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Luo Z, Han L, Qian J, Li L. Circular RNAs exhibit extensive intraspecific variation in maize. PLANTA 2019; 250:69-78. [PMID: 30904942 DOI: 10.1007/s00425-019-03145-y] [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: 01/19/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Comprehensive transcriptome profiling uncovers extensive intraspecific variation of circular RNAs in maize, shedding light on genomic and phenotypic variation among maize inbred lines. Circular RNAs (circRNAs) are single-strand, covalently closed transcripts. A substantial number of circRNAs have been identified and shown to be associated with phenotypic variation in various species. However, little is known about the intraspecific variation of circRNAs in maize (Zea mays L.). Here, we collected a large transcriptomic dataset (by circRNA-seq and mRNA-seq) from seedling leaves of the reference maize inbred lines B73 and Mo17. We identified over 1500 circRNAs in these lines using two circRNA detection methods, CIRCexplorer2 and CIRI. Notably, a substantial proportion of circRNAs varied in terms of sequence or expression level between lines, pointing to extensive intraspecific variation of circRNAs in maize. GO and KEGG analyses showed that genes producing circRNAs with intraspecific variation were more likely to be enriched in multiple functional groups, compared with those that did not produce circRNAs. These findings suggest that circRNAs could be utilized as an indicator of genomic and phenotypic variation among maize inbred lines. Ribosomal profiling revealed that several circRNAs might have translational capacity in maize. These results uncover the extensive intraspecific variation of circRNAs and pave the way for further understanding the molecular mechanisms underlying phenotypic variation at the circRNA level in maize.
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Affiliation(s)
- Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jia Qian
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan, 430070, China.
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52
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A pistil-expressed pectin methylesterase confers cross-incompatibility between strains of Zea mays. Nat Commun 2019; 10:2304. [PMID: 31127100 PMCID: PMC6534598 DOI: 10.1038/s41467-019-10259-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/29/2019] [Indexed: 11/08/2022] Open
Abstract
A central problem in speciation is the origin and mechanisms of reproductive barriers that block gene flow between sympatric populations. Wind-pollinated plant species that flower in synchrony with one another rely on post-pollination interactions to maintain reproductive isolation. In some locations in Mexico, sympatric populations of domesticated maize and annual teosinte grow in intimate associate and flower synchronously, but rarely produce hybrids. This trait is typically conferred by a single haplotype, Teosinte crossing barrier1-s. Here, we show that the Teosinte crossing barrier1-s haplotype contains a pistil-expressed, potential speciation gene, encoding a pectin methylesterase homolog. The modification of the pollen tube cell wall by the pistil, then, is likely a key mechanism for pollen rejection in Zea and may represent a general mechanism for reproductive isolation in grasses. Domesticated maize and some varieties of wild teosinte grow in close proximity in parts of Mexico but rarely cross-fertilize. Here the authors show that a pistil-expressed pectin methylesterase, encoded by a gene within the Teosinte crossing barrier1-s haplotype, prevents fertilization of these teosintes by incompatible pollen.
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53
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Lu X, Fu X, Wang D, Wang J, Chen X, Hao M, Wang J, Gervers KA, Guo L, Wang S, Yin Z, Fan W, Shi C, Wang X, Peng J, Chen C, Cui R, Shu N, Zhang B, Han M, Zhao X, Mu M, Yu JZ, Ye W. Resequencing of cv CRI-12 family reveals haplotype block inheritance and recombination of agronomically important genes in artificial selection. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:945-955. [PMID: 30407717 PMCID: PMC6587942 DOI: 10.1111/pbi.13030] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 05/21/2023]
Abstract
Although efforts have been taken to exploit diversity for yield and quality improvements, limited progress on using beneficial alleles in domesticated and undomesticated cotton varieties is limited. Given the complexity and limited amount of genomic information since the completion of four cotton genomes, characterizing significant variations and haplotype block inheritance under artificial selection has been challenging. Here we sequenced Gossypium hirsutum L. cv CRI-12 (the cotton variety with the largest acreage in China), its parental cultivars, and progeny cultivars, which were bred by the different institutes in China. In total, 3.3 million SNPs were identified and 118, 126 and 176 genes were remarkably correlated with Verticillium wilt, salinity and drought tolerance in CRI-12, respectively. Transcriptome-wide analyses of gene expression, and functional annotations, have provided support for the identification of genes tied to these tolerances. We totally discovered 58 116 haplotype blocks, among which 23 752 may be inherited and 1029 may be recombined under artificial selection. This survey of genetic diversity identified loci that may have been subject to artificial selection and documented the haplotype block inheritance and recombination, shedding light on the genetic mechanism of artificial selection and guiding breeding efforts for the genetic improvement of cotton.
