plant breeders have made major contributions to the productivity of this crop; however, this has led to decreasing the genetic variation among Egyptian cotton varieties. Enhancing the productivity of cotton could be addressed through improving different agronomic traits including early flowering and maturation. In the present investigation, an interspecific cross (G. barbadense x G. hirsutum) was performed between two genotypes, Giza83 (late flowering) and Deltapine (early flowering) to develop F2 segregating population. Analysis of segregation among the 71 F2 individuals was performed using 3 RAPD, 10 SSR, 6 AFLP primer combinations. Twenty four AFLP primer combinations were used in bulked segregant analysis for flowering time. Linkage analysis and map construction were performed using Map Manager. The map showed 22 linkage groups with 140 markers covered a total length of 1556.7 cM. The average length of linkage groups ranged from 1.4 to 649.5. Single point analysis was used to identify the genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total, 30 significant QTL were identified for the five traits on ten linkage groups, among these 11 QTL for plant height, 8 for number of bolls, 4 QTL for each of days to flowering and bolling date and 3 QTL for number of nodes at flowering time. This work represents the first linkage map for the intercross between Giza83 and Deltapine showing chromosomal regions associated with some agronomic traits.
Durum wheat (Triticum turgidum ssp. durum) is an economically and nutritionally important cereal ... more Durum wheat (Triticum turgidum ssp. durum) is an economically and nutritionally important cereal crop in the Mediterranean region and its production is largely influenced by environmental stresses, such as drought, salinity, heat and nutrient deficiency. The objective of this study was to dissect quantitative trait loci (QTL) controlling grain yield, yield components and drought tolerance in durum. A molecular genetic linkage map for F2 durum mapping population derived from an intraspecific cross between Baniswif-1 x Sohag-2 was constructed using 114 DNA markers (9 SSRs, 14 SCoTs, 90 AFLPs and 1 RAPDs) distributed over the 14 linkage groups and spanning 2040.9 cM of the durum wheat genome. The size of linkage groups varied greatly from 6.8cM for LG11 to 317.5cM for LG4 with an average length of 145.8cM. Based on the used anchor SSR markers, only eight linkage groups were assigned to chromosomes, where LG1, LG3, LG5, LG6, LG7, LG9, LG13 and LG14 were assigned to chromosomes 1B, 3B, 5B, 6A, 6B, 7A, 3A and 2B, respectively. Single point analysis was used to identify genomic regions controlling eleven morpho-physiological traits related to grain yield, yield components and drought tolerance. A total of 74 QTL were identified for the eleven traits on all linkage groups except (LG10 and LG11). These included 3 QTL for root length (RL), 11 QTL for plant height (PH), 7 QTL for spike length (SL), 3 QTL for number of branches/plant (NBP), 3 QTL for number of spike/plant (NSP), 8 QTL for number of spikelets/spike (NSS), 15 QTL for number of kernel/spike (NKS), 10 QTL for thousand-kernel weight (TKW), 4 QTL for fresh weight (FW), 5 QTL for dry weight (DW) and 5 QTL for total amino acids (TAA). This work represents the first genetic linkage map for durum wheat population derived from an intraspecific cross between ‗Baniswif-1' and ‗Sohag-2' showing chromosomal regions associated with 11 morpho-physiological traits related to grain yield, yield components and drought tolerance in durum wheat.
The date palm (Phoenix dactylifera L.), 2n=36, is a dioecious long-lived monocotyledonous plant, ... more The date palm (Phoenix dactylifera L.), 2n=36, is a dioecious long-lived monocotyledonous plant, which belongs to
the family Arecaceae. It is one of the excellent candidate crops in arid and semiarid regions of the world. Recently,
fluorescence in situ hybridization (FISH) has become a powerful and useful tool for the direct detection of specific
DNA fragments in the genome. In this technique, ribosomal DNA genes (45S and 5S rDNA) are commonly used as
markers for the physical mapping of plant chromosomes to analyze genomic organization. To date, there is no report
on rDNA loci in Phoenix dactylifera detected by FISH. The objective of this study was to develop a sex-specific
fluorescence in situ hybridization (FISH) markers with 5S and 45S rDNA in Egyptian Date Palm Trees (cv.
Zaghloul and Siwi). The results successfully revealed clear differences between males and females belonging to
both cv. Zaghloul and Siwi by using 45S rDNA FISH. The fluorescence in situ hybridization (FISH) with 45S
rDNA localized two clear telomeric intermediate -signals in female palm trees belonging to cv. Zaghloul and Siwi.
While, it exhibited three clear telomeric intermediate-signals in male trees belonging to cv. Zaghloul and Siwi. On
the other hand, results of fluorescence in situ hybridization (FISH) with 5S rDNA didn’t reveal any clear differences
between males and females belonging to cv. Siwi. Based on the above results, we hypothesize that the third signal
(unpaired signal) of 45S rDNA probe characterized in both Siwi and Zaghloul males is located on a male
chromosome (Y chromosome). This finding can be utilized and used as cytological marker to differentiate between
male and female trees in Egyptian date palm at an early stage.
