Molecular Plant Breeding
Mojtaba Khayam Nekouei; Mohammad Reza Ghaffari; Mohsen Mardi; Zahra Ghorbanzadeh; Rasmieh Hamid; Mehrshad Zeinalabedini
Abstract
Today, using advanced technologies such as the global positioning system (GPS), agricultural drones, satellite mapping, remote sensors, and precision agriculture machinery provides farmers with a lot of big data during production. According to the reports, this can be considered a part of the digital ...
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Today, using advanced technologies such as the global positioning system (GPS), agricultural drones, satellite mapping, remote sensors, and precision agriculture machinery provides farmers with a lot of big data during production. According to the reports, this can be considered a part of the digital economy in precision agriculture and be economically exploited. The analysis of this data cannot be processed by traditional processing systems due to its complexity. Given the size and complexity of big data, artificial intelligence can transform this data into valuable information through machine learning algorithms. This technology is being used to performance prediction algorithms, reducing agricultural inputs such as fertilizers and poisons, monitoring the growing conditions, pest management, breeding, molecular studies and finally value chain management. Developing programs using artificial intelligence technology will soon be able to manage the time of agricultural products entering the market, in addition to determining the planting time in order to increase productivity. The production of bio fertilizer from agricultural waste can be another achievement of the development of algorithms based on artificial intelligence to reduce the negative environmental effects and increase the economic productivity of the remaining waste from agricultural products. This study discusses the important applications of artificial intelligence in agriculture and its impact on Precision agriculture.
Molecular Plant Breeding
Sina Ghanbari; Kianoosh Cheghamirza; leila zarei; Roghayeh Naseri; Elisabetta Mazzucotelli
Abstract
Among cereals, durum wheat (Triticum turgidum L. var. durum) is one of the most important protein and energy sources after bread wheat. It has a significant role in human nutrition in most countries. In this study, to identify and localization of QTLs controlling traits related to starch and Neutral ...
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Among cereals, durum wheat (Triticum turgidum L. var. durum) is one of the most important protein and energy sources after bread wheat. It has a significant role in human nutrition in most countries. In this study, to identify and localization of QTLs controlling traits related to starch and Neutral detergent fiber, 118 durum wheat recombinant inbred lines obtained from the cross between the local genotype of Iran-249 originated from the west of Iran and the local cultivar of Zardak from Kermanshah were evaluated in two environments (2014 and 2015) under rainfall conditions using randomized complete block design along with parents in three replications. QTL analysis for each trait was performed using the inclusive composite interval mapping method to identify genomic regions that significantly affected the studied traits. A total of six QTLs were identified for the two traits measured, grain starch content and neutral detergent fiber. Three QTLs were identified on chromosome 7A and one QTL on chromosome 4B for the grain starch content trait. For the neutral detergent fiber trait, one QTL was localization on chromosome 6B and one QTL on chromosome 7A. Identifying and localization QTLs controlling traits related to seed quality characteristics can provide an opportunity to improve these traits through marker-assisted selection. Also, these results can create a basis for identifying candidate genes and map-based cloning and confirming QTL function.
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
Leila Farhadi; Ali Arminian; sajad Rashidi Monfared
Abstract
MicroRNAs (miRNAs) are endogenous and noncoding small RNA molecules with a length of 19-24 nucleotides (nts) that regulate target genes at the post-transcriptional level in plants. In this study, several miRNAs in Camelina were identified, and their potential roles were reported. Camelina with its scientific ...
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MicroRNAs (miRNAs) are endogenous and noncoding small RNA molecules with a length of 19-24 nucleotides (nts) that regulate target genes at the post-transcriptional level in plants. In this study, several miRNAs in Camelina were identified, and their potential roles were reported. Camelina with its scientific name (Camelina Sativa L.) is an oil-medicinal plant belonging to the Brassicaceae family. First the RNA was extracted from C. sativa leaf and sent to the Beijing genome institute for RNA-sequencing. Then the data were assembled denovo with Trinity software after removing the reads with lower quality than the threshold level and trimming them. Detection of miRNAs was then performed by miRDeep2 software. Accordingly, we identified 33 miRNAs from the leaf dataset, and their secondary structures were evaluated. The target genes of the detected miRNAs were identified by the psRNAtarget website. Examining the target genes showed that a total of 1415 genes are regulated by these microRNAs, which belong to several gene families with different biological functions, including the genes of proteins that bind to the Squamusa promoter, the protein kinase family, etc. Comparing the expression of microRNA carrying genes (TPM) in the two studied doubled haploid lines, showed that except for miR296 and miR474 which were more expressed in line number 1, the other miRNAs had higher expression in line number 2. Considering the lower amount of oil production in line number 1 compared to line number 2, this indicates the relationship of these two microRNAs with oil production. miR483 was not expressed in any of the lines. miR113 and miR206 had the highest expression levels among all microRNAs. The higher expression of micro RNAs in line 2 probably indicates the higher activity of the silencing mechanism at the transcription level for the target genes in this line compared to line number 1.
