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Valliyodan B, Cannon SB, Bayer PE, Shu S, Brown AV, Ren L, Jenkins J, Chung CYL, Chan TF, Daum CG, Plott C, Hastie A, Baruch K, Barry KW, Huang W, Patil G, Varshney RK, Hu H, Batley J, Yuan Y, Song Q, Stupar RM, Goodstein DM, Stacey G, Lam HM, Jackson SA, Schmutz J, Grimwood J, Edwards D, Nguyen HT. Construction and comparison of three reference-quality genome assemblies for soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1066-1082. [PMID: 31433882 DOI: 10.1111/tpj.14500] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 05/15/2023]
Abstract
We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.
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Affiliation(s)
- Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, 65101, MO, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, 50011, IA, USA
| | - Philipp E Bayer
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Anne V Brown
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, 50011, IA, USA
| | - Longhui Ren
- Interdepartmental Genetics Program, Iowa State University, Ames, 50011, IA, USA
| | - Jerry Jenkins
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Claire Y-L Chung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Ting-Fung Chan
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Christopher G Daum
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Christopher Plott
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | | | | | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Wei Huang
- Department of Agronomy, Iowa State University, Ames, 50011, IA, USA
| | - Gunvant Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Haifei Hu
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Yuxuan Yuan
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Qijian Song
- Soybean Genomics and Improvement Lab, US Department of Agriculture - Agricultural Research Service, Beltsville, 20705, MD, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, 55108, MN, USA
| | - David M Goodstein
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Gary Stacey
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
| | - Jeremy Schmutz
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Jane Grimwood
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
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Gumber HK, McKenna JF, Tolmie AF, Jalovec AM, Kartick AC, Graumann K, Bass HW. MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation. Nucleus 2019; 10:144-166. [PMID: 31221013 PMCID: PMC6649574 DOI: 10.1080/19491034.2019.1629795] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/13/2019] [Accepted: 05/28/2019] [Indexed: 01/25/2023] Open
Abstract
The linker of nucleoskeleton and cytoskeleton (LINC) complex is an essential multi-protein structure spanning the eukaryotic nuclear envelope. The LINC complex functions to maintain nuclear architecture, positioning, and mobility, along with specialized functions in meiotic prophase and chromosome segregation. Members of the LINC complex were recently identified in maize, an important scientific and agricultural grass species. Here we characterized Maize LINC KASH AtSINE-like2, MLKS2, which encodes a highly conserved SINE-group plant KASH protein with characteristic N-terminal armadillo repeats (ARM). Using a heterologous expression system, we showed that actively expressed GFP-MLKS2 is targeted to the nuclear periphery and colocalizes with F-actin and the endoplasmic reticulum, but not microtubules in the cell cortex. Expression of GFP-MLKS2, but not GFP-MLKS2ΔARM, resulted in nuclear anchoring. Genetic analysis of transposon-insertion mutations, mlks2-1 and mlks2-2, showed that the mutant phenotypes were pleiotropic, affecting root hair nuclear morphology, stomatal complex development, multiple aspects of meiosis, and pollen viability. In male meiosis, the mutants showed defects for bouquet-stage telomere clustering, nuclear repositioning, perinuclear actin accumulation, dispersal of late prophase bivalents, and meiotic chromosome segregation. These findings support a model in which the nucleus is connected to cytoskeletal F-actin through the ARM-domain, predicted alpha solenoid structure of MLKS2. Functional conservation of MLKS2 was demonstrated through genetic rescue of the misshapen nuclear phenotype of an Arabidopsis (triple-WIP) KASH mutant. This study establishes a role for the SINE-type KASH proteins in affecting the dynamic nuclear phenomena required for normal plant growth and fertility. Abbreviations: FRAP: Fluorescence recovery after photobleaching; DPI: Days post infiltration; OD: Optical density; MLKS2: Maize LINC KASH AtSINE-like2; LINC: Linker of nucleoskeleton and cytoskeleton; NE: Nuclear envelope; INM: Inner nuclear membrane; ONM: Outer nuclear membrane.
