Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales.
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TLDR
Results support a model whereby segmental CNV and the genes encoded within these regions contribute to adaptive capacity of plants through natural genome variation.Abstract:
Arabidopsis thaliana is the model plant and is grown worldwide by plant biologists seeking to dissect the molecular underpinning of plant growth and development. Gene copy number variation (CNV) is a common form of genome natural diversity that is currently poorly studied in plants and may have broad implications for model organism research, evolutionary biology, and crop science. Herein, comparative genomic hybridization (CGH) was used to identify and interrogate regions of gene CNV across the A. thaliana genome. A common temperature condition used for growth of A. thaliana in our laboratory and many around the globe is 22 °C. The current study sought to test whether A. thaliana, grown under different temperature (16 and 28 °C) and stress regimes (salicylic acid spray) for five generations, selecting for fecundity at each generation, displayed any differences in CNV relative to a plant lineage growing under normal conditions. Three siblings from each alternative temperature or stress lineage were also compared with the reference genome (22 °C) by CGH to determine repetitive and nonrepetitive CNVs. Findings document exceptional rates of CNV in the genome of A. thaliana over immediate family generational scales. A propensity for duplication and nonrepetitive CNVs was documented in 28 °C CGH, which was correlated with the greatest plant stress and infers a potential CNV–environmental interaction. A broad diversity of gene species were observed within CNVs, but transposable elements and biotic stress response genes were notably overrepresented as a proportion of total genes and genes initiating CNVs. Results support a model whereby segmental CNV and the genes encoded within these regions contribute to adaptive capacity of plants through natural genome variation.read more
Citations
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Journal ArticleDOI
The Theory of Island Biogeography
TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
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Copy number variation in association studies of human disease
TL;DR: In this article, the authors discuss evidence that copy-number variants affect phenotypes, directions for basic knowledge to support clinical study of CNVs, the challenge of genotyping CNPs in clinical cohorts, the use of SNPs as markers for CNPs and statistical challenges in testing CNVs for association with disease.
Journal ArticleDOI
Gene duplication as a mechanism of genomic adaptation to a changing environment
TL;DR: The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve the understanding of gene duplication as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.
Journal ArticleDOI
The genome of the extremophile crucifer Thellungiella parvula.
Maheshi Dassanayake,Dong Ha Oh,Jeffrey S. Haas,Alvaro G. Hernandez,Hyewon Hong,Hyewon Hong,Shahjahan Ali,Dae-Jin Yun,Ray A. Bressan,Ray A. Bressan,Ray A. Bressan,Jian-Kang Zhu,Jian-Kang Zhu,Hans J. Bohnert,John M. Cheeseman +14 more
TL;DR: The draft genome for Thellungiella parvula is presented and it is shown that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information.
Journal ArticleDOI
Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor).
Lei-Ying Zheng,Xiaosen Guo,Bing He,Lian-Jun Sun,Yao Peng,Shan-Shan Dong,Teng-Fei Liu,Shu-Ye Jiang,Shu-Ye Jiang,Srinivasan Ramachandran,Srinivasan Ramachandran,Chun-Ming Liu,Hai-Chun Jing +12 more
TL;DR: This is a first report of the identification of genome-wide patterns of genetic variation in sorghum, and high-density SNP and indel markers reported here will be a valuable resource for future gene-phenotype studies and the molecular breeding of this important crop and related species.
References
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Journal ArticleDOI
The Theory of Island Biogeography
TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Book
The Theory of Island Biogeography
TL;DR: The Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201
Journal ArticleDOI
Large-Scale Copy Number Polymorphism in the Human Genome
Jonathan Sebat,B. Lakshmi,Jennifer Troge,Joan Alexander,Janet M. Young,Pär Lundin,Susanne Månér,Hillary Massa,Megan Walker,Maoyen Chi,Nicholas Navin,Robert Lucito,John Healy,James W. Hicks,Kenny Q. Ye,Andrew Reiner,T. Conrad Gilliam,Barbara J. Trask,Nick Patterson,Anders Zetterberg,Michael Wigler +20 more
TL;DR: It is shown that large-scale copy number polymorphisms (CNPs) (about 100 kilobases and greater) contribute substantially to genomic variation between normal humans.
Journal ArticleDOI
The significance of responses of the genome to challenge
TL;DR: An attempt is made to outline several experiments conducted by the author that revealed how a genome may react to conditions for which it is unprepared, but to which it responds in a discernible, but initially unforeseen manner.
Journal ArticleDOI
Breeding Technologies to Increase Crop Production in a Changing World
Mark Tester,Peter Langridge +1 more
TL;DR: New technologies must be developed to accelerate breeding through improving genotyping and phenotyping methods and by increasing the available genetic diversity in breeding germplasm.
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