Molecular Plant Breeding
Mohammad Saleh Shahvardi; Mohammad mohsenzadeh; Habibollah Habibollah Samizadeh Lahiji
Abstract
This experiment was conducted in order to assess genetic variation and determination of the best genetic structure and the grouping of safflower genotypes using ISSR and retrotransposon markers and different agricultural traits. In this study, 28 safflower genotypes were evaluated using 7 ISSR markers, ...
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This experiment was conducted in order to assess genetic variation and determination of the best genetic structure and the grouping of safflower genotypes using ISSR and retrotransposon markers and different agricultural traits. In this study, 28 safflower genotypes were evaluated using 7 ISSR markers, 3 retrotransposon markers and 12 combined ISSR and retrotransposon markers, as well as eight different morphological traits with different statistical methods. From 22 primers, 117 polymorphic bands were created. The primers, primer-of UBC-827 and TOS-1 with 13 band maximum number of bands, and primer UBC-811 and UBC-822 in combination with 5-band TOS-1 with the lowest band for ISSR primers and Retrotransposons. The average percent polymorphism obtained in this study for markers ISSR, Retrotransposons and primer combinations was from 38.46 to 88.88 percent ISSR and Retrotransposons is variable and the mean percentage of polymorphic for this is equal to 62. High standards of straw gene diversity, Shannon index, the PIC and the number of effective allele primer UBC-810, UBC-811 and primer combination TOS-2 + HB-12, TOS-1 + HB12 and TOS-1+ UBC822 show performance Primers on the assessment of genetic diversity in this article. The morphological traits of 28 genotypes by UPGMA and Euclidean distance criteria were divided into 4 groups. Grouping results of cluster analysis by linear discriminant analysis using Fisher's focal 82.1 percent for morphological traits were confirmed. Principal component analysis showed that the main vectors of the first and second respectively are 8.22 and 6.84 and the 10 first components validated 63.47 percent of total variance. Mantel test the relationship between molecular and morphological data matrix equivalent 0.214 that show little correlation between the two data. Overall, the results showed that there is a considerable genetic variation in safflower germplasm that can be used to select parents and desirable genotypes in safflower breeding programs.
Tissue culture and Micropropagation
Zeinab Chaghakaboodi; Mahdi Kakaei; Alireza Zebarjadi; danial kahrizi
Abstract
Rapeseed (Brassica napus) is recognized as one of the most important oilseed crops worldwide and its development of cultivation has received attention due to the importance of importing oil. The current study aimed to investigate the effect of drought stress on some Rapeseed genotypes under tissue culture ...
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Rapeseed (Brassica napus) is recognized as one of the most important oilseed crops worldwide and its development of cultivation has received attention due to the importance of importing oil. The current study aimed to investigate the effect of drought stress on some Rapeseed genotypes under tissue culture and field conditions and to identify stable genotypes in the field. The possible responses of 14 different canola genotypes to Callus induction resulting from Hypocotyl cultivation and evaluation their drought tolerance were studied using Polyethylene Glycol 6000 (PEG 6000) at five different levels, including zero (as control), 10%, 20%, 30%, and 40% PEG concentrations based on a completely randomized design (CRD) with three replications. Measured traits included relative growth rate, growth rate, relative water content, and proline content of the Callus. Furthermore, in the field sector, the genotypes were investigated in four environments (two consecutive years in 2016-2018 under rainfed and irrigated conditions) based on randomized complete block design with three replications. According to the Callus culture results, the assessed traits, except the Proline content of Callus, decreased with increasing stress level. In laboratory conditions, genotype number seven (Dante) was introduced as the superior genotype. The results of Additive Main effects and Multiplicative Interaction (AMMI) analysis showed the significance of both additive effects of genotype and environment and the multiplicative effect of genotype × environment interaction. The results of cumulative additive effects (decomposition of variance) and multiplicative interaction effects (decomposition into principal components) showed that the first two components explained 53.02 and 33.65% of the variance of the interaction effect for oil yield. Dante and SLM-046 genotypes were introduced as stable genotypes.
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
nadali bagheri; zeinab Masoudi Jozchal
Abstract
Grain length is one of the most important characteristics in rice breeding, which affects the yield and quality of the grain. In this study, the genetic diversity of grain length and width and 1000 seed weight were evaluated in the F2 population resulting from the crossing of L44 line (maternal parent) ...