Date palm is one of the most successful fruit crops in tropical and sub-tropical hab... more Date palm is one of the most successful fruit crops in tropical and sub-tropical habitats. In the present investigation a multidisciplinary molecular marker approaches including three novel marker types (SCoT, CDDP and ITAP) in addition to (SSR, AFLP and RAPD) were employed to assess the genetic diversity and genetic relationships within and among different Egyptian cultivars. Males and females genotypes representingthree or five Egyptian cultivars were assayed using 14 AFLP, 48 SCoT, 14 SSR, 21 CDDP, 18 ITAP and 100 RAPD primers or primer combinations. Amplification products yielded a total no. of bands591, 484, 83, 192, 204 and 1084, with a percentageof polymorphism 37.4%, 41.3%, 59%, 31.7%, 34% and 24.9%, respectively. The average no. of bands/primer ranged from 5.9for SSR to 42.2 for AFLP. The cluster analysis of the studied genotypes using these different marker systems revealed five dendrograms exhibited unique topology with some similarities. The generated dendrograms from these marker systems successfully clustered the studied genotypes based on cultivar or gender. The data scored from AFLP, SCoT, SSR, CDDP and ITAP were combined and computed to generate more accurate relationships based on large and versatile genome coverage. The dendrogram based on the combined data exhibited the closest relationships to those illustrated by the AFLP-based dendrogram. On the other hand, the RAPD dendrogram exhibited also a unique topology with some similarities comparing with other marker systems. These results confirmed that different marker systems differ in the mechanism of detecting polymorphism, genome coverage and the ease of application. Therefore, they could complement each other to draw more accurate conclusions.
Date palm (Phoenix dactylifera L., 2n=36) is outstanding for the economic value of its different ... more Date palm (Phoenix dactylifera L., 2n=36) is outstanding for the economic value of its different parts and its socio-economic significance in agro-systems of arid zones. Date palm trees are propagated either from seed or vegetative offshoots. Propagation with seeds is unsuitable for commercial production because half of the progeny are males and to date there is no way to distinguish the sex in date palm plants at an early stage of development. During the past decade, there have been numerous attempts to use molecular markers to discriminate among male and female trees in date palm. Here, we employed an effective approach to develop sex-specific PCR-based markers to distinguish the genders in Egyptian date palm. A set of 23 SCoT and 122 RAPD primers were applied against five superior Egyptian date palm cultivars to identify any sex-specific markers. Two SCoT (SCoT36 and SCoT41) and four RAPD primers (OP-A11, OP-M11, OP-O07 and OP-S07) exhibited differential fragments/bands between males and females (Two male-associated markers and five female-associated markers). To verify these results, the PCR reactions were repeated at least three times by different professional hands and by using different commercial reagents (Promega, Ferments and Takara). Then, these differential bands were extracted, cloned to pGEM-T Easy Vector System and transformed into DH5-alpha E. coli competent cells for subsequent sequencing analysis. The BLAST analysis results indicated that SCoT36 revealed high degree of similarity with mitochondrial rpl2 gene in date palm while, SCoT41 revealed high degree of similarity with putative DEIH-box RNA/DNA helicase gene (Os01g0767700) in Oryza sativa Japonica. On the other hand, the BLAST analysis of (OP-A11, OP-O07 and OP-S07) revealed no significant similarity to any well-defined sequences or protein on databases. While, they showed very low similarity with the date palm published sequences which give high probability that this sequences may be a novel or non-sequenced parts of the date palm genome. Meanwhile, OP-M11 exhibited high degree of similarity with the date palm genome (cultivar Deglet Noor, fosmid 9B12) and partial similarity with both putative glucuronoxylan glucuronosyltransferase protein (Triticum urartu) and Exostosin-like family protein (Oryza sativa). These results represent the first case-study focusing on the applications of SCoT technique as a gene targeting marker in sex-determination in date palm. Moreover, indicate that these promising primers should be helpful in rapidly distinguishing between male and female trees in date palm at earliest stages.
Durum wheat (Triticum turgidum ssp. durum) is an economically and nutritionally important cereal ... more Durum wheat (Triticum turgidum ssp. durum) is an economically and nutritionally important cereal crop in the Mediterranean region and its production is largely influenced by environmental stresses, such as drought, salinity, heat and nutrient deficiency. The objective of this study was to dissect quantitative trait loci (QTL) controlling grain yield, yield components and drought tolerance in durum. A molecular genetic linkage map for F2 durum mapping population derived from an intraspecific cross between Baniswif-1 x Sohag-2 was constructed using 114 DNA markers (9 SSRs, 14 SCoTs, 90 AFLPs and 1 RAPDs) distributed over the 14 linkage groups and spanning 2040.9 cM of the durum wheat genome. The size of linkage groups varied greatly from 6.8cM for LG11 to 317.5cM for LG4 with an average length of 145.8cM. Based on the used anchor SSR markers, only eight linkage groups were assigned to chromosomes, where LG1, LG3, LG5, LG6, LG7, LG9, LG13 and LG14 were assigned to chromosomes 1B, 3B, 5B, 6A, 6B, 7A, 3A and 2B, respectively. Single point analysis was used to identify genomic regions controlling eleven morpho-physiological traits related to grain yield, yield components and drought tolerance. A total of 74 QTL were identified for the eleven traits on all linkage groups except (LG10 and LG11). These included 3 QTL for root length (RL), 11 QTL for plant height (PH), 7 QTL for spike length (SL), 3 QTL for number of branches/plant (NBP), 3 QTL for number of spike/plant (NSP), 8 QTL for number of spikelets/spike (NSS), 15 QTL for number of kernel/spike (NKS), 10 QTL for thousand-kernel weight (TKW), 4 QTL for fresh weight (FW), 5 QTL for dry weight (DW) and 5 QTL for total amino acids (TAA). This work represents the first genetic linkage map for durum wheat population derived from an intraspecific cross between ‗Baniswif-1‘ and ‗Sohag-2‘ showing chromosomal regions associated with 11 morpho-physiological traits related to grain yield, yield components and drought tolerance in durum wheat.
