Tracing the Evolution and Economic Potential of Konjac Glucomannan in Amorphophallus species (Araceae) using Molecular Phylogeny and RAPD Markers

Phytotaxa ◽  
2016 ◽  
Vol 282 (2) ◽  
pp. 81 ◽  
Author(s):  
ORACHORN MEKKERDCHOO ◽  
CHALEEDA BOROMPICHAICHARTKUL ◽  
ALLISON PERRIGO ◽  
GEORGE SRZEDNICKI ◽  
CHEUNJIT PRAKITCHAIWATTANA ◽  
...  
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Its Region ◽  
Pharmaceutical Products ◽  
Konjac Glucomannan ◽  
Closely Related Species ◽  
Dna Variation ◽  
Amorphophallus Konjac ◽  
Genome Wide ◽  
Present Understanding

The genus Amorphophallus is an economically important taxon that is abundant in Old World tropical forests (Asia, Oceania and Africa). It includes many species that are used with increasing frequency as a source of food and pharmaceutical products worldwide. Amorphophallus konjac is an important economic crop and has been used widely in China and Japan for commercial konjac glucomannan (KGM) production. However, the species’ range does not extend to Thailand, where other closely related species may be more suitable for commercial KGM production. Present understanding of genetic relationships among Thai Amorphophallus species is still limited, and the connection between evolutionary history and KGM content is unknown. Here, the genetic relationships among various accessions of Amorphophallus spp. collected in Thailand are investigated using the chloroplast trnL-trnF spacer, nuclear ribosomal internal transcribed spacer (ITS) region and the second intron of LEAFY (FLint2) together with genome-wide DNA variation analysis, Randomly Amplified Polymorphic DNA (RAPD) technique. RAPD primers are also developed to quickly and efficiently identify species producing high levels of KGM. This study finds that two monophyletic clades include high KGM content species. RAPD analyses indicate that primer AC-10 generates specific bands identifying species belonging only to the high and medium KGM content clades.  These primers can be used as a screening tool for economical species, aiming at improving the industrial production of KGM in Thailand and the world.

scholarly journals Biosystematic Study on Some Egyptian Species of Astragalus L. (Fabaceae)

Agriculture ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 125
Author(s):  
Monier M. Abd El-Ghani ◽  
Ashraf S. A. El-Sayed ◽  
Ahmed Moubarak ◽  
Rabab Rashad ◽  
Hala Nosier ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Dna Barcode ◽  
Plant Morphology ◽  
Its Region ◽  
Its2 Region ◽  
Whole Plant ◽  
Three Samples ◽  
Two Samples ◽  
Region 10 ◽  
Unique Banding Pattern

Astragalus L. is one of the largest angiosperm complex genera that belongs to the family Fabaceae, subfamily Papilionoideae or Faboideae under the subtribe Astragalinae of the tribe Galegeae. The current study includes the whole plant morphology, DNA barcode (ITS2), and molecular marker (SCoT). Ten taxa representing four species of Astragalus were collected from different localities in Egypt during the period from February 2018 to May 2019. Morphologically, identification and classification of collected Astragalus plants occurred by utilizing the light microscope, regarding the taxonomic revisions of the reference collected Astragalus specimens in other Egyptian Herbaria. For molecular validation, ten SCoT primers were used in this study, producing a unique banding pattern to differentiate between ten samples of Astragalus taxa which generated 212 DNA fragments with an average of 12.2 bands per 10 Astragalus samples, with 8 to 37 fragments per primer. The 212 fragments amplified were distributed as 2 monomorphic bands, 27 polymorphic without unique bands, 183 unique bands (210 Polymorphic with unique bands), and ITS2 gene sequence was showed as the optimal barcode for identifying Astragalus L. using BLAST searched on NCBI database, and afterward, analyzing the chromatogram for ITS region, 10 samples have been identified as two samples representing A. hauarensis, four samples representing A. sieberi, three samples representing A. spinosus and one sample representing A. vogelii. Based on the ITS barcode, A. hauarensis RMG1, A. hauarensis RMG2, A. sieberi RMG1, A. sieberi RMG2, A. sieberi RMG3, A. sieberi RMG4, A. spinosus RMG1, A. spinosus RMG2, A. spinosus RMG3, A. vogelii RMG were deposited into GenBank with accession # MT367587.1, MT367591.1, MT367593.1, MT367585.1, MT367586.1, MT367588.1, MT160347.1, MT367590.1, MT367589.1, MT367592.1, respectively. These results indicated the efficiency of SCoT markers and ITS2 region in identifying and determining genetic relationships between Astragalus species.

scholarly journals Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

2019 ◽  
Vol 15 ◽  
pp. 117693431988994
Author(s):  
Shulin Zhang ◽  
Yaling Cai ◽  
Jinggong Guo ◽  
Kun Li ◽  
Renhai Peng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Association Analyses ◽  
Genome Wide ◽  
Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

Mitochondrial and nuclear DNA variation, genotype fingerprinting and genetic relationships in lentil (Lens culinaris Medik.)