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Grain length is one of the most important characteristics in rice breeding, which affects the yield and quality of the grain. In this study, the genetic diversity of grain length and width and 1000 seed weight were evaluated in the F2 population resulting from the crossing of L44 line (maternal parent) and IR-229R genotype (paternal parent). Also, molecular markers correlated with grain length were used to identify genotypes with longer grain length in the F2 population. The results of the evaluation of morphological traits showed that the average length of rice grain in the second generation L44 × IR-229R population is 11.16 mm, which is close to the average grain length in the mother genotype L44 (11 mm). Also, 10 genotypes showed longer seed length than the paternal parent, and among these genotypes, 6 genotypes (numbers 8, 10, 76, 82, 91 and 96) had greater seed width and 1000 seed weight than the population average. In the molecular evaluation, it was found that primers RM488 and RM234 (correlated with rice grain length on chromosome 1 and 7, respectively) showed polymorphism between parent’s genotypes. In examining the grain length trait with markers RM488 and RM234, genotypes 76, 82, 91 and 101 with grain length of 12.96, 12.66, 12.79 and 12.53 mm respectively were identified as long seed genotypes.
Molecular Plant Breeding
Sanaz Khalifani; Reza Darvishzadeh; Fariba Morsali Aghajari
Abstract
A B S T R A C T
Sunflower (Helianthus annuus L.) is an important oilseed crop that is cultivated worldwide because of its high-quality oil and be rich in linoleic acid. The present study is a review of the effects of salinity on morphological and physiological traits, resistance mechanisms, breeding, ...
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A B S T R A C T
Sunflower (Helianthus annuus L.) is an important oilseed crop that is cultivated worldwide because of its high-quality oil and be rich in linoleic acid. The present study is a review of the effects of salinity on morphological and physiological traits, resistance mechanisms, breeding, and agronomic methods to deal with salinity tolerance in sunflower. Sunflower is classified as semi-tolerant species. The negative effects of salt stress on sunflower include browning of root tips, reduction of cotyledons and root proliferation, leaf surface, accumulation of dry matter, yield, and seed oil content. Salt stress also leads to decrease in CO2 absorption, transpiration rate and stomatal conductance, and photosynthetic capacity in sunflower. The resistance reactions to salinity stress in sunflower include: modulating the expression of oubain-sensitive ATPases through calcium, delaying the degradation of membrane proteins of oil bodies, increase serotonin and melatonin, increase the expression of nitric oxide, increase S-nitrosylation of cytosolic proteins, increased content of lipid peroxide, activity of glutathione peroxidase, and the abundance of heme oxygenase-1 (HO-1) in the cells around the secretory channels . Among the important breeding approaches to cope salinity stress in sunflower are the identification of HT089, HT175, HT185, HT215, HT216, and HT227 salinity resistance genes, the identification of H. paradoxus as the most salinity resistant species, the production of HA429 and HA430 lines tolerant to salinity, the transfer of the TaNHX2 gene from wheat to sunflower that improved its salinity tolerance and the identification of genes involved in salinity stress in sunflower by next generation sequencing technology. The results of this extensive study will be important in achieving a comprehensive plan for sustainable improvement of yield and quality of sunflower oil under salt stress conditions.
Molecular Plant Breeding
Somayeh Ebrahimi; Ahmad Ismaili; Seyed Sajad Sohrabi; Hasan Torabi Podeh
Abstract
Abiotic stresses, including drought in plants, lead to physiological and biochemical changes that are controlled by regulating gene expression. Transcription factors are considered as the most key molecular elements for regulating genes in response to biotic or abiotic stresses. The role of Heat shock ...
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Abiotic stresses, including drought in plants, lead to physiological and biochemical changes that are controlled by regulating gene expression. Transcription factors are considered as the most key molecular elements for regulating genes in response to biotic or abiotic stresses. The role of Heat shock transcription factors (HSFs) in the molecular mechanism of response to various abiotic stresses has been confirmed; therefore, this study used the analysis of RNA sequencing data to identify, classify and evaluate changes in HSF expression in lentil under water-deficit stress, and finally, the expression of some transcripts were examined using qRT-PCR. From the total assembled transcripts of lentil, 35 transcripts belonging to three HSF classes were identified. Also, according to the results, the expression of 14.28% of the identified transcripts, which often belonged to class A, is altered in lentil under water-deficit stress. The expression of 14.28% of the identified transcripts, most of which belonged to class A, is altered in lentil under water-deficit stress. In general, the results show that changes in the expression of some transcripts of one HSF gene take precedence over those of other transcripts of that gene in response to drought stress; therefore, it is of particular importance to study alternative splicing in response to this environmental factor in lentil. The HSF genes identified in this study can be used in future experiments to understand better the molecular mechanism of water-deficit stress tolerance in lentil.
