FARZAD FAYAZ - Academia.edu (original) (raw)

Papers by FARZAD FAYAZ

Phylogenetic diversity and relationship among annual Cicer species using random amplified polymor... more Phylogenetic diversity and relationship among annual Cicer species using random amplified polymorphic DNA markers

Molecular Biology Reports, 2020

Safflower (Carthamus tinctorius L.) is one of the most important oilseed crops for its seed oil r... more Safflower (Carthamus tinctorius L.) is one of the most important oilseed crops for its seed oil rich in unsaturated fatty acids. Precise utilization of diverse genetic resources is fundamental in breeding programs to improve high yield genotypes with desirable traits. In this study, for the first time we report successful application of DArTseq technology; an efficient genotyping-by-sequencing (NGS); to analysis genetic diversity and population structure of 89 safflower accessions from worldwide origins. Totally, 19,639 DArTseq markers (10,130 SilicoDArTs and 9509 SNPs) generated through DArTseq genotyping. After filtering the data, 3431 polymorphic DArTseq markers (1136 SilicoDArTs and 2295 SNPs) used for genetic diversity, population structure and linkage disequilibrium analysis in safflower genotypes. All the SilicoDArT and SNP markers showed high reproducibility and call rate. Polymorphism information content (PIC) values ranged from 0.1 to 0.5, while ≥ 0.50% of SilicoDArTs and ≥ 0.64% SNPs showed PIC values more than median. Genotypes grouping using DArTseq markers resulted in three distinct clusters. Results showed weak correlation between safflower diversity pattern and origins. Analysis of molecular variance revealed that the majority of genetic variation was attributed to the differences among varieties within cluster populations and there was no significant molecular variance between origins. However, safflower of accessions belonged to Iran, Turkey, Pakistan and India indeed appear to be genetically similar and grouped close in referred cluster, while the accessions from Near East (Afghanistan, China) being distinct. Our results were in agreement with hypothesis that safflower domesticated in somewhere west of Fertile Crescent and then expanded through Africa and Europe. Present study using a panel of globally diverse safflower accessions and large number of DArTseq markers set the stage for future analysis of safflower domestication using large germplasm from proposed domestication centers. Also, studied germplasm in this study can be used as a valuable source for future genomic studies in safflower for mapping desirable traits through genome-wide association mapping studies.

Molecular Biology Reports, 2019

Acetolactate synthase (ALS)-inhibiting herbicides have been widely used for effective management ... more Acetolactate synthase (ALS)-inhibiting herbicides have been widely used for effective management and control of wild mustard (Sinapis arvensis) biotypes in Iran. The resistance of the ALS inhibitor to weeds is attributed to either target site alteration or enhanced herbicide degradation. Molecular and genetic characterization of the resistance mechanism is relevant to the evolution and management of herbicide resistance. The aims of this research were (a) to characterize the mechanism molecular suspected to Granstar (tribenuron methyl) and Atlantis (Mesosulfuron + Iodosulfuron) resistance in S. arvensis biotypes in the greenhouse and laboratory (b) to investigate the organization of the target-site loci in field selected S. arvensis populations and (c) instantly recognize the mutations that cause resistance to ALS inhibitors. Eighty resistant populations of S. arvensis were carefully collected from fields repeatedly treated with Granstar and Atlantis. The resistance level and pattern of the population were determined through a greenhouse dose-response experiment by applying the above-mentioned herbicides. Extraction of genomic DNA was carried out for PCR and ALS gene analysis. Our results showed that by greenhouse experiment across 80 biotypes suspected to resistance collected in the fields of whole Kermanshah Province, 30 biotypes (37.5%) conferred S. arvensis resistance species reported in the farm. Among 30 biotypes screened in a greenhouse experiment, six biotypes (20%), No. 9, 14, 17, 19, 23 and 28 revealed a mutation in the ALS gene that was detected by PCR-based method. Biotype No. 9 in the position 376 (Asp376-Gly, GAC to GGC), biotypes 14 and 19 in the position 197 (Pro197-Ala, CCT to GCT), biotypes 17, 23 and 28 in the position 574 (Trp574-Leu, TGG to TTG) and biotype No. 23 in the position 122 (Thr-122-Ala, ACA to GCA) showed herbicide resistance. The specific mutation in the position of 122 of the ALS gene in S. arvensis is the first report. Other biotypes showed resistance in the greenhouse but didn't indicate any mutation by PCR-based method. Most of the resistance to Granstar and Atlantis are genetic and are induced by mutations in the ALS gene. The resistance to herbicides may contain a non-mutagenic and non-genetic origin. The reason of herbicide resistance as non-target-site in some of the biotypes may relate to the activity of the herbicide-metabolizing enzyme(s) or transporter proteins that will naturally lead to an increase in herbicide degradation or compartmentation away from its active site.