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Affiliation(s)
- Xuke Lu
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Xiaoqiong Fu
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Delong Wang
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Junyi Wang
- Hangzhou 1 Gene Technology CO., LTDHangzhouZhejiangChina
| | - Xiugui Chen
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Meirong Hao
- Hangzhou 1 Gene Technology CO., LTDHangzhouZhejiangChina
| | - Junjuan Wang
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Kyle A. Gervers
- Crop Germplasm Research UnitSouthern Plains Agricultural Research CenterUS Department of Agriculture—Agricultural Research Service (USDA‐ARS)College StationTXUSA
| | - Lixue Guo
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Shuai Wang
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Zujun Yin
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Weili Fan
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Chunwei Shi
- Hangzhou 1 Gene Technology CO., LTDHangzhouZhejiangChina
| | - Xiaoge Wang
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Jun Peng
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Chao Chen
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Ruifeng Cui
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Na Shu
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Binglei Zhang
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Mingge Han
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Xiaojie Zhao
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Min Mu
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - John Z. Yu
- Crop Germplasm Research UnitSouthern Plains Agricultural Research CenterUS Department of Agriculture—Agricultural Research Service (USDA‐ARS)College StationTXUSA
| | - Wuwei Ye
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
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54
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Fuentes RR, Chebotarov D, Duitama J, Smith S, De la Hoz JF, Mohiyuddin M, Wing RA, McNally KL, Tatarinova T, Grigoriev A, Mauleon R, Alexandrov N. Structural variants in 3000 rice genomes. Genome Res 2019; 29:870-880. [PMID: 30992303 PMCID: PMC6499320 DOI: 10.1101/gr.241240.118] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 03/11/2019] [Indexed: 12/24/2022]
Abstract
Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million allelic variants. We found enrichment of long SVs in promoters and an excess of shorter variants in 5′ UTRs. Across the rice genomes, we identified regions of high SV frequency enriched in stress response genes. We demonstrated how SVs may help in finding causative variants in genome-wide association analysis. These new insights into rice genome biology are valuable for understanding the effects SVs have on gene function, with the prospect of identifying novel agronomically important alleles that can be utilized to improve cultivated rice.
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Affiliation(s)
- Roven Rommel Fuentes
- International Rice Research Institute, Laguna 4031, Philippines.,Bioinformatics Group, Wageningen University and Research, 6708 PB Wageningen, the Netherlands
| | | | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de Los Andes, Bogotá 111711, Colombia.,Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | - Sean Smith
- Biology Department, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
| | - Juan Fernando De la Hoz
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | | | - Rod A Wing
- International Rice Research Institute, Laguna 4031, Philippines.,Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA.,King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | | | - Tatiana Tatarinova
- Department of Biology, University of La Verne, La Verne, California 91750, USA.,Vavilov Institute of General Genetics, Moscow 119333, Russia.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia.,Laboratory of Forest Genomics, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Andrey Grigoriev
- Biology Department, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
| | - Ramil Mauleon
- International Rice Research Institute, Laguna 4031, Philippines
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55
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Lye ZN, Purugganan MD. Copy Number Variation in Domestication. TRENDS IN PLANT SCIENCE 2019; 24:352-365. [PMID: 30745056 DOI: 10.1016/j.tplants.2019.01.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 05/22/2023]
Abstract
Domesticated plants have long served as excellent models for studying evolution. Many genes and mutations underlying important domestication traits have been identified, and most causal mutations appear to be SNPs. Copy number variation (CNV) is an important source of genetic variation that has been largely neglected in studies of domestication. Ongoing work demonstrates the importance of CNVs as a source of genetic variation during domestication, and during the diversification of domesticated taxa. Here, we review how CNVs contribute to evolutionary processes underlying domestication, and review examples of domestication traits caused by CNVs. We draw from examples in plant species, but also highlight cases in animal systems that could illuminate the roles of CNVs in the domestication process.