Molecular Plant Breeding
Mohammad Hassan Kaffash Moghaddam; Forough Sanjarian; Alaeddin Kordnaeeje; Mehrdad Chaichi; Amir Mohammad Naji
Abstract
Bread wheat is one of the most important crops in the world, which is essential in terms of global food security. However, its production is extremely compromised in agricultural regions affected by water deficiency during part of the growing season and mostly in the later stages of growth. Therefore, ...
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Bread wheat is one of the most important crops in the world, which is essential in terms of global food security. However, its production is extremely compromised in agricultural regions affected by water deficiency during part of the growing season and mostly in the later stages of growth. Therefore, it is promising to identify the native drought-tolerant germplasms and molecular mechanisms used to enhance drought stress resistance. The aim of this study was to investigate the expression level of eight selected genes related to drought tolerance NCED, ABF, HKT, PAL, bHLH, ABC transporter and lipoxygenase in two native germplasms of Iranian winter wheat, one is sensitive and the other is drought tolerant. For this purpose, drought treatment was applied on native germplasms in a completely randomized design with three replications and two levels of treatment in the greenhouse. Selected gene fragments were amplified, gene expression was measured by Reverse Northern Blot and quantified using total lip software. Analysis of variance of the mean relative expression of each gene compared to the internal control gene showed that drought stress had a significant effect on the expression of all genes except bHLH gene. Biplot based on the first and second components made it possible to isolate genotypes in dehydration stress based on the expression of the seven genes evaluated. This method can be used in screening and identifying tolerant genotypes in landrace population of wheat.
Molecular Plant Breeding
Sahar Ghahramani; Reza Darvishzadeh
Abstract
Maize is the third most important cereal after wheat and rice in the world and is a major seed source for many people in Africa, Latin America and Asia. Knowledge on function and extent of genes effect is one of the necessities to achieve high yielding cultivars. In this regard, molecular marker technology ...
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Maize is the third most important cereal after wheat and rice in the world and is a major seed source for many people in Africa, Latin America and Asia. Knowledge on function and extent of genes effect is one of the necessities to achieve high yielding cultivars. In this regard, molecular marker technology has eliminated the need to know the pedigree of genotypes for estimating the kinship matrix to evaluate genotypes breeding values. In this research, 97 genotypes of maize were evaluated in a randomized complete block design (RCBD) with 6 replications for agronomical traits. In the molecular experiment, the molecular profiles of the genotypes were prepared with 28 pairs of Inter-retro transposon amplified polymorphism (IRAP) and Retro transposon-microsatellite amplified polymorphism )REMAP( primers. Estimation the breeding valueofstudied traits in maize genotypes was done through the best linear unbiased prediction (BLUP) in the mixed linear model framewo rk by integrating molecular data based calculated kinship matrix. Considering the sum of estimated breeding values ranks for the studied traits, genotypes P3L11, P10L9, P9L6, P19L5 Kahia and (Paternal) OH43 / 1042 had the highest ranks. Positive breeding value shows that these genotypes have the greatest potential in transmitting the value of traits to the next generation. Genotype P14L2 with positive and high breeding value for leaf length, leaf area, cob weight and leaf area index and P16L6 Kahia with positive and high breeding value for plant height to cob height, cob length and grain weight in the plant, can be introduced as desirable parents to improve these traits in maize breeding programs.
Molecular Plant Breeding
Marjan Jannatdoust; Reza Darvishzadeh; Sattar Tahmasebi Enferadi; Maryam Monazzah
Abstract
Salinity is a major abiotic stress that limits the growth and productivity of plants in many parts of the world due to increased use of poor-quality water for irrigation and soil salinity. Plant adaptation or tolerance to salinity stress involves alteration in physiological processes and metabolic pathways ...
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Salinity is a major abiotic stress that limits the growth and productivity of plants in many parts of the world due to increased use of poor-quality water for irrigation and soil salinity. Plant adaptation or tolerance to salinity stress involves alteration in physiological processes and metabolic pathways and activating molecular or gene networks. In this study, 2DE technique was used to identify proteins responsive to salinity stress in maize. Two maize lines with different responses to salinity stress; R10 (tolerant) and S46 (sensitive) were selected. In the eight-leaf stage, salinity stress treatment of 8 dS/m was applied to plants for 20 days and then leaf proteins were extracted. Spots with more than a 1.5-fold increase or decrease in their expression were isolated and sequenced by mass spectrometry. Functional classification of protein spots per line after MS/MS revealed that the differentlly expressed proteins have different metabolic activities. In the tolerant line (R10), 5 spots including Pyruvate orthophosphate dikinase proteins, ATP synthase subunit beta, Germin-like protein, Chlorophyll a-b binding protein, Triosephosphate isomerase, and 40S ribosomal protein, respectively showed an increased expression level. Moreover, in the sensitive line (S46), one spot showed an increased expression level that related to Proteasome subunit beta proteins, and two spots including Chlorophyll a-b binding protein and Ribulose bisphosphate carboxylase small chain protein showed a decreased expression level. The proteins identified in this study and the possible related biochemical pathways provide new information on the response of maize lines (R10 and S46) to salinity stress.
