A DNA fingerprinting-based taxonomic allocation of Kamut wheat

2006 ◽  
Vol 4 (3) ◽  
pp. 172-180 ◽  
Author(s):  
Elena K. Khlestkina ◽  
Marion S. Röder ◽  
Heinrich Grausgruber ◽  
Andreas Börner
Keyword(s):  
Polymorphic Information Content ◽  
Tetraploid Wheat ◽  
Diversity Analysis ◽  
Natural Hybrid ◽  
Wheat Species ◽  
Microsatellite Genotyping ◽  
B Genome ◽  
Triticum Polonicum ◽  
Fertile Crescent ◽  
Seed Admixture

AbstractKamut wheat, said to have been derived from seed found in the Egyptian pyramids, appeared on the market about 25 years ago. We have investigated its taxonomic placement using microsatellite genotyping. In all, 89 accessions of 13 tetraploid wheat species, along with samples of Kamut wheat, were genotyped using two A and B genome wheat microsatellite markers per chromosome, generating 453 alleles (8–33 alleles per locus), and a mean allelic polymorphic information content (PIC) of 0.80. A diversity analysis showed that nine major accession groups could be defined, and these were inconsistent with formal taxonomic classifications of about 10% of the material. Most of these misclassifications are due to either species introgression or seed admixture. Some accessions appear to be duplicates. The Kamut wheats grouped together in a cluster containing three accessions of Triticum polonicum and three of T. durum, originating from Turkey, Iraq, Iran and Israel. We suggest that Kamut perhaps derived from a natural hybrid between T. durum and T. polonicum, which occurred in the Fertile Crescent.

scholarly journals Analysis of gliadin patterns and diversity in Triticum polonicum L. accessions from Ethiopia

2021 ◽  
Vol 117 (1) ◽  
pp. 1
Author(s):  
Eleni SHIFERAW
Keyword(s):  
Genetic Diversity ◽  
Gel Electrophoresis ◽  
Polyacrylamide Gel Electrophoresis ◽  
Tetraploid Wheat ◽  
Genetic Distances ◽  
Wheat Species ◽  
Triticum Polonicum ◽  
Wheat Improvement ◽  
Polymorphic Bands ◽  
Gliadin Patterns

<p>Gliadins from 25 accessions represented by 350 individual seed samples were analysed by acid-polyacrylamide gel electrophoresis (A-PAGE) with the objective of identifying gliadin band patterns and examine the extent of diversity in <em>Triticum polonicum </em>L. collections from Ethiopia. Seventy polymorphic bands and 68 different patterns were identified. Eighteen different mobility bands and 16 patterns were identified in <em>ω</em>-gliadin region, 22 bands and 20 patterns in <em>γ-</em>gliadin region, 12 bands and 22 patterns in <em>β-</em>gliadin region and 18 bands and 10 patterns in <em>α</em>-gliadin region. The average genetic diversity calculated from the data of the four gliadin zones of the analysed samples was 0.15. The γ region have the highest diversity (H = 0.193), followed by ω regions (H = 0.177) and β region (H = 0.168) and the lowest diversity was observed in α region (H = 0.127). Cluster analysis based on genetic distances resulted in grouping of the analysed accessions in to seven main groups. Though the level of diversity was relatively lower than other tetraploid wheat species from Ethiopia, the findings are indicative of the existence of variation in the collections which can be exploited for wheat improvement.</p>

scholarly journals The Independent Domestication of Timopheev’s Wheat: Insights from Haplotype Analysis of the Brittle rachis 1 (BTR1-A) Gene

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 338
Author(s):  
Moran Nave ◽  
Mihriban Taş ◽  
John Raupp ◽  
Vijay K. Tiwari ◽  
Hakan Ozkan ◽  
...  
Keyword(s):  
Promoter Region ◽  
Haplotype Analysis ◽  
Common Ancestor ◽  
Triticum Turgidum ◽  
Tetraploid Wheat ◽  
Wheat Species ◽  
Loss Of Function ◽  
Brittle Rachis ◽  
Gene Level ◽  
Large Panel

