Molecular Plant Breeding
Nasrin Akbari; Reza Darvishzadeh
Abstract
Knowledge on genes effect and action (additive/dominance) is one of the necessities to achieve cultivars with high performance and quality. Estimating the breeding value (additive effect) can be done thanks to molecular markers through best linear unbiased prediction (BLUP). In the present study, 100 ...
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Knowledge on genes effect and action (additive/dominance) is one of the necessities to achieve cultivars with high performance and quality. Estimating the breeding value (additive effect) can be done thanks to molecular markers through best linear unbiased prediction (BLUP). In the present study, 100 oilseed sunflower genotypes were evaluated based on the 10×10 lattice design during two crop years of 1392-1393 under normal and drought stress (irrigation limitation) conditions. The breeding value of 13 traits in 78 genotypes out of 100 was estimated due to having genotyping data with SSR and Retrotransposon based markers in each one of normal and drought stress (irrigation limitation) conditions through BLUP. For this purpose, the kinship matrix was calculated by SSR and Retrotransposon based markers data. According to total ranks of breeding values of all studied traits estimated by molecular data of both markers, in normal conditions, genotypes 47, 11, 8 and 35 and under drought stress (irrigation limitation) conditions, genotypes 8, 11 and 35 showed the highest breeding value. Based on SSR markers data in normal conditions; genotypes 76, 36, 34 and 41 and based on Retrotransposon based markers data; genotypes 61, 78, 72 and 52, and in drought stress (irrigation limitation) conditions based on SSR markers data; genotypes 76, 38, 34, 29 and 70 and based on Retrotransposon based markers data; genotypes 16, 71, 78 and 61 showed the lowest breeding value. Considering both studied conditions and all studied traits and both molecular markers information, genotypes 8, 11 and 35 with high breeding value are introduced as desirable parents for breeding programs.
Molecular Plant Breeding
Nasrin Akbari; Reza Darvishzadeh
Abstract
With expensing the amount of data, speed and accuracy in breeding evaluations are very important. The multivariate statistical methods, such as GGE Biplot that reduce the data volume and computational complexity, help in this direction. The use of GGE is useful for introducing genotypes with high stability ...
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With expensing the amount of data, speed and accuracy in breeding evaluations are very important. The multivariate statistical methods, such as GGE Biplot that reduce the data volume and computational complexity, help in this direction. The use of GGE is useful for introducing genotypes with high stability and performance. Therefore, in order to introduce a stable genotype with high adaptation to drought stress, 100 oilseed sunflower genotypes were evaluated in a 10×10 simple lattice design under normal and limited irrigation conditions during two successive years (2013-2014). The results of composite variance analysis revealed a significant difference among genotypes in terms of the evaluated agromorphological traits. Based on graphical evaluation of genotype × environment interaction using GGE Biplot in metan program under R, genotypes 57 (SDR19), 41 (F1250/03), 8 (254-ENSAT), 24 (8ASB2) and 26 (H049+FSB) were introduced as the best genotypes in terms of stability and performance. The genotype 8 (254-ENSAT) had the highest performance among all genotypes in all environments. Meanwhile, genotypes 26 (H049+FSB) had the highest performance in Y1D (First year-limited irrigation) and Y1N (First year-normal irrigation) environments, and genotypes 57 (SDR19), 41 (F1250/03) and 24 (8ASB2) had the highest performance in Y2D (Second year -limited irrigation) and Y2N (Second year -normal irrigation) environments. Based on the results, genotype with code number of 8 with high and stable performance can be used in all environments as a parent in the development of high-yielding and stress-tolerant hybrids. The results show that GGE Biplot is a useful statistical method to achieve practical and accurate results.
Molecular Plant Breeding
Maryam Rasoulzadeh Aghdam; Reza Darvishzadeh; Ebrahim Sepehr; Hadi Alipour
Abstract
In order to breeding phosphorus-efficient genotypes, 100 sunflower genotypes coming from different parts of the glob were evaluated based on agro-morphological traits under optimal and phosphorus deficient (7.2 mg/kg) conditions in a completely randomized design with three replications in potted conditions ...
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In order to breeding phosphorus-efficient genotypes, 100 sunflower genotypes coming from different parts of the glob were evaluated based on agro-morphological traits under optimal and phosphorus deficient (7.2 mg/kg) conditions in a completely randomized design with three replications in potted conditions in Faculty of Agriculture and Natural Resources, Urmia University in 2017 cropping season. In molecular experiments, the molecular profile of genotypes was prepared with 30 pairs microsatellite (SSR) primers. The results showed that the mean of most studied traits such as stem diameter, leaf wide, leaf surface, chlorophyll rate and 1000 grain weight was reduced significantly in phosphorus deficient conditions compared to optimal ones, which shows that phosphorus deficiency has a negative effect on the studied traits. The polymorphic information content (PIC) in the studied genotypes ranged from 0.055 for ORS718 primer to 0.687 for HA3040 primer. In population structure analysis, based on 30 SSR loci, potentially 2 sub-populations (K=2) were identified in the association panel. About 1.15% of possible SSR locus pairs showed significant level of linkage disequilibrium (P
Molecular Plant Breeding
Hossein Zeinalzadeh Tabrizi; Kamil Haliloglu; Ahmad Razban Haqiqi3 Razban Haqiqi
Volume 5, Issue 12 , February 2016, , Pages 39-53
Abstract
In order to investigate genetic diversity of sunflower genotypes, TRAP markers were used with six fixed and arbitrary primers. Nineteen primer combinations generated a total of 116 bands in which 109 of them were polymorphic. Restorer inbred lines with a mean of 22.76 polymorphic bands had the highest ...