Cotton is the world’s leading natural fiber and second most important oilseed crop and has been a... more Cotton is the world’s leading natural fiber and second most important oilseed crop and has been a focus of genetic, systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. “Giza 83” and “Deltapine” was used in this study. Different molecular markers including SS R, ES T, ES T-SS R, AFLP and RAPD were employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with 140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11 and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19 and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton cultivars with improved agronomic traits
Cotton is the world's leading fiber crop and the second most important oil seed crop. In Egypt,
p... more Cotton is the world's leading fiber crop and the second most important oil seed crop. In Egypt, plant breeders have made major contributions to the productivity of this crop; however, this has led to decreasing the genetic variation among Egyptian cotton varieties. Enhancing the productivity of cotton could be addressed through improving different agronomic traits including early flowering and maturation. In the present investigation, an interspecific cross (G. barbadense x G. hirsutum) was performed between two genotypes, Giza83 (late flowering) and Deltapine (early flowering) to develop F2 segregating population. Analysis of segregation among the 71 F2 individuals was performed using 3 RAPD, 10 SSR, 6 AFLP primer combinations. Twenty four AFLP primer combinations were used in bulked segregant analysis for flowering time. Linkage analysis and map construction were performed using Map Manager. The map showed 22 linkage groups with 140 markers covered a total length of 1556.7 cM. The average length of linkage groups ranged from 1.4 to 649.5. Single point analysis was used to identify the genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total, 30 significant QTL were identified for the five traits on ten linkage groups, among these 11 QTL for plant height, 8 for number of bolls, 4 QTL for each of days to flowering and bolling date and 3 QTL for number of nodes at flowering time. This work represents the first linkage map for the intercross between Giza83 and Deltapine showing chromosomal regions associated with some agronomic traits.
In this study, we undertook a survey to analyze the distribution and frequency of microsatellites... more In this study, we undertook a survey to analyze the distribution and frequency of microsatellites or Simple Sequence Repeats (SSRs) in Spodoptera littoralis multiple nucleopolyhedrovirus (SpliMNPV) genome (isolate AN–1956). Out of the 55 microsatellite motifs, identified in the SpliMNPV-AN1956 genome using in silico analysis (inclusive of mono-, di-, tri- and hexa-nucleotide repeats), 39 were found to be distributed within coding regions (cSSRs), whereas 16 were observed to lie within intergenic or noncoding regions. Among the 39 motifs located in coding regions, 21 were located in annotated functional genes whilst 18 were identified in unknown functional genes (hypothetical proteins). Among the identified motifs, trinucleotide (80%) repeats were found to be the most abundant followed by dinucleotide (13%), mononucleotide (5%) and hexanucleotide (2%) repeats. The 39 motifs located within coding regions were further validated in vitro by using PCR analysis, while the 21 motifs located within known functional genes (15 genes) were characterized using nucleotide sequencing. A comparison of the sequence analysis data of the 21 sequenced cSSRs with the published sequences is presented. Finally, the developed SSR markers of the 39 motifs were further mapped/localized onto the SpliMNPV-AN1956 genome. In conclusion, the SSR markers specific to SpliMNPV, developed in this study, could be a useful tool for the identification of isolates and analysis of genetic diversity and viral evolutionary status.
Cotton is the world’s leading natural fiber and second most important oilseed crop and has been a... more Cotton is the world’s leading natural fiber and second most important oilseed crop and has been a focus of genetic, systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. “Giza 83” and “Deltapine” was used in this study. Different molecular markers including SS R, ES T, ES T-SS R, AFLP and RAPD were employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with 140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11 and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19 and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton cultivars with improved agronomic traits
Cotton is the world's leading fiber crop and the second most important oil seed crop. In Egypt, p... more Cotton is the world's leading fiber crop and the second most important oil seed crop. In Egypt, plant breeders have made major contributions to the productivity of this crop; however, this has led to decreasing the genetic variation among Egyptian cotton varieties. Enhancing the productivity of cotton could be addressed through improving different agronomic traits including early flowering and maturation. In the present investigation, an interspecific cross (G. barbadense x G. hirsutum) was performed between two genotypes, Giza83 (late flowering) and Deltapine (early flowering) to develop F2 segregating population. Analysis of segregation among the 71 F2 individuals was performed using 3 RAPD, 10 SSR, 6 AFLP primer combinations. Twenty four AFLP primer combinations were used in bulked segregant analysis for flowering time. Linkage analysis and map construction were performed using Map Manager. The map showed 22 linkage groups with 140 markers covered a total length of 1556.7 cM. The average length of linkage groups ranged from 1.4 to 649.5. Single point analysis was used to identify the genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total, 30 significant QTL were identified for the five traits on ten linkage groups, among these 11 QTL for plant height, 8 for number of bolls, 4 QTL for each of days to flowering and bolling date and 3 QTL for number of nodes at flowering time. This work represents the first linkage map for the intercross between Giza83 and Deltapine showing chromosomal regions associated with some agronomic traits.