Triticum turgidum and T. timopheevii are two tetraploid wheat species sharing T. urartu as a common ancestor, and domesticated accessions from both of these allopolyploids exhibit nonbrittle rachis (i.e., nonshattering spikes). We previously described the loss-of-function mutations in the Brittle Rachis 1 genes BTR1-A and BTR1-B in the A and B subgenomes, respectively, that are responsible for this most visible domestication trait in T. turgidum. Resequencing of a large panel of wild and domesticated T. turgidum accessions subsequently led to the identification of the two progenitor haplotypes of the btr1-A and btr1-B domesticated alleles. Here, we extended the haplotype analysis to other T. turgidum subspecies and to the BTR1 homologues in the related T. timopheevii species. Our results showed that all the domesticated wheat subspecies within T. turgidum share common BTR1-A and BTR1-B haplotypes, confirming their common origin. In T. timopheevii, however, we identified a novel loss-of-function btr1-A allele underlying a partially brittle spike phenotype. This novel recessive allele appeared fixed within the pool of domesticated Timopheev’s wheat but was also carried by one wild timopheevii accession exhibiting partial brittleness. The promoter region for BTR1-B could not be amplified in any T. timopheevii accessions with any T. turgidum primer combination, exemplifying the gene-level distance between the two species. Altogether, our results support the concept of independent domestication processes for the two polyploid, wheat-related species.

Molecular characterization and chromosome-specific TRAP-marker development for Langdon durum D-genome disomic substitution lines

Genome ◽  
2006 ◽  
Vol 49 (12) ◽  
pp. 1545-1554 ◽  
Author(s):  
J. Li ◽  
D.L. Klindworth ◽  
F. Shireen ◽  
X. Cai ◽  
J. Hu ◽  
...  
Keyword(s):  
Triticum Turgidum ◽  
Tetraploid Wheat ◽  
Substitution Lines ◽  
Genome Chromosome ◽  
D Genome ◽  
Single Chromosome ◽  
B Genome ◽  
The Individual ◽  
Trap Marker

The aneuploid stocks of durum wheat ( Triticum turgidum L. subsp. durum (Desf.) Husnot) and common wheat ( T. aestivum L.) have been developed mainly in ‘Langdon’ (LDN) and ‘Chinese Spring’ (CS) cultivars, respectively. The LDN-CS D-genome chromosome disomic substitution (LDN-DS) lines, where a pair of CS D-genome chromosomes substitute for a corresponding homoeologous A- or B-genome chromosome pair of LDN, have been widely used to determine the chromosomal locations of genes in tetraploid wheat. The LDN-DS lines were originally developed by crossing CS nulli-tetrasomics with LDN, followed by 6 backcrosses with LDN. They have subsequently been improved with 5 additional backcrosses with LDN. The objectives of this study were to characterize a set of the 14 most recent LDN-DS lines and to develop chromosome-specific markers, using the newly developed TRAP (target region amplification polymorphism)-marker technique. A total of 307 polymorphic DNA fragments were amplified from LDN and CS, and 302 of them were assigned to individual chromosomes. Most of the markers (95.5%) were present on a single chromosome as chromosome-specific markers, but 4.5% of the markers mapped to 2 or more chromosomes. The number of markers per chromosome varied, from a low of 10 (chromosomes 1A and 6D) to a high of 24 (chromosome 3A). There was an average of 16.6, 16.6, and 15.9 markers per chromosome assigned to the A-, B-, and D-genome chromosomes, respectively, suggesting that TRAP markers were detected at a nearly equal frequency on the 3 genomes. A comparison of the source of the expressed sequence tags (ESTs), used to derive the fixed primers, with the chromosomal location of markers revealed that 15.5% of the TRAP markers were located on the same chromosomes as the ESTs used to generate the fixed primers. A fixed primer designed from an EST mapped on a chromosome or a homoeologous group amplified at least 1 fragment specific to that chromosome or group, suggesting that the fixed primers might generate markers from target regions. TRAP-marker analysis verified the retention of at least 13 pairs of A- or B-genome chromosomes from LDN and 1 pair of D-genome chromosomes from CS in each of the LDN-DS lines. The chromosome-specific markers developed in this study provide an identity for each of the chromosomes, and they will facilitate molecular and genetic characterization of the individual chromosomes, including genetic mapping and gene identification.

