scholarly journals Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 481 ◽  
Author(s):  
Hayba Badro ◽  
Agnelo Furtado ◽  
Robert Henry
Keyword(s):  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Plastid Genome ◽  
Evolutionary Relationships ◽  
Rice Varieties ◽  
Tropical Japonica ◽  
Asian Rice ◽  
Sequence Read Archive ◽  
Long Time ◽  
Southern Iraq

Due to the importance of the rice crop in Iraq, this study was conducted to determine the origin of the major varieties and understand the evolutionary relationships between Iraqi rice varieties and other Asian rice accessions that could be significant in the improvement of this crop. Five varieties of Oryza sativa were obtained from Baghdad/Iraq, and the whole genomic DNA was sequenced, among these varieties, Amber33, Furat, Yasmin, Buhooth1 and Amber al-Baraka. Raw sequence reads of 33 domesticated Asian rice accessions were obtained from the Sequence Read Archive (SRA-NCBI). The sequence of the whole chloroplast-genome was assembled while only the sequence of 916 concatenated nuclear-genes was assembled. The phylogenetic analysis of both chloroplast and nuclear genomes showed that two main clusters, Indica and Japonica, and further five sub-clusters based upon their ecotype, indica, aus, tropical-japonica, temperate-japonica and basmati were created; moreover, Amber33, Furat, Yasmin and Buhooth1 belonged to the basmati, indica and japonica ecotypes, respectively, where Amber33 was placed in the basmati group as a sister of cultivars from Pakistan and India. This confirms the traditional story that Amber was transferred by a group of people who had migrated from India and settled in southern Iraq a long time ago.

scholarly journals Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels

Proceedings ◽  
2019 ◽  
Vol 36 (1) ◽  
pp. 24
Author(s):  
Badro ◽  
Furtado ◽  
Henry
Keyword(s):  
Genomic Dna ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Nuclear Genome ◽  
Rice Varieties ◽  
Asian Rice ◽  
National Centre ◽  
Long Time ◽  
Nuclear Genomes ◽  
Southern Iraq

Due to the importance of the rice crop in Iraq, this study was conducted to determine the origin of the major varieties and understand the evolutionary relationships between Iraqi rice varieties and other Asian-rice accessions that could be significant in the improvement of this crop. Five varieties of Oryza sativa were obtained from Baghdad, Iraq; among these varieties, one, Amber33, is local and is one of the most highly valued varieties in Iraq because of its fragrance, and two varieties, Furat and Yasmin were introduced from Vietnam while the other two, Buhoot1 and Amber al-Baraka, were improved varieties; the whole genomic DNA was sequenced. Raw sequence reads of 33 domesticated Asian-rice accessions were obtained from the National Centre for Biotechnology Information (NCBI). The sequence of the whole chloroplast genome of 5 Iraqi varieties and 34 domesticated rice accessions was assembled while for nuclear genome analysis, only the sequences of 916 concatenated nuclear genes were assembled. The phylogenetic trees of both chloroplast and nuclear genomes were similar with insignificant differences at the end of the clades. Two main clusters, Indica and Japonica, and further five subclusters based upon their ecotype, indica, aus, tropical-japonica, temperate-japonica and basmati were created, where Amber33, Furat, Yasmin and Buhooth1 belonged to the basmati, indica and japonica ecotypes, respectively. The phylogenetic analysis of both chloroplast and nuclear genomes placed Amber33 in the basmati ecotype group as a sister of cultivars from Pakistan and India. This confirms the old traditional story that the Amber variety was transferred by a group of people who had migrated from India (the Southeast) and settled in southern Iraq a long time ago

scholarly journals Tailoring rice varieties to consumer preferences induced by cultural and colonial heritage: Lessons from New Rice for Africa (NERICA) in The Gambia

2021 ◽  
pp. 003072702110197
Author(s):  
Kofi Britwum ◽  
Matty Demont
Keyword(s):  
Consumer Preferences ◽  
Rice Variety ◽  
Import Substitution ◽  
The Gambia ◽  
Rice Varieties ◽  
Auction Market ◽  
Asian Rice ◽  
Market Competitiveness ◽  
New Varieties ◽  
Locally Grown