Durum wheat (Triticum turgidum ssp. durum) is an economically and nutritionally important cereal ... more Durum wheat (Triticum turgidum ssp. durum) is an economically and nutritionally important cereal crop in the Mediterranean region and its production is largely influenced by environmental stresses, such as drought, salinity, heat and nutrient deficiency. The objective of this study was to dissect quantitative trait loci (QTL) controlling grain yield, yield components and drought tolerance in durum. A molecular genetic linkage map for F2 durum mapping population derived from an intraspecific cross between Baniswif-1 x Sohag-2 was constructed using 114 DNA markers (9 SSRs, 14 SCoTs, 90 AFLPs and 1 RAPDs) distributed over the 14 linkage groups and spanning 2040.9 cM of the durum wheat genome. The size of linkage groups varied greatly from 6.8cM for LG11 to 317.5cM for LG4 with an average length of 145.8cM. Based on the used anchor SSR markers, only eight linkage groups were assigned to chromosomes, where LG1, LG3, LG5, LG6, LG7, LG9, LG13 and LG14 were assigned to chromosomes 1B, 3B, 5B, 6A, 6B, 7A, 3A and 2B, respectively. Single point analysis was used to identify genomic regions controlling eleven morpho-physiological traits related to grain yield, yield components and drought tolerance. A total of 74 QTL were identified for the eleven traits on all linkage groups except (LG10 and LG11). These included 3 QTL for root length (RL), 11 QTL for plant height (PH), 7 QTL for spike length (SL), 3 QTL for number of branches/plant (NBP), 3 QTL for number of spike/plant (NSP), 8 QTL for number of spikelets/spike (NSS), 15 QTL for number of kernel/spike (NKS), 10 QTL for thousand-kernel weight (TKW), 4 QTL for fresh weight (FW), 5 QTL for dry weight (DW) and 5 QTL for total amino acids (TAA). This work represents the first genetic linkage map for durum wheat population derived from an intraspecific cross between ‗Baniswif-1' and ‗Sohag-2' showing chromosomal regions associated with 11 morpho-physiological traits related to grain yield, yield components and drought tolerance in durum wheat.
The date palm (Phoenix dactylifera L.), 2n=36, is a dioecious long-lived monocotyledonous plant, ... more The date palm (Phoenix dactylifera L.), 2n=36, is a dioecious long-lived monocotyledonous plant, which belongs to
the family Arecaceae. It is one of the excellent candidate crops in arid and semiarid regions of the world. Recently,
fluorescence in situ hybridization (FISH) has become a powerful and useful tool for the direct detection of specific
DNA fragments in the genome. In this technique, ribosomal DNA genes (45S and 5S rDNA) are commonly used as
markers for the physical mapping of plant chromosomes to analyze genomic organization. To date, there is no report
on rDNA loci in Phoenix dactylifera detected by FISH. The objective of this study was to develop a sex-specific
fluorescence in situ hybridization (FISH) markers with 5S and 45S rDNA in Egyptian Date Palm Trees (cv.
Zaghloul and Siwi). The results successfully revealed clear differences between males and females belonging to
both cv. Zaghloul and Siwi by using 45S rDNA FISH. The fluorescence in situ hybridization (FISH) with 45S
rDNA localized two clear telomeric intermediate -signals in female palm trees belonging to cv. Zaghloul and Siwi.
While, it exhibited three clear telomeric intermediate-signals in male trees belonging to cv. Zaghloul and Siwi. On
the other hand, results of fluorescence in situ hybridization (FISH) with 5S rDNA didn’t reveal any clear differences
between males and females belonging to cv. Siwi. Based on the above results, we hypothesize that the third signal
(unpaired signal) of 45S rDNA probe characterized in both Siwi and Zaghloul males is located on a male
chromosome (Y chromosome). This finding can be utilized and used as cytological marker to differentiate between
male and female trees in Egyptian date palm at an early stage.