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Affiliation(s)
- Zoe N Lye
- Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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56
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Zhou P, Hirsch CN, Briggs SP, Springer NM. Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development. MOLECULAR PLANT 2019; 12:410-425. [PMID: 30593858 DOI: 10.1016/j.molp.2018.12.015] [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: 07/27/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 05/26/2023]
Abstract
Gene expression variation is a key component underlying phenotypic variation and heterosis. Transcriptome profiling was performed on 23 different tissues or developmental stages of two maize inbreds, B73 and Mo17, as well as their F1 hybrid. The obtained large-scale datasets provided opportunities to monitor the developmental dynamics of differential expression, additivity for gene expression, and regulatory variation. The transcriptome can be divided into ∼30 000 genes that are expressed in at least one tissue of one inbred and an additional ∼10 000 ″silent" genes that are not expressed in any tissue of any genotype, 90% of which are non-syntenic relative to other grasses. Many (∼74%) of the expressed genes exhibit differential expression in at least one tissue. However, the majority of genes with differential expression do not exhibit consistent differential expression in different tissues. These genes often exhibit tissue-specific differential expression with equivalent expression in other tissues, and in many cases they switch the directionality of differential expression in different tissues. This suggests widespread variation for tissue-specific regulation of gene expression between the two maize inbreds B73 and Mo17. Nearly 5000 genes are expressed in only one parent in at least one tissue (single parent expression) and 97% of these genes are expressed at mid-parent levels or higher in the hybrid, providing extensive opportunities for hybrid complementation in heterosis. In general, additive expression patterns are much more common than non-additive patterns, and this trend is more pronounced for genes with strong differential expression or single parent expression. There is relatively little evidence for non-additive expression patterns that are maintained in multiple tissues. The analysis of allele-specific expression allowed classification of cis- and trans-regulatory variation. Genes with cis-regulatory variation often exhibit additive expression and tend to have more consistent regulatory variation throughout development. In contrast, genes with trans-regulatory variation are enriched for non-additive patterns and often show tissue-specific differential expression. Taken together, this study provides a deeper understanding of regulatory variation and the degree of additive gene expression throughout maize development. The dynamic nature of differential expression, additivity, and regulatory variation imply abundant variability for tissue-specific regulatory mechanisms and suggest that connections between transcriptome and phenome will require expression data from multiple tissues.
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Affiliation(s)
- Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Steven P Briggs
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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57
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Gabur I, Chawla HS, Snowdon RJ, Parkin IAP. Connecting genome structural variation with complex traits in crop plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:733-750. [PMID: 30448864 DOI: 10.1007/s00122-018-3233-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/07/2018] [Indexed: 05/05/2023]
Abstract
Structural genome variation is a major determinant of useful trait diversity. We describe how genome analysis methods are enabling discovery of trait-associated structural variants and their potential impact on breeding. As our understanding of complex crop genomes continues to grow, there is growing evidence that structural genome variation plays a major role in determining traits important for breeding and agriculture. Identifying the extent and impact of structural variants in crop genomes is becoming increasingly feasible with ongoing advances in the sophistication of genome sequencing technologies, particularly as it becomes easier to generate accurate long sequence reads on a genome-wide scale. In this article, we discuss the origins of structural genome variation in crops from ancient and recent genome duplication and polyploidization events and review high-throughput methods to assay such variants in crop populations in order to find associations with phenotypic traits. There is increasing evidence from such studies that gene presence-absence and copy number variation resulting from segmental chromosome exchanges may be at the heart of adaptive variation of crops to counter abiotic and biotic stress factors. We present examples from major crops that demonstrate the potential of pangenomic diversity as a key resource for future plant breeding for resilience and sustainability.
