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Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana

Marco Todesco,Sureshkumar Balasubramanian,Tina T. Hu,M. Brian Traw,Matthew Horton,Petra Epple,Christine Kuhns,Sridevi Sureshkumar,Christopher Schwartz,Christa Lanz,Roosa A. E. Laitinen,Yu Huang,Joanne Chory,Volker Lipka,Justin O. Borevitz,Jeffery L. Dangl,Joy Bergelson,Magnus Nordborg& Detlef Weigel

Journal name:Nature Volume:465,Pages:632–636 Date published:(03 June 2010) DOI: doi:10.1038/nature09083 Received10 July 2009 Accepted 14 April 2010

Plants can defend themselves against a wide array of enemies, from microbes to large animals, yet there is great variability in the effectiveness of such defences, both within and between species. Some of this variation can be explained by conflicting pressures from pathogens with different modes of attack¹. A second explanation comes from an evolutionary ‘tug of war’, in which pathogens adapt to evade detection, until the plant has evolved new recognition capabilities for pathogen invasion^{2, 3, 4, 5}. If selection is, however, sufficiently strong, susceptible hosts should remain rare. That this is not the case is best explained by costs incurred from constitutive defences in a pest-free environment^{6, 7, 8, 9, 10, 11}. Using a combination of forward genetics and genome-wide association analyses, we demonstrate that allelic diversity at a single locus, ACCELERATED CELL DEATH 6 (ACD6)^{12, 13}, underpins marked pleiotropic differences in both vegetative growth and resistance to microbial infection and herbivory among natural Arabidopsis thaliana strains. A hyperactive ACD6 allele, compared to the reference allele, strongly enhances resistance to a broad range of pathogens from different phyla, but at the same time slows the production of new leaves and greatly reduces the biomass of mature leaves. This allele segregates at intermediate frequency both throughout the worldwide range of A. thaliana and within local populations, consistent with this allele providing substantial fitness benefits despite its marked impact on growth.

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High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases.

from PNAS

Publication Date: 2010 May 27 PMID: 20508152
Authors: Zhang, F. – Maeder, M. L. – Unger-Wallace, E. – Hoshaw, J. P. – Reyon, D. – Christian, M. – Li, X. – Pierick, C. J. – Dobbs, D. – Peterson, T. – Joung, J. K. – Voytas, D. F.
Journal: Proc Natl Acad Sci U S A

We report here an efficient method for targeted mutagenesis of Arabidopsis genes through regulated expression of zinc finger nucleases (ZFNs)-enzymes engineered to create DNA double-strand breaks at specific target loci. ZFNs recognizing the Arabidopsis ADH1 and TT4 genes were made by Oligomerized Pool ENgineering (OPEN)-a publicly available, selection-based platform that yields high quality zinc finger arrays. The ADH1 and TT4 ZFNs were placed under control of an estrogen-inducible promoter and introduced into Arabidopsis plants by floral-dip transformation. Primary transgenic Arabidopsis seedlings induced to express the ADH1 or TT4 ZFNs exhibited somatic mutation frequencies of 7% or 16%, respectively. The induced mutations were typically insertions or deletions (1-142 bp) that were localized at the ZFN cleavage site and likely derived from imprecise repair of chromosome breaks by nonhomologous end-joining. Mutations were transmitted to the next generation for 69% of primary transgenics expressing the ADH1 ZFNs and 33% of transgenics expressing the TT4 ZFNs. Furthermore, approximately 20% of the mutant-producing plants were homozygous for mutations at ADH1 or TT4, indicating that both alleles were disrupted. ADH1 and TT4 were chosen as targets for this study because of their selectable or screenable phenotypes (adh1, allyl alcohol resistance; tt4, lack of anthocyanins in the seed coat). However, the high frequency of observed ZFN-induced mutagenesis suggests that targeted mutations can readily be recovered by simply screening progeny of primary transgenic plants by PCR and DNA sequencing. Taken together, our results suggest that it should now be possible to obtain mutations in any Arabidopsis target gene regardless of its mutant phenotype.

Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases.

from PNAS

Publication Date: 2010 May 27 PMID: 20508151
Authors: Osakabe, K. – Osakabe, Y. – Toki, S.
Journal: Proc Natl Acad Sci U S A

Site-directed mutagenesis in higher plants remains a significant technical challenge for basic research and molecular breeding. Here, we demonstrate targeted-gene inactivation for an endogenous gene in Arabidopsis using zinc finger nucleases (ZFNs). Engineered ZFNs for a stress-response regulator, the ABA-INSENSITIVE4 (ABI4) gene, cleaved their recognition sequences specifically in vitro, and ZFN genes driven by a heat-shock promoter were introduced into the Arabidopsis genome. After heat-shock induction, gene mutations with deletion and substitution in the ABI4 gene generated via ZFN-mediated cleavage were observed in somatic cells at frequencies as high as 3%. The homozygote mutant line zfn_abi4-1-1 for ABI4 exhibited the expected mutant phenotypes, i.e., ABA and glucose insensitivity. In addition, ZFN-mediated mutagenesis was applied to the DNA repair-deficient mutant plant, atku80. We found that lack of AtKu80, which plays a role in end-protection of dsDNA breaks, increased error-prone rejoining frequency by 2.6-fold, with increased end-degradation. These data demonstrate that an approach using ZFNs can be used for the efficient production of mutant plants for precision reverse genetics.

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An Environment-Wide Association Study (EWAS) on Type 2 Diabetes Mellitus

Type 2 Diabetes (T2D) and other chronic diseases are caused by a complex combination of many genetic and environmental factors. Few methods are available to comprehensively associate specific physical environmental factors with disease. We conducted a pilot Environmental-Wide Association Study (EWAS), in which epidemiological data are comprehensively and systematically interpreted in a manner analogous to a Genome Wide Association Study (GWAS).

We performed multiple cross-sectional analyses associating 266 unique environmental factors with clinical status for T2D defined by fasting blood sugar (FBG) concentration ≥126 mg/dL. We utilized available Centers for Disease Control (CDC) National Health and Nutrition Examination Survey (NHANES) cohorts from years 1999 to 2006. Within cohort sample numbers ranged from 503 to 3,318. Logistic regression models were adjusted for age, sex, body mass index (BMI), ethnicity, and an estimate of socioeconomic status (SES). As in GWAS, multiple comparisons were controlled and significant findings were validated with other cohorts. We discovered significant associations for the pesticide-derivative heptachlor epoxide (adjusted OR in three combined cohorts of 1.7 for a 1 SD change in exposure amount; p<0.001), and the vitamin γ-tocopherol (adjusted OR 1.5; p<0.001). Higher concentrations of polychlorinated biphenyls (PCBs) such as PCB170 (adjusted OR 2.2; p<0.001) were also found. Protective factors associated with T2D included β-carotenes (adjusted OR 0.6; p<0.001).

Despite difficulty in ascertaining causality, the potential for novel factors of large effect associated with T2D justify the use of EWAS to create hypotheses regarding the broad contribution of the environment to disease. Even in this study based on prior collected epidemiological measures, environmental factors can be found with effect sizes comparable to the best loci yet found by GWAS.

Chirag J. Patel^1,2,3, Jayanta Bhattacharya⁴, Atul J. Butte^1,2,3*

1 Department of Pediatrics and Medicine, Stanford University School of Medicine, Stanford, California, United States of America, 2 Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California, United States of America, 3 Lucile Packard Children's Hospital, Palo Alto, California, United States of America, 4 Center For Primary Care and Outcomes Research, Stanford University School of Medicine, Stanford, California, United States of America

Abstract

Background

Type 2 Diabetes (T2D) and other chronic diseases are caused by a complex combination of many genetic and environmental factors. Few methods are available to comprehensively associate specific physical environmental factors with disease. We conducted a pilot Environmental-Wide Association Study (EWAS), in which epidemiological data are comprehensively and systematically interpreted in a manner analogous to a Genome Wide Association Study (GWAS).

Methods and Findings

We performed multiple cross-sectional analyses associating 266 unique environmental factors with clinical status for T2D defined by fasting blood sugar (FBG) concentration ≥126 mg/dL. We utilized available Centers for Disease Control (CDC) National Health and Nutrition Examination Survey (NHANES) cohorts from years 1999 to 2006. Within cohort sample numbers ranged from 503 to 3,318. Logistic regression models were adjusted for age, sex, body mass index (BMI), ethnicity, and an estimate of socioeconomic status (SES). As in GWAS, multiple comparisons were controlled and significant findings were validated with other cohorts. We discovered significant associations for the pesticide-derivative heptachlor epoxide (adjusted OR in three combined cohorts of 1.7 for a 1 SD change in exposure amount; p<0.001), and the vitamin γ-tocopherol (adjusted OR 1.5; p<0.001). Higher concentrations of polychlorinated biphenyls (PCBs) such as PCB170 (adjusted OR 2.2; p<0.001) were also found. Protective factors associated with T2D included β-carotenes (adjusted OR 0.6; p<0.001).