Date palm is one of the most successful fruit crops in tropical and sub-tropical hab... more Date palm is one of the most successful fruit crops in tropical and sub-tropical habitats. In the present investigation a multidisciplinary molecular marker approaches including three novel marker types (SCoT, CDDP and ITAP) in addition to (SSR, AFLP and RAPD) were employed to assess the genetic diversity and genetic relationships within and among different Egyptian cultivars. Males and females genotypes representingthree or five Egyptian cultivars were assayed using 14 AFLP, 48 SCoT, 14 SSR, 21 CDDP, 18 ITAP and 100 RAPD primers or primer combinations. Amplification products yielded a total no. of bands591, 484, 83, 192, 204 and 1084, with a percentageof polymorphism 37.4%, 41.3%, 59%, 31.7%, 34% and 24.9%, respectively. The average no. of bands/primer ranged from 5.9for SSR to 42.2 for AFLP. The cluster analysis of the studied genotypes using these different marker systems revealed five dendrograms exhibited unique topology with some similarities. The generated dendrograms from these marker systems successfully clustered the studied genotypes based on cultivar or gender. The data scored from AFLP, SCoT, SSR, CDDP and ITAP were combined and computed to generate more accurate relationships based on large and versatile genome coverage. The dendrogram based on the combined data exhibited the closest relationships to those illustrated by the AFLP-based dendrogram. On the other hand, the RAPD dendrogram exhibited also a unique topology with some similarities comparing with other marker systems. These results confirmed that different marker systems differ in the mechanism of detecting polymorphism, genome coverage and the ease of application. Therefore, they could complement each other to draw more accurate conclusions.
Date palm (Phoenix dactylifera L., 2n=36) is outstanding for the economic value of its different ... more Date palm (Phoenix dactylifera L., 2n=36) is outstanding for the economic value of its different parts and its socio-economic significance in agro-systems of arid zones. Date palm trees are propagated either from seed or vegetative offshoots. Propagation with seeds is unsuitable for commercial production because half of the progeny are males and to date there is no way to distinguish the sex in date palm plants at an early stage of development. During the past decade, there have been numerous attempts to use molecular markers to discriminate among male and female trees in date palm. Here, we employed an effective approach to develop sex-specific PCR-based markers to distinguish the genders in Egyptian date palm. A set of 23 SCoT and 122 RAPD primers were applied against five superior Egyptian date palm cultivars to identify any sex-specific markers. Two SCoT (SCoT36 and SCoT41) and four RAPD primers (OP-A11, OP-M11, OP-O07 and OP-S07) exhibited differential fragments/bands between males and females (Two male-associated markers and five female-associated markers). To verify these results, the PCR reactions were repeated at least three times by different professional hands and by using different commercial reagents (Promega, Ferments and Takara). Then, these differential bands were extracted, cloned to pGEM-T Easy Vector System and transformed into DH5-alpha E. coli competent cells for subsequent sequencing analysis. The BLAST analysis results indicated that SCoT36 revealed high degree of similarity with mitochondrial rpl2 gene in date palm while, SCoT41 revealed high degree of similarity with putative DEIH-box RNA/DNA helicase gene (Os01g0767700) in Oryza sativa Japonica. On the other hand, the BLAST analysis of (OP-A11, OP-O07 and OP-S07) revealed no significant similarity to any well-defined sequences or protein on databases. While, they showed very low similarity with the date palm published sequences which give high probability that this sequences may be a novel or non-sequenced parts of the date palm genome. Meanwhile, OP-M11 exhibited high degree of similarity with the date palm genome (cultivar Deglet Noor, fosmid 9B12) and partial similarity with both putative glucuronoxylan glucuronosyltransferase protein (Triticum urartu) and Exostosin-like family protein (Oryza sativa). These results represent the first case-study focusing on the applications of SCoT technique as a gene targeting marker in sex-determination in date palm. Moreover, indicate that these promising primers should be helpful in rapidly distinguishing between male and female trees in date palm at earliest stages.
Durum wheat (Triticum turgidum ssp. durum) is an economically and nutritionally important cereal ... more Durum wheat (Triticum turgidum ssp. durum) is an economically and nutritionally important cereal crop in the Mediterranean region and its production is largely influenced by environmental stresses, such as drought, salinity, heat and nutrient deficiency. The objective of this study was to dissect quantitative trait loci (QTL) controlling grain yield, yield components and drought tolerance in durum. A molecular genetic linkage map for F2 durum mapping population derived from an intraspecific cross between Baniswif-1 x Sohag-2 was constructed using 114 DNA markers (9 SSRs, 14 SCoTs, 90 AFLPs and 1 RAPDs) distributed over the 14 linkage groups and spanning 2040.9 cM of the durum wheat genome. The size of linkage groups varied greatly from 6.8cM for LG11 to 317.5cM for LG4 with an average length of 145.8cM. Based on the used anchor SSR markers, only eight linkage groups were assigned to chromosomes, where LG1, LG3, LG5, LG6, LG7, LG9, LG13 and LG14 were assigned to chromosomes 1B, 3B, 5B, 6A, 6B, 7A, 3A and 2B, respectively. Single point analysis was used to identify genomic regions controlling eleven morpho-physiological traits related to grain yield, yield components and drought tolerance. A total of 74 QTL were identified for the eleven traits on all linkage groups except (LG10 and LG11). These included 3 QTL for root length (RL), 11 QTL for plant height (PH), 7 QTL for spike length (SL), 3 QTL for number of branches/plant (NBP), 3 QTL for number of spike/plant (NSP), 8 QTL for number of spikelets/spike (NSS), 15 QTL for number of kernel/spike (NKS), 10 QTL for thousand-kernel weight (TKW), 4 QTL for fresh weight (FW), 5 QTL for dry weight (DW) and 5 QTL for total amino acids (TAA). This work represents the first genetic linkage map for durum wheat population derived from an intraspecific cross between ‗Baniswif-1‘ and ‗Sohag-2‘ showing chromosomal regions associated with 11 morpho-physiological traits related to grain yield, yield components and drought tolerance in durum wheat.
