551
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Genetic Engineering Contribution to Forest Tree Breeding Efforts. BIOSAFETY OF FOREST TRANSGENIC TREES 2016. [DOI: 10.1007/978-94-017-7531-1_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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552
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Chen C, E Z, Lin HX. Evolution and Molecular Control of Hybrid Incompatibility in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1208. [PMID: 27563306 PMCID: PMC4980391 DOI: 10.3389/fpls.2016.01208] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/29/2016] [Indexed: 05/09/2023]
Abstract
Postzygotic reproductive isolation (RI) plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, or hybrid breakdown. In this review, we summarized new findings about hybrid incompatibilities in plants, most of which are from studies on Arabidopsis and rice. Recent progress suggests that hybrid incompatibility is a by-product of co-evolution either with "parasitic" selfish elements in the genome or with invasive microbes in the natural environment. We discuss the environmental influences on the expression of hybrid incompatibility and the possible effects of environment-dependent hybrid incompatibility on sympatric speciation. We also discuss the role of domestication on the evolution of hybrid incompatibilities.
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Affiliation(s)
- Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- *Correspondence: Chen Chen,
| | - Zhiguo E
- China National Rice Research InstituteHangzhou, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics and CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
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553
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Zhang J, Zhou X, Yan W, Zhang Z, Lu L, Han Z, Zhao H, Liu H, Song P, Hu Y, Shen G, He Q, Guo S, Gao G, Wang G, Xing Y. Combinations of the Ghd7, Ghd8 and Hd1 genes largely define the ecogeographical adaptation and yield potential of cultivated rice. THE NEW PHYTOLOGIST 2015; 208:1056-66. [PMID: 26147403 DOI: 10.1111/nph.13538] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/27/2015] [Indexed: 05/04/2023]
Abstract
Rice cultivars have been adapted to favorable ecological regions and cropping seasons. Although several heading date genes have separately made contributions to this adaptation, the roles of gene combinations are still unclear. We employed a map-based cloning approach to isolate a heading date gene, which coordinated the interaction between Ghd7 and Ghd8 to greatly delay rice heading. We resequenced these three genes in a germplasm collection to analyze natural variation. Map-based cloning demonstrated that the gene largely affecting the interaction between Ghd7 and Ghd8 was Hd1. Natural variation analysis showed that a combination of loss-of-function alleles of Ghd7, Ghd8 and Hd1 contributes to the expansion of rice cultivars to higher latitudes; by contrast, a combination of pre-existing strong alleles of Ghd7, Ghd8 and functional Hd1 (referred as SSF) is exclusively found where ancestral Asian cultivars originated. Other combinations have comparatively larger favorable ecological scopes and acceptable grain yield. Our results indicate that the combinations of Ghd7, Ghd8 and Hd1 largely define the ecogeographical adaptation and yield potential in rice cultivars. Breeding varieties with the SSF combination are recommended for tropical regions to fully utilize available energy and light resources and thus produce greater yields.
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Affiliation(s)
- Jia Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Lu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongmin Han
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyang Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Pan Song
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yong Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Guojing Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin He
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Sibin Guo
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Naning, 530007, China
| | - Guoqing Gao
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Naning, 530007, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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554
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Hazzouri KM, Flowers JM, Visser HJ, Khierallah HSM, Rosas U, Pham GM, Meyer RS, Johansen CK, Fresquez ZA, Masmoudi K, Haider N, El Kadri N, Idaghdour Y, Malek JA, Thirkhill D, Markhand GS, Krueger RR, Zaid A, Purugganan MD. Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. Nat Commun 2015; 6:8824. [PMID: 26549859 PMCID: PMC4667612 DOI: 10.1038/ncomms9824] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 10/07/2015] [Indexed: 12/13/2022] Open
Abstract
Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.
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Affiliation(s)
- Khaled M Hazzouri
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Jonathan M Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.,Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Hendrik J Visser
- Date Palm Research and Development Unit, United Arab Emirates University, Al-Ain, PO Box 15551, Abu Dhabi, United Arab Emirates
| | - Hussam S M Khierallah
- Date Palm Research Unit, College of Agriculture, PO Box 47054, University of Baghdad, Baghdad, Iraq
| | - Ulises Rosas
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Gina M Pham
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Rachel S Meyer
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.,Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Caryn K Johansen
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Zoë A Fresquez
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Khaled Masmoudi
- International Center for Biosaline Agriculture, Academic City, Al Ruwayyah 2, PO Box 14660, Dubai, United Arab Emirates
| | - Nadia Haider
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, PO Box 6091, Damascus, Syria
| | - Nabila El Kadri
- Technical Center of Dates, Ministry of Agriculture, Kebili, Tunisia
| | - Youssef Idaghdour
- Division of Science and Mathematics, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Joel A Malek
- Genomics Core Laboratory, Weill Cornell Medical College in Qatar, Doha 24144, Qatar
| | - Deborah Thirkhill
- Arizona State University Date Palm Collection, Arizona State University Tempe, Arizona, Arizona 85281, USA
| | - Ghulam S Markhand
- Date Palm Research Institute (DPRI), Shah Abdul Latif University, Khairpur, Sindh, Pakistan
| | - Robert R Krueger
- United States Department of Agriculture, Riverside, California 92507, USA
| | - Abdelouahhab Zaid
- Date Palm Research and Development Unit, United Arab Emirates University, Al-Ain, PO Box 15551, Abu Dhabi, United Arab Emirates
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.,Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
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555
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Liu S, Sehgal SK, Lin M, Li J, Trick HN, Gill BS, Bai G. Independent mis-splicing mutations in TaPHS1 causing loss of preharvest sprouting (PHS) resistance during wheat domestication. THE NEW PHYTOLOGIST 2015; 208:928-35. [PMID: 26255630 DOI: 10.1111/nph.13489] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/30/2015] [Indexed: 05/19/2023]
Abstract
Preharvest sprouting (PHS) is one of the major constraints of wheat production in areas where prolonged rainfall occurs during harvest. TaPHS1 is a gene that regulates PHS resistance on chromosome 3A of wheat, and two causal mutations in the positions +646 and +666 of the TaPHS1 coding region result in wheat PHS susceptibility. Three competitive allele-specific PCR (KASP) markers were developed based on the two mutations in the coding region and one in the promoter region and validated in 82 wheat cultivars with known genotypes. These markers can be used to transfer TaPHS1 in breeding through marker-assisted selection. Screening of 327 accessions of wheat A genome progenitors using the three KASP markers identified different haplotypes in both diploid and tetraploid wheats. Only one Triticum monococcum accession, however, carries both causal mutations in the TaPHS1 coding region and shows PHS susceptibility. Five of 249 common wheat landraces collected from the Fertile Crescent and surrounding areas carried the mutation (C) in the promoter (-222), and one landrace carries both the causal mutations in the TaPHS1 coding region, indicating that the mis-splicing (+646) mutation occurred during common wheat domestication. PHS assay of wheat progenitor accessions demonstrated that the wild-types were highly PHS-resistant, whereas the domesticated type showed increased PHS susceptibility. The mis-splicing TaPHS1 mutation for PHS susceptibility was involved in wheat domestication and might arise independently between T. monococcum and Triticum aestivum.
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Affiliation(s)
- Shubing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Sunish K Sehgal
- Department of Plant Science, South Dakota State University, Brookings, SD, 57006, USA
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Meng Lin
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Jiarui Li
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
- Hard Winter Wheat Genetic Research Unit, USDA-ARS, Manhattan, KS, 66506, USA
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556
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Baer B, Millar AH. Proteomics in evolutionary ecology. J Proteomics 2015; 135:4-11. [PMID: 26453985 DOI: 10.1016/j.jprot.2015.09.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 01/09/2023]
Abstract
Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein modifications and protein interactions of interest with high accuracy and assess protein diversity and function. Therefore, proteomic technologies can be viewed as providing evolutionary biologist with exciting novel opportunities to understand very early events in functional variation of cellular molecular machinery that are acting as part of evolutionary processes.