Development of EST-SSR markers and genetic diversity analysis among three Artemia species from different geographic populations

Crustaceana ◽  
2019 ◽  
Vol 92 (7) ◽  
pp. 841-851
Author(s):  
Xuekai Han ◽  
Ruyi Xu ◽  
Yuyu Zheng ◽  
Meirong Gao ◽  
Liying Sui
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Polymorphic Information Content ◽  
Diversity Analysis ◽  
Food Items ◽  
Geographical Populations ◽  
Geographic Populations ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Artemia is one of the most important live food items used in larviculture. In order to study the genetic diversity of Artemia in China, 170 novel simple sequence repeats (SSR) markers were identified from expressed sequence tags (ESTs) of the transcriptome library of Artemia parthenogenetica. Of these, 8 microsatellite loci were developed to characterize three geographical populations of Artemia. The results showed the expected and observed heterozygosity varied from 0.43 to 0.50 and from 0.59 to 0.64, respectively. The PIC (polymorphic information content) ranged from 0.37 to 0.45. These observations indicated that the Yuncheng population has the highest genetic diversity, whereas the Shuanghu population has the lowest. The Fst value (genetic differentiation coefficient) indicated that the three populations are highly differentiated. Genetic identity analyses revealed that the Yuncheng and Shuanghu populations have the closest relationship. The SSR markers described here will serve as a valuable tool for further studies in population and conservation genetics on Artemia.

scholarly journals New hyper-variable SSRs for diversity analysis in mango (Mangifera indica L.)

2021 ◽  
Vol 81 (01) ◽  
pp. 119-126
Author(s):  
Manish Srivastav ◽  
Sanjay K. Singh ◽  
Jai Prakash ◽  
Rakesh Singh ◽  
Neha Sharma ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Polymorphic Information Content ◽  
Mangifera Indica ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Diversity Analysis ◽  
Genome Wide ◽  
Improvement Programme ◽  
The Mean ◽  
Simple Sequence

Whole genome sequence in mango offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, simple sequence repeats (SSRs) were predicted from genome sequence of mango. Based on the SSR length (? 50 bp), highly-variable mango SSRs (MSSRs) were sorted. A sub-set of 129 MSSRs was validated on a set of 24 diverse mango genotypes yielding marker validation and polymorphism of 88.96 and 85.27 per cent, respectively. One hundred and ten polymorphic markers were identified for the present set of mango genotypes. Polymorphic information content (PIC) ranged from 0.10 to 0.78 and the highest value was observed with MSSR133. The mean PIC value was 0.40 but 33 MSSR markers showed PIC values ? 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs) in mango. MSSRs data was further used for diversity analysis of mango genotypes belonging to different agro-ecological conditions including chance seedlings, landraces, exotic and indigenous germplasm and hybrids. Cluster analysis using UPGMA of 24 mango genotypes revealed that these MSSRs were informative in diversity analysis and distinguished mango genotypes based on their origin, parentage and embryo types. A novel set of 110 hyper-variable SSR markers have been added to the mango repository depicting usefulness in discriminating closely related mango germplasm and their use in mango improvement programme.

scholarly journals Genetic Diversity Analysis of Hybrid Rice Parental Lines and Genetic Purity Assessment of Hybrid Seeds of China

