Germplasm genetic diversity & plant breeding
Abdol reza Bagheri; Valiollah Ghasemi Omran; Mostafa Haghpanah
Abstract
Genetic relationships among twenty-three Chickpea genotypes include seven Chickpea cultivars, and 16 wild genotypes were analysed by 10 ISSR markers. On average, 11 bands per primer were observed, and 83.4 % polymorphic bands were shared in ISSR analysis. The results of clustering demonstrated the efficiency ...
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Genetic relationships among twenty-three Chickpea genotypes include seven Chickpea cultivars, and 16 wild genotypes were analysed by 10 ISSR markers. On average, 11 bands per primer were observed, and 83.4 % polymorphic bands were shared in ISSR analysis. The results of clustering demonstrated the efficiency of ISSR markers (particularly ISSR1 (UBC-834) and ISSR8 (UBC-864)) for reporting appropriate parents for breeding programs to biotic and abiotic stresses. Principle Coordinate Analysis (PCoA) clustered 23 Chickpea genotypes in two groups by which six cultivars separated in one group. Genetic data extracted from ISSR analysis are practical in Chickpea to choose parental sources for inbreeding programs.
Molecular markers & plant breeding
Jithin Thomas; V.J. Dominic
Abstract
Rice (Oryza sativa L.) is one of the most significant cereal crops, about 3 billion people, nearly half the world's population; depend on rice for survival and it offers up to 80% of daily energy intake in most of the Asian countries. Knowledge of the distribution, extent and pattern of genetic variation ...
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Rice (Oryza sativa L.) is one of the most significant cereal crops, about 3 billion people, nearly half the world's population; depend on rice for survival and it offers up to 80% of daily energy intake in most of the Asian countries. Knowledge of the distribution, extent and pattern of genetic variation is useful for estimation of any possible loss of genetic diversity and its role in breeding programs. This work assessed the genetic diversity among 25 coastal rice populations of five regions of Kerala (South India) using 18 microsatellite markers. A mean PIC value of 0.37 and an average of 3.5 alleles per loci were observed. Mean Heterozygosity value of 0.29 and gene diversity value of 0.41 was attained. AMOVA demonstrated that genetic differentiation was significant at P< 0.001 and FST index value of 0.035 was obtained. Of the total diversity, 57.76% was attributed within individuals, 38.71% was attributed among individuals within populations and 3.53% among populations. Information regarding the amount of genetic variations in these salt tolerant coastal accessions and genetic relationship between genotypes are essential for designing effective breeding programs. Especially, to meet the differentiated goals of plant breeding such as breeding for increasing yield, wider adaptation, desirable quality, pest and disease resistance.
Germplasm genetic diversity & plant breeding
Farnaz Goodarzi; Reza Darvishzadeh; Abbas Hassani
Abstract
Castor (Ricinus communis L.) is one of the most ancient medicinal oil crops in the world. It has been vastly distributed in different parts of Iran. In the present study, the inter simple sequence repeat (ISSR) markers were used to evaluate the molecular genetic diversity among and within 12 castor accessions ...
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Castor (Ricinus communis L.) is one of the most ancient medicinal oil crops in the world. It has been vastly distributed in different parts of Iran. In the present study, the inter simple sequence repeat (ISSR) markers were used to evaluate the molecular genetic diversity among and within 12 castor accessions collected from 7 regions of Iran. Totally, 16 ISSR primers amplified 166 loci, of which 116 loci (69.89 %) were polymorph, indicating high genetic variability in castor germplasm. An accession-specific ISSR band was detected in ‘80-29’accession. Genetic distance among accessions ranged from 0.2 to 0.056. Analysis of molecular variance revealed a higher level of genetic variation within (80%) than between (20%) accessions. A model-based Bayesian approach subdivided 60 genotypes from 12 accessions into 6 subgroups. UPGMA dendrogram based on Nei’s genetic distance classified 12 accessions into 4 groups. The result indicates that there was no association between geographical origin and ISSR patterns. The results suggest that ISSR technique is a useful tool for studying genetic diversity in castor germplasm.
Molecular markers & plant breeding
Robabeh Mollaheydari Bafghi; Amin Baghizadeh; Ghasem Mohammadi-Nejad; Babak Nakhoda
Abstract
In this study, genetic diversity of 20 wheat genotypes was evaluated using 126 simple sequence repeats (SSR) alleles, covering all three wheat genomes. A total of 1557 allelic variants were detected for 126 SSR loci. The number of alleles per locus ranged from 4 to 19 and the allelic polymorphism information ...