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Affiliation(s)
- B Baer
- Centre for Integrative Bee Research (CIBER) and ARC Centre of Excellence in Plant Energy Biology, Bayliss Building, The University of Western Australia, 6009 Crawley, Australia.
| | - A H Millar
- Centre for Integrative Bee Research (CIBER) and ARC Centre of Excellence in Plant Energy Biology, Bayliss Building, The University of Western Australia, 6009 Crawley, Australia
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557
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Milla R, Morente-López J, Alonso-Rodrigo JM, Martín-Robles N, Chapin FS. Shifts and disruptions in resource-use trait syndromes during the evolution of herbaceous crops. Proc Biol Sci 2015; 281:rspb.2014.1429. [PMID: 25185998 DOI: 10.1098/rspb.2014.1429] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Trait-based ecology predicts that evolution in high-resource agricultural environments should select for suites of traits that enable fast resource acquisition and rapid canopy closure. However, crop breeding targets specific agronomic attributes rather than broad trait syndromes. Breeding for specific traits, together with evolution in high-resource environments, might lead to reduced phenotypic integration, according to predictions from the ecological literature. We provide the first comprehensive test of these hypotheses, based on a trait-screening programme of 30 herbaceous crops and their wild progenitors. During crop evolution plants became larger, which enabled them to compete more effectively for light, but they had poorly integrated phenotypes. In a subset of six herbaceous crop species investigated in greater depth, competitiveness for light increased during early plant domestication, whereas diminished phenotypic integration occurred later during crop improvement. Mass-specific leaf and root traits relevant to resource-use strategies (e.g. specific leaf area or tissue density of fine roots) changed during crop evolution, but in diverse and contrasting directions and magnitudes, depending on the crop species. Reductions in phenotypic integration and overinvestment in traits involved in competition for light may affect the chances of upgrading modern herbaceous crops to face current climatic and food security challenges.
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Affiliation(s)
- Rubén Milla
- Departamento de Biología y Geología, Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/Tulipán s/n, Móstoles 28933, Spain
| | - Javier Morente-López
- Departamento de Biología y Geología, Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/Tulipán s/n, Móstoles 28933, Spain
| | - J Miguel Alonso-Rodrigo
- Departamento de Biología y Geología, Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/Tulipán s/n, Móstoles 28933, Spain
| | - Nieves Martín-Robles
- Departamento de Biología y Geología, Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/Tulipán s/n, Móstoles 28933, Spain
| | - F Stuart Chapin
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
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558
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Shi T, Dimitrov I, Zhang Y, Tax FE, Yi J, Gou X, Li J. Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication. PLANT MOLECULAR BIOLOGY 2015; 89:253-261. [PMID: 26362289 DOI: 10.1007/s11103-015-0366-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/21/2015] [Indexed: 06/05/2023]
Abstract
Traits related to grain and reproductive organs in grass crops have been under continuous directional selection during domestication. Barley is one of the oldest domesticated crops in human history. Thus genes associated with the grain and reproductive organs in barley may show evidence of dramatic evolutionary change. To understand how artificial selection contributes to protein evolution of biased genes in different barley organs, we used Digital Gene Expression analysis of six barley organs (grain, pistil, anther, leaf, stem and root) to identify genes with biased expression in specific organs. Pairwise comparisons of orthologs between barley and Brachypodium distachyon, as well as between highland and lowland barley cultivars mutually indicated that grain and pistil biased genes show relatively higher protein evolutionary rates compared with the median of all orthologs and other organ biased genes. Lineage-specific protein evolutionary rates estimation showed similar patterns with elevated protein evolution in barley grain and pistil biased genes, yet protein sequences generally evolve much faster in the lowland barley cultivar. Further functional annotations revealed that some of these grain and pistil biased genes with rapid protein evolution are related to nutrient biosynthesis and cell cycle/division. Our analyses provide insights into how domestication differentially shaped the evolution of genes specific to different organs of a crop species, and implications for future functional studies of domestication genes.
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Affiliation(s)
- Tao Shi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Ivan Dimitrov
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Yinling Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Frans E Tax
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jing Yi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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559
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Abstract
Convincing evidence has accumulated that unintended transgene escape occurs in oilseed rape, maize, cotton and creeping bentgrass. The escaped transgenes are found in variant cultivars, in wild type plants as well as in hybrids of sexually compatible species. The fact that in some cases stacked events are present that have not been planted commercially, implies unintended recombination of transgenic traits. As the consequences of this continuous transgene escape for the ecosystem cannot be reliably predicted, I propose to use more sophisticated approaches of gene technology in future. If possible GM plants should be constructed using either site-directed mutagenesis or cisgenic strategies to avoid the problem of transgene escape. In cases where a transgenic trait is needed, efficient containment should be the standard approach. Various strategies available or in development are discussed. Such a cautious approach in developing novel types of GM crops will enhance the sustainable potential of GM crops and thus increase the public trust in green gene technology.
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Affiliation(s)
- Gerhart U Ryffel
- a Institut für Zellbiologie (Tumorforschung); Universitätsklinikum Essen ; Essen , Germany
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560
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Moczek AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu CH, Cohen CS, Tomaso AWD, Gilbert SF, Hall B, Love AC, Lyons DC, Sanger TJ, Smith J, Specht C, Vallejo-Marin M, Extavour CG. The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evol Dev 2015; 17:198-219. [PMID: 25963198 DOI: 10.1111/ede.12125] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century.
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Affiliation(s)
- Armin P Moczek
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - Karen E Sears
- School of Integrative Biology and Institute for Genomic Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London, E1 4NS, UK
| | - Patricia J Wittkopp
- Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Pamela Diggle
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Ian Dworkin
- Department of Biology, McMaster University, 1280 Main St. West Hamilton, Ontario, L8S 4K1, Canada
| | - Cristina Ledon-Rettig
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, 412 Life Sciences Building, Stony Brook, NY, 11794-5215, USA
| | - Siegfried Roth
- University of Cologne, Institute of Developmental Biology, Biocenter, Zülpicher Straße 47b, D-50674, Cologne, Germany
| | - Ehab Abouheif
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montréal Québec, H3A 1B1, Canada
| | - Federico D Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, no. 101, 05508-090, São Paulo, Brazil
| | - Chi-Hua Chiu
- Department of Biological Sciences, Kent State University, OH, USA
| | - C Sarah Cohen
- Biology Department, Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| | | | - Scott F Gilbert
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA and Biotechnology Institute, University of Helsinki, 00014, Helsinki, Finland
| | - Brian Hall
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, CA, B3H 4R2, USA
| | - Alan C Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, USA
| | - Deirdre C Lyons
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Thomas J Sanger
- Department of Molecular Genetics and Microbiology, University of Florida, P.O. Box 103610, Gainesville, FL, 32610, USA
| | - Joel Smith
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Chelsea Specht
- Plant and Microbial Biology, Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, FK9 4LA, Scotland, UK
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, BioLabs 4103, Cambridge, MA, 02138, USA
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561
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Milla R, Osborne CP, Turcotte MM, Violle C. Plant domestication through an ecological lens. Trends Ecol Evol 2015; 30:463-9. [DOI: 10.1016/j.tree.2015.06.006] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 01/20/2023]
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562
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Sanseverino W, Hénaff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM. Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome. Mol Biol Evol 2015; 32:2760-74. [PMID: 26174143 DOI: 10.1093/molbev/msv152] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution.