Environmental and Experimental Biology, 2016

Genetic diversity and relationships among 38 Iranian durum wheat accessions were analysed using c... more Genetic diversity and relationships among 38 Iranian durum wheat accessions were analysed using conserved DNA-derived polymorphism (CDDP) and start codon targeted (SCoT) markers. A total of 10 CDDP and 10 SCoT primers were used to estimate genetic polymorphism among 38 durum wheat accessions. Comparatively, both CDDP and SCoT markers proved to be more effective and in terms of percentage of polymorphisms and polymorphic information content value were relatively similar. The average polymorphic information content value of CDDP was 0.39 which was relatively higher than those of SCoT where the respective values of polymorphic information content was 0.35. Using the neighbor joining clustering method, CDDP and SCoT markers were used to generate dendrograms, which revealed that the durum accessions were clustered into three and two major groups, respectively. According to the present results, CDDP markers proved more informative in studying genetic diversity among durum accessions. In both marker types, low correlation between genetic distances and geographical origin in examined durum landrace accessions was found. However, accessions from the same geographical regions mostly showed more genetic similarity than those with origins far apart. The results demostrated that CDDP and SCoT markers are useful for genetic diversity analysis of durum accessions. This information is useful for future germplasm collection and efficient utilization of landrace durum germplasm in plant breeding.

Drought is a widespread problem seriously influencing durum wheat (Triticum durum Desf.) producti... more Drought is a widespread problem seriously influencing durum wheat (Triticum durum Desf.) production and quality, but development of resistant cultivars is hampered by the lack of effective selection criteria. The objective of this study was to evaluate the ability of several selection indices to identify drought resistance cultivars under a variety of environmental conditions. Twenty four durum wheat lines and cultivars were evaluated under both moisture stress (E 1) and non-stress (E 2) field environments using a randomized complete block design for each environment. Seven drought tolerance indices including stress susceptibility index, stress tolerance index, tolerance, yield index, yield stability index, mean productivity and geometric mean productivity were used. The indices were adjusted based on grain yield under drought and normal conditions. The significant and positive correlation of Y p and MP, GMP and STI showed that these indices were more effective in identifying high yielding cultivars under different moisture conditions. The results of calculated gain from indirect selection from moisture stress environment would improve yield in moisture stress environment better than selection from non moisture stress environment. Wheat breeders should, therefore, take into account the stress severity of the environment in choosing an index.

Wheat (Triticum aestivum) is one of the most important food staples in Iran. Understanding of the... more Wheat (Triticum aestivum) is one of the most important food staples in Iran. Understanding of the genetic variability among landrace wheat germplasm is important for breeding. The aim of this work was to characterize sixty landrace wheat accessions collected from northwest Iran, and to assess mutual genetic distances by use of morphometric and AFLP markers. In morphometric trait assay, results of variance analysis and descriptive statistics indicated that the genotypes differed significantly for all of the traits, and indicated considerable diversity. A dendrogram was constructed from morphological traits. The genotypes were grouped into two clusters, between which the mean Euclidian distance was 4.77. Twelve AFLP primer pairs detected 128 polymorphic bands among the sixty genotypes. The mean polymorphism rate based on AFLP data was 31%; however, wide polymorphism among primer pairs was observed (22 to 40%). Polymorphic information content, calculated to assess the informativeness of each marker ranged from 0.28 to 0.4, with a mean of 0.37. Five distinct clusters were obtained by using the un-weighted neighbour-joining method with arithmetic means analysis. In this study, the landrace genotypes did not demonstrate significant association between agronomic performance and genetic diversity determined using AFLPs. Clearly the study showed that there are genotypes with similar agronomic performance and different genetic constitutions. This information can be used to protect intellectual property and for breeding and selection programmes.

Plant Molecular Biology Reporter, 2014

In order to identify yield and yield component QTLs under control and salt-stress conditions, a p... more In order to identify yield and yield component QTLs under control and salt-stress conditions, a population of 254 recombinant inbred lines (RILs), derived from a cross between two bread wheat cultivars, (Roshan / Sabalan), was assessed. Parents and their 254 recombinant inbred lines (RILs) were evaluated in an alpha-lattice design with two replications in two control and saline environments of Yazd in 2011-2012 cropping season. Yield and yieldrelated traits were evaluated at harvest time. The genotyping was carried out using SSR and DArT markers. A, B and D genomes were covered by 411.8, 620.4 and 67.5 cM, respectively. Also, a total of 48 QTLs were detected on 11 chromosomes for grain yield, biological yield, harvest index, thousand-kernel weight, grain number per spike, spike weight and spikelet number per spike. Roshan (salt tolerance) alleles were associated with an increase yield under saline conditions. SSR markers including gwm146, gwm577, gwm249 (on chromosomes 2A and 7B) were tightly associated with different QTLs. The major effect QTLs were located on chromosomes 1A and 7B for grain yield, harvest index and spike weight, which were explained 10.2%, 12.98% and 29 % of the total phenotypic variance, respectively. These QTLs and markers could be suitable for marker-assisted selection and gene stacking techniques. Moreover, co-located QTLs were detected on chromosome 2B for evaluated traits.