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Affiliation(s)
- Hardeep K. Gumber
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Joseph F. McKenna
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Andrea F. Tolmie
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Alexis M. Jalovec
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Andre C. Kartick
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Katja Graumann
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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103
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Im J, Kim HS. Genetic features of Haliotis discus hannai by infection of vibrio and virus. Genes Genomics 2019; 42:117-125. [PMID: 31776802 DOI: 10.1007/s13258-019-00892-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/14/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Haliotis discus hannai more commonly referred to as the Pacific Abalone is of significant commercial and economical value in South Korea, with it being the second largest producer in the world. Despite this significance there is a lack of genetic studies with regards to the species. Most existing studies focused mainly on environmental factors. OBJECTIVE To provide a comprehensive review describing the genetic feature of Haliotis discus hannai by infection of vibrio and virus. METHODS This review summarized the immune response in the Haliotis spp. with regards to immunological genes such as Cathepsin B, C-type lectin and Toll-like receptors. Genetic studies with regards to transposable elements and miRNAs are few and far between. A study identified LTR retrotransposon Ty3/gypsy in the species. As to miRNA, a single study identified numerous miRNAs in the Haliotis discus hannai. CONCLUSION This paper sought to provide an overview of genetic perspective with regards to immune response genes, transposable elements and miRNAs.
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Affiliation(s)
- Jennifer Im
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea. .,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea.
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104
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Dai Z, Li T, Li J, Han Z, Pan Y, Tang S, Diao X, Luo M. High-throughput long paired-end sequencing of a Fosmid library by PacBio. PLANT METHODS 2019; 15:142. [PMID: 31788019 PMCID: PMC6878638 DOI: 10.1186/s13007-019-0525-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Large insert paired-end sequencing technologies are important tools for assembling genomes, delineating associated breakpoints and detecting structural rearrangements. To facilitate the comprehensive detection of inter- and intra-chromosomal structural rearrangements or variants (SVs) and complex genome assembly with long repeats and segmental duplications, we developed a new method based on single-molecule real-time synthesis sequencing technology for generating long paired-end sequences of large insert DNA libraries. RESULTS A Fosmid vector, pHZAUFOS3, was developed with the following new features: (1) two 18-bp non-palindromic I-SceI sites flank the cloning site, and another two sites are present in the skeleton of the vector, allowing long DNA inserts (and the long paired-ends in this paper) to be recovered as single fragments and the vector (~ 8 kb) to be fragmented into 2-3 kb fragments by I-SceI digestion and therefore was effectively removed from the long paired-ends (5-10 kb); (2) the chloramphenicol (Cm) resistance gene and replicon (oriV), necessary for colony growth, are located near the two sides of the cloning site, helping to increase the proportion of the paired-end fragments to single-end fragments in the paired-end libraries. Paired-end libraries were constructed by ligating the size-selected, mechanically sheared pooled Fosmid DNA fragments to the Ampicillin (Amp) resistance gene fragment and screening the colonies with Cm and Amp. We tested this method on yeast and Setaria italica Yugu1. Fosmid-size paired-ends with an average length longer than 2 kb for each end were generated. The N50 scaffold lengths of the de novo assemblies of the yeast and S. italica Yugu1 genomes were significantly improved. Five large and five small structural rearrangements or assembly errors spanning tens of bp to tens of kb were identified in S. italica Yugu1 including deletions, inversions, duplications and translocations. CONCLUSIONS We developed a new method for long paired-end sequencing of large insert libraries, which can efficiently improve the quality of de novo genome assembly and identify large and small structural rearrangements or assembly errors.
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Affiliation(s)
- Zhaozhao Dai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jiadong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhifei Han
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yonglong Pan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10081 China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10081 China
| | - Meizhong Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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105
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Xue W, Anderson SN, Wang X, Yang L, Crisp PA, Li Q, Noshay J, Albert PS, Birchler JA, Bilinski P, Stitzer MC, Ross-Ibarra J, Flint-Garcia S, Chen X, Springer NM, Doebley JF. Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize. Genetics 2019; 213:143-160. [PMID: 31320409 PMCID: PMC6727801 DOI: 10.1534/genetics.119.302378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/03/2019] [Indexed: 11/18/2022] Open
Abstract
In the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1 plants appear similar to typical maize × teosinte F1s. However, upon backcrossing to maize, the BC1 and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set, and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. A de novo assembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 upregulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation, and small RNAs are similar between sickly plants and normal controls, although a few upregulated transcripts and transposable elements are associated with altered small RNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon "hybrid decay" and present ideas on the mechanism that may underlie it.