Conclusions and Significance

Despite difficulty in ascertaining causality, the potential for novel factors of large effect associated with T2D justify the use of EWAS to create hypotheses regarding the broad contribution of the environment to disease. Even in this study based on prior collected epidemiological measures, environmental factors can be found with effect sizes comparable to the best loci yet found by GWAS.

Source: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010746

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Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza.

from Plant Journal

Publication Date: 2010 May 6 PMID: 20487382
Authors: Ammiraju, J. S. – Fan, C. – Yu, Y. – Song, X. – Cranston, K. A. – Pontaroli, A. C. – Lu, F. – Sanyal, A. – Jiang, N. – Rambo, T. – Currie, J. – Collura, K. – Talag, J. – Bennetzen, J. L. – Chen, M. – Jackson, S. – Wing, R. A.
Journal: Plant J

SUMMARY Despite knowledge that polyploidy is wide-spread and a major evolutionary force for flowering plant diversification, detailed comparative molecular studies on polyploidy have been confined to only few species and families. The genus Oryza is composed of twenty-three species that are classified into 10 distinct "genome types" (6 diploid and 4 polyploid) and is emerging as a powerful new model system to study polyploidy. Here we report the identification, sequence and comprehensive comparative annotation of eight homoeologous genomes from a single orthologous region – Adh1-Adh2 – from four allopolyploid species representing each of the known Oryza genome types (BC, CD, HJ and KL). Detailed comparative phylogenomic analyses of these regions within and across species and ploidy levels, provided several insights into spatio-temporal dynamics of genome organization and evolution of this region in "natural" polyploids of Oryza. The major findings from this study are: a) homoeologous genomic regions within the same nucleus experienced both independent and parallel evolution; b) differential lineage specific selection pressures were not found between polyploids and their diploid progenitors; c) no dramatic structural changes relative to the diploid ancestors were detected; d) even though the BC and CD polyploid species appear to have arisen less than 2 MYA, molecular evolutionary rate variation between the two genomes in the BC complex species could be detected; and e) no clear distinction in the patterns of genome evolution in the diploid vs. polyploid species were detected.

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Production and identification of wheat-Agropyron cristatum 6P translocation lines.

Planta. 2010 May 19. [Epub ahead of print]

Luan Y, Wang X, Liu W, Li C, Zhang J, Gao A, Wang Y, Yang X, Li L.

National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Abstract

The narrow genetic background of wheat is the primary factor that has restricted the improvement of crop yield in recent years. The kernel number per spike is the most important factor of the many potential characteristics that determine wheat yield. Agropyron cristatum (L.) Gaertn., a wild relative of wheat, has the characteristics of superior numbers of florets and kernels per spike, which are controlled by chromosome 6P. In this study, the wheat-A. cristatum disomic addition and substitution lines were used as bridge materials to produce wheat-A. cristatum 6P translocation lines induced by gametocidal chromosomes and irradiation. The results of genomic in situ hybridization showed that the frequency of translocation induced by gametocidal chromosomes was 5.08%, which was higher than the frequency of irradiated hybrids (2.78%) and irradiated pollen (2.12%). The fluorescence in situ hybridization results of the translocation lines showed that A. cristatum chromosome 6P could be translocated to wheat ABD genome, and the recombination frequency was A genome > B genome > D genome. The alien A. cristatum chromosome 6P was translocated to wheat homoeologous groups 1, 2, 3, 5 and 6. We obtained abundant translocation lines that possessed whole-arm, terminal, segmental and intercalary translocations. Three 6PS-specific and four 6PL-specific markers will be useful to rapidly identify and trace the translocated fragments. The different wheat-A. cristatum 6P translocation lines obtained in this study can provide basic materials for analyzing the alien genes carried by chromosome 6P. The translocation line WAT33-1-3 and introgression lines WAI37-2 and WAI41-1, which had significant characteristics of multikernel (high numbers of kernels per spike), could be utilized as novel germplasms for high-yield wheat breeding.

