scholarly journals Genome-wide homology analysis reveals new insights into the origin of the wheat B genome

2017 ◽  
Author(s):  
Wei Zhang ◽  
Mingyi Zhang ◽  
Xianwen Zhu ◽  
Yaping Cao ◽  
Qing Sun ◽  
...  
Keyword(s):  
Wheat Chromosome ◽  
Genomic Region ◽  
Aegilops Speltoides ◽  
Origin And Evolution ◽  
Homology Analysis ◽  
B Genome ◽  
Genome Wide ◽  
Polyploid Genome ◽  
Relationship Of ◽  
The Relationship

AbstractWheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The ancestors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a candidate for the ancestor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure, which has puzzled the wheat research community for nearly a century. In the present study, the genome-wide homology analysis identified perceptible homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was identified on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome in wheat species. Thereby, we conclude that Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive ancestor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings provide significant insights into the origin and evolution of the wheat B genome, and will facilitate polyploid genome studies in wheat and other plants as well.

scholarly journals Validation of Hosta alata (Asparagaceae) as a new species and its phylogenetic affinity

PhytoKeys ◽  
2021 ◽  
Vol 181 ◽  
pp. 79-93
Author(s):  
Tetsukazu Yahara ◽  
Shun K. Hirota ◽  
Kengo Fuse ◽  
Hiroyuki Sato ◽  
Shuichiro Tagane ◽  
...  
Keyword(s):  
New Species ◽  
Genotyping By Sequencing ◽  
Phylogenetic Affinity ◽  
Phylogenetic Studies ◽  
Genome Wide ◽  
Molecular Phylogenetic ◽  
Flowering Periods ◽  
Relationship Of ◽  
The Relationship ◽  
A New Species

Molecular phylogenetic studies of Hosta pulchella (Asparagaceae) and its relatives, which are native to Japan, have been conducted and resulted in a highly resolved phylogeny. Specifically, the relationship of H. pulchella to H. alata Hatusima, nom. nud. is investigated. These data include genome-wide SNPs obtained through conducting multiplexed ISSR genotyping by sequencing (MIG-seq). Based on these phylogenetic results, morphological observations, distribution, and differences in flowering periods of H. alata collections sympatric with H. pulchella, we find the two species closely related, but distinct. As such, we formally describe Hosta alatasp. nov. from the Oita Prefecture of Kyushu island, southwestern Japan.

scholarly journals On the relationship between high-order linkage disequilibrium and epistasis

2018 ◽  
Author(s):  
Yanjun Zan ◽  
Simon K. G. Forsberg ◽  
Örjan Carlborg
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Architecture ◽  
Genomic Region ◽  
High Order ◽  
Common Assumption ◽  
Association Analyses ◽  
Functional Polymorphisms ◽  
Genome Wide ◽  
The Common ◽  
The Relationship

AbstractA plausible explanation for statistical epistasis revealed in genome wide association analyses is the presence of high order linkage disequilibrium (LD) between the genotyped markers tested for interactions and unobserved functional polymorphisms. Based on findings in experimental data, it has been suggested that high order LD might be a common explanation for statistical epistasis inferred between local polymorphisms in the same genomic region. Here, we empirically evaluate how prevalent high order LD is between local, as well as distal, polymorphisms in the genome. This could provide insights into whether we should account for this when interpreting results from genome wide scans for statistical epistasis. An extensive and strong genome wide high order LD was revealed between pairs of markers on the high density 250k SNP-chip and individual markers revealed by whole genome sequencing in the A. thaliana 1001-genomes collection. The high order LD was found to be more prevalent in smaller populations, but present also in samples including several hundred individuals. An empirical example illustrates that high order LD might be an even greater challenge in cases when the genetic architecture is more complex than the common assumption of bi-allelic loci. The example shows how significant statistical epistasis is detected for a pair of markers in high order LD with a complex multi allelic locus. Overall, our study illustrates the importance of considering also other explanations than functional genetic interactions when genome wide statistical epistasis is detected, in particular when the results are obtained in small populations of inbred individuals.