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Affiliation(s)
- Walter Sanseverino
- Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Elizabeth Hénaff
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Cristina Vives
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Sara Pinosio
- Dipartimento di szience agrarie e ambientali, Università degli studi di Udine, Udine, Italy
| | - William Burgos-Paz
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Michele Morgante
- Dipartimento di szience agrarie e ambientali, Università degli studi di Udine, Udine, Italy
| | | | - Jordi Garcia-Mas
- Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
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563
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Illa-Berenguer E, Van Houten J, Huang Z, van der Knaap E. Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1329-42. [PMID: 25893466 DOI: 10.1007/s00122-015-2509-x] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 03/20/2015] [Indexed: 05/22/2023]
Abstract
Bulk segregant analysis coupled with whole genome sequencing is a powerful approach and cost-effective method to identify loci controlling fruit traits in tomato. Domestication of fruit and vegetable crops was accompanied by selection for weight of the edible parts. Increases in fruit weight are controlled by multiple quantitative trait loci (QTL). To date, only two fruit weight genes have been cloned and a third has been fine-mapped. Genes that control locule number also impact fruit weight and two of them are known. To efficiently identify additional tomato fruit weight (FW) and locule number (LC) loci, six F2 populations were generated from crosses between closely related tomato accessions for which the alleles of the cloned FW and LC genes were known. We employed the bulk segregant approach coupled to whole genome sequencing (QTL-seq) which led to the identification of three highly significant and newly mapped FW QTL. fw11.2 was located in the distal part of chromosome 11 above the known loci fas and fw11.3; fw1.1 in the pericentromeric region of chromosome 1; and fw3.3 located ~1.6 Mb below the known fruit weight gene, SlKLUH/FW3.2. In addition, we mapped three LC QTL (lcn2.4, lcn5.1, and lcn6.1) although their significance was generally low. To confirm the location of the gene underlying fw11.2, we developed additional markers and conducted progeny tests. These results allowed us to narrow down the fw11.2 QTL to a region of ~750 kb corresponding to 66 candidate genes. Our research approach provided a cost-effective and time-efficient method for the identification of additional genes involved in FW and LC that could be used for both fruit development studies and crop improvement programs.
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Affiliation(s)
- Eudald Illa-Berenguer
- Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, 44691, USA
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564
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Chen T, Chen Q, Luo Y, Huang ZL, Zhang J, Tang HR, Pan DM, Wang XR. Phylogeography of Chinese cherry (Prunus pseudocerasus Lindl.) inferred from chloroplast and nuclear DNA: insights into evolutionary patterns and demographic history. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:787-97. [PMID: 25521479 DOI: 10.1111/plb.12294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 12/10/2014] [Indexed: 05/16/2023]
Abstract
Chinese cherry (Prunus pseudocerasus Lindl.) is a commercially valuable fruit crop in China. In order to obtain new insights into its evolutionary history and provide valuable recommendations for resource conservation, phylogeographic patterns of 26 natural populations (305 total individuals) from six geographic regions were analyzed using chloroplast and nuclear DNA fragments. Low levels of haplotype and nucleotide diversity were found in these populations, especially in landrace populations. It is likely that a combined effect of botanical characteristics impact the effective population size, such as inbreeding mating system, long life span, as well as vegetative reproduction. In addition, strong bottleneck effect caused by domestication, together with founder effect after dispersal and subsequent demographic expansion, might also accelerate the reduction of the genetic variation in landrace populations. Interestingly, populations from Longmen Mountain (LMM) and Daliangshan Mountain (DLSM) exhibited relatively higher levels of genetic diversity, inferring the two historical genetic diversity centers of the species. Moreover, moderate population subdivision was also detected by both chloroplast DNA (GST = 0.215; NST = 0.256) and nuclear DNA (GST = 0.146; NST = 0.342), respectively. We inferred that the episodes of efficient gene flow through seed dispersal, together with features of long generation cycle and inbreeding mating system, were likely the main contributors causing the observed phylogeographic patterns. Finally, factors that led to the present demographic patterns of populations from these regions and taxonomic varieties were also discussed.
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Affiliation(s)
- T Chen
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Q Chen
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Y Luo
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Z-L Huang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - J Zhang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - H-R Tang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - D-M Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - X-R Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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565
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Qi X, Liu Y, Vigueira CC, Young ND, Caicedo AL, Jia Y, Gealy DR, Olsen KM. More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms. Mol Ecol 2015; 24:3329-44. [PMID: 26031196 DOI: 10.1111/mec.13256] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 02/06/2023]
Abstract
Many different crop species were selected for a common suite of 'domestication traits', which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica crop variety and representatives of each of the two independently evolved weed strains found in US rice fields, strawhull (S) and blackhull awned (B). Genotyping-by-sequencing provided dense marker coverage for linkage map construction (average marker interval <0.25 cM), with 6016 and 13 730 SNPs mapped in F5 lines of the S and B populations, respectively. For some weediness traits (awn length, hull pigmentation and pericarp pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed that trait variation was largely attributable to individual loci. However, for more complex quantitative traits (including heading date, panicle length and seed shattering), we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Candidate gene sequencing revealed causal genetic bases for 8 of 27 total mapped QTL. Together these findings suggest that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in this crop to allow agricultural weed evolution through multiple genetic mechanisms.
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Affiliation(s)
- Xinshuai Qi
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Yan Liu
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, 72160, USA
| | - Cynthia C Vigueira
- Department of Biology, Washington University, St. Louis, MO, 63130, USA.,Department of Biology, High Point University, High Point, NC, 27268, USA
| | - Nelson D Young
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Yulin Jia
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, 72160, USA
| | - David R Gealy
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, 72160, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
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566
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Dong Y, Zhang X, Xie M, Arefnezhad B, Wang Z, Wang W, Feng S, Huang G, Guan R, Shen W, Bunch R, McCulloch R, Li Q, Li B, Zhang G, Xu X, Kijas JW, Salekdeh GH, Wang W, Jiang Y. Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. BMC Genomics 2015; 16:431. [PMID: 26044654 PMCID: PMC4455334 DOI: 10.1186/s12864-015-1606-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 05/01/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics. RESULTS We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits. CONCLUSION Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.
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Affiliation(s)
- Yang Dong
- Kunming University of Science and Technology, Kunming, 650093, China.
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Xiaolei Zhang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Min Xie
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Babak Arefnezhad
- Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
| | - Zongji Wang
- BGI-Shenzhen, Shenzhen, 518083, China.
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China.
| | | | | | | | - Rui Guan
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Wenjing Shen
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Rowan Bunch
- CSIRO, Agriculture Flagship, Brisbane, 4065, QLD, Australia.
| | | | - Qiye Li
- BGI-Shenzhen, Shenzhen, 518083, China.
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Bo Li
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - James W Kijas
- CSIRO, Agriculture Flagship, Brisbane, 4065, QLD, Australia.
| | - Ghasem Hosseini Salekdeh
- Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Wen Wang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Yu Jiang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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567
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Gaut BS. Evolution Is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution. Mol Biol Evol 2015; 32:1661-71. [DOI: 10.1093/molbev/msv105] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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568
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Evidence That the Origin of Naked Kernels During Maize Domestication Was Caused by a Single Amino Acid Substitution in tga1. Genetics 2015; 200:965-74. [PMID: 25943393 DOI: 10.1534/genetics.115.175752] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/27/2015] [Indexed: 12/11/2022] Open
Abstract
teosinte glume architecture1 (tga1), a member of the SBP-box gene family of transcriptional regulators, has been identified as the gene conferring naked kernels in maize vs. encased kernels in its wild progenitor, teosinte. However, the identity of the causative polymorphism within tga1 that produces these different phenotypes has remained unknown. Using nucleotide diversity data, we show that there is a single fixed nucleotide difference between maize and teosinte in tga1, and this difference confers a Lys (teosinte allele) to Asn (maize allele) substitution. This substitution transforms TGA1 into a transcriptional repressor. While both alleles of TGA1 can bind a GTAC motif, maize-TGA1 forms more stable dimers than teosinte-TGA1. Since it is the only fixed difference between maize and teosinte, this alteration in protein function likely underlies the differences in maize and teosinte glume architecture. We previously reported a difference in TGA1 protein abundance between maize and teosinte based on relative signal intensity of a Western blot. Here, we show that this signal difference is not due to tga1 but to a second gene, neighbor of tga1 (not1). Not1 encodes a protein that has 92% amino acid similarity to TGA1 and that is recognized by the TGA1 antibody. Genetic mapping and phenotypic data show that tga1, without a contribution from not1, controls the difference in covered vs. naked kernels. No trait differences could be associated with the maize vs. teosinte alleles of not1. Our results document how morphological evolution can be driven by a simple nucleotide change that alters protein function.