Molecular Plant Breeding
Amir Forghani Saravani; Babak Rabiei; AliAkbar Ebadi
Abstract
Rice grain quality is a complex characteristic that can be divided into milling quality, appearance quality, cooking quality, and nutritional quality. Most studies on rice grain quality show the importance of chromosomes number one and six in the genetic control of various traits in rice. In the present ...
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Rice grain quality is a complex characteristic that can be divided into milling quality, appearance quality, cooking quality, and nutritional quality. Most studies on rice grain quality show the importance of chromosomes number one and six in the genetic control of various traits in rice. In the present study, the validation of 35 microsatellite markers linked to grain quality characteristics which all located on two chromosomes one and six, was performed in 144 recombinant inbred lines of F10 population resulted from the cross between Sepidrood (an Iranian improved cultivar with inferior quality) and Gharib (an Iranian local cultivar with good quality). The results of regression analysis showed that 25 markers were linked to different quantitative and qualitative traits, and explained from 16 to 39% of the variance of different traits, but the markers RM253, RM246, RM190, RM104, RM314, RM3827 and RM7434 had stronger linkage. Construction of the linkage map of 35 microsatellite markers in the studied population showed that the map length was 236.5 cM and the average distance between adjacent markers was 6.95 cM. QTL analysis by the composite interval mapping method showed that 40 QTLs controlled the measured traits in the studied population and the phenotypic variance controlled by the identified QTLs ranged from 7.57 to 37.41% for milling quality and head rice percentage, respectively. Based on this analysis, 23 markers were closer to the QTLs controlling the studied traits in this research. Of these, some markers were linked to several different traits. In total, the results of regression analysis and QTL analysis showed that the markers RM253, RM246, RM340, RM243, RM4128, RM314, RM3827, RM7434, RM104 and RM190 were the informative markers linked to grain quality characteristics, which can be used in marker-assisted selection programs in the future.
Molecular Plant Breeding
Alireza Nabipour; Reza Darvishzadeh; Ahmad Sarrafi
Abstract
Oilseeds are undoubtedly one of the most strategic agricultural products; their production is of basic needs for food security in any society. Sunflower with the scientific name of Helianthus annuus L. is an annual, monoecy, dicotyledonous plant that belongs to composite family. This genus consists diploid, ...
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Oilseeds are undoubtedly one of the most strategic agricultural products; their production is of basic needs for food security in any society. Sunflower with the scientific name of Helianthus annuus L. is an annual, monoecy, dicotyledonous plant that belongs to composite family. This genus consists diploid, tetraploid and hexaploid species, and common sunflower is a diploid species with a base chromosome number of x=17. Sunflower is grown mainly for its edible oil. Environmental stresses such as drought, salinity, unusual temperatures, heavy metal and UV radiation are serious threats to plant growth, metabolism and productivity. In recent years, astonishing advances in biotechnology, genetic engineering, and computer science have made breeding programs much faster, more accurate, and more efficient than ever before. New techniques, if properly incorporated into breeding programs, can dramatically increase the speed and accuracy of these programs and can reduce costs by an extraordinary amount. In this article, while briefly referring to conventional breeding methods, new methods and their application in sunflower breeding are discussed. In the last 10 years, the science of genomic has expanded the genetic information of quantitative traits, and marker assisted selection has become a practical tool.
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
Ashkboos Amini; Sheida Khadam kheir; Iraj Bernousi
Abstract
In order to evaluate variation and reaction of 40 wheat genotypes to salinity tolerance and assess the association of 27 microsatellite markers with salinity tolerance and morpho-physiological traits measured under normal and salt stress conditions, the present study was conducted. The results of analysis ...