1997 ◽  
Vol 77 (4) ◽  
pp. 515-521 ◽  
Author(s):  
Om P. Rajora ◽  
John D. Mahon
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Fragment ◽  
Lens Culinaris ◽  
Nuclear Dna ◽  
Genetic Relationships ◽  
Restriction Enzymes ◽  
Dna Variation ◽  
Apocytochrome B ◽  
Nuclear Dna Variation ◽  
Mean Similarity

Mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) variations were examined in six cultivars of Lens culinaris ssp. culinaris and two (mtDNA) or one (nuDNA) accession(s) of L. culinaris ssp. orientalis. Total leaf DNA was digested with up to 15 restriction endonucleases, separated by agarose gel electrophoresis and trasferred to nylon membranes. To examine mtDNA variation, blots were probed with mtDNA coding for cytochrome c oxidase I (coxI) and ATPase 6 (atp6) of both wheat and maize as well as apocytochrome b (cob) and Orf25 (orf25) of wheat. Sixteen combinations of mtDNA probes and restriction enzymes revealed 34 fragments that discriminated between at least two lentil accessions. For nuDNA analysis, probes from cDNA and genomic DNA clones of lentil were used to probe the same blots, and identified 46 diagnostic fragments from 19 probe/enzyme combinations. Each lentil accession could be unequivocably distinguished from all others on the basis of both mitochondrial and nuclear DNA fragment patterns. The mitochondrial restriction fragment similarities ranged from 0.944 to 0.989, with a mean of 0.970 but nuclear restriction fragment similarities varied from 0.582 to 0.987, with a mean of 0.743. The apparent genetic relationships among accessions differed according to the source of DNA examined, although the commercial varieties Laird, Brewer and Redchief showed similarly high levels of mean similarity with both nuclear (0.982) and mitochondrial DNA (0.983). Key words: Lens culinaris Medik., genetic variation, mitochondrial, nuclear, DNA, lentil

scholarly journals Endocrine Fertility Parameters—Genomic Background and Their Genetic Relationship to Boar Taint in German Landrace and Large White

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 231
Author(s):  
Ines Brinke ◽  
Christine Große-Brinkhaus ◽  
Katharina Roth ◽  
Maren Julia Pröll-Cornelissen ◽  
Sebastian Klein ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Young Male ◽  
Boar Taint ◽  
Genetic Progress ◽  
Large White ◽  
Genome Wide ◽  
A Genome ◽  
Different Origins ◽  
Fertility Traits

The surgical castration of young male piglets without anesthesia is no longer allowed in Germany from 2021. One alternative is breeding against boar taint, but shared synthesis pathways of androstenone (AND) and several endocrine fertility parameters (EFP) indicate a risk of decreasing fertility. The objective of this study was to investigate the genetic background between AND, skatole (SKA), and six EFP in purebred Landrace (LR) and Large White (LW) populations. The animals were clustered according to their genetic relatedness because of their different origins. Estimated heritabilities (h2) of AND and SKA ranged between 0.52 and 0.34 in LR and LW. For EFP, h2 differed between the breeds except for follicle-stimulating hormone (FSH) (h2: 0.28–0.37). Both of the breeds showed unfavorable relationships between AND and testosterone, 17-β estradiol, and FSH. The genetic relationships (rg) between SKA and EFP differed between the breeds. A genome-wide association analysis revealed 48 significant associations and confirmed a region for SKA on Sus Scrofa chromosome (SSC) 14. For EFP, the results differed between the clusters. In conclusion, rg partly confirmed physiologically expected antagonisms between AND and EFP. Particular attention should be spent on fertility traits that are based on EFP when breeding against boar taint to balance the genetic progress in both of the trait complexes.