Cotton is the world’s leading natural fiber and second most important oilseed crop and has been a... more Cotton is the world’s leading natural fiber and second most important oilseed crop and has been a focus of genetic, systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. “Giza 83” and “Deltapine” was used in this study. Different molecular markers including SS R, ES T, ES T-SS R, AFLP and RAPD were employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with 140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11 and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19 and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton cultivars with improved agronomic traits
Cotton is the world's leading fiber crop and the second most important oil seed crop. In Egypt,
p... more Cotton is the world's leading fiber crop and the second most important oil seed crop. In Egypt, plant breeders have made major contributions to the productivity of this crop; however, this has led to decreasing the genetic variation among Egyptian cotton varieties. Enhancing the productivity of cotton could be addressed through improving different agronomic traits including early flowering and maturation. In the present investigation, an interspecific cross (G. barbadense x G. hirsutum) was performed between two genotypes, Giza83 (late flowering) and Deltapine (early flowering) to develop F2 segregating population. Analysis of segregation among the 71 F2 individuals was performed using 3 RAPD, 10 SSR, 6 AFLP primer combinations. Twenty four AFLP primer combinations were used in bulked segregant analysis for flowering time. Linkage analysis and map construction were performed using Map Manager. The map showed 22 linkage groups with 140 markers covered a total length of 1556.7 cM. The average length of linkage groups ranged from 1.4 to 649.5. Single point analysis was used to identify the genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total, 30 significant QTL were identified for the five traits on ten linkage groups, among these 11 QTL for plant height, 8 for number of bolls, 4 QTL for each of days to flowering and bolling date and 3 QTL for number of nodes at flowering time. This work represents the first linkage map for the intercross between Giza83 and Deltapine showing chromosomal regions associated with some agronomic traits.
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Papers by Assoc. Prof. Mohamed Atia Omar
systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton
were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating
F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. “Giza 83”
and “Deltapine” was used in this study. Different molecular markers including SS R, ES T, ES T-SS R, AFLP and RAPD were
employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with
140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these
new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11
and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic
regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number
of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19
and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal
assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in
this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton
cultivars with improved agronomic traits
the family Arecaceae. It is one of the excellent candidate crops in arid and semiarid regions of the world. Recently,
fluorescence in situ hybridization (FISH) has become a powerful and useful tool for the direct detection of specific
DNA fragments in the genome. In this technique, ribosomal DNA genes (45S and 5S rDNA) are commonly used as
markers for the physical mapping of plant chromosomes to analyze genomic organization. To date, there is no report
on rDNA loci in Phoenix dactylifera detected by FISH. The objective of this study was to develop a sex-specific
fluorescence in situ hybridization (FISH) markers with 5S and 45S rDNA in Egyptian Date Palm Trees (cv.
Zaghloul and Siwi). The results successfully revealed clear differences between males and females belonging to
both cv. Zaghloul and Siwi by using 45S rDNA FISH. The fluorescence in situ hybridization (FISH) with 45S
rDNA localized two clear telomeric intermediate -signals in female palm trees belonging to cv. Zaghloul and Siwi.
While, it exhibited three clear telomeric intermediate-signals in male trees belonging to cv. Zaghloul and Siwi. On
the other hand, results of fluorescence in situ hybridization (FISH) with 5S rDNA didn’t reveal any clear differences
between males and females belonging to cv. Siwi. Based on the above results, we hypothesize that the third signal
(unpaired signal) of 45S rDNA probe characterized in both Siwi and Zaghloul males is located on a male
chromosome (Y chromosome). This finding can be utilized and used as cytological marker to differentiate between
male and female trees in Egyptian date palm at an early stage.
investigation a multidisciplinary molecular marker approaches including three novel marker types (SCoT, CDDP and
ITAP) in addition to (SSR, AFLP and RAPD) were employed to assess the genetic diversity and genetic relationships
within and among different Egyptian cultivars. Males and females genotypes representingthree or five Egyptian cultivars
were assayed using 14 AFLP, 48 SCoT, 14 SSR, 21 CDDP, 18 ITAP and 100 RAPD primers or primer combinations.
Amplification products yielded a total no. of bands591, 484, 83, 192, 204 and 1084, with a percentageof polymorphism
37.4%, 41.3%, 59%, 31.7%, 34% and 24.9%, respectively. The average no. of bands/primer ranged from 5.9for SSR to
42.2 for AFLP. The cluster analysis of the studied genotypes using these different marker systems revealed five
dendrograms exhibited unique topology with some similarities. The generated dendrograms from these marker systems
successfully clustered the studied genotypes based on cultivar or gender. The data scored from AFLP, SCoT, SSR, CDDP
and ITAP were combined and computed to generate more accurate relationships based on large and versatile genome
coverage. The dendrogram based on the combined data exhibited the closest relationships to those illustrated by the
AFLP-based dendrogram. On the other hand, the RAPD dendrogram exhibited also a unique topology with some
similarities comparing with other marker systems.
These results confirmed that different marker systems differ in the mechanism of detecting polymorphism,
genome coverage and the ease of application. Therefore, they could complement each other to draw more accurate
conclusions.