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Affiliation(s)
- Wei Xue
- College of Agronomy, Shenyang Agricultural University, 110866 Liaoning Province, China
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Xufeng Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, 518060 Guangdong Province, China
| | - Liyan Yang
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- Life Science College, Shanxi Normal University, 041004 Shanxi Province, China
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Qing Li
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jaclyn Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Patrice S Albert
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Paul Bilinski
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Michelle C Stitzer
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Sherry Flint-Garcia
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
- Agricultural Research Service, United States Department of Agriculture, Columbia, Missouri 65211
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, 518060 Guangdong Province, China
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - John F Doebley
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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106
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Noshay JM, Anderson SN, Zhou P, Ji L, Ricci W, Lu Z, Stitzer MC, Crisp PA, Hirsch CN, Zhang X, Schmitz RJ, Springer NM. Monitoring the interplay between transposable element families and DNA methylation in maize. PLoS Genet 2019; 15:e1008291. [PMID: 31498837 PMCID: PMC6752859 DOI: 10.1371/journal.pgen.1008291] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 09/19/2019] [Accepted: 07/05/2019] [Indexed: 12/15/2022] Open
Abstract
DNA methylation and epigenetic silencing play important roles in the regulation of transposable elements (TEs) in many eukaryotic genomes. A majority of the maize genome is derived from TEs that can be classified into different orders and families based on their mechanism of transposition and sequence similarity, respectively. TEs themselves are highly methylated and it can be tempting to view them as a single uniform group. However, the analysis of DNA methylation profiles in flanking regions provides evidence for distinct groups of chromatin properties at different TE families. These differences among TE families are reproducible in different tissues and different inbred lines. TE families with varying levels of DNA methylation in flanking regions also show distinct patterns of chromatin accessibility and modifications within the TEs. The differences in the patterns of DNA methylation flanking TE families arise from a combination of non-random insertion preferences of TE families, changes in DNA methylation triggered by the insertion of the TE and subsequent selection pressure. A set of nearly 70,000 TE polymorphisms among four assembled maize genomes were used to monitor the level of DNA methylation at haplotypes with and without the TE insertions. In many cases, TE families with high levels of DNA methylation in flanking sequence are enriched for insertions into highly methylated regions. The majority of the >2,500 TE insertions into unmethylated regions result in changes in DNA methylation in haplotypes with the TE, suggesting the widespread potential for TE insertions to condition altered methylation in conserved regions of the genome. This study highlights the interplay between TEs and the methylome of a major crop species.
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Affiliation(s)
- Jaclyn M. Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul MN, United States of America
| | - Sarah N. Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul MN, United States of America
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul MN, United States of America
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens GA, United States of America
| | - William Ricci
- Department of Plant Biology, University of Georgia, Athens GA, United States of America
| | - Zefu Lu
- Department of Genetics, University of Georgia, Athens GA, United States of America
| | - Michelle C. Stitzer
- Department of Plant Sciences, University of California Davis, Davis CA, United States of America
| | - Peter A. Crisp
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul MN, United States of America
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul MN, United States of America
| | - Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens GA, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens GA, United States of America
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul MN, United States of America
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107
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Roessler K, Muyle A, Diez CM, Gaut GRJ, Bousios A, Stitzer MC, Seymour DK, Doebley JF, Liu Q, Gaut BS. The genome-wide dynamics of purging during selfing in maize. NATURE PLANTS 2019; 5:980-990. [PMID: 31477888 DOI: 10.1038/s41477-019-0508-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 07/26/2019] [Indexed: 05/07/2023]
Abstract
Self-fertilization (also known as selfing) is an important reproductive strategy in plants and a widely applied tool for plant genetics and plant breeding. Selfing can lead to inbreeding depression by uncovering recessive deleterious variants, unless these variants are purged by selection. Here we investigated the dynamics of purging in a set of eleven maize lines that were selfed for six generations. We show that heterozygous, putatively deleterious single nucleotide polymorphisms are preferentially lost from the genome during selfing. Deleterious single nucleotide polymorphisms were lost more rapidly in regions of high recombination, presumably because recombination increases the efficacy of selection by uncoupling linked variants. Overall, heterozygosity decreased more slowly than expected, by an estimated 35% to 40% per generation instead of the expected 50%, perhaps reflecting pervasive associative overdominance. Finally, three lines exhibited marked decreases in genome size due to the purging of transposable elements. Genome loss was more likely to occur for lineages that began with larger genomes with more transposable elements and chromosomal knobs. These three lines purged an average of 398 Mb from their genomes, an amount equivalent to three Arabidopsis thaliana genomes per lineage, in only a few generations.