scholarly journals Genetic Diversity of Salvia Species Assessed by ISSR and RAPD Markers

2016 ◽  
Vol 44 (2) ◽  
pp. 431-436 ◽  
Author(s):  
Masoumeh YOUSEFIAZARKHANIAN ◽  
Ali ASGHARI ◽  
Jafar AHMADI ◽  
Behvar ASGHARI ◽  
Ali Ashraf JAFARI
Keyword(s):  
Genetic Diversity ◽  
Genetic Polymorphisms ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Genetic Variations ◽  
Molecular Techniques ◽  
Wild Populations ◽  
Similarity Coefficients ◽  
The World

The genus Salvia includes an enormous assemblage of nearly 1,000 species dispersed around the world. Due to possible threats to this genus, there is an immediate requirement to evaluate the diversity of its wild populations. ISSR and RAPD molecular techniques were used to evaluate the genetic relationships among twenty-one ecotypes of eight Salvia species. Amplification of genomic DNA using 23 primers (15 RAPD and eight ISSR) produced 280 bands, of which 91% were polymorphic. The results of marker parameters showed no clear difference between two marker systems. It was generally observed that both ISSR and RAPD markers had similar efficiency in detecting genetic polymorphisms with remarkable ability to differentiate the closely related ecotypes of Salvia. Nei’s similarity coefficients for these techniques ranged from 0.48 to 0.98. Based on the results of clustering, PCoA and AMOVA, the genetic diversity between and within species was confirmed. So, conservation and domestication of the genus Salvia must be due to levels of genetic variations.

Genetic relationships among Brazilian strains of Aspergillus ochraceus based on RAPD and ITS sequences

2004 ◽  
Vol 50 (11) ◽  
pp. 985-988 ◽  
Author(s):  
Maria Helena Pelegrinelli Fungaro ◽  
Marciane Magnani ◽  
Laurival Antônio Vilas-Boas ◽  
Patrícia Cristina Vissotto ◽  
Márcia Cristina Furlaneto ◽  
...  
Keyword(s):  
Ochratoxin A ◽  
Sequence Data ◽  
Genetic Relationships ◽  
Its Region ◽  
Aspergillus Ochraceus ◽  
Coffee Bean ◽  
Coffee Beans ◽  
Major Species ◽  
Group A ◽  
Group B

Ochratoxin A (OA) is a mycotoxin that has been found in coffee beans and coffee beverages. Its toxicological profile includes carcinogenicity, nephrotoxicity, and immunotoxicity. Aspergillus ochraceus is the major species responsible for OA production in Brazilian coffee beans. The genetic relationships among 25 A. ochraceus strains collected from Brazilian coffee-bean samples were determined based on RAPD and internal transcribed spacer (ITS) sequence data. The isolates were resolved into 2 distinct groups, one with 4 strains (group A) and the other with 21 strains (group B). Specific nucleotide variations characterizing group A and B were found for both ITS1 and ITS2 regions. Group B is a new group proposed here to accommodate the majority of the Brazilian isolates. Each group was found to contain both toxigenic and nontoxigenic strains, indicating that there is no association between molecular genotypes and the ability to produce OA.Key words: Aspergillus ochraceus, ochratoxin A, ITS region (ITS1–5.8S–ITS2), RAPD.

scholarly journals Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species

2015 ◽  
Vol 26 (21) ◽  
pp. 3777-3787 ◽  
Author(s):  
Maike Claußen ◽  
Thomas Lingner ◽  
Claudia Pommerenke ◽  
Lennart Opitz ◽  
Gabriela Salinas ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Global Analysis ◽  
Primordial Germ Cells ◽  
Binding Studies ◽  
Closely Related Species ◽  
Cis Acting ◽  
Genome Wide ◽  
Vegetal Cortex ◽  
Gain Loss ◽  
Germ Layer Patterning

RNAs that localize to the vegetal cortex during Xenopus laevis oogenesis have been reported to function in germ layer patterning, axis determination, and development of the primordial germ cells. Here we report on the genome-wide, comparative analysis of differentially localizing RNAs in Xenopus laevis and Xenopus tropicalis oocytes, revealing a surprisingly weak degree of conservation in respect to the identity of animally as well as vegetally enriched transcripts in these closely related species. Heterologous RNA injections and protein binding studies indicate that the different RNA localization patterns in these two species are due to gain/loss of cis-acting localization signals rather than to differences in the RNA-localizing machinery.

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