Mediterranean region and its production is largely influenced by environmental stresses, such as drought, salinity, heat and
nutrient deficiency. The objective of this study was to dissect quantitative trait loci (QTL) controlling grain yield, yield
components and drought tolerance in durum. A molecular genetic linkage map for F2 durum mapping population derived
from an intraspecific cross between Baniswif-1 x Sohag-2 was constructed using 114 DNA markers (9 SSRs, 14 SCoTs, 90
AFLPs and 1 RAPDs) distributed over the 14 linkage groups and spanning 2040.9 cM of the durum wheat genome. The
size of linkage groups varied greatly from 6.8cM for LG11 to 317.5cM for LG4 with an average length of 145.8cM. Based
on the used anchor SSR markers, only eight linkage groups were assigned to chromosomes, where LG1, LG3, LG5, LG6,
LG7, LG9, LG13 and LG14 were assigned to chromosomes 1B, 3B, 5B, 6A, 6B, 7A, 3A and 2B, respectively. Single point
analysis was used to identify genomic regions controlling eleven morpho-physiological traits related to grain yield, yield
components and drought tolerance. A total of 74 QTL were identified for the eleven traits on all linkage groups except
(LG10 and LG11). These included 3 QTL for root length (RL), 11 QTL for plant height (PH), 7 QTL for spike length (SL),
3 QTL for number of branches/plant (NBP), 3 QTL for number of spike/plant (NSP), 8 QTL for number of spikelets/spike
(NSS), 15 QTL for number of kernel/spike (NKS), 10 QTL for thousand-kernel weight (TKW), 4 QTL for fresh weight
(FW), 5 QTL for dry weight (DW) and 5 QTL for total amino acids (TAA). This work represents the first genetic linkage
map for durum wheat population derived from an intraspecific cross between ‗Baniswif-1‘ and ‗Sohag-2‘ showing
chromosomal regions associated with 11 morpho-physiological traits related to grain yield, yield components and drought
tolerance in durum wheat.
systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton
were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating
F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. “Giza 83”
and “Deltapine” was used in this study. Different molecular markers including SS R, ES T, ES T-SS R, AFLP and RAPD were
employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with
140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these
new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11
and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic
regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number
of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19
and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal
assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in
this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton
cultivars with improved agronomic traits
plant breeders have made major contributions to the productivity of this crop; however, this has led to
decreasing the genetic variation among Egyptian cotton varieties. Enhancing the productivity of cotton
could be addressed through improving different agronomic traits including early flowering and maturation.
In the present investigation, an interspecific cross (G. barbadense x G. hirsutum) was performed between
two genotypes, Giza83 (late flowering) and Deltapine (early flowering) to develop F2 segregating
population. Analysis of segregation among the 71 F2 individuals was performed using 3 RAPD, 10 SSR,
6 AFLP primer combinations. Twenty four AFLP primer combinations were used in bulked segregant
analysis for flowering time. Linkage analysis and map construction were performed using Map Manager.
The map showed 22 linkage groups with 140 markers covered a total length of 1556.7 cM. The average
length of linkage groups ranged from 1.4 to 649.5. Single point analysis was used to identify the genomic
regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to
flowering and number of bolls. In total, 30 significant QTL were identified for the five traits on ten
linkage groups, among these 11 QTL for plant height, 8 for number of bolls, 4 QTL for each of days to
flowering and bolling date and 3 QTL for number of nodes at flowering time. This work represents the
first linkage map for the intercross between Giza83 and Deltapine showing chromosomal regions
associated with some agronomic traits.
systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton
were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating
F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. “Giza 83”
and “Deltapine” was used in this study. Different molecular markers including SS R, ES T, ES T-SS R, AFLP and RAPD were
employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with
140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these
new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11
and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic
regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number
of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19
and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal
assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in
this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton
cultivars with improved agronomic traits
the family Arecaceae. It is one of the excellent candidate crops in arid and semiarid regions of the world. Recently,
fluorescence in situ hybridization (FISH) has become a powerful and useful tool for the direct detection of specific
DNA fragments in the genome. In this technique, ribosomal DNA genes (45S and 5S rDNA) are commonly used as
markers for the physical mapping of plant chromosomes to analyze genomic organization. To date, there is no report
on rDNA loci in Phoenix dactylifera detected by FISH. The objective of this study was to develop a sex-specific
fluorescence in situ hybridization (FISH) markers with 5S and 45S rDNA in Egyptian Date Palm Trees (cv.
Zaghloul and Siwi). The results successfully revealed clear differences between males and females belonging to
both cv. Zaghloul and Siwi by using 45S rDNA FISH. The fluorescence in situ hybridization (FISH) with 45S
rDNA localized two clear telomeric intermediate -signals in female palm trees belonging to cv. Zaghloul and Siwi.