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In order to evaluate variation and reaction of 40 wheat genotypes to salinity tolerance and assess the association of 27 microsatellite markers with salinity tolerance and morpho-physiological traits measured under normal and salt stress conditions, the present study was conducted. The results of analysis of variance in two environments showed significant difference among genotypes for all traits, indicating genetic variation among them. Based on the results of combined analysis of variance, the effect of the environment for all traits and the effect of Genotype × environment on most of the traits was significant and it was determined that the response of the evaluated genotypes to salinity stress was different In two environment, the highest variation was belonged to grain yield and its component and biological yield. Cluster analysis in salinity stress based on traits with significant genotype × environment, classified the genotypes into 3 groups i.e. tolerant moderate and sensitive. Association analysis using 27 microsatellite markers, SSR markers with 11 traits measured in two normal conditions and salinity stress for all genotypes was conducted through a mixed linear model (MLM) The study of population structure as a precondition for communication analysis showed that there are 2 probable subgroups (K = 2) in the population studied, which was confirmed by the results of the plot formula. The decomposition of the association analysis using 27 SSR markers with 11 traits measured in two conditions based on mixed linear model (MLM) was carried out using the population structure matrix. Based on the results, 29 locations had a significant relationship with the evaluated traits in the normal environment, while in the salinity stress environment, this number increased to 40 locations. The existence of common markers among some of the studied traits such as the significant associate between S16-1 and 3 traits in normal conditions and with 5 traits in the salinity medium can be due to the polytrophic effects of these markers and possibly the connectivity of genomic locations controlling these traits. S6-3 and S12-1 markers were identified as markers that associated with grain yield in salinity condition and S11-4 marker was identified as marker that related with biological yield in both environmental Conditions. Finally, given the results obtained, if the results are confirmed in other genetic fields, these markers can be used in corrective programs.
Molecular Plant Breeding
Morteza Oladi Ghadicolaei; Ghorban Ali Nematzadeh; Ali Ranjbar; Hamidreza Hashemi
Abstract
Marker-assisted selection (MAS), a selective method which is not influenced by environmental factors. The success of MAS-based breeding programs depends on the selection and validation of the markers used. In this study, to validate the gene(s) associated with salinity stress and evaluation of allelic ...
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Marker-assisted selection (MAS), a selective method which is not influenced by environmental factors. The success of MAS-based breeding programs depends on the selection and validation of the markers used. In this study, to validate the gene(s) associated with salinity stress and evaluation of allelic diversity of these markers in mutant rice lines, Band pattern of 18 SSR markers on a leaf sample of 14 mutant lines (M9) of rice, along with 2 susceptible controls (IR29 and Sepidrood) and 2 tolerant controls (Nonabokra and Dylmani) in 1398 in Genetics & Agricultural Biotechnology Institute of Tabarestan (GABIT). 11 primers were selected based on band pattern analysis in susceptible / tolerant cultivars. The molecular analysis results showed that OsMAPK4, OsCML11 and OsCPK17 had highest polymorphic information content (PIC). OsMAPK4 and OsCML11 had highest marker index (MI) at a rate of 0.23. The lowest PIC (0.05) and MI (0. 11) was accounted for OsCAX (D). Cluster analysis of molecular data, divided rice genotypes into three distinct groups. However, analysis of Biplot classified the genotypes into four different groups. In this study, 3 genes OsCML11, OsMAPK4 and OsCPK17 were identified on chromosomes 1, 6 and 7 respectively, as the most efficient primers in identifying the genetic diversity between the rice genotypes, considering that these primers have a very high linkage with salinity resistance genes, can be predicted that 3 lines G1 (M9-P1-7-2-1), G8 (M9-P3-21-1-1) and G9 (M9-P6 -7-1-1) have high tolerance to salinity stress.
Molecular Plant Breeding
Zeinab Shahabzadeh; Reza Darvishzadeh; Reza Mohammadi; Morad Jafari; Hadi Alipour
Abstract
Study of genetic diversity and association analysis of agronomic traits with ISSR and EST-SSR markers in tall fescue (Festuca arundinacea)
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Study of genetic diversity and association analysis of agronomic traits with ISSR and EST-SSR markers in tall fescue (Festuca arundinacea)
Molecular Plant Breeding
Maryam Shirani-Bidabadi; Farhad Nazarian-Firouzabadi; Karim Sorkheh; Ahmad Ismaili
Abstract
Potato is the fourth most valuable plant for human nutrition. In addition to carbohydrates, potato tuber contains important vitamins and micronutrients for human health. During developmental stages of Potato; morphological, physiological and molecular changes occur. From the genetic point of view, studying ...