Rice breeding priorities in Africa often focus on agronomic gains. However, being a net importer of rice, the continent’s varietal replacement success also crucially hinges on new varieties’ market competitiveness vis-à-vis imports. Markets have been profoundly shaped by cultural and colonial heritage. Indigenous preferences for African rice can be traced back to ancient rice domestication and have been subsequently influenced by Asian rice import standards as a result of colonial import substitution policies. New Rice for Africa (NERICA) crosses between African and Asian rice species have the potential to reconcile these dual indigenous/import preferences, but little is known about their market competitiveness. We use auction market data to assess the intrinsic and extrinsic consumer value of NERICA in The Gambia relative to two market standards: branded, Asian rice imports and the most popular locally grown Asian rice variety. We categorize rice consumers into four market segments, based on their heritage as evidenced by their preferences and genealogical lineages. NERICA outperforms both Asian rice standards in terms of market competitiveness, and its value is further reinforced by colonial heritage and labeling, but somewhat weakened by cultural heritage. Consumers were found to pay price premiums for NERICA in the range of 5% to 22% relative to Asian rice imports, with the highest premiums offered by consumers with colonial heritage, representing 86% of the sample. Maintaining and expanding this market will require breeders to incorporate trait mixes that reconcile agronomic gains and consumer preferences induced by cultural and colonial heritage.

scholarly journals Molecular record for the first authentication of Isaria cicadae from Vietnam

2021 ◽  
Vol 16 (1) ◽  
pp. 711-718
Author(s):  
Thuan Duc Lao ◽  
Hanh Van Trinh ◽  
Loi Vuong ◽  
Luyen Tien Vu ◽  
Thuy Ai Huyen Le ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Neighbor Joining ◽  
Pcr Assay ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Cordyceps Cicadae ◽  
High Bootstrap

Abstract The entomopathogenic fungus T011, parasitizing on nymph of Cicada, collected in the coffee garden in Dak Lak Province, Vietnam, was preliminarily morphologically identified as Isaria cicadae, belonged to order Hypocreales and family Clavicipitaceae. To ensure the authenticity of T011, phylogenetic analysis of the concatenated set of multiple genes including ITS, nrLSU, nrSSU, Rpb1, and Tef1 was applied to support the identification. Genomic DNA was isolated from dried sample T011. The PCR assay sequencing was applied to amplify ITS, nrLSU, nrSSU, Rpb1, and Tef1 gene. For phylogenetic analysis, the concatenated data of both target gens were constructed with MEGAX with a 1,000 replicate bootstrap based on the neighbor-joining, maximum likelihood, maximum parsimony method. As the result, the concatenated data containing 62 sequences belonged to order Hypocreales, families Clavicipitaceae, and 2 outgroup sequences belonged to order Hypocreales, genus Verticillium. The phylogenetic analysis results indicated that T011 was accepted at subclade Cordyceps and significantly formed the monophyletic group with referent Cordyceps cicadae (Telemorph of Isaria cicadae) with high bootstrap value. The phylogenetically analyzed result was strongly supported by our morphological analysis described as the Isaria cicadae. In summary, phylogenetic analyses based on the concatenated dataset were successfully applied to strengthen the identification of T011 as Isaria cicadae.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

Bulinus species on Madagascar: molecular evolution, genetic markers and compatibility with Schistosoma haematobium

Parasitology ◽  
2001 ◽  
Vol 123 (7) ◽  
pp. 261-275 ◽  
Author(s):  
J. R. STOTHARD ◽  
P. BRÉMOND ◽  
L. ANDRIAMARO ◽  
B. SELLIN ◽  
E. SELLIN ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Subunit ◽  
Population Genetic Analysis ◽  
Basal Node ◽  
Pcr Rflp ◽  
Dna Sequence Variation ◽  
Long Time ◽  
Laboratory Infection ◽  
Species Groups ◽  
Nucleotide Divergence