While, it exhibited three clear telomeric intermediate-signals in male trees belonging to cv. Zaghloul and Siwi. On
the other hand, results of fluorescence in situ hybridization (FISH) with 5S rDNA didn’t reveal any clear differences
between males and females belonging to cv. Siwi. Based on the above results, we hypothesize that the third signal
(unpaired signal) of 45S rDNA probe characterized in both Siwi and Zaghloul males is located on a male
chromosome (Y chromosome). This finding can be utilized and used as cytological marker to differentiate between
male and female trees in Egyptian date palm at an early stage.
investigation a multidisciplinary molecular marker approaches including three novel marker types (SCoT, CDDP and
ITAP) in addition to (SSR, AFLP and RAPD) were employed to assess the genetic diversity and genetic relationships
within and among different Egyptian cultivars. Males and females genotypes representingthree or five Egyptian cultivars
were assayed using 14 AFLP, 48 SCoT, 14 SSR, 21 CDDP, 18 ITAP and 100 RAPD primers or primer combinations.
Amplification products yielded a total no. of bands591, 484, 83, 192, 204 and 1084, with a percentageof polymorphism
37.4%, 41.3%, 59%, 31.7%, 34% and 24.9%, respectively. The average no. of bands/primer ranged from 5.9for SSR to
42.2 for AFLP. The cluster analysis of the studied genotypes using these different marker systems revealed five
dendrograms exhibited unique topology with some similarities. The generated dendrograms from these marker systems
successfully clustered the studied genotypes based on cultivar or gender. The data scored from AFLP, SCoT, SSR, CDDP
and ITAP were combined and computed to generate more accurate relationships based on large and versatile genome
coverage. The dendrogram based on the combined data exhibited the closest relationships to those illustrated by the
AFLP-based dendrogram. On the other hand, the RAPD dendrogram exhibited also a unique topology with some
similarities comparing with other marker systems.
These results confirmed that different marker systems differ in the mechanism of detecting polymorphism,
genome coverage and the ease of application. Therefore, they could complement each other to draw more accurate
conclusions.
Mediterranean region and its production is largely influenced by environmental stresses, such as drought, salinity, heat and
nutrient deficiency. The objective of this study was to dissect quantitative trait loci (QTL) controlling grain yield, yield
components and drought tolerance in durum. A molecular genetic linkage map for F2 durum mapping population derived
from an intraspecific cross between Baniswif-1 x Sohag-2 was constructed using 114 DNA markers (9 SSRs, 14 SCoTs, 90
AFLPs and 1 RAPDs) distributed over the 14 linkage groups and spanning 2040.9 cM of the durum wheat genome. The
size of linkage groups varied greatly from 6.8cM for LG11 to 317.5cM for LG4 with an average length of 145.8cM. Based
on the used anchor SSR markers, only eight linkage groups were assigned to chromosomes, where LG1, LG3, LG5, LG6,
LG7, LG9, LG13 and LG14 were assigned to chromosomes 1B, 3B, 5B, 6A, 6B, 7A, 3A and 2B, respectively. Single point
analysis was used to identify genomic regions controlling eleven morpho-physiological traits related to grain yield, yield
components and drought tolerance. A total of 74 QTL were identified for the eleven traits on all linkage groups except
(LG10 and LG11). These included 3 QTL for root length (RL), 11 QTL for plant height (PH), 7 QTL for spike length (SL),
3 QTL for number of branches/plant (NBP), 3 QTL for number of spike/plant (NSP), 8 QTL for number of spikelets/spike
(NSS), 15 QTL for number of kernel/spike (NKS), 10 QTL for thousand-kernel weight (TKW), 4 QTL for fresh weight
(FW), 5 QTL for dry weight (DW) and 5 QTL for total amino acids (TAA). This work represents the first genetic linkage
map for durum wheat population derived from an intraspecific cross between ‗Baniswif-1‘ and ‗Sohag-2‘ showing
chromosomal regions associated with 11 morpho-physiological traits related to grain yield, yield components and drought
tolerance in durum wheat.
systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton
were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating
F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. “Giza 83”
and “Deltapine” was used in this study. Different molecular markers including SS R, ES T, ES T-SS R, AFLP and RAPD were
employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with
140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these
new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11
and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic
regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number
of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19
and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal
assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in
this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton
cultivars with improved agronomic traits
plant breeders have made major contributions to the productivity of this crop; however, this has led to
decreasing the genetic variation among Egyptian cotton varieties. Enhancing the productivity of cotton
could be addressed through improving different agronomic traits including early flowering and maturation.
In the present investigation, an interspecific cross (G. barbadense x G. hirsutum) was performed between
two genotypes, Giza83 (late flowering) and Deltapine (early flowering) to develop F2 segregating
population. Analysis of segregation among the 71 F2 individuals was performed using 3 RAPD, 10 SSR,
6 AFLP primer combinations. Twenty four AFLP primer combinations were used in bulked segregant
analysis for flowering time. Linkage analysis and map construction were performed using Map Manager.
The map showed 22 linkage groups with 140 markers covered a total length of 1556.7 cM. The average
length of linkage groups ranged from 1.4 to 649.5. Single point analysis was used to identify the genomic
regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to
flowering and number of bolls. In total, 30 significant QTL were identified for the five traits on ten
linkage groups, among these 11 QTL for plant height, 8 for number of bolls, 4 QTL for each of days to
flowering and bolling date and 3 QTL for number of nodes at flowering time. This work represents the
first linkage map for the intercross between Giza83 and Deltapine showing chromosomal regions
associated with some agronomic traits.