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Affiliation(s)
- Kyria Roessler
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Aline Muyle
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | | | | | | | | | - Danelle K Seymour
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - John F Doebley
- Department of Genetics, University of Wisconsin, Madison, WI, USA
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zheijang Province, College of Agriculture and Food Sciences, Zhejiang A&F University, Lin'an, Hangzhou, China.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA.
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108
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Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, Beridze T, Cantu D, Gaut BS. The population genetics of structural variants in grapevine domestication. NATURE PLANTS 2019; 5:965-979. [PMID: 31506640 DOI: 10.1038/s41477-019-0507-8] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/26/2019] [Indexed: 05/20/2023]
Abstract
Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their evolutionary genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution.
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Affiliation(s)
- Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, UC Davis, Davis, CA, USA
| | | | - Edwin Solares
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Yuanda Lv
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Tengiz Beridze
- Institute of Molecular Genetics, Agricultural University of Georgia, Tbilisi, Georgia
| | - Dario Cantu
- Department of Viticulture and Enology, UC Davis, Davis, CA, USA.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA.
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109
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Cho KT, Portwood JL, Gardiner JM, Harper LC, Lawrence-Dill CJ, Friedberg I, Andorf CM. MaizeDIG: Maize Database of Images and Genomes. FRONTIERS IN PLANT SCIENCE 2019; 10:1050. [PMID: 31555312 PMCID: PMC6724615 DOI: 10.3389/fpls.2019.01050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/29/2019] [Indexed: 05/23/2023]
Abstract
Background: An organism can be described by its observable features (phenotypes) and the genes and genomic information (genotypes) that cause these phenotypes. For many decades, researchers have tried to find relationships between genotypes and phenotypes, and great strides have been made. However, improved methods and tools for discovering and visualizing these phenotypic relationships are still needed. The maize genetics and genomics database (MaizeGDB, www.maizegdb.org) provides an array of useful resources for diverse data types including thousands of images related to mutant phenotypes in Zea mays ssp. mays (maize). To integrate mutant phenotype images with genomics information, we implemented and enhanced the web-based software package BioDIG (Biological Database of Images and Genomes). Findings: We developed a genotype-phenotype database for maize called MaizeDIG. MaizeDIG has several enhancements over the original BioDIG package. MaizeDIG, which supports multiple reference genome assemblies, is seamlessly integrated with genome browsers to accommodate custom tracks showing tagged mutant phenotypes images in their genomic context and allows for custom tagging of images to highlight the phenotype. This is accomplished through an updated interface allowing users to create image-to-gene links and is accessible via the image search tool. Conclusions: We have created a user-friendly and extensible web-based resource called MaizeDIG. MaizeDIG is preloaded with 2,396 images that are available on genome browsers for 10 different maize reference genomes. Approximately 90 images of classically defined maize genes have been manually annotated. MaizeDIG is available at http://maizedig.maizegdb.org/. The code is free and open source and can be found at https://github.com/Maize-Genetics-and-Genomics-Database/maizedig.
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Affiliation(s)
- Kyoung Tak Cho
- Department of Computer Science, Iowa State University, Ames, IA, United States
| | - John L. Portwood
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, United States
| | - Jack M. Gardiner
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Lisa C. Harper
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, United States
| | - Carolyn J. Lawrence-Dill
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, United States
| | - Iddo Friedberg
- Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, United States
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
| | - Carson M. Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, United States
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110
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Boehlein SK, Liu P, Webster A, Ribeiro C, Suzuki M, Wu S, Guan JC, Stewart JD, Tracy WF, Settles AM, McCarty DR, Koch KE, Hannah LC, Hennen-Bierwagen TA, Myers AM. Effects of long-term exposure to elevated temperature on Zea mays endosperm development during grain fill. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:23-40. [PMID: 30746832 DOI: 10.1111/tpj.14283] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 05/28/2023]
Abstract
Cereal yields decrease when grain fill proceeds under conditions of prolonged, moderately elevated temperatures. Endosperm-endogenous processes alter both rate and duration of dry weight gain, but underlying mechanisms remain unclear. Heat effects could be mediated by either abnormal, premature cessation of storage compound deposition or accelerated implementation of normal development. This study used controlled environments to isolate temperature as the sole environmental variable during Zea mays kernel-fill, from 12 days after pollination to maturity. Plants subjected to elevated day, elevated night temperatures (38°C day, 28°C night (38/28°C])) or elevated day, normal night (38/17°C), were compared with those from controls grown under normal day and night conditions (28/17°C). Progression of change over time in endosperm tissue was followed to dissect contributions at multiple levels, including transcriptome, metabolome, enzyme activities, product accumulation, and tissue ultrastructure. Integrated analyses indicated that the normal developmental program of endosperm is fully executed under prolonged high-temperature conditions, but at a faster rate. Accelerated development was observed when both day and night temperatures were elevated, but not when daytime temperature alone was increased. Although transcripts for most components of glycolysis and respiration were either upregulated or minimally affected, elevated temperatures decreased abundance of mRNAs related to biosynthesis of starch and storage proteins. Further analysis of 20 central-metabolic enzymes revealed six activities that were reduced under high-temperature conditions, indicating candidate roles in the observed reduction of grain dry weight. Nonetheless, a striking overall resilience of grain filling in the face of elevated temperatures can be attributed to acceleration of normal endosperm development.