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Potato is the fourth most valuable plant for human nutrition. In addition to carbohydrates, potato tuber contains important vitamins and micronutrients for human health. During developmental stages of Potato; morphological, physiological and molecular changes occur. From the genetic point of view, studying these events is crucial for breeding potatoes with nutritional values and a higher yield. The next-generation sequencing methods generate abundant and useful genetic data for molecular breeding of crop plants. In this study, two different potato tuber developmental stages (S1 and S2) were chosen and sampled. Following RNA extraction and cDNA synthesis, Illumina RNA sequencing was performed in two replications for each stage. Bioinformatics analysis, gene ontology, and gene set enrichment analysis were performed. Finally, out of 1829 differential expression genes, 1186 genes were identified and valided by bioinformatics resources. The result of gene ontology comparison showed that 393, 483 and 669 genes were involved in biological processes, cellular components, and molecular functions, respectively. Most genes were present in the phenylpropanoid biosynthesis, biosynthesis of secondary metabolites and metabolic pathways. Peroxidase and membrane transporters coding genes were the most important genes at the beginning of tuber onset to tuberization. These results suggested that development in potato tuber activates metabolic pathways, which not only promotes growth and development but also activates the pathways involved in stress responses and synthesis of different compounds. Ten key genes were identified involved in starch biosynthesis, most of which showed a significant up-regulation, suggesting that the starch biosynthesis pathway starts from the onset of stolon development to tuber maturation.
Molecular Plant Breeding
Parvin Amani Daz; Hossein Hossein Moghaddam; Hossein Sabouri; Ebrahim Gholamalipour Alamdari; Sayedeh Masoomeh Hosseini; Somayeh Sanchouli
Abstract
Identification of the linked markers to drought tolerance genes are needed for the breeding of rice varieties. In order to mapping of QTLs controlling related to drought tolerance, 96 rice Inbred lines caused Ahlamitarom × Neda cross planted as complementary randomized design with 3 replications under ...
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Identification of the linked markers to drought tolerance genes are needed for the breeding of rice varieties. In order to mapping of QTLs controlling related to drought tolerance, 96 rice Inbred lines caused Ahlamitarom × Neda cross planted as complementary randomized design with 3 replications under drought stress in Gonbad Kavous University lab in 2014. Given the genetic variation among the studied lines, it was possible to the detection of QTLs in this study. In calculating the correlation of traits evaluated under drought stress, the highest correlation was for root diameter with root area density (0.96 **). The results of cluster analysis based on total traits under drought stress, lines assigned to four groups: tolerant, semi-tolerant, semi-sensitive and sensitive. Linkage map provided using F8 population, 30 SSR markers, and 20 ISSR markers and covered 1413.2 cM with an average distance between two markers 12.18. QTL analysis indicated that containing totally 13 distances were found, in this way, 2 QTL stem length, 1 QTL root number, 3 QTL leaf width, 1 QTL stem weight, 3 QTL leaf surface, 1 QTL stomata density before stress, 1 QTL stomata density after stress, 1 QTL ratio of total stomata surfaces total area after stress were controlled. Of the detected QTLs, qLL-2 and qSA-12, explained a high percentage of phenotypic variation for leaf area and stomata density after stress. The major QTLs detected in this study, can be used in marker-assisted selection breeding programs after validation
Molecular Plant Breeding
Sajjad Zare; Farhad Nazarian-Firouzabadi; Ahmad Ismaili; Hassan Pakniyat
Abstract
Study of stress tolerance in barley can help for a better understanding of the genetic basis of drought stress tolerance mechanisms and lead to improve the genetic properties associated with drought tolerance through modern molecular genetic techniques. To this end, microRNAs associated with drought ...
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Study of stress tolerance in barley can help for a better understanding of the genetic basis of drought stress tolerance mechanisms and lead to improve the genetic properties associated with drought tolerance through modern molecular genetic techniques. To this end, microRNAs associated with drought stress in barley leaf and root ESTs were analyzed in Nimruz and spantaneum barley genotypes. Bioinformatics databases were mined for relevant EST libraries and bioinformatics services were used for pre-processing and identify genes with different expressions among libraries. The expression profile of candidate genes was studied, by using Real time-PCR in a factorial-split plot design, including Nimruz as tolerant and Spontaneum as a drought sensitive in pots with three replications. Sampling time was also considered at 0, 24 and 72 hours after drought stress as sub factor. Results of this study led to identification of three highly-expressed miRNAs (ath-miR414, os-miR2102-5p and osa-miR414). The expression analysis showed that miR414 and miR2102 expression was significantly (P< 0.05) increased in both genotypes in response to drought stress. After 72h in Nimruz and Spontaneum, the expression of miR414 reached 2.61 and 2-fold and the expression of miR2102 was 2.4 and 2.8-fold of that of control (Spontaneum at control condition at 0 times), respectively.
Molecular Plant Breeding
ََAyda Dorreshte; Alireza Tarang
Abstract
Rice is the most important source of food for more than half of the world's population. Currently, Hashemi rice has the highest area under rice in Guilan province and is better than other varieties in terms of cooking quality and customer satisfaction. In this study, for the study the genetic diversity ...