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In order to investigate genetic diversity of sunflower genotypes, TRAP markers were used with six fixed and arbitrary primers. Nineteen primer combinations generated a total of 116 bands in which 109 of them were polymorphic. Restorer inbred lines with a mean of 22.76 polymorphic bands had the highest polymorphic loci (84.48 %), and Iranian hybrids with a mean of 2.97 polymorphic bands had the lowest polymorphic loci (40.52 %). Maximum and minimum genetic distances were between restorer lines and Iranian hybrids (0.151) and foreign hybrids and open pollinated cultivars (0.064), respectively. Maximum genetic similarity was between restorer and CMS lines (0.066). AMOVA analysis revealed that 87 % of total variance was within groups, and 13 % was between groups. Using UPGMA method of clustering and principal coordinate analysis, three distinctive groups were identified. Minimum similarity coefficient (0.472) was observed between R42 and CMS328 inbred lines. Results showed that TRAP marker was useful in genetic diversity estimation of sunflower genotypes. Higher similarity coefficient (0.755) for the studied genotypes indicated a narrow genetic base suggesting increasing genetic diversity of sunflower germplasm and selection of high diversity of new inbred lines in the future sunflower breeding programs.
Molecular Plant Breeding
Arezo Mohamadian Farsani; Hamid Hatami Maleki; Reza Darvishzadeh; Faramarz Hoshyardel
Volume 4, Issue 7 , December 2015, , Pages 15-23
Abstract
Black stem disease is one of the most important fungi diseases of sunflower. The use of resistant genotypes is potentially one of the economical ways for its control. In this study, expression level of genes including phenylalanine ammonia-lyase 2 (PAL2) and thaumatin-like protein (TLP) were measured ...
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Black stem disease is one of the most important fungi diseases of sunflower. The use of resistant genotypes is potentially one of the economical ways for its control. In this study, expression level of genes including phenylalanine ammonia-lyase 2 (PAL2) and thaumatin-like protein (TLP) were measured in sunflower genotypes including ENSAT-B5, AS613 and mutant genotype M5-54-1 infected with MA6, MP8 and MP10 isolates of Phoma macdonaldii via quantitative RT-PCR technique. Results revealed that transcript levels of the both PAL2 and TLP genes were significantly affected by isolate and genotype and genotype-isolate interactions. In this study, the expression levels of genes PAL2 and TLP showed higher increase against the MP8 isolate. Among studied genotypes, genotype ENSAT-B5 possessed highest increasing in expression levels of genes PAL2 and TLP. The resistant and susceptible genotypes had possessed high and low transcript levels of PAL2 and TLP and disease symptoms were seen in susceptible genotypes.
Genomics
Hamid Hatami Maleki; Marjan Jannatdoust; Reza Darvishzadeh
Volume 5, Issue 11 , December 2015, , Pages 51-63
Abstract
Salinity stress is one of the abiotic stresses which threaten plant species. Achieving any progress in breeding for tolerance to stresses needs existence of genetic diversity. In this research, reaction of 53 sunflower mutant lines seedlings accompanied by their parental line was studied in several salinity ...
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Salinity stress is one of the abiotic stresses which threaten plant species. Achieving any progress in breeding for tolerance to stresses needs existence of genetic diversity. In this research, reaction of 53 sunflower mutant lines seedlings accompanied by their parental line was studied in several salinity levels including 0, 2, 4, 6, 8 ds/m. Also, in molecular experiment, genetic diversity of mutant lines was inspected using AFLP markers. Results revealed significant differences among the studied lines in each of salinity level based on seedling characteristics. Two hundreds loci were amplified using 17 combinations of AFLP primers in the studied lines. Analysis of population structure classified studied mutant lines in two subgroups. Considering association mapping, 43 AFLP markers had significant relation with seedling characteristics. Phenotypic variance of the identified markers varied between 0.13 and 0.42.
Molecular Plant Breeding
Fatemeh Sahranavard Azartamar; Reza Darvishzadeh; Mortaza Ghadimzadeh; Heydar Azizi; Zahra Aboulghasemi
Volume 5, Issue 10 , September 2015, , Pages 73-87
Abstract
Since the economic value of cultivar depends on different characteristics, thus detailed knowledge on genetic behavior and identification of genomic loci linked to these traits will help to improve plant cultivars. In this investigation, relation and linkage between of 30 microsatellite markers with ...
