scholarly journals Accelerating structure-function mapping using the ViVa webtool to mine natural variation

2018 ◽  
Author(s):  
Morgan O Hamm ◽  
Britney L Moss ◽  
Alexander R Leydon ◽  
Hardik P Gala ◽  
Amy Lanctot ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Network ◽  
Natural Variation ◽  
Genetic Resource ◽  
Gene Families ◽  
Auxin Signaling ◽  
Human Genetic Variation ◽  
Auxin Signaling Pathway ◽  
Accelerating Structure ◽  
Or Gene

Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of this data remains inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project (http://snp-seek.irri.org/) and human genetic variation (https://www.ncbi.nlm.nih.gov/clinvar/).

scholarly journals Aux/IAA and ARF Gene Families in Salix suchowensis: Identification, Evolution, and Dynamic Transcriptome Profiling During the Plant Growth Process

2021 ◽  
Vol 12 ◽  
Author(s):  
Suyun Wei ◽  
Yingnan Chen ◽  
Jing Hou ◽  
Yonghua Yang ◽  
Tongming Yin
Keyword(s):  
Plant Growth ◽  
Growth Process ◽  
Transcriptome Profiling ◽  
Gene Families ◽  
Auxin Signaling ◽  
Vascular Differentiation ◽  
Auxin Signaling Pathway ◽  
Functional Involvement ◽  
Functional Features ◽  
Gene Structures

The phytohormone auxin plays a pivotal role in the regulation of plant growth and development, including vascular differentiation and tree growth. The auxin/indole-3-acetic acid (Aux/IAA) and auxin response transcription factor (ARF) genes are key components of plant auxin signaling. To gain more insight into the regulation and functional features of Aux/IAA and ARF genes during these processes, we identified 38 AUX/IAA and 34 ARF genes in the genome of Salix suchowensis and characterized their gene structures, conserved domains, and encoded amino acid compositions. Phylogenetic analysis of some typical land plants showed that the Aux/IAA and ARF genes of Salicaceae originated from a common ancestor and were significantly amplified by the ancestral eudicot hexaploidization event and the “salicoid” duplication that occurred before the divergence of poplar and willow. By analyzing dynamic transcriptome profiling data, some Aux/IAA and ARF genes were found to be involved in the regulation of plant growth, especially in the initial plant growth process. Additionally, we found that the expression of several miR160/miR167-ARFs was in agreement with canonical miRNA–ARF interactions, suggesting that miRNAs were possibly involved in the regulation of the auxin signaling pathway and the plant growth process. In summary, this study comprehensively analyzed the sequence features, origin, and expansion of Aux/IAA and ARF genes, and the results provide useful information for further studies on the functional involvement of auxin signaling genes in the plant growth process.

scholarly journals Genome Duplication in Soybean (Glycine subgenus soja)

Genetics ◽  
1996 ◽  
Vol 144 (1) ◽  
pp. 329-338 ◽  
Author(s):  
R C Shoemaker ◽  
K Polzin ◽  
J Labate ◽  
J Specht ◽  
E C Brummer ◽  
...  
Keyword(s):  
Seed Protein ◽  
Genome Duplication ◽  
Fragment Length Polymorphism ◽  
Gene Families ◽  
Soybean Genome ◽  
Seed Composition ◽  
Linkage Groups ◽  
Mapping Data ◽  
Or Gene ◽  
Average Size

Abstract Restriction fragment length polymorphism mapping data from nine populations (Glycine max × G. soja and G. max × G. max) of the Glycine subgenus soja genome led to the identification of many duplicated segments of the genome. Linkage groups contained up to 33 markers that were duplicated on other linkage groups. The size of homoeologous regions ranged from 1.5 to 106.4 cM, with an average size of 45.3 cM. We observed segments in the soybean genome that were present in as many as six copies with an average of 2.55 duplications per segment. The presence of nested duplications suggests that at least one of the original genomes may have undergone an additional round of tetraploidization. Tetraploidization, along with large internal duplications, accounts for the highly duplicated nature of the genome of the subgenus. Quantitative trait loci for seed protein and oil showed correspondence across homoeologous regions, suggesting that the genes or gene families contributing to seed composition have retained similar functions throughout the evolution of the chromosomes.

Revitalizing Difference in the HapMap: Race and Contemporary Human Genetic Variation Research

2008 ◽  
Vol 36 (3) ◽  
pp. 471-477 ◽  
Author(s):  
Jennifer A. Hamilton
Keyword(s):  
Genetic Variation ◽  
Human Genome ◽  
Genetic Research ◽  
The United States ◽  
Genome Project ◽  
Human Genetic Variation ◽  
Early 21St Century ◽  
The Social ◽  
English Speaking ◽  
The Human Genome Project

In 2000, researchers from the Human Genome Project (HGP) proclaimed that the initial sequencing of the human genome definitively proved, among other things, that there was no genetic basis for race. The genetic fact that most humans were 99.9% the same at the level of their DNA was widely heralded and circulated in the English-speaking press, especially in the United States. This pronouncement seemed proof that long-term antiracist efforts to de-biologize race were legitimized by scientific findings. Yet, despite the seemingly widespread acceptance of the social construction of race, post-HGP genetic science has seen a substantial shift toward the use of race variables in genetic research and, according to a number of prominent scholars, is re-invoking the specter of earlier forms of racial science in some rather discomfiting ways. During the past seven years, the main thrust of human genetic research, especially in the realm of biomedicine, has shifted from a concern with the 99.9% of the shared genome — what is thought to make humans alike — towards an explicit focus on the 0.1% that constitutes human genetic variation. Here I briefly explore some of the potential implications of the conceptualization and practice of early 21st century genetic variation research, especially as it relates to questions of race.

GENETIC DIVERSITY

PEDIATRICS ◽  
1977 ◽  
Vol 59 (3) ◽  
pp. 432-432
Author(s):  
R. C. Lewontin ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Skin Color ◽  
Human Genetic Variation ◽  
Human Species

Only about 7% of all human genetic diversity is between major races. It would appear then that the superficial characters of skin color, hair form, lip, nose, and eye shape that we use to distinguish human races are atypical and do not represent the mode of human genetic variation. The taxonomic division of the human species into races places a completely disproportionate emphasis on a very small fraction of total human genetic diversity.

An overview of human genetic variation

2018 ◽  
pp. 361-396 ◽  
Author(s):  
Tom Strachan ◽  
Andrew P Read
Keyword(s):  
Genetic Variation ◽  
Human Genetic Variation
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