2020 ◽  
Vol 12 (5) ◽  
pp. 37
Author(s):  
Haiya Cai ◽  
Yuxia Lu ◽  
Gang Liu ◽  
Shuo Zhang ◽  
Haitao Jia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Hybrid Rice ◽  
Southern China ◽  
Polymorphic Information Content ◽  
Diversity Analysis ◽  
Japonica Rice ◽  
Similarity Coefficients ◽  
Genetic Purity ◽  
Genetic Diversity Analysis ◽  
Parental Lines

Thirty-five pairs of SSR primers were used for genetic diversity analysis and DNA fingerprinting of 31 hybrid rice core parental lines developed in central- and southern-China using one japonica rice line and three inbred rice lines as the check varieties. The average number of alleles (Na) per SSR locus was 4.02, with a range of two to eight, the effective number of alleles (Ne) was 83.16 with a mean of 2.38, ranging from 1.19 to 4.66. The polymorphic information content (PIC) ranged from 0.16 to 0.79, with an average number of 0.52. The results of the cluster analysis indicated that the check varieties viz., one japonica rice and three inbred rice, were clustered into two groups with similarity coefficients of 0.62 and 0.71 respectively indicating their relatedness. Thirty-one hybrid rice parental lines were clustered into 6 groups according to their different types, pedigrees and regions of development with similarity coefficients of approximately 0.76. The highest genetic similarity coefficient (0.94) was observed between Y58S and C815S, and the lowest (0.63) was observed between Quan9311A and Peiai64S. The purity of one hybrid rice cultivar was tested using characteristic marker and the field test, and it was demonstrated that the purities obtained using the two methods were similar. This research will be helpful for rice breeding, new cultivar registration and seed production.

scholarly journals Morpho-Molecular Diversity Analysis of Local Rice (Oryza sativa L.) Genotypes Using Microsatellite Markers

2020 ◽  
pp. 92-104
Author(s):  
S. K. Singh ◽  
Charupriya Singh ◽  
Mounika Korada ◽  
Sonali Habde ◽  
D. K. Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Diversity ◽  
Agricultural Research ◽  
Polymorphic Information Content ◽  
Block Design ◽  
Genetic Enhancement ◽  
Diversity Analysis ◽  
Cluster Distance ◽  
Breeding Programmes ◽  
Rice Genotypes

Aim: The knowledge of genetic diversity and relationship among the genotypes play a significant role for genetic enhancement in breeding programmes to increase production, improve quality, biotic and abiotic stresses, and also for the selection of superior parental lines in rice. The present field experiment was conducted to study the diversity present in 29 local genotypes of rice using both morphological and molecular ways. Methodology: The experiment was conducted at Agricultural Research Farm, Banaras Hindu University, during Kharif-2017 in an augmented block design with 29 rice genotypes including 3 checks. Mahalanobis’ D2 analysis was carried out to assess the morphological diversity present among the genotypes and molecular analysis was done with 21 polymorphic SSR markers using the NTSYSpc software. Results: Mahalanobis’ D2 grouped the 29 genotypes into 6 clusters based on the inter-se genetic distance. The highest intra-cluster distance was recorded in the Cluster I (32.73), which comprised of 7 genotypes. The highest inter-cluster distance (65.86) was observed between Clusters IV and V. Molecular diversity analysis grouped the 29 rice genotypes into 2 main clusters i.e. cluster I and cluster II with dissimilarity coefficient of 0.34, which were further divided into sub-clusters. Polymorphic Information Content (PIC) value is an evidence of diversity and frequency among the varieties. The level of polymorphism varied from 0.164 to 0.694, with an average 0.521. The highest PIC value was observed for locus RM 5 (0.694) followed by RM 510 (0.692). All the 21 primers showed polymorphism and the number of alleles ranged from 2 to 4 with an average of 3.04.  Conclusion: This study established the presence of considerable amount of genetic diversity among the genotypes studied, the most diverse genotypes being Anupam gold and HUR-1309 followed by Kalanamak-2 and HUR-1304. Breeders may attempt hybridization among the above genotypes which showed maximum diversity, for creating more variability in rice and can be used for planning further breeding programmes.

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