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Affiliation(s)
- Susan K Boehlein
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Peng Liu
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ashley Webster
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Camila Ribeiro
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Masaharu Suzuki
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Shan Wu
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jiahn-Chou Guan
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jon D Stewart
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - William F Tracy
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - A Mark Settles
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Karen E Koch
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Larkin C Hannah
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Tracie A Hennen-Bierwagen
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Alan M Myers
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
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111
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Yan J, Tan BC. Maize biology: From functional genomics to breeding application. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:654-657. [PMID: 31099156 DOI: 10.1111/jipb.12819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University (HZAU), Wuhan, 430070, China
| | - Bao-Cai Tan
- School of Life Sciences, Shandong University, Jinan, 266237, China
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112
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Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nat Genet 2019; 51:1052-1059. [DOI: 10.1038/s41588-019-0427-6] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/25/2019] [Indexed: 01/15/2023]
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113
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Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions. Proc Natl Acad Sci U S A 2019; 116:10734-10743. [PMID: 30992374 DOI: 10.1073/pnas.1903809116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
While studying spontaneous mutations at the maize bronze (bz) locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate new bz mutations from several Bz stocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stable bz mutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneous wx mutations [Wessler S (1997) The Mutants of Maize, pp 385-386]. Similar mutations were recovered at the closely linked sh locus. These events occurred with a frequency of 2-4 × 10-5 in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, like Hopscotch, Magellan, and Bs2, a Bs1 variant, were described previously; others, like Foto and Focou in 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition of Hopscotch, Magellan, and Bs2 occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.
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114
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Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nat Genet 2019; 51:739-748. [PMID: 30886425 DOI: 10.1038/s41588-019-0371-5] [Citation(s) in RCA: 453] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 02/11/2019] [Indexed: 11/08/2022]
Abstract
Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo-assembled genomes for these two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that species-specific alterations in gene expression, structural variations and expanded gene families were responsible for speciation and the evolutionary history of these species. These findings help to elucidate the evolution of cotton genomes and their domestication history. The information generated not only should enable breeders to improve fiber quality and resilience to ever-changing environmental conditions but also can be translated to other crops for better understanding of their domestication history and use in improvement.
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115
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Mejía-Guerra MK, Buckler ES. A k-mer grammar analysis to uncover maize regulatory architecture. BMC PLANT BIOLOGY 2019; 19:103. [PMID: 30876396 PMCID: PMC6419808 DOI: 10.1186/s12870-019-1693-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 02/21/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Only a small percentage of the genome sequence is involved in regulation of gene expression, but to biochemically identify this portion is expensive and laborious. In species like maize, with diverse intergenic regions and lots of repetitive elements, this is an especially challenging problem that limits the use of the data from one line to the other. While regulatory regions are rare, they do have characteristic chromatin contexts and sequence organization (the grammar) with which they can be identified. RESULTS We developed a computational framework to exploit this sequence arrangement. The models learn to classify regulatory regions based on sequence features - k-mers. To do this, we borrowed two approaches from the field of natural language processing: (1) "bag-of-words" which is commonly used for differentially weighting key words in tasks like sentiment analyses, and (2) a vector-space model using word2vec (vector-k-mers), that captures semantic and linguistic relationships between words. We built "bag-of-k-mers" and "vector-k-mers" models that distinguish between regulatory and non-regulatory regions with an average accuracy above 90%. Our "bag-of-k-mers" achieved higher overall accuracy, while the "vector-k-mers" models were more useful in highlighting key groups of sequences within the regulatory regions. CONCLUSIONS These models now provide powerful tools to annotate regulatory regions in other maize lines beyond the reference, at low cost and with high accuracy.