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In this study, genetic diversity of 20 wheat genotypes was evaluated using 126 simple sequence repeats (SSR) alleles, covering all three wheat genomes. A total of 1557 allelic variants were detected for 126 SSR loci. The number of alleles per locus ranged from 4 to 19 and the allelic polymorphism information content (PIC) varied from 0.66 (Xgwm429) to 0.94 (Xgwm212 and Xgwm515). The highest polymorphism was observed in Xgwm212 and Xgwm515 primerswith 19 alleles, while the lowest polymorphism belonged to Xgwm429 with 4 alleles. The highest number of alleles per locus was detected in the genome A with 594 , compared to 552 and 411 for B and D genomes, respectively. Dendrogram was constructed using Dice similarity coefficient and UPGMA algorithm by NTSYSpc2.0 software and genotypes were grouped in to six clusters. The knowledge about the genetic relationships of genotypes provides useful information to address breeding programs and germplasm resource management. This study also confirms the usefulness of SSR markers to study wheat genetic diversity.
Molecular markers & plant breeding
Nesa Jafari; Reza Behroozi; Abdolreza Bagheri; Nasrin Moshtaghi
Abstract
Expressed sequence tags simple sequence repeats (EST-SSRs) are important sources for investigation of genetic diversity and molecular marker development. Similar to genomic SSRs, the EST-SSRs are useful markers for many applications in genetics and plant breeding such as genetic diversity analysis, molecular ...
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Expressed sequence tags simple sequence repeats (EST-SSRs) are important sources for investigation of genetic diversity and molecular marker development. Similar to genomic SSRs, the EST-SSRs are useful markers for many applications in genetics and plant breeding such as genetic diversity analysis, molecular mapping and cross-transferability across related species and genera. In spite of low polymorphism, these markers show variation in the expressed part of the genome. In this study, Medicago truncatula EST-SSRs were used for investigation of transferability between M. truncatula and some chickpea (Cicer arietinum L.) genotypes, also genetic diversity between used chickpea genotypes was determined. In this research, 650 M. truncatula ESTs were searched to find simple sequence repeats (SSRs). A total of 131 EST-SSRs were contained di-and trinucleotide motif SSRs. In this study, thirty pairs of primers were designed to amplify over 10 chickpea genotypes. Thirteen primer pairs (43%) generated reproducible bands in at least one chickpea genotype that eight bands (61.5%) were polymorphic in the chickpea genotypes. A total of 24 alleles were amplified with an average of 3 alleles per primer. The average of polymorphism information content (PIC) was 78.75% and transferability across M. truncatula and C. arietinum was 43.32%. The results indicate that the developed EST-SSR markers from M. truncatula as a model plant are valuable genetic markers for legume species such as chickpea. In addition to suitability of EST-SSR markers for genetic diversity analysis, their broad range of transferability also proved their potential for comparative genomics studies.
Molecular markers & plant breeding
Somaye Sardouie Nasab; Ghasem Mohammadi Nejad; Babak Nakhoda
Abstract
Narrow genetic variability may lead to genetic vulnerability of field crops against biotic and abiotic stresses which can cause yield reduction. In this study a set of 37 wheat microsatellite markers linked with identified QTLs for salinity tolerance were used for the assessment of genetic diversity ...
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Narrow genetic variability may lead to genetic vulnerability of field crops against biotic and abiotic stresses which can cause yield reduction. In this study a set of 37 wheat microsatellite markers linked with identified QTLs for salinity tolerance were used for the assessment of genetic diversity for salinity in 30 promising lines of hexaploid bread wheat (Triticum aestivum L.). A total of 438 alleles were detected with an average allele number of 11.84 per locus using 37 microsatellite markers. The number of alleles per locus ranged from two to twenty, the maximum number of alleles was observed at Xgwm312. Gene diversity statistic for 37 microsatellite loci was varied from 0.66 to 0.94 and also polymorphic information content value was varied from 0.64 to 0.93 for Xgwm445 and Xgwm312 respectively. Result showed Xgwm312 SSR marker with the highest PIC value was distinguished as the best marker for genetic diversity analysis to improve of salinity tolerance. Obtained dendrogram by UPGMA method categorized genotypes in to 3 different groups, which had different reaction to salinity. A wide range of genomic diversity was observed among all the genotypes. Principal Coordinates Analysis (PCoA) also confirmed this pattern of genetic diversity, proving them can be use as the prime candidates in order to improve of salinity tolerance in breeding programs of wheat. The present study also indicates that microsatellite markers permit the fast and high throughput fingerprinting of numbers of genotypes from a germplasm collection in order to assess genetic diversity.