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569
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Yadav UP, Ayre BG, Bush DR. Transgenic approaches to altering carbon and nitrogen partitioning in whole plants: assessing the potential to improve crop yields and nutritional quality. FRONTIERS IN PLANT SCIENCE 2015; 6:275. [PMID: 25954297 PMCID: PMC4405696 DOI: 10.3389/fpls.2015.00275] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/06/2015] [Indexed: 05/18/2023]
Abstract
The principal components of plant productivity and nutritional value, from the standpoint of modern agriculture, are the acquisition and partitioning of organic carbon (C) and nitrogen (N) compounds among the various organs of the plant. The flow of essential organic nutrients among the plant organ systems is mediated by its complex vascular system, and is driven by a series of transport steps including export from sites of primary assimilation, transport into and out of the phloem and xylem, and transport into the various import-dependent organs. Manipulating C and N partitioning to enhance yield of harvested organs is evident in the earliest crop domestication events and continues to be a goal for modern plant biology. Research on the biochemistry, molecular and cellular biology, and physiology of C and N partitioning has now matured to an extent that strategic manipulation of these transport systems through biotechnology are being attempted to improve movement from source to sink tissues in general, but also to target partitioning to specific organs. These nascent efforts are demonstrating the potential of applied biomass targeting but are also identifying interactions between essential nutrients that require further basic research. In this review, we summarize the key transport steps involved in C and N partitioning, and discuss various transgenic approaches for directly manipulating key C and N transporters involved. In addition, we propose several experiments that could enhance biomass accumulation in targeted organs while simultaneously testing current partitioning models.
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Affiliation(s)
- Umesh P. Yadav
- Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Brian G. Ayre
- Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Daniel R. Bush
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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570
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Cheeseman JM. The evolution of halophytes, glycophytes and crops, and its implications for food security under saline conditions. THE NEW PHYTOLOGIST 2015; 206:557-70. [PMID: 25495078 DOI: 10.1111/nph.13217] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/12/2014] [Indexed: 05/09/2023]
Abstract
The effective development of salt tolerant crops requires an understanding that the evolution of halophytes, glycophytes and our major grain crops has involved significantly different processes. Halophytes (and other edaphic endemics) generally arose through colonization of habitats in severe disequilibrium by pre-adapted individuals, rather than by gradual adaptation from populations of 'glycophytes'. Glycophytes, by contrast, occur in low sodium ecosystems, where sodium was and is the major limiting nutrient in herbivore diets, suggesting that their evolution reflects the fact that low sodium individuals experienced lower herbivory and had higher fitness. For domestication/evolution of crop plants, the selective pressure was human imposed and involved humans co-opting functions of defense and reproductive security. Unintended consequences of this included loss of tolerance to various stresses and loss of the genetic variability needed to correct that. Understanding, combining and manipulating all three modes of evolution are now critical to the development of salt tolerant crops, particularly those that will offer food security in countries with few economic resources and limited infrastructure. Such efforts will require exploiting the genetic structures of recently evolved halophytes, the genetic variability of model plants, and endemic halophytes and 'minor' crops that already exist.
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Affiliation(s)
- John M Cheeseman
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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571
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Baute GJ, Kane NC, Grassa CJ, Lai Z, Rieseberg LH. Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives. THE NEW PHYTOLOGIST 2015; 206:830-8. [PMID: 25641359 DOI: 10.1111/nph.13255] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/24/2014] [Indexed: 05/22/2023]
Abstract
The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study, we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower (Helianthus annuus), a globally important oilseed. To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes, including wild, landrace, and modern lines of H. annuus, as well as two cross-compatible wild relatives, Helianthus argophyllus and Helianthus petiolaris. Outlier analyses identified 122 and 15 candidate genes associated with domestication and improvement, respectively. As in several previous studies, genes putatively involved in oil biosynthesis were the most extreme outliers. Additionally, several promising associations were observed with previously mapped quantitative trait loci (QTLs), such as branching. Admixture analyses revealed that all the modern cultivar genomes we examined contained one or more introgressions from wild populations, with every chromosome having evidence of introgression in at least one modern line. Cumulatively, introgressions cover c. 10% of the cultivated sunflower genome. Surprisingly, introgressions do not avoid candidate domestication genes, probably because of the reintroduction of branching.
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Affiliation(s)
- Gregory J Baute
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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572
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Shi J, Lai J. Patterns of genomic changes with crop domestication and breeding. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:47-53. [PMID: 25656221 DOI: 10.1016/j.pbi.2015.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/15/2015] [Accepted: 01/15/2015] [Indexed: 05/20/2023]
Abstract
Crop domestication and further breeding improvement have long been important areas of genetics and genomics studies. With the rapid advancing of next-generation sequencing (NGS) technologies, the amount of population genomics data has surged rapidly. Analyses of the mega genomics data have started to uncover a previously unknown pattern of genome-wide changes with crop domestication and breeding. Selection during domestication and breeding drastically reshaped crop genomes, which have ended up with regions of greatly reduced genetic diversity and apparent enrichment of potentially beneficial alleles located in both genic and non-genic regions. Increasing evidences suggest that epigenetic modifications also played an important role during domestication and breeding.
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Affiliation(s)
- Junpeng Shi
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
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573
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Dussert Y, Snirc A, Robert T. Inference of domestication history and differentiation between early- and late-flowering varieties in pearl millet. Mol Ecol 2015; 24:1387-402. [PMID: 25705965 DOI: 10.1111/mec.13119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 02/04/2023]
Abstract
Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early- and late-flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early- and late-flowering domesticated varieties were not differentiated over their whole distribution area, despite a clear difference in their isolation-by-distance pattern. Conversely, our data brought evidence for two well-differentiated genetic pools in wild pearl millet, allowing us to test scenarios with different numbers and origins of domestication using approximate Bayesian computation (ABC). The ABC analysis showed the likely existence of asymmetric migration between wild and domesticated populations. The model choice procedure indicated that a single domestication from the eastern wild populations was the more likely scenario to explain the polymorphism patterns observed in cultivated pearl millet.
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Affiliation(s)
- Y Dussert
- Ecologie, Systématique et Evolution, UMR 8079 CNRS, Université Paris-Sud, 91405, Orsay, France; Sorbonne Universités, UPMC Univ Paris06, IFD, 4 Place Jussieu, 75252, Paris Cedex 05, France
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574
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Abstract
The domestication of African rice, Oryza glaberrima, occurred separately from that of the much more widespread Asian rice species Oryza sativa. Analysis of the whole-genome sequence for O. glaberrima shows the extent to which the same genes were involved in these distinct but parallel evolutionary events.