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Affiliation(s)
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, 14853 NY USA
- USDA-ARS, Research Geneticist, USDA ARS Robert Holley Center, Ithaca, 14853 NY USA
- Department of Plant Breeding and Genetics, Cornell University, 159 Biotechnology Building, Ithaca, 14853 NY USA
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116
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Li C, Song W, Luo Y, Gao S, Zhang R, Shi Z, Wang X, Wang R, Wang F, Wang J, Zhao Y, Su A, Wang S, Li X, Luo M, Wang S, Zhang Y, Ge J, Tan X, Yuan Y, Bi X, He H, Yan J, Wang Y, Hu S, Zhao J. The HuangZaoSi Maize Genome Provides Insights into Genomic Variation and Improvement History of Maize. MOLECULAR PLANT 2019; 12:402-409. [PMID: 30807824 DOI: 10.1016/j.molp.2019.02.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 01/31/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequenced maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZS-related lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity-by-descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we demonstrated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function-related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize.
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Affiliation(s)
- Chunhui Li
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Wei Song
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Yingfeng Luo
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Shenghan Gao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ruyang Zhang
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Zi Shi
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Xiaqing Wang
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Ronghuan Wang
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Fengge Wang
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Jidong Wang
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Yanxin Zhao
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Aiguo Su
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Shuai Wang
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Xin Li
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Meijie Luo
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Shuaishuai Wang
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Yunxia Zhang
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Jianrong Ge
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China
| | - Xinyu Tan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ye Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiaochun Bi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuandong Wang
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China.
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Jiuran Zhao
- Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Shuguang Garden Middle Road No. 9, Beijing 100097, China.
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117
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Su W, Gu X, Peterson T. TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome. MOLECULAR PLANT 2019; 12:447-460. [PMID: 30802553 DOI: 10.1016/j.molp.2019.02.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 05/21/2023]
Abstract
Transposable elements (TEs) make up a large and rapidly evolving proportion of plant genomes. Among Class II DNA TEs, TIR elements are flanked by characteristic terminal inverted repeat sequences (TIRs). TIR TEs may play important roles in genome evolution, including generating allelic diversity, inducing structural variation, and regulating gene expression. However, TIR TE identification and annotation has been hampered by the lack of effective tools, resulting in erroneous TE annotations and a significant underestimation of the proportion of TIR elements in the maize genome. This problem has largely limited our understanding of the impact of TIR elements on plant genome structure and evolution. In this paper, we propose a new method of TIR element detection and annotation. This new pipeline combines the advantages of current homology-based annotation methods with powerful de novo machine-learning approaches, resulting in greatly increased efficiency and accuracy of TIR element annotation. The results show that the copy number and genome proportion of TIR elements in maize is much larger than that of current annotations. In addition, the distribution of some TIR superfamily elements is reduced in centromeric and pericentromeric positions, while others do not show a similar bias. Finally, the incorporation of machine-learning techniques has enabled the identification of large numbers of new DTA (hAT) family elements, which have all the hallmarks of bona fide TEs yet which lack high homology with currently known DTA elements. Together, these results provide new tools for TE research and new insight into the impact of TIR elements on maize genome diversity.
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Affiliation(s)
- Weijia Su
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Thomas Peterson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA; Department of Agronomy, Iowa State University, Ames, IA 50011-3260, USA.
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118
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Andorf C, Beavis WD, Hufford M, Smith S, Suza WP, Wang K, Woodhouse M, Yu J, Lübberstedt T. Technological advances in maize breeding: past, present and future. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:817-849. [PMID: 30798332 DOI: 10.1007/s00122-019-03306-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 02/05/2019] [Indexed: 05/18/2023]
Abstract
Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and utilization, (3) manipulation of genetic diversity by transformation and genome editing, (4) inbred line development and hybrid seed production, (5) understanding and prediction of hybrid performance, (6) breeding methodology and (7) synthesis of opportunities and challenges for future maize breeding.
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Affiliation(s)
| | - William D Beavis
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Matthew Hufford
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011-1010, USA
| | - Stephen Smith
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Walter P Suza
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | | | - Jianming Yu
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA.