Molecular markers & plant breeding
Keivan Salehi; Farhad Nazarian Firouzabadi
Abstract
Chamomile (Matricaria chamomilla), an important medicinal plant belonging to the Asteraceae family, has a wide distribution in Iran and other parts of the world. The medicinal and pharmacological effects of chamomile are mainly associated with its essential oil content and it is widely used in food, ...
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Chamomile (Matricaria chamomilla), an important medicinal plant belonging to the Asteraceae family, has a wide distribution in Iran and other parts of the world. The medicinal and pharmacological effects of chamomile are mainly associated with its essential oil content and it is widely used in food, cosmetics and pharmaceutical industries. Despite its wide geographical distribution in Iran, little is known about its molecular genetic diversity and distribution. In this study, intron-exon splice junction (ISJ) markers, including both intron-targeted (IT) and exon-targeted (ET) primers, were used to assess the genetic diversity of thirty-one chamomile populations, including 28 populations from different parts of Iran, one Hungarian population, and two of unknown origin. Twenty-six out of thirty-five primers used in the study, were reliable, producing a total number of 566 sharp and precise bands, of which 557 bands were polymorphic (98%). The average polymorphic information content (PIC) and the average marker index (MI) were calculated at 0.33 and 7.34, respectively. The average total genetic diversity (HT), average genetic diversity within population (HST) and gene differentiation coefficient (Gst) were 0.293, 0.219, and 0.251, respectively. The diversity data revealed that the Matricaria chamomilla species exhibited the closest relationship with the Tripleurospermum disciforme and Tripleurospermum sevanense species.
Mutation breeding
Mozhgan Abtahi; Ahmad Arzani
Abstract
Mutation induction is considered as an effective way to enrich plant genetic variation, particularly for traits with a very low level of genetic variation. This research was conducted to assess genetic variation induced by gamma radiation in M2 and M3 mutant lines of canola (Brassica napus L.) by SSR ...
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Mutation induction is considered as an effective way to enrich plant genetic variation, particularly for traits with a very low level of genetic variation. This research was conducted to assess genetic variation induced by gamma radiation in M2 and M3 mutant lines of canola (Brassica napus L.) by SSR and morphological characteristics and to identify useful mutants in terms of agronomic traits. Sixty-two mutant lines derived from gamma mutagenesis and their wild-type progenitors (‘RGS003’ and ‘Sarigol’ cvs) were used. Twenty-five polymorphic SSR primers were used in this study. Results of cluster analysis based on both morphological traits comprising plant height, days to flowering, days to maturity, number of pods/plant, number of seeds/pod, 1000-seed weight and seed yield/plant and SSR data revealed a separate grouping of mutant lines from control cultivars. SSR data analysis of mutant lines and controls demonstrated a considerable genetic variation among mutant lines, where 83% of primers generated polymorphic bands with 3.32 alleles per locus. The genetic distance calculated between mutant lines and their controls indicated a significant difference between mutant lines and controls. Although both morphological and SSR markers successfully discriminated mutant lines from controls, SSR primers could further discriminate between the mutant lines derived from the related cultivar. Mutant lines 24 derived from ‘RGS003’ and 16 and 26 from ‘Sarigol’ were considered as superior for breeding canola, which could be utilized in future genetic and breeding programs. Distinct classification of genotypes based on agromorphological and SSR data in the present study implies that morphological and SSR markers reflected different aspects of genetic variation among mutant lines.
Molecular markers & plant breeding
Mahdieh Modareskia; Reza Darvishzadeh; Abbas Hassani; Maryam Kholghi
Abstract
Study of genetic relationships is a prerequisite for plant breeding activities as well as for conservation of genetic resources. In the present study, genetic diversity among and within 15 Iranian native Ajowan(Carum copticum L.) populations were determined using inter simple sequence repeat (ISSR) markers. ...
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Study of genetic relationships is a prerequisite for plant breeding activities as well as for conservation of genetic resources. In the present study, genetic diversity among and within 15 Iranian native Ajowan(Carum copticum L.) populations were determined using inter simple sequence repeat (ISSR) markers. Twelve selected primers produced 153 discernible bands, with 93 (60.78%) being polymorphic, indicating considerable genetic diversity at the population level. Number of polymorphic bands per primer ranged from 4 to 11 with an average of 7.75. The largest percentage of polymorphic loci was 78.57% for primer UBC818. Based on an un-weighted pair-group method using arithmetic average (UPGMA) clustering algorithm, four distinct groups were established. Results of the principal coordinate analysis (PCoA) corresponded to those obtained through cluster analysis. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly within populations (61%), but variance among populations was only 39%. This study has detected significant genetic differentiation among C. copticum populations. The current study confirmed the importance of molecular studies in detecting genetic variation among genotypes in selecting diverse parents to carry out crossing program successfully.