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Interpopulation differences of retroduplication variations (RDVs) in rice retrogenes and their phenotypic correlations
- Source :
- Computational and Structural Biotechnology Journal, Computational and Structural Biotechnology Journal, Vol 19, Iss, Pp 600-611 (2021)
- Publication Year :
- 2021
- Publisher :
- Research Network of Computational and Structural Biotechnology, 2021.
-
Abstract
- Graphical abstract<br />Retroduplication variation (RDV), a type of retrocopy polymorphism, is considered to have essential biological significance, but its effect on gene function and species phenotype is still poorly understood. To this end, we analyzed the retrocopies and RDVs in 3,010 rice genomes. We calculated the RDV frequencies in the genome of each rice population; detected the mutated, ancestral and expressed retrogenes in rice genomes; and analyzed their RDV influence on rice phenotypic traits. Collectively, 73 RDVs were identified, and 14 RDVs in ancestral retrogenes can significantly affect rice phenotypes. Our research reveals that RDV plays an important role in rice migration, domestication and evolution. We think that RDV is a good molecular breeding marker candidate. To our knowledge, this is the first study on the relationship between retrogene function, expression, RDV and species phenotype.
- Subjects :
- RDV, Retroduplication variation
Population
Biophysics
MF, Molecular function
Biology
Biochemistry
Genome
03 medical and health sciences
Retrocopy
0302 clinical medicine
Structural Biology
CC, Cellular component
Genetics
Domestication
education
GO, Gene ontology
BP, Biological process
Gene
Retroposition
030304 developmental biology
ComputingMethodologies_COMPUTERGRAPHICS
RDV
Molecular breeding
0303 health sciences
education.field_of_study
FPKM, Fragments per kilobase per million mapped reads
food and beverages
Phenotypic trait
Phenotype
MST, monosaccharide transporter
Computer Science Applications
030220 oncology & carcinogenesis
Retrogene
ORF, Open reading frame
Indel, Insertion-deletion
Rice
TP248.13-248.65
Function (biology)
Biotechnology
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 20010370
- Volume :
- 19
- Database :
- OpenAIRE
- Journal :
- Computational and Structural Biotechnology Journal
- Accession number :
- edsair.doi.dedup.....6b585f54bb8800a9e354b734ad21d6ff