Of the four species of Bulinus found on Madagascar, three species: B. obtusispira, B. liratus and B. bavayi are endemic while the fourth, B. forskalii, is probably a recent introduction from the African mainland. The evolutionary relationships of these species with Bulinus species from Africa were studied by phylogenetic analysis of DNA sequence variation at two mitochondrial loci: cytochrome oxidase subunit I (COI) and large ribosomal subunit (LSU) or 16S. The observed levels of nucleotide divergence within Bulinus were substantial but may underestimate the true levels as there was evidence of ‘saturation' of transitional substitutions at both loci. A putative secondary structure model for the sequenced segment of the 16S was developed. Subsequent phylogenetic analysis using transversional changes only for both loci, showed that there were contrasting levels of divergence within the four species groups. B. obtusispira was consistently placed within the B. africanus group, appearing ancestral to this group and was closest to the basal node within Bulinus. Together with B. bavayi, the two species appear to have been isolated on Madagascar for a long time, contrasting with both B. liratus and B. forskalii that appear more recent colonisers; however, estimate of exact times of divergence is problematic. A PCR-RFLP assay was developed to enable identification and discrimination of B. obtusispira and B. liratus using discriminatory variation within the COI. To enable population genetic analysis within B. obtusispira, microsatellite markers were developed using an enrichment method and 8 primer pairs are reported. Laboratory infection experiments using Madasgacan S. haematobium from the Mahabo area showed that certain populations of B. obtusispira, B. liratus and B. bavayi were compatible.

scholarly journals Marker identification and phylogenetic analysis of saline tolerant rice varieties

2021 ◽  
Vol 746 (1) ◽  
pp. 012014
Author(s):  
Suprayogi ◽  
P S Dewi ◽  
E Oktaviani ◽  
A W Aisya ◽  
R G N Prasetia
Keyword(s):  
Phylogenetic Analysis ◽  
Rice Varieties ◽  
Marker Identification

scholarly journals Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers

2018 ◽  
Vol 14 (1) ◽  
pp. 1
Author(s):  
Joko Prasetiyono ◽  
Nurul Hidayatun ◽  
Tasliah Tasliah
Keyword(s):  
Genetic Diversity ◽  
Morphological Characters ◽  
Snp Markers ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Tropical Japonica ◽  
Rice Chromosomes ◽  
Improvement Programs ◽  
Rice Genotypes ◽  
Genotypic Mixtures

<p>Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.</p>

scholarly journals Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

2021 ◽  
Author(s):  
Marcia Gumiel ◽  
Oscar M Rollano-Penaloza ◽  
Carmelo Peralta-Rivero ◽  
Leslie Tejeda ◽  
Valeria D. Palma Encinas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Theobroma Cacao ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Next Generation ◽  
Center Of Origin ◽  
Chloroplast Genomes ◽  
Geographical Locations ◽  
Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

Clidicus minilankanus sp. n., with notes on remaining Sri Lankan Clidicus species (Coleoptera, Staphylinidae, Scydmaeninae)

Zootaxa ◽  
2020 ◽  
Vol 4718 (1) ◽  
pp. 87-94
Author(s):  
PAWEŁ JAŁOSZYŃSKI
Keyword(s):  
Phylogenetic Analysis ◽  
Sri Lanka ◽  
Junior Synonym ◽  
Monophyletic Group ◽  
Evolutionary Relationships ◽  
Sri Lankan

Until now, four species of Clidicus Laporte were found in Sri Lanka, three known from female specimens only. Clidicus minilankanus sp. n., is described, and compared to all remaining sympatric congeners. The Sri Lankan species may form a monophyletic group characterized by several morphological oddities: the head only slightly impressed posteromedially, with a large portion of vertex and frons not divided longitudinally; the pronotum quadrangular and flattened, with vestigial or absent posterior ‘collar’, and the transverse groove that demarcates it from the disc lacking pits or even entirely or partly obliterated; and the metaventrite strongly shortened, so that meso- and metacoxae are nearly adjacent. These characters may justify resurrecting Erineus Walker, a junior synonym of Clidicus (proposed for the first described Sri Lankan species, C. monstrosus (Walker)), as a valid name for a subgenus. This problem must be addressed by a phylogenetic analysis of all Clidicus species, to establish evolutionary relationships within this interesting genus. 

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