Asian Journal of Plant Sciences, 2007

Biotechnology & Biotechnological Equipment, 2020

This study was conducted to investigate the genetic diversity and population structure of globall... more This study was conducted to investigate the genetic diversity and population structure of globally diverse mini core collection of safflower (Carthamus tinctorius L.) using agro-morphological, sequence-related amplified polymorphism (SRAP) and simple-sequence repeats (SSR) molecular markers. Field experiment results showed significant differences between genotypes for agro-morphological traits such as: number of capitula per plant, number of seeds per plant, 1000-seed weight and seed yield. Ten SRAP primer combinations generated 120 polymorphic bands with an average polymorphism information content (PIC) value of 0.23. High allelic variation using 10 SSR markers observed across genotypes, with an average value of 6.8 alleles per locus and relatively high value for PIC (0.69). Pooled molecular data (SSR þ SRAP) were used to identify the population structure and genetic diversity using discriminant analysis of principal components (DAPC) and STRUCTURE analysis. The results revealed four clusters within the safflower accessions, while there was no strong correlation between geographical origins and estimated genetic diversity. Our results showed high genetic diversity for both agro-morphological and molecular analysis in the examined safflower germplasm. This mini core germplasm can be used for germplasm management and future safflower breeding programs.

The objective of this study was to evaluate the genetic relationships of 28 chickpea accessions f... more The objective of this study was to evaluate the genetic relationships of 28 chickpea accessions from diverse origin using AFLP markers. On average, 13 polymorphic bands per primer were observed in AFLP analysis. The average polymorphic information content (PIC) was 0.71, ranging from 0.48 to 0.92. The lowest and the highest PIC value were recorded for primer P-GAG/M-GC and P-AT/M-GC, respectively. The average GD, based on F st values among the 21 accessions was 0.42, ranging from 0.61 to 0.16. From the UPGMA dendrogram, it is discernible that material taken for the analysis can be divided in four clusters. The results indicate that the greatest genetic diversity occurs in Afghanistan, Iran and Lebanon. In many cases, the diversity between individuals of an accession is as great as between individuals of different accessions. Based on DNA markers it is concluded that there are three centers of diversity for chickpea: Pakistan-Afghanistan, Iran-Turkey and Syria-Lebanon. India and Ethiopia, which were previously considered as a secondary center of diversity for chickpea, showed lower diversity than the above regions.

Archives of Agronomy and Soil Science, 2012

This study was undertaken to compare patterns of agronomic characters and yellow pigment content ... more This study was undertaken to compare patterns of agronomic characters and yellow pigment content diversity between Iranian durum landraces and modern varieties. In four field experiments, a collection of 127 accessions of landraces and 23 modern cultivars tetraploid wheat representing Iranian and global genetic diversity were tested under optimum and rain-fed conditions. Across the environments, the yellow pigment concentrations ranged from 1.85 mg kg−1 to 8.95 mg kg−1 in the field-grown samples. Multivariate analysis detected five groups, four including landraces and one comprising modern cultivars. As a group, modern cultivars were the most productive and showed high mean values for harvest index, grains per spike and yellow pigment, but they had the lowest plant height. Landraces had the highest mean number of spikes per m2 and 1000-kernel weight, but were characterized by low plant height and yellow pigment content. Clustering analysis also showed that, based on yield and yellow pigment content, the accessions in different groups were of different origins, suggesting that there was no clear relationship between accessions and geographical diversity. According to our results, Iranian landraces can be particularly useful as germplasm in breeding programmes to improve spikes per m2 and 1000-kernel weights.

Genetic variation among cultivated chickpea (Cicer arietinum L.) and six other related annual wil... more Genetic variation among cultivated chickpea (Cicer arietinum L.) and six other related annual wild species of Cicer was evaluated with random amplified polymorphic DNA (RAPD). Among the 42 random 10-mer primers tested, only 9 amplified genomic DNA across all species. Three main species groups were identified by UPGMA clustering using Nei's pair-wise distance calculations. Group I included the cultivated species C. arietinum, C. reticulatum and C. echinospermum. Within this group, C. reticulatum accessions were clustered closest to the C. C. arietinum. C. yamashitae. The second cluster was separated from the other clusters. Group III (the annual tertiary group) included C. judaicum, C. pinnatifidum and C. cuneatum. These results were in accordance with the common hypothesis that C. reticulatum was the progenitor species of cultivated chickpea. Our results also show that RAPD markers can be used for studying Cicer species and largely confirm the known relationships among taxonomic units in this genus.