Molecular evidence for the origin and evolution of chromosome 4A in polyploidy wheats

1985 ◽  
Vol 27 (2) ◽  
pp. 246-250 ◽  
Author(s):  
A. Lane Rayburn ◽  
B. S. Gill
Keyword(s):  
In Situ Hybridization ◽  
Chinese Spring ◽  
Diploid Species ◽  
Aegilops Speltoides ◽  
Molecular Evidence ◽  
Wheat Evolution ◽  
D Genome ◽  
Origin And Evolution ◽  
B Genome

The chromosomes of polyploid Triticum species and the putative donor diploid species were analyzed by in situ hybridization with a repeated DNA sequence clone pSc 119 isolated from rye and also found in wheat. In Triticum aestivum cv. Chinese Spring, chromosome 4A showed one terminal site in the short arm and one terminal and two interstitial sites of hybridization in the long arm. Triticum turgidum contained a 4A chromosome identical to 'Chinese Spring' with respect to hybridization sites. Chromosome 4A of the timopheevi wheats differed from 4A of 'Chinese Spring' in that the site of the sequence on the short arm was subterminal rather than terminal. Of the A-, B-, and D-genome progenitor species, only potential B-genome donors Aegilops speltoides and Aegilops sharonensis each showed a chromosome with hybridization sites similar to 4A. This suggested that 4A belongs to the B genome. Moreover, with regard to this sequence, chromosome 4A has undergone only minor changes during the evolution of the polyploid wheats.Key words: wheat evolution, in situ hybridization, biotin labeling.

scholarly journals Genome-wide meta-analysis of phytosterols reveals five novel loci and a detrimental effect on coronary atherosclerosis

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Markus Scholz ◽  
Katrin Horn ◽  
Janne Pott ◽  
Arnd Gross ◽  
Marcus E. Kleber ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Significant Snps ◽  
Serum Concentrations ◽  
Locus Heterogeneity ◽  
Genome Wide ◽  
A Genome ◽  
Artery Disease ◽  
Relationship Of ◽  
Functional Mechanisms ◽  
The Relationship

AbstractPhytosterol serum concentrations are under tight genetic control. The relationship between phytosterols and coronary artery disease (CAD) is controversially discussed. We perform a genome-wide meta-analysis of 32 phytosterol traits reflecting resorption, cholesterol synthesis and esterification in six studies with up to 9758 subjects and detect ten independent genome-wide significant SNPs at seven genomic loci. We confirm previously established associations at ABCG5/8 and ABO and demonstrate an extended locus heterogeneity at ABCG5/8 with different functional mechanisms. New loci comprise HMGCR, NPC1L1, PNLIPRP2, SCARB1 and APOE. Based on these results, we perform Mendelian Randomization analyses (MR) revealing a risk-increasing causal relationship of sitosterol serum concentrations and CAD, which is partly mediated by cholesterol. Here we report that phytosterols are polygenic traits. MR add evidence of both, direct and indirect causal effects of sitosterol on CAD.

THE PROBLEM OF ETHNIC KURDS IN THE MIDDLE EASTERN REGION: THE HISTORY OF ORIGIN AND EVOLUTION

2021 ◽  
pp. 67-73
Author(s):  
Farhod karimov
Keyword(s):  
Middle East ◽  
Middle Eastern ◽  
Eastern Region ◽  
Regional Stability ◽  
Origin And Evolution ◽  
Middle East Countries ◽  
History Of ◽  
External Power ◽  
Relationship Of ◽  
The Relationship

This article examines the problem of the Kurds in ensuring regional stability and security in the Middle East, the history of this problem in comparison with the history of the countries of the region in the 14-19 centuries. The analysis of the facts presented in the historical literature about the Kurds is carried out. The attitude of the Middle East countries to these issues, the factor of external power in this matter, the relationship of the problem with other confessional problems in the region are also being studied.