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119
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Hoopes GM, Hamilton JP, Wood JC, Esteban E, Pasha A, Vaillancourt B, Provart NJ, Buell CR. An updated gene atlas for maize reveals organ-specific and stress-induced genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:1154-1167. [PMID: 30537259 PMCID: PMC6850026 DOI: 10.1111/tpj.14184] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/19/2018] [Accepted: 11/22/2018] [Indexed: 05/09/2023]
Abstract
Maize (Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide. The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long-read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA-sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36 207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4154 organ-specific and 7704 differentially expressed (DE) genes following stress treatment. Gene co-expression network analyses revealed 12 modules associated with distinct biological processes containing 13 590 genes providing a resource for further association of gene function based on co-expression patterns. Presence-absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ-specific and stress-induced DE genes suggesting that PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average have significantly fewer co-expression network connections suggesting that a subset of PAVs may be on an evolutionary path to pseudogenization. To facilitate use by the community, we developed the Maize Genomics Resource website (maize.plantbiology.msu.edu) for viewing and data-mining these resources and deployed two new views on the maize electronic Fluorescent Pictograph Browser (bar.utoronto.ca/efp_maize).
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Affiliation(s)
| | - John P. Hamilton
- Department of Plant BiologyMichigan State UniversityEast LansingMI48824USA
- Department of Energy Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
| | - Joshua C. Wood
- Department of Plant BiologyMichigan State UniversityEast LansingMI48824USA
- Department of Energy Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - Brieanne Vaillancourt
- Department of Plant BiologyMichigan State UniversityEast LansingMI48824USA
- Department of Energy Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
| | - Nicholas J. Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - C. Robin Buell
- Department of Plant BiologyMichigan State UniversityEast LansingMI48824USA
- Department of Energy Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
- Plant Resilience InstituteMichigan State UniversityEast LansingMI48824USA
- Michigan State University AgBioResearchEast LansingMI48824USA
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120
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Bragina MK, Afonnikov DA, Salina EA. Progress in plant genome sequencing: research directions. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.
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Affiliation(s)
| | - D. A. Afonnikov
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
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121
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Vaattovaara A, Leppälä J, Salojärvi J, Wrzaczek M. High-throughput sequencing data and the impact of plant gene annotation quality. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1069-1076. [PMID: 30590678 PMCID: PMC6382340 DOI: 10.1093/jxb/ery434] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/28/2018] [Indexed: 06/02/2023]
Abstract
The use of draft genomes of different species and re-sequencing of accessions and populations are now common tools for plant biology research. The de novo assembled draft genomes make it possible to identify pivotal divergence points in the plant lineage and provide an opportunity to investigate the genomic basis and timing of biological innovations by inferring orthologs between species. Furthermore, re-sequencing facilitates the mapping and subsequent molecular characterization of causative loci for traits, such as those for plant stress tolerance and development. In both cases high-quality gene annotation-the identification of protein-coding regions, gene promoters, and 5'- and 3'-untranslated regions-is critical for investigation of gene function. Annotations are constantly improving but automated gene annotations still require manual curation and experimental validation. This is particularly important for genes with large introns, genes located in regions rich with transposable elements or repeats, large gene families, and segmentally duplicated genes. In this opinion paper, we highlight the impact of annotation quality on evolutionary analyses, genome-wide association studies, and the identification of orthologous genes in plants. Furthermore, we predict that incorporating accurate information from manual curation into databases will dramatically improve the performance of automated gene predictors.
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Affiliation(s)
- Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
| | - Johanna Leppälä
- Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 6, Umeå, Sweden
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
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Muchlinski A, Chen X, Lovell JT, Köllner TG, Pelot KA, Zerbe P, Ruggiero M, Callaway L, Laliberte S, Chen F, Tholl D. Biosynthesis and Emission of Stress-Induced Volatile Terpenes in Roots and Leaves of Switchgrass ( Panicum virgatum L.). FRONTIERS IN PLANT SCIENCE 2019; 10:1144. [PMID: 31608090 PMCID: PMC6761604 DOI: 10.3389/fpls.2019.01144] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 08/21/2019] [Indexed: 05/18/2023]
Abstract
Switchgrass (Panicum virgatum L.), a perennial C4 grass, represents an important species in natural and anthropogenic grasslands of North America. Its resilience to abiotic and biotic stress has made switchgrass a preferred bioenergy crop. However, little is known about the mechanisms of resistance of switchgrass against pathogens and herbivores. Volatile compounds such as terpenes have important activities in plant direct and indirect defense. Here, we show that switchgrass leaves emit blends of monoterpenes and sesquiterpenes upon feeding by the generalist insect herbivore Spodoptera frugiperda (fall armyworm) and in a systemic response to the treatment of roots with defense hormones. Belowground application of methyl jasmonate also induced the release of volatile terpenes from roots. To correlate the emission of terpenes with the expression and activity of their corresponding biosynthetic genes, we identified a gene family of 44 monoterpene and sesquiterpene synthases (mono- and sesqui-TPSs) of the type-a, type-b, type-g, and type-e subfamilies, of which 32 TPSs were found to be functionally active in vitro. The TPS genes are distributed over the K and N subgenomes with clusters occurring on several chromosomes. Synteny analysis revealed syntenic networks for approximately 30-40% of the switchgrass TPS genes in the genomes of Panicum hallii, Setaria italica, and Sorghum bicolor, suggesting shared TPS ancestry in the common progenitor of these grass lineages. Eighteen switchgrass TPS genes were substantially induced upon insect and hormone treatment and the enzymatic products of nine of these genes correlated with compounds of the induced volatile blends. In accordance with the emission of volatiles, TPS gene expression was induced systemically in response to belowground treatment, whereas this response was not observed upon aboveground feeding of S. frugiperda. Our results demonstrate complex above and belowground responses of induced volatile terpene metabolism in switchgrass and provide a framework for more detailed investigations of the function of terpenes in stress resistance in this monocot crop.