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Since the economic value of cultivar depends on different characteristics, thus detailed knowledge on genetic behavior and identification of genomic loci linked to these traits will help to improve plant cultivars. In this investigation, relation and linkage between of 30 microsatellite markers with some of important agromorphological traits in 106 different sunflower lines was evaluated through GLM and MLM association models in Structure and TASSEL software. Based on the 30 microsatellite markers used in this study, population genetic structure subdivided into five subpopulations (K=5) that barplat results also confirmed it. In association analysis based on GLM and MLM models, 9 and 16 loci showed significant relation with assessed traits, respectively, and explained considerable variations of this studied traits. In this study, some co-localized QTLs were identified for studied traits. Common markers between of traits can be due to pleiotropic effects or linkage between of genomic regions involved in these traits. Results of the current study presented useful information about the genetic basis of the studied traits and can be used in different sunflower breeding programs including marker aided selection. In future studies, coding genes of important agronomical traits could be identified by sequencing of loci with highest R2 (ORS1209, ORS822 and ORS649). Markers with highest association to traits can be used for saturating linkage maps.
Genomics
Reza Darvishzadeh
Volume 5, Issue 9 , June 2015, , Pages 15-28
Abstract
Since the economic value of cultivars depends on different characteristics, thus procedure of selection for several traits to maximizing the economic value always has been considered by plant breeders. Detailed knowledge on genetic behavior and association between economic traits will help breeders to ...
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Since the economic value of cultivars depends on different characteristics, thus procedure of selection for several traits to maximizing the economic value always has been considered by plant breeders. Detailed knowledge on genetic behavior and association between economic traits will help breeders to improve plant populations. In this study, 12 retrotransposons-based primers (7 IRAP and 5 REMAP primers) and general and mixed linear models (GLM and MLM) were used to identify molecular markers associated to 9 seed related important traits including oil yield, oil percentage, protein yield, protein percentage, grain length, grain diameter, grain weight, dehulled kernel weight, percentage of dehulled kernel weight to whole grain in 48 confectionery sunflower landraces under normal irrigation, mild and severe drought stress conditions. By applying Bayesian model, the whole confectionery sunflower populations were classified into two sub-populations. Based on general linear model, 2, 5 and 12 loci and through mixed linear model 2, 5 and 11 loci showed significant (P
Genomics
Marjan Jannatdoust; Reza Darvishzadeh; Mohammad Ali Ebrahimi
Volume 4, Issue 6 , October 2014, , Pages 61-72
Abstract
In this study, genetic variability among and within 50 confectionery sunflower populations was investigated using 10 microsatellite markers (SSR). The number of alleles per locus ranged from 2 to 3 with an average of 2.1. The number of effective alleles per locus was estimated from 1.948 (locus ORS785) ...
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In this study, genetic variability among and within 50 confectionery sunflower populations was investigated using 10 microsatellite markers (SSR). The number of alleles per locus ranged from 2 to 3 with an average of 2.1. The number of effective alleles per locus was estimated from 1.948 (locus ORS785) to 1.468 (locus ORS1088) with an average of 1.825. The highest expected heterozygosity (0.484) was estimated for ORS785 locus and the lowest one (0.268) estimated for ORS1088. The mean of expected and observed heterozygosity was 0.435 and 0.722, respectively. Polymorphic information content varied between 0.572 in ORS785 locus and 0.334 in ORS1088 with an average of 0.503. A principal co-ordinates analysis (PCoA) showed that the first two Eigen-values explained 31.71% of the cumulative variation. Cluster analysis based on complete algorithm and Nei genetic distance grouped the studied populations in 3 main classes. Analysis of molecular variance revealed that the high part of total variation was due to within populations. So it will be better to do selection within populations in breeding programs.
Bioinformatics
Reyhaneh Ebrahimi; Behrouz Shiran; Esmaeil Ebrahimi; Hossein Fallahi
Volume 3, Issue 5 , February 2013, , Pages 49-51
Abstract
microRNAs are small non-coding RNAs approximately 21-22 nucleotides long and have been identified as negative regulators of gene expression in the post-transcriptional level in plants and animals. Temperature is one of the most important climate change factors and higher temperatures affect agriculture ...
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microRNAs are small non-coding RNAs approximately 21-22 nucleotides long and have been identified as negative regulators of gene expression in the post-transcriptional level in plants and animals. Temperature is one of the most important climate change factors and higher temperatures affect agriculture and crop production adversely. In this study, the expression pattern of miR398 and its target gene NtGT5b were measured in root and leaf tissues of sunflower (Helianthus annuus) in various heat stress conditions (0h, 1.5h, 3h , 6h) at 42 °C by qRT-PCR. The results showed different pattern of miRNA expression in both root and leaf tissues during mild, moderate and severe heat stress, respectively. miR398 was highly up regulated and its target gene down regulated in leaf tissue that showed thermo tolerance of this tissue in term of heat stress. There is a different miRNA expression patterns in leaf and root tissues under various stress conditions which is an indication of induced signal transmission after heat stress. Investigating miR398 network shows that this miRNA through presences of important genes and transcription factors such as AFO and INO has the ability to change the pattern of gene expression of many processes such as growth, development and response to stress.