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Affiliation(s)
- Iulian Gabur
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N OX2, Canada
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58
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Haas M, Schreiber M, Mascher M. Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:204-225. [PMID: 30414305 DOI: 10.1111/jipb.12737] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/27/2018] [Indexed: 05/02/2023]
Abstract
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of next-generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.
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Affiliation(s)
- Matthew Haas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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59
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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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60
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Wang X, Lebarbier E, Aubert J, Robin S. Variational Inference for Coupled Hidden Markov Models Applied to the Joint Detection of Copy Number Variations. Int J Biostat 2019; 15:/j/ijb.ahead-of-print/ijb-2018-0023/ijb-2018-0023.xml. [PMID: 30779702 DOI: 10.1515/ijb-2018-0023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 11/21/2018] [Indexed: 02/04/2023]
Abstract
Hidden Markov models provide a natural statistical framework for the detection of the copy number variations (CNV) in genomics. In this context, we define a hidden Markov process that underlies all individuals jointly in order to detect and to classify genomics regions in different states (typically, deletion, normal or amplification). Structural variations from different individuals may be dependent. It is the case in agronomy where varietal selection program exists and species share a common phylogenetic past. We propose to take into account these dependencies inthe HMM model. When dealing with a large number of series, maximum likelihood inference (performed classically using the EM algorithm) becomes intractable. We thus propose an approximate inference algorithm based on a variational approach (VEM), implemented in the CHMM R package. A simulation study is performed to assess the performance of the proposed method and an application to the detection of structural variations in plant genomes is presented.
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Affiliation(s)
- Xiaoqiang Wang
- School of Mathematics and Statistics, Shandong University (Weihai), Weihai,Shandong, China
| | - Emilie Lebarbier
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | - Julie Aubert
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | - Stéphane Robin
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
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61
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Tao Y, Zhao X, Mace E, Henry R, Jordan D. Exploring and Exploiting Pan-genomics for Crop Improvement. MOLECULAR PLANT 2019; 12:156-169. [PMID: 30594655 DOI: 10.1016/j.molp.2018.12.016] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 05/19/2023]
Abstract
Genetic variation ranging from single-nucleotide polymorphisms to large structural variants (SVs) can cause variation of gene content among individuals within the same species. There is an increasing appreciation that a single reference genome is insufficient to capture the full landscape of genetic diversity of a species. Pan-genome analysis offers a platform to evaluate the genetic diversity of a species via investigation of its entire genome repertoire. Although a recent wave of pan-genomic studies has shed new light on crop diversity and improvement using advanced sequencing technology, the potential applications of crop pan-genomics in crop improvement are yet to be fully exploited. In this review, we highlight the progress achieved in understanding crop pan-genomics, discuss biological activities that cause SVs, review important agronomical traits affected by SVs, and present our perspective on the application of pan-genomics in crop improvement.
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Affiliation(s)
- Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD 4370, Australia
| | - Xianrong Zhao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD 4370, Australia
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD 4370, Australia; Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD 4370, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD 4072, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD 4370, Australia.