Source: http://www.springerlink.com/content/g760x50171186131/

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NSF, Gates Foundation to Support WSU Research on Developing ‘Desert Wheat’

May 20, 2010

FOR IMMEDIATE RELEASE

Kathy Barnard, Marketing and News Services
509-335-2806, kbarnard@wsu.edu

Source Contacts

Professor Kulvinder Gill, Department of Crop and Soil Sciences
509/335-4666, ksgill@wsu.edu

Ralph Cavalieri, director, WSU Agricultural Research center
509/335-4563, cavalieri@wsu.edu

PULLMAN, Wash. – Washington State University researchers working on developing wheat varieties that grow under severe drought conditions — “desert wheat” — have earned a $1.6 million grant from the National Science Foundation and the Bill & Melinda Gates Foundation.Part of the two foundations’ BREAD program, the grant will help fund WSU scientist Kulvinder Gill’s research on identifying genes that will increase wheat yields under drought stress. BREAD stands for Basic Research to Enable Agricultural Development; it is a five-year program aimed at generating sustainable, science-based solutions to agricultural problems in developing countries. More than 130 U.S. institutions in 45 states, partnering with counterparts in 68 countries, submitted proposals for the inaugural BREAD competition.

“It is an honor for WSU to be a part of this prestigious, international effort to help feed the world,” said Dan Bernardo, dean of the WSU College of Agricultural, Human, and Natural Resource Sciences. “The potential for truly changing the circumstances of people around the globe is real and powerful.”

Ralph Cavalieri, director of WSU’s Agricultural Research Center, said the award speaks to the quality of the university’s plant sciences research.

“This award is national recognition of WSU’s strength in wheat genetics and breeding,” he said. “It will have positive impacts globally and for U.S. wheat producers.”

Gill, who holds the Vogel Chair for Wheat Breeding and Genetics at WSU, will lead a team of researchers at WSU, Purdue University, the University of Wisconsin-Stevens Point, the Punjab Agricultural University in India, COMSATS University in Pakistan, and Pioneer Hi-Bred International, Inc. The team will focus on developing alternate gene systems to reduce plant height in wheat and other cereals. Currently used dwarfing genes that helped double wheat and rice production during the “Green Revolution” of the 1960s limit yields under drought and other environmental stress conditions, especially in wheat. Approximately 50 percent of the world’s wheat is grown in arid climates.

“Successful completion of our project will help maximize the benefits of the dwarfing trait without the adverse effects under drought conditions that are usually associated with the currently used mutants. The project is particularly important for the U.S. where 85 percent of the wheat is grown under limited water conditions,” said Gill.

A complete list of 2010 BREAD awards is available at http://www.nsf.gov/bio/pubs/awards/bread10.htm.

Source:http://www.wsunews.wsu.edu/pages/publications.asp?Action=Detail&PublicationID=20188&TypeID=1

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RESEARCH ARTICLES

Published Online May 20, 2010 Science   DOI: 10.1126/science.1190719

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

Daniel G. Gibson,¹ 

John I. Glass,¹ 

Carole Lartigue,¹ Vladimir N. Noskov,¹ Ray-Yuan Chuang,¹Mikkel A. Algire,¹ Gwynedd A. Benders,² Michael G. Montague,¹ Li Ma,¹ Monzia M. Moodie,¹Chuck Merryman,¹ Sanjay Vashee,¹ Radha Krishnakumar,¹ Nacyra Assad-Garcia,¹Cynthia Andrews-Pfannkoch,¹ Evgeniya A. Denisova,¹ Lei Young,¹ Zhi-Qing Qi,¹Thomas H. Segall-Shapiro,¹ Christopher H. Calvey,¹ Prashanth P. Parmar,¹ Clyde A. Hutchison, III,²Hamilton O. Smith,² J. Craig Venter^1,2,*

We report the design, synthesis, and assembly of the 1.08-Mbp Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a Mycoplasma capricolum recipient cell to create new Mycoplasma mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletionsand polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.

¹ The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
² The J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA 92121, USA.

^* To whom correspondence should be addressed. E-mail: jcventer@jcvi.org

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Received for publication 9 April 2010. Accepted for publication 13 May 2010.

Source:http://www.sciencemag.org/cgi/content/abstract/science.1190719

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