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Affiliation(s)
- Andrew Muchlinski
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - John T. Lovell
- Genome Sequencing Center, Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Tobias G. Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Kyle A. Pelot
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Philipp Zerbe
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Meredith Ruggiero
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - LeMar Callaway
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Suzanne Laliberte
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- *Correspondence: Feng Chen, ; Dorothea Tholl,
| | - Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
- *Correspondence: Feng Chen, ; Dorothea Tholl,
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Enders TA, St. Dennis S, Oakland J, Callen ST, Gehan MA, Miller ND, Spalding EP, Springer NM, Hirsch CD. Classifying cold-stress responses of inbred maize seedlings using RGB imaging. PLANT DIRECT 2019; 3:e00104. [PMID: 31245751 PMCID: PMC6508840 DOI: 10.1002/pld3.104] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/12/2018] [Accepted: 12/06/2018] [Indexed: 05/05/2023]
Abstract
Increasing the tolerance of maize seedlings to low-temperature episodes could mitigate the effects of increasing climate variability on yield. To aid progress toward this goal, we established a growth chamber-based system for subjecting seedlings of 40 maize inbred genotypes to a defined, temporary cold stress while collecting digital profile images over a 9-daytime course. Image analysis performed with PlantCV software quantified shoot height, shoot area, 14 other morphological traits, and necrosis identified by color analysis. Hierarchical clustering of changes in growth rates of morphological traits and quantification of leaf necrosis over two time intervals resulted in three clusters of genotypes, which are characterized by unique responses to cold stress. For any given genotype, the set of traits with similar growth rates is unique. However, the patterns among traits are different between genotypes. Cold sensitivity was not correlated with the latitude where the inbred varieties were released suggesting potential further improvement for this trait. This work will serve as the basis for future experiments investigating the genetic basis of recovery to cold stress in maize seedlings.
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Affiliation(s)
- Tara A. Enders
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesota
| | - Susan St. Dennis
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesota
| | - Justin Oakland
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesota
| | - Steven T. Callen
- Donald Danforth Plant Science CenterSt. LouisMissouri
- Present address:
Bayer U.S. Crop ScienceSt. LouisMissouri
| | | | - Nathan D. Miller
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWisconsin
| | | | - Nathan M. Springer
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesota
| | - Cory D. Hirsch
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMinnesota
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Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C. Ten things you should know about transposable elements. Genome Biol 2018; 19:199. [PMID: 30454069 PMCID: PMC6240941 DOI: 10.1186/s13059-018-1577-z] [Citation(s) in RCA: 659] [Impact Index Per Article: 109.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of genomics and large-scale functional assays has shed new light on the multi-faceted activities of TEs and implies that they should no longer be marginalized. Here, we introduce the fundamental properties of TEs and their complex interactions with their cellular environment, which are crucial to understanding their impact and manifold consequences for organismal biology. While we draw examples primarily from mammalian systems, the core concepts outlined here are relevant to a broad range of organisms.
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Affiliation(s)
- Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0G1, Canada.
- Canadian Center for Computational Genomics, McGill University, Montréal, Québec, H3A 0G1, Canada.
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Michaël Imbeault
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Henry L Levin
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
| | - Dixie L Mager
- Terry Fox Laboratory, British Columbia Cancer Agency and Department of Medical Genetics, University of BC, Vancouver, BC, V5Z1L3, Canada
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
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