The relationship of leaf rust resistance gene Lr13 and hybrid necrosis gene Ne2m on wheat chromosome 2BS

2015 ◽  
Vol 129 (3) ◽  
pp. 485-493 ◽  
Author(s):  
Peng Zhang ◽  
Colin W. Hiebert ◽  
Robert A. McIntosh ◽  
Brent D. McCallum ◽  
Julian B. Thomas ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Resistance Gene ◽  
Rust Resistance ◽  
Wheat Chromosome ◽  
Leaf Rust Resistance ◽  
Rust Resistance Gene ◽  
Leaf Rust Resistance Gene ◽  
Hybrid Necrosis ◽  
Relationship Of ◽  
The Relationship

scholarly journals Redefining the origin and evolution of ovarian cancer: a hormonal connection

2016 ◽  
Vol 23 (9) ◽  
pp. R411-R422 ◽  
Author(s):  
Carlos Cardenas ◽  
Ayesha B Alvero ◽  
Bo Seong Yun ◽  
Gil Mor
Keyword(s):  
Ovarian Cancer ◽  
Ovarian Function ◽  
Developmental Process ◽  
Reproductive Age ◽  
Origin And Evolution ◽  
Tumorigenesis And Progression ◽  
Reproductive Cancers ◽  
Ovarian Tumorigenesis ◽  
Relationship Of ◽  
The Relationship

Ovarian cancer has the highest mortality of all female reproductive cancers. Late diagnosis, tumour heterogeneity and the development of chemoresistance contribute to this statistic and work against patient survival. Current studies have revealed novel concepts that impact our view on how ovarian cancer develops. The greatest impact is on our understanding that, as a disease, ovarian cancer has multiple cellular origins and that these malignant precursors are mostly derived from outside of the ovaries. In this review, we propose a new concept of a step-wise developmental process that may underwrite ovarian tumorigenesis and progression: (1) migration/recruitment to the ovaries; (2) seeding and establishment in the ovaries; (3) induction of a dormant cancer stage; and (4) expansion and tumor progression. We will discuss the relationship of each step with the changing ovarian function and milieu during the reproductive age and the subsequent occurrence of menopause. The realization that ovarian cancer development and progression occurs in distinct steps is critical for the search of adequate markers for early detection that will offer personalized strategies for prevention and therapy.

scholarly journals Monocyte polarization: the relationship of genome-wide changes in H4 acetylation with polarization

2011 ◽  
Vol 12 (6) ◽  
pp. 445-456 ◽  
Author(s):  
Z Zhang ◽  
L Song ◽  
K Maurer ◽  
A Bagashev ◽  
K E Sullivan
Keyword(s):  
Genome Wide ◽  
Relationship Of ◽  
The Relationship

scholarly journals Shortened leukocyte telomere length in young adults who use methamphetamine

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yen-Feng Lin ◽  
Po-Yu Chen ◽  
Hsing-Cheng Liu ◽  
Yi-Lung Chen ◽  
Wei-Hern Chou ◽  
...  
Keyword(s):  
Young Adults ◽  
Young Adult ◽  
Telomere Length ◽  
Multivariate Regression Analysis ◽  
Biological Aging ◽  
Leukocyte Telomere Length ◽  
Negatively Associated ◽  
Genome Wide ◽  
Relationship Of ◽  
The Relationship

AbstractMethamphetamine (METH) use, most prevalent in young adults, has been associated with high rates of morbidity and mortality. The relationship between METH use and accelerated biological aging, which can be measured using leukocyte telomere length (LTL), remains unclear. We examined whether young adult METH users have shorter LTL and explored the relationship between characteristics of METH use and LTL by using Mendelian randomization (MR) analysis. We compared the LTL for 187 METH users and 159 healthy individuals aged between 25 and 34 years and examined the relationship of LTL with METH use variables (onset age, duration, and maximum frequency of METH use) by using regression analyses. In addition, 2-stage-least-squares (2SLS) MR was also performed to possibly avoid uncontrolled confounding between characteristics of METH use and LTL. We found METH users had significantly shorter LTL compared to controls. Multivariate regression analysis showed METH use was negatively associated with LTL (β = −0.36, P < .001). Among METH users, duration of METH use was negatively associated with LTL after adjustment (β = −0.002, P = .01). We identified a single nucleotide polymorphism (SNP) rs6585206 genome-wide associated with duration of METH use. This SNP was used as an instrumental variable to avoid uncontrolled confounding for the relationship between the use duration and LTL shortening. In conclusion, we show that young adult METH users may have shorter LTL compared with controls and longer duration of METH use was significantly associated with telomere shortening. These observations suggest that METH use may accelerate biological senescence.

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