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Cultrera NGM, Sarri V, Lucentini L, Ceccarelli M, Alagna F, Mariotti R, Mousavi S, Ruiz CG, Baldoni L. High Levels of Variation Within Gene Sequences of Olea europaea L. FRONTIERS IN PLANT SCIENCE 2019; 9:1932. [PMID: 30671076 PMCID: PMC6331486 DOI: 10.3389/fpls.2018.01932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/12/2018] [Indexed: 05/08/2023]
Abstract
Gene sequence variation in cultivated olive (Olea europaea L. subsp. europaea var. europaea), the most important oil tree crop of the Mediterranean basin, has been poorly evaluated up to now. A deep sequence analysis of fragments of four genes, OeACP1, OeACP2, OeLUS and OeSUT1, in 90 cultivars, revealed a wide range of polymorphisms along all recognized allele forms and unexpected allele frequencies and genotype combinations. High linkage values among most polymorphisms were recorded within each gene fragment. The great sequence variability corresponded to a low number of alleles and, surprisingly, to a small fraction of genotype combinations. The distribution, frequency, and combination of the different alleles at each locus is possibly due to natural and human pressures, such as selection, ancestrality, or fitness. Phylogenetic analyses of allele sequences showed distant and complex patterns of relationships among cultivated olives, intermixed with other related forms, highlighting an evolutionary connection between olive cultivars and the O. europaea subspecies cuspidata and cerasiformis. This study demonstrates how a detailed and complete sequence analysis of a few gene portions and a thorough genotyping on a representative set of cultivars can clarify important issues related to sequence polymorphisms, reconstructing the phylogeny of alleles, as well as the genotype combinations. The identification of regions representing blocks of recombination could reveal polymorphisms that represent putatively functional markers. Indeed, specific mutations found on the analyzed OeACP1 and OeACP2 fragments seem to be correlated to the fruit weight.
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Affiliation(s)
- Nicolò G. M. Cultrera
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Vania Sarri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Livia Lucentini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Fiammetta Alagna
- ENEA Italian National Agency for New Technologies Energy and Sustainable Economic Development, Trisaia Research Center, Rotondella, Italy
| | - Roberto Mariotti
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Soraya Mousavi
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | | | - Luciana Baldoni
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
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Penning BW, McCann MC, Carpita NC. Evolution of the Cell Wall Gene Families of Grasses. FRONTIERS IN PLANT SCIENCE 2019; 10:1205. [PMID: 31681352 PMCID: PMC6805987 DOI: 10.3389/fpls.2019.01205] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/02/2019] [Indexed: 05/06/2023]
Abstract
Grasses and related commelinid monocot species synthesize cell walls distinct in composition from other angiosperm species. With few exceptions, the genomes of all angiosperms contain the genes that encode the enzymes for synthesis of all cell-wall polysaccharide, phenylpropanoid, and protein constituents known in vascular plants. RNA-seq analysis of transcripts expressed during development of the upper and lower internodes of maize (Zea mays) stem captured the expression of cell-wall-related genes associated with primary or secondary wall formation. High levels of transcript abundances were not confined to genes associated with the distinct walls of grasses but also of those associated with xyloglucan and pectin synthesis. Combined with proteomics data to confirm that expressed genes are translated, we propose that the distinctive cell-wall composition of grasses results from sorting downstream from their sites of synthesis in the Golgi apparatus and hydrolysis of the uncharacteristic polysaccharides and not from differential expression of synthases of grass-specific polysaccharides.