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Affiliation(s)
- Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA, and in the New York University Abu Dhabi Center for Genomics and Systems Biology, Abu Dhabi, United Arab Emirates
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575
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Bo K, Ma Z, Chen J, Weng Y. Molecular mapping reveals structural rearrangements and quantitative trait loci underlying traits with local adaptation in semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis Qi et Yuan). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:25-39. [PMID: 25358412 DOI: 10.1007/s00122-014-2410-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 10/01/2014] [Indexed: 05/02/2023]
Abstract
Comparative genetic mapping revealed the origin of Xishuangbanna cucumber through diversification selection after domestication. QTL mapping provided insights into the genetic basis of traits under diversification selection during crop evolution. The Xishuangbanna cucumber, Cucumis sativus L. var. xishuangbannanesis Qi et Yuan (XIS), is a semi-wild landrace from the tropical southwest China with some unique traits that are very useful for cucumber breeding, such as tolerance to low light, large fruit size, heavy fruit weight, and orange flesh color in mature fruits. In this study, using 124 recombinant inbred lines (RILs) derived from the cross of the XIS cucumber with a cultivated cucumber inbred line, we developed a linkage map with 269 microsatellite (or simple sequence repeat) markers which covered 705.9 cM in seven linkage groups. Comparative analysis of orders of common marker loci or marker-anchored draft genome scaffolds among the wild (C. sativus var. hardwickii), semi-wild, and cultivated cucumber genetic maps revealed that the XIS cucumber shares major chromosomal rearrangements in chromosomes 4, 5, and 7 between the wild and cultivated cucumbers suggesting that the XIS cucumber originated through diversifying selection after cucumber domestication. Several XIS-specific minor structural changes were identified in chromosomes 1 and 6. QTL mapping with the 124 RILs in four environments identified 13 QTLs for domestication and diversifying selection-related traits including 2 for first female flowering time (fft1.1, fft6.1), 5 for mature fruit length (fl1.1, fl3.1, fl4.1, fl6.1, and fl7.1), 3 for fruit diameter (fd1.1, fd4.1, and fd6.1), and 3 for fruit weight (fw2.1, fw4.1, and fw6.1). Six of the 12 QTLs were consistently detected in all four environments. Among the 13 QTLs, fft1.1, fl1.1, fl3.1, fl7.1, fd4.1, and fw6.1 were major-effect QTLs for respective traits with each explaining at least 10 % of the observed phenotypic variations. Results from this study provide insights into the cytological and genetic basis of crop evolution leading to the XIS cucumber. The molecular markers associated with the QTLs should be useful in exploring the XIS cucumber genetic resources for cucumber breeding.
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Affiliation(s)
- Kailiang Bo
- Horticulture College, Nanjing Agricultural University, Nanjing, 210095, China
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576
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Bargsten JW, Nap JP, Sanchez-Perez GF, van Dijk ADJ. Prioritization of candidate genes in QTL regions based on associations between traits and biological processes. BMC PLANT BIOLOGY 2014; 14:330. [PMID: 25492368 PMCID: PMC4274756 DOI: 10.1186/s12870-014-0330-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/10/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Elucidation of genotype-to-phenotype relationships is a major challenge in biology. In plants, it is the basis for molecular breeding. Quantitative Trait Locus (QTL) mapping enables to link variation at the trait level to variation at the genomic level. However, QTL regions typically contain tens to hundreds of genes. In order to prioritize such candidate genes, we show that we can identify potentially causal genes for a trait based on overrepresentation of biological processes (gene functions) for the candidate genes in the QTL regions of that trait. RESULTS The prioritization method was applied to rice QTL data, using gene functions predicted on the basis of sequence- and expression-information. The average reduction of the number of genes was over ten-fold. Comparison with various types of experimental datasets (including QTL fine-mapping and Genome Wide Association Study results) indicated both statistical significance and biological relevance of the obtained connections between genes and traits. A detailed analysis of flowering time QTLs illustrates that genes with completely unknown function are likely to play a role in this important trait. CONCLUSIONS Our approach can guide further experimentation and validation of causal genes for quantitative traits. This way it capitalizes on QTL data to uncover how individual genes influence trait variation.
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Affiliation(s)
- Joachim W Bargsten
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
- />Laboratory for Plant Breeding, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Jan-Peter Nap
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
| | - Gabino F Sanchez-Perez
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Laboratory of Bioinformatics, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Aalt DJ van Dijk
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
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577
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Dolferus R. To grow or not to grow: a stressful decision for plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:247-261. [PMID: 25443851 DOI: 10.1016/j.plantsci.2014.10.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 05/18/2023]
Abstract
Progress in improving abiotic stress tolerance of crop plants using classic breeding and selection approaches has been slow. This has generally been blamed on the lack of reliable traits and phenotyping methods for stress tolerance. In crops, abiotic stress tolerance is most often measured in terms of yield-capacity under adverse weather conditions. "Yield" is a complex trait and is determined by growth and developmental processes which are controlled by environmental signals throughout the life cycle of the plant. The use of model systems has allowed us to gradually unravel how plants grow and develop, but our understanding of the flexibility and opportunistic nature of plant development and its capacity to adapt growth to environmental cues is still evolving. There is genetic variability for the capacity to maintain yield and productivity under abiotic stress conditions in crop plants such as cereals. Technological progress in various domains has made it increasingly possible to mine that genetic variability and develop a better understanding about the basic mechanism of plant growth and abiotic stress tolerance. The aim of this paper is not to give a detailed account of all current research progress, but instead to highlight some of the current research trends that may ultimately lead to strategies for stress-proofing crop species. The focus will be on abiotic stresses that are most often associated with climate change (drought, heat and cold) and those crops that are most important for human nutrition, the cereals.
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Affiliation(s)
- Rudy Dolferus
- CSIRO, Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia.
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578
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Yuan L, Grotewold E. Metabolic engineering to enhance the value of plants as green factories. Metab Eng 2014; 27:83-91. [PMID: 25461830 DOI: 10.1016/j.ymben.2014.11.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 11/08/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022]
Abstract
The promise of plants to serve as the green factories of the future is ever increasing. Plants have been used traditionally for construction, energy, food and feed. Bioactive compounds primarily derived from specialized plant metabolism continue to serve as important scaffold molecules for pharmaceutical drug production. Yet, the past few years have witnessed a growing interest on plants as the ultimate harvesters of carbon and energy from the sun, providing carbohydrate and lipid biofuels that would contribute to balancing atmospheric carbon. How can the metabolic output from plants be increased even further, and what are the bottlenecks? Here, we present what we perceive to be the main opportunities and challenges associated with increasing the efficiency of plants as chemical factories. We offer some perspectives on when it makes sense to use plants as production systems because the amount of biomass needed makes any other system unfeasible. However, there are other instances in which plants serve as great sources of biological catalysts, yet are not necessarily the best-suited systems for production. We also present emerging opportunities for manipulating plant genomes to make plant synthetic biology a reality.
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Affiliation(s)
- Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, United States
| | - Erich Grotewold
- Center for Applied Plant Sciences (CAPS), Department of Molecular Genetics and Department of Horticulture and Crop Science, The Ohio State University, 012 Rightmire Hall, 1060 Carmack Rd, Columbus, OH 43210, United States.
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579
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Park SJ, Jiang K, Tal L, Yichie Y, Gar O, Zamir D, Eshed Y, Lippman ZB. Optimization of crop productivity in tomato using induced mutations in the florigen pathway. Nat Genet 2014; 46:1337-42. [PMID: 25362485 DOI: 10.1038/ng.3131] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 10/07/2014] [Indexed: 12/16/2022]
Abstract
Naturally occurring genetic variation in the universal florigen flowering pathway has produced major advancements in crop domestication. However, variants that can maximize crop yields may not exist in natural populations. Here we show that tomato productivity can be fine-tuned and optimized by exploiting combinations of selected mutations in multiple florigen pathway components. By screening for chemically induced mutations that suppress the bushy, determinate growth habit of field tomatoes, we isolated a new weak allele of the florigen gene SINGLE FLOWER TRUSS (SFT) and two mutations affecting a bZIP transcription factor component of the 'florigen activation complex' (ref. 11). By combining heterozygous mutations, we pinpointed an optimal balance of flowering signals, resulting in a new partially determinate architecture that translated to maximum yields. We propose that harnessing mutations in the florigen pathway to customize plant architecture and flower production offers a broad toolkit to boost crop productivity.
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Affiliation(s)
- Soon Ju Park
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Ke Jiang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Lior Tal
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Yichie
- Institute of Plant Sciences, Hebrew University of Jerusalem Faculty of Agriculture, Rehovot, Israel
| | - Oron Gar
- Institute of Plant Sciences, Hebrew University of Jerusalem Faculty of Agriculture, Rehovot, Israel
| | - Dani Zamir
- Institute of Plant Sciences, Hebrew University of Jerusalem Faculty of Agriculture, Rehovot, Israel
| | - Yuval Eshed
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
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580
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Turcotte MM, Turley NE, Johnson MTJ. The impact of domestication on resistance to two generalist herbivores across 29 independent domestication events. THE NEW PHYTOLOGIST 2014; 204:671-681. [PMID: 25039644 DOI: 10.1111/nph.12935] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/09/2014] [Indexed: 05/09/2023]
Abstract
The domestication of crops is among the most important innovations in human history. Here, we test the hypothesis that cultivation and artificial selection for increased productivity of crops reduced plant defenses against herbivores. We compared the performance of two economically important generalist herbivores - the leaf-chewing beet armyworm (Spodoptera exigua) and the phloem-feeding green peach aphid (Myzus persicae) - across 29 crop species and their closely related wild relatives. We also measured putative morphological and chemical defensive traits and correlated them with herbivore performance. We show that, on average, domestication significantly reduced resistance to S. exigua, but not M. persicae, and that most independent domestication events did not cause differences in resistance to either herbivore. In addition, we found that multiple plant traits predicted resistance to S. exigua and M. persicae, and that domestication frequently altered the strength and direction of correlations between these traits and herbivore performance. Our results show that domestication can alter plant defenses, but does not cause strong allocation tradeoffs as predicted by plant defense theory. These results have important implications for understanding the evolutionary ecology of species interactions and for the search for potential resistance traits to be targeted in crop breeding.
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Affiliation(s)
- Martin M Turcotte
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Nash E Turley
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Marc T J Johnson
- Department of Biology, University of Toronto-Mississauga, Mississauga, ON, L5L 1C6, Canada
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581
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Chen L, Tang L, Xiang H, Jin L, Li Q, Dong Y, Wang W, Zhang G. Advances in genome editing technology and its promising application in evolutionary and ecological studies. Gigascience 2014; 3:24. [PMID: 25414792 PMCID: PMC4238018 DOI: 10.1186/2047-217x-3-24] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 10/04/2014] [Indexed: 12/26/2022] Open
Abstract
Genetic modification has long provided an approach for “reverse genetics”, analyzing gene function and linking DNA sequence to phenotype. However, traditional genome editing technologies have not kept pace with the soaring progress of the genome sequencing era, as a result of their inefficiency, time-consuming and labor-intensive methods. Recently, invented genome modification technologies, such as ZFN (Zinc Finger Nuclease), TALEN (Transcription Activator-Like Effector Nuclease), and CRISPR/Cas9 nuclease (Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 nuclease) can initiate genome editing easily, precisely and with no limitations by organism. These new tools have also offered intriguing possibilities for conducting functional large-scale experiments. In this review, we begin with a brief introduction of ZFN, TALEN, and CRISPR/Cas9 technologies, then generate an extensive prediction of effective TALEN and CRISPR/Cas9 target sites in the genomes of a broad range of taxonomic species. Based on the evidence, we highlight the potential and practicalities of TALEN and CRISPR/Cas9 editing in non-model organisms, and also compare the technologies and test interesting issues such as the functions of candidate domesticated, as well as candidate genes in life-environment interactions. When accompanied with a high-throughput sequencing platform, we forecast their potential revolutionary impacts on evolutionary and ecological research, which may offer an exciting prospect for connecting the gap between DNA sequence and phenotype in the near future.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
| | - Linyi Tang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hui Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
| | - Lijun Jin
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiye Li
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Yang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650223, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223, China ; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
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582
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DeHaan LR, Van Tassel DL. Useful insights from evolutionary biology for developing perennial grain crops. AMERICAN JOURNAL OF BOTANY 2014; 101:1801-1819. [PMID: 25326622 DOI: 10.3732/ajb.1400084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Annual grain crops dominate agricultural landscapes and provide the majority of calories consumed by humanity. Perennial grain crops could potentially ameliorate the land degradation and off-site impacts associated with annual grain cropping. However, herbaceous perennial plants with constitutively high allocation to harvestable seeds are rare to absent in nature. Recent trade-off theory models suggest that rugged fitness landscapes may explain the absence of this form better than sink competition models. Artificial selection for both grain production and multiyear lifespan can lead to more rapid progress in the face of fitness and genetic trade-offs than natural selection but is likely to result in plant types that differ substantially from all current domestic crops. Perennial grain domestication is also likely to require the development of selection strategies that differ from published crop breeding methods, despite their success in improving long-domesticated crops; for this purpose, we have reviewed literature in the areas of population and evolutionary genetics, domestication, and molecular biology. Rapid domestication will likely require genes with large effect that are expected to exhibit strong pleiotropy and epistasis. Cryptic genetic variation will need to be deliberately exposed both to purge mildly deleterious alleles and to generate novel agronomic phenotypes. We predict that perennial grain domestication programs will benefit from population subdivision followed by selection for simple traits in each subpopulation, the evaluation of very large populations, high selection intensity, rapid cycling through generations, and heterosis. The latter may be particularly beneficial in the development of varieties with stable yield and tolerance to crowding.
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Affiliation(s)
- Lee R DeHaan
- The Land Institute, 2440 E. Water Well Rd., Salina, Kansas 67401 USA
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583
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Higgins RH, Thurber CS, Assaranurak I, Brown PJ. Multiparental mapping of plant height and flowering time QTL in partially isogenic sorghum families. G3 (BETHESDA, MD.) 2014; 4:1593-602. [PMID: 25237111 PMCID: PMC4169151 DOI: 10.1534/g3.114.013318] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 06/11/2014] [Indexed: 12/31/2022]
Abstract
Sorghum varieties suitable for grain production at temperate latitudes show dwarfism and photoperiod insensitivity, both of which are controlled by a small number of loci with large effects. We studied the genetic control of plant height and flowering time in five sorghum families (A-E), each derived from a cross between a tropical line and a partially isogenic line carrying introgressions derived from a common, temperate-adapted donor. A total of 724 F2:3 lines were phenotyped in temperate and tropical environments for plant height and flowering time and scored at 9139 SNPs using genotyping-by-sequencing. Biparental mapping was compared with multiparental mapping in different subsets of families (AB, ABC, ABCD, and ABCDE) using both a GWAS approach, which fit each QTL as a single effect across all families, and using a joint linkage approach, which fit QTL effects as nested within families. GWAS using all families (ABCDE) performed best at the cloned Dw3 locus, whereas joint linkage using all families performed best at the cloned Ma1 locus. Both multiparental approaches yielded apparently synthetic associations due to genetic heterogeneity and were highly dependent on the subset of families used. Comparison of all mapping approaches suggests that a GA2-oxidase underlies Dw1, and that a mir172a gene underlies a Dw1-linked flowering time QTL.
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Affiliation(s)
- R H Higgins
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801 Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
| | - C S Thurber
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
| | - I Assaranurak
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - P J Brown
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801 Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
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584
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Abstract
Grain size is one of the most important factors determining rice yield. As a quantitative trait, grain size is predominantly and tightly controlled by genetic factors. Several quantitative trait loci (QTLs) for grain size have been molecularly identified and characterized. These QTLs may act in independent genetic pathways and, along with other identified genes for grain size, are mainly involved in the signaling pathways mediated by proteasomal degradation, phytohormones, and G proteins to regulate cell proliferation and cell elongation. Many of these QTLs and genes have been strongly selected for enhanced rice productivity during domestication and breeding. These findings have paved new ways for understanding the molecular basis of grain size and have substantial implications for genetic improvement of crops.
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Affiliation(s)
- Jianru Zuo
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
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585
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Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JSS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KFX, Rounsley S, Wing RA. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet 2014; 46:982-8. [PMID: 25064006 PMCID: PMC7036042 DOI: 10.1038/ng.3044] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
Abstract
Mingsheng Chen, Klaus Mayer, Steve Rounsley, Rod Wing and colleagues report the genome sequence of African rice (Oryza glaberrima), a different species than Asian rice. The authors resequenced 20 O. glaberrima accessions and 94 Oryza barthii accessions (the putative progenitor species of O. glaberrima), and their analyses support the hypothesis that O. glaberrima was domesticated in a single region along the upper Niger river. The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.
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Affiliation(s)
- Muhua Wang
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2]
| | - Yeisoo Yu
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2]
| | - Georg Haberer
- 1] Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany. [2]
| | | | - Chuanzhu Fan
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Jose Luis Goicoechea
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Xiang Song
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jetty S S Ammiraju
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] DuPont Pioneer, Johnston, Iowa, USA
| | - Rosa Maria Cossu
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Carlos Maldonado
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jinfeng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Nick Sisneros
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Kristi de Baynast
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Wolfgang Golser
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Marina Wissotski
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Woojin Kim
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Paul Sanchez
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] US Arid Land Agricultural Research Center, Maricopa, Arizona, USA
| | | | | | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Judith Carney
- Department of Geography, Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/Institut de Recherche pour le Développement/l'Université de Perpignan Via Domitia, Université de Perpignan, Perpignan, France
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
| | | | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
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586
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Kellner R, Hanschke C, Begerow D. Patterns of variation at Ustilago maydis virulence clusters 2A and 19A largely reflect the demographic history of its populations. PLoS One 2014; 9:e98837. [PMID: 24887029 PMCID: PMC4041787 DOI: 10.1371/journal.pone.0098837] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/07/2014] [Indexed: 12/18/2022] Open
Abstract
The maintenance of an intimate interaction between plant-biotrophic fungi and their hosts over evolutionary times involves strong selection and adaptative evolution of virulence-related genes. The highly specialised maize pathogen Ustilago maydis is assigned with a high evolutionary capability to overcome host resistances due to its high rates of sexual recombination, large population sizes and long distance dispersal. Unlike most studied fungus-plant interactions, the U. maydis – Zea mays pathosystem lacks a typical gene-for-gene interaction. It exerts a large set of secreted fungal virulence factors that are mostly organised in gene clusters. Their contribution to virulence has been experimentally demonstrated but their genetic diversity within U. maydis remains poorly understood. Here, we report on the intraspecific diversity of 34 potential virulence factor genes of U. maydis. We analysed their sequence polymorphisms in 17 isolates of U. maydis from Europe, North and Latin America. We focused on gene cluster 2A, associated with virulence attenuation, cluster 19A that is crucial for virulence, and the cluster-independent effector gene pep1. Although higher compared to four house-keeping genes, the overall levels of intraspecific genetic variation of virulence clusters 2A and 19A, and pep1 are remarkably low and commensurate to the levels of 14 studied non-virulence genes. In addition, each gene is present in all studied isolates and synteny in cluster 2A is conserved. Furthermore, 7 out of 34 virulence genes contain either no polymorphisms or only synonymous substitutions among all isolates. However, genetic variation of clusters 2A and 19A each resolve the large scale population structure of U. maydis indicating subpopulations with decreased gene flow. Hence, the genetic diversity of these virulence-related genes largely reflect the demographic history of U. maydis populations.
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Affiliation(s)
- Ronny Kellner
- MPRG Fungal Biodiversity, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Geobotany, Ruhr-Universität Bochum, Bochum, Germany
- * E-mail:
| | | | - Dominik Begerow
- Department of Geobotany, Ruhr-Universität Bochum, Bochum, Germany
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587
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Abbo S, Pinhasi van-Oss R, Gopher A, Saranga Y, Ofner I, Peleg Z. Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes. TRENDS IN PLANT SCIENCE 2014; 19:351-60. [PMID: 24398119 DOI: 10.1016/j.tplants.2013.12.002] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/25/2013] [Accepted: 12/10/2013] [Indexed: 05/19/2023]
Abstract
'Domestication syndrome' (DS) denotes differences between domesticated plants and their wild progenitors. Crop plants are dynamic entities; hence, not all parameters distinguishing wild progenitors from cultigens resulted from domestication. In this opinion article, we refine the DS concept using agronomic, genetic, and archaeobotanical considerations by distinguishing crucial domestication traits from traits that probably evolved post-domestication in Near Eastern grain crops. We propose that only traits showing a clear domesticated-wild dimorphism represent the pristine domestication episode, whereas traits showing a phenotypic continuum between wild and domesticated gene pools mostly reflect post-domestication diversification. We propose that our approach may apply to other crop types and examine its implications for discussing the timeframe of plant domestication and for modern plant science and breeding.
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Affiliation(s)
- Shahal Abbo
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
| | - Ruth Pinhasi van-Oss
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Avi Gopher
- Sonia and Marco Nadler Institute of Archaeology, Tel-Aviv University, Ramat Aviv 6997801, Israel
| | - Yehoshua Saranga
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Itai Ofner
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Zvi Peleg
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
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588
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Gepts P. The contribution of genetic and genomic approaches to plant domestication studies. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:51-9. [PMID: 24631844 DOI: 10.1016/j.pbi.2014.02.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/04/2014] [Accepted: 02/09/2014] [Indexed: 05/25/2023]
Abstract
The application of genomic approaches to the phenomenon of plant domestication promises a better understanding of the origins of agriculture, but also of the way plant genomes in general are organized and expressed. Building on earlier genetic research, more detailed information has become available on the organization of genetic diversity at the genome level and the effects of gene flow on diversity in different regions of the genome. In addition, putative domestication genes have been identified through population genomics approaches (selective sweeps or divergence scanning). Further information has been obtained on the origin of domestication syndrome mutations and the dispersal and adaptation of crops after domestication. For the future, increasingly multidisciplinary approaches using combinations of genomics and other approaches will prevail.
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Affiliation(s)
- Paul Gepts
- University of California, Department of Plant Sciences/MS 1, Section of Crop and Ecosystem Sciences, 1 Shields Avenue, Davis, CA 95616, United States of America.
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589
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Vendramin E, Pea G, Dondini L, Pacheco I, Dettori MT, Gazza L, Scalabrin S, Strozzi F, Tartarini S, Bassi D, Verde I, Rossini L. A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach. PLoS One 2014; 9:e90574. [PMID: 24595269 PMCID: PMC3940905 DOI: 10.1371/journal.pone.0090574] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/01/2014] [Indexed: 12/30/2022] Open
Abstract
Nectarines play a key role in peach industry; the fuzzless skin has implications for consumer acceptance. The peach/nectarine (G/g) trait was described as monogenic and previously mapped on chromosome 5. Here, the position of the G locus was delimited within a 1.1 cM interval (635 kb) based on linkage analysis of an F2 progeny from the cross ‘Contender’ (C, peach) x ‘Ambra’ (A, nectarine). Careful inspection of the genes annotated in the corresponding genomic sequence (Peach v1.0), coupled with variant discovery, led to the identification of MYB gene PpeMYB25 as a candidate for trichome formation on fruit skin. Analysis of genomic re-sequencing data from five peach/nectarine accessions pointed to the insertion of a LTR retroelement in exon 3 of the PpeMYB25 gene as the cause of the recessive glabrous phenotype. A functional marker (indelG) developed on the LTR insertion cosegregated with the trait in the CxA F2 progeny and was validated on a broad panel of genotypes, including all known putative donors of the nectarine trait. This marker was shown to efficiently discriminate between peach and nectarine plants, indicating that a unique mutational event gave rise to the nectarine trait and providing a useful diagnostic tool for early seedling selection in peach breeding programs.
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Affiliation(s)
- Elisa Vendramin
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura – Centro di Ricerca per la Frutticoltura (CRA-FRU), Rome, Italy
| | - Giorgio Pea
- Parco Tecnologico Padano, Via Einstein, Loc. C.na Codazza, Lodi, Italy
| | | | - Igor Pacheco
- Università degli Studi di Milano, DiSAA, Milan, Italy
| | - Maria Teresa Dettori
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura – Centro di Ricerca per la Frutticoltura (CRA-FRU), Rome, Italy
| | - Laura Gazza
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura – Centro di Ricerca per la Frutticoltura (CRA-FRU), Rome, Italy
| | | | - Francesco Strozzi
- Parco Tecnologico Padano, Via Einstein, Loc. C.na Codazza, Lodi, Italy
| | | | - Daniele Bassi
- Università degli Studi di Milano, DiSAA, Milan, Italy
| | - Ignazio Verde
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura – Centro di Ricerca per la Frutticoltura (CRA-FRU), Rome, Italy
- * E-mail: (IV); (LR)
| | - Laura Rossini
- Parco Tecnologico Padano, Via Einstein, Loc. C.na Codazza, Lodi, Italy
- Università degli Studi di Milano, DiSAA, Milan, Italy
- * E-mail: (IV); (LR)
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590
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Moray C, Lanfear R, Bromham L. Domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated mammals and birds and their wild relatives. Genome Biol Evol 2014; 6:161-9. [PMID: 24459286 PMCID: PMC3914681 DOI: 10.1093/gbe/evu005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2013] [Indexed: 11/14/2022] Open
Abstract
Studies of domesticated animals have led to the suggestion that domestication could have significant effects on patterns of molecular evolution. In particular, analyses of mitochondrial genome sequences from domestic dogs and yaks have yielded higher ratios of non-synonymous to synonymous substitutions in the domesticated lineages than in their wild relatives. These results are important because they imply that changes to selection or population size operating over a short timescale can cause significant changes to the patterns of mitochondrial molecular evolution. In this study, our aim is to test whether the impact on mitochondrial genome evolution is a general feature of domestication or whether it is specific to particular examples. We test whether domesticated mammals and birds have consistently different patterns of molecular evolution than their wild relatives for 16 phylogenetically independent comparisons of mitochondrial genome sequences. We find no consistent difference in branch lengths or dN/dS between domesticated and wild lineages. We also find no evidence that our failure to detect a consistent pattern is due to the short timescales involved or low genetic distance between domesticated lineages and their wild relatives. However, removing comparisons where the wild relative may also have undergone a bottleneck does reveal a pattern consistent with reduced effective population size in domesticated lineages. Our results suggest that, although some domesticated lineages may have undergone changes to selective regime or effective population size that could have affected mitochondrial evolution, it is not possible to generalize these patterns over all domesticated mammals and birds.
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Affiliation(s)
- Camile Moray
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Robert Lanfear
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- National Evolutionary Synthesis Center, Durham, NC
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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591
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van der Knaap E, Chakrabarti M, Chu YH, Clevenger JP, Illa-Berenguer E, Huang Z, Keyhaninejad N, Mu Q, Sun L, Wang Y, Wu S. What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape. FRONTIERS IN PLANT SCIENCE 2014; 5:227. [PMID: 24904622 PMCID: PMC4034497 DOI: 10.3389/fpls.2014.00227] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/06/2014] [Indexed: 05/19/2023]
Abstract
Domestication of fruit and vegetables resulted in a huge diversity of shapes and sizes of the produce. Selections that took place over thousands of years of alleles that increased fruit weight and altered shape for specific culinary uses provide a wealth of resources to study the molecular bases of this diversity. Tomato (Solanum lycopersicum) evolved from a wild ancestor (S. pimpinellifolium) bearing small and round edible fruit. Molecular genetic studies led to the identification of two genes selected for fruit weight: FW2.2 encoding a member of the Cell Number Regulator family; and FW3.2 encoding a P450 enzyme and the ortholog of KLUH. Four genes were identified that were selected for fruit shape: SUN encoding a member of the IQD family of calmodulin-binding proteins leading to fruit elongation; OVATE encoding a member of the OVATE family proteins involved in transcriptional repression leading to fruit elongation; LC encoding most likely the ortholog of WUSCHEL controlling meristem size and locule number; FAS encoding a member in the YABBY family controlling locule number leading to flat or oxheart shape. For this article, we will provide an overview of the putative function of the known genes, when during floral and fruit development they are hypothesized to act and their potential importance in regulating morphological diversity in other fruit and vegetable crops.
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Affiliation(s)
- Esther van der Knaap
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
- *Correspondence: Esther van der Knaap, Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA e-mail:
| | - Manohar Chakrabarti
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Yi Hsuan Chu
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Josh P. Clevenger
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Eudald Illa-Berenguer
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Zejun Huang
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Neda Keyhaninejad
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Qi Mu
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Liang Sun
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Yanping Wang
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
- Department of Pomology, College of Agriculture and Biotechnology, China Agricultural UniversityBeijing, China
| | - Shan Wu
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
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592
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Pabón-Mora N, Wong GKS, Ambrose BA. Evolution of fruit development genes in flowering plants. FRONTIERS IN PLANT SCIENCE 2014; 5:300. [PMID: 25018763 PMCID: PMC4071287 DOI: 10.3389/fpls.2014.00300] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/07/2014] [Indexed: 05/18/2023]
Abstract
The genetic mechanisms regulating dry fruit development and opercular dehiscence have been identified in Arabidopsis thaliana. In the bicarpellate silique, valve elongation and differentiation is controlled by FRUITFULL (FUL) that antagonizes SHATTERPROOF1-2 (SHP1/SHP2) and INDEHISCENT (IND) at the dehiscence zone where they control normal lignification. SHP1/2 are also repressed by REPLUMLESS (RPL), responsible for replum formation. Similarly, FUL indirectly controls two other factors ALCATRAZ (ALC) and SPATULA (SPT) that function in the proper formation of the separation layer. FUL and SHP1/2 belong to the MADS-box family, IND and ALC belong to the bHLH family and RPL belongs to the homeodomain family, all of which are large transcription factor families. These families have undergone numerous duplications and losses in plants, likely accompanied by functional changes. Functional analyses of homologous genes suggest that this network is fairly conserved in Brassicaceae and less conserved in other core eudicots. Only the MADS box genes have been functionally characterized in basal eudicots and suggest partial conservation of the functions recorded for Brassicaceae. Here we do a comprehensive search of SHP, IND, ALC, SPT, and RPL homologs across core-eudicots, basal eudicots, monocots and basal angiosperms. Based on gene-tree analyses we hypothesize what parts of the network for fruit development in Brassicaceae, in particular regarding direct and indirect targets of FUL, might be conserved across angiosperms.
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Affiliation(s)
- Natalia Pabón-Mora
- Instituto de Biología, Universidad de AntioquiaMedellín, Colombia
- The New York Botanical GardenBronx, NY, USA
- *Correspondence: Natalia Pabón-Mora, Instituto de Biología, Universidad de Antioquia, Calle 70 No 52-21, AA 1226 Medellín, Colombia e-mail:
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
- Department of Medicine, University of AlbertaEdmonton, AB, Canada
- BGI-Shenzhen, Beishan Industrial ZoneShenzhen, China
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