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Rice is the most important source of food for more than half of the world's population. Currently, Hashemi rice has the highest area under rice in Guilan province and is better than other varieties in terms of cooking quality and customer satisfaction. In this study, for the study the genetic diversity of 20 Hashemi cultivars genotypes and two varieties as control (Hashemi and gowhar- introduced by the Rice Research Institute of Iran), 21 polymorphic markers, morphological traits and grain quality were used. The results showed that all of studied traits had a significant difference at 1% level. The cluster analysis with the help of software R divided the studied genotypes into four groups. Based on the data from 21 markers, in total, 96 alleles were detected with the average of 4.57 alleles per locus. The highest number of alleles was observed in markers RM19 and RM1109 with 6 alleles and minimum number of alleles in marker RM249 with 3 alleles. The average number of effective alleles was 3.97. The RM249 had the lowest value of 2.25 and the RM413 and RM1109 markers had the highest values of 5.65 and 5.21, respectively. The average value of polymorphic information content (PIC) was 0.69 for SSR markers. Based on cluster analysis by using Jaccard coefficient and UPGMA method on the SSR markers, the genotypes were grouped in 4 clusters. In general, the results of cluster analysis of morphological traits and microsatellite markers were in good agreement and they could group individuals based on their geographical origin. Understanding the genetic diversity can further help to breeders in their breeding programs, especially in purification the best genotypes and preserving these genotypes in Iran's rice gene bank.
Molecular Plant Breeding
Bahareh Ghasemi; Hossein Sabouri; Hossein Hossein Moghaddam; Abbas Biabani; Mohamad Javad Sheikhzadeh
Abstract
Genetic diversity is of great importance for breeding programs. In order to study the genetic diversity of 102 different rice genotypes based on seedling traits and molecular experiments, an experiment was conducted in a Completely Randomized Design with three replications. The studied traits including ...
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Genetic diversity is of great importance for breeding programs. In order to study the genetic diversity of 102 different rice genotypes based on seedling traits and molecular experiments, an experiment was conducted in a Completely Randomized Design with three replications. The studied traits including Plumule length, radicle length, length of the largest leaf, width of the largest leaf, number of root, fresh shoot weight, fresh weight of root and root volume, and dry weight of shoot, dry weight of root were measured. The average of the Polymorphic of information content (PIC) was estimated to be 0.2716, indicating RM1029 with the of least 0.175 and the RM216 with the highest of 0.435 (PIC). The results of Association analysis between microsatellite marker and seeding traits at normal condition indicated that the RM60B allele for root length, RM127A allele for root, RM231G allele for the fresh weight of the stem explained high percentage of variations. In saline condition, RM129H allele for stem length trait, RM12091 B allele for root attribute, RM263G allele for stem fresh weight, RM127C allele for width of largest leaf explained high percentage of phenotypic variations and were identified as important markers. The results of this experiment can be used in breeding programs.
Molecular Plant Breeding
Omid Sofalian; Fatemeh Ajri; Atefeh Sabouri; Ali Asghari; Samira Hasanian
Abstract
One way to assessing the validity of recognized markers is studing the consistency of case grouping based on molecular markers and phenotypic data obtained from the normal and drought stress conditions. In this study in order to assessing probable relationship between SSR molecular markers and drought ...
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One way to assessing the validity of recognized markers is studing the consistency of case grouping based on molecular markers and phenotypic data obtained from the normal and drought stress conditions. In this study in order to assessing probable relationship between SSR molecular markers and drought tolerance indices in studding genotypes and grouping these genotypes based on SSR molecular markers and tolerance indices, 40 rice genotypes was used based on randomized complete block design with three replications in both normal and stress conditions. In addition, 26 microsattelite markers in relation with drought tolerance were used. Our results showed that 128 polymorphic alleles with 4.92 mean allele for each marker locus were amplified. The highest PIC value related to RM5672 (0.829) and the least related to RM523 (0.047). The corelation analysis between yield and tolerance indices in both two conditions confirmed that four indices; mean productivity (MP), geometric mean productivity (GMP), stress tolerance index (STI) and yield index (YI) were the best indices for sensitive and tolerant genotype discrimination. Grouping of genotypes based on cluster analysis using WARD method divided all of studding genotypes into three groups including tolerant, semi tolerant and sensitive. Considering the higher values of second group than the mean of the above indicators, they were introduced as tolerant genotypes, which often included upland genotypes and a Hashemi genotype. Based on our results thre firs group represent semi tolerant genotypes ant the third group represents sensitive genotypes. The cluster analysis based on microsatellite markers also divided genotypes into two groups. Comparison of these two types of grouping showed a significant correlation between them, so that in both groups the Hashemi genotype showed close proximity to the upland genotypes and was associated with them in one group.