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Affiliation(s)
- Bryan W. Penning
- Corn, Soybean and Wheat Quality Research, USDA-ARS, Wooster, OH, United States
| | - Maureen C. McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, West Lafayette, IN, United States
| | - Nicholas C. Carpita
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, West Lafayette, IN, United States
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN, United States
- *Correspondence: Nicholas C. Carpita,
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64
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Lyra DH, Galli G, Alves FC, Granato ÍSC, Vidotti MS, Bandeira E Sousa M, Morosini JS, Crossa J, Fritsche-Neto R. Modeling copy number variation in the genomic prediction of maize hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:273-288. [PMID: 30382311 DOI: 10.1007/s00122-018-3215-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 10/20/2018] [Indexed: 06/08/2023]
Abstract
Our study indicates that copy variants may play an essential role in the phenotypic variation of complex traits in maize hybrids. Moreover, predicting hybrid phenotypes by combining additive-dominance effects with copy variants has the potential to be a viable predictive model. Non-additive effects resulting from the actions of multiple loci may influence trait variation in single-cross hybrids. In addition, complementation of allelic variation could be a valuable contributor to hybrid genetic variation, especially when crossing inbred lines with higher contents of copy gains. With this in mind, we aimed (1) to study the association between copy number variation (CNV) and hybrid phenotype, and (2) to compare the predictive ability (PA) of additive and additive-dominance genomic best linear unbiased prediction model when combined with the effects of CNV in two datasets of maize hybrids (USP and HELIX). In the USP dataset, we observed a significant negative phenotypic correlation of low magnitude between copy number loss and plant height, revealing a tendency that more copy losses lead to lower plants. In the same set, when CNV was combined with the additive plus dominance effects, the PA significantly increased only for plant height under low nitrogen. In this case, CNV effects explicitly capture relatedness between individuals and add extra information to the model. In the HELIX dataset, we observed a pronounced difference in PA between additive (0.50) and additive-dominance (0.71) models for predicting grain yield, suggesting a significant contribution of dominance. We conclude that copy variants may play an essential role in the phenotypic variation of complex traits in maize hybrids, although the inclusion of CNVs into datasets does not return significant gains concerning PA.
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Affiliation(s)
- Danilo Hottis Lyra
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil.
- Department of Computational and Analytical Sciences, Rothamsted Research, West Common, Harpenden, AL52JQ, UK.
| | - Giovanni Galli
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Filipe Couto Alves
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Ítalo Stefanine Correia Granato
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Miriam Suzane Vidotti
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Massaine Bandeira E Sousa
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Júlia Silva Morosini
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - José Crossa
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), 06600, Texcoco, D.F, Mexico
| | - Roberto Fritsche-Neto
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
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65
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Owens GL, Baute GJ, Hubner S, Rieseberg LH. Genomic sequence and copy number evolution during hybrid crop development in sunflowers. Evol Appl 2019; 12:54-65. [PMID: 30622635 PMCID: PMC6304689 DOI: 10.1111/eva.12603] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 01/18/2018] [Indexed: 01/21/2023] Open
Abstract
Hybrid crops, an important part of modern agriculture, rely on the development of male and female heterotic gene pools. In sunflowers, heterotic gene pools were developed through the use of crop-wild relatives to produce cytoplasmic male sterile female and branching, fertility restoring male lines. Here, we use genomic data from a diversity panel of male, female, and open-pollinated lines to explore the genetic changes brought during modern improvement. We find the male lines have diverged most from their open-pollinated progenitors and that genetic differentiation is concentrated in chromosomes, 8, 10 and 13, due to introgressions from wild relatives. Ancestral variation from open-pollinated varieties almost universally evolved in parallel for both male and female lines suggesting little or no selection for heterotic overdominance. Furthermore, we show that gene content differs between the male and female lines and that differentiation in gene content is concentrated in high FST regions. This means that the introgressions that brought branching and fertility restoration to the male lines, brought with them different gene content from the ancestral haplotypes, including the removal of some genes. Although we find no evidence that gene complementation genomewide is responsible for heterosis between male and female lines, several of the genes that are largely absent in either the male or female lines are associated with pathogen defense, suggesting complementation may be functionally relevant for crop breeders.
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Affiliation(s)
- Gregory L. Owens
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCCanada
| | - Gregory J. Baute
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCCanada
| | - Sariel Hubner
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCCanada
- Department of BiotechnologyTel‐Hai Academic CollegeUpper GalileeIsrael
- MIGAL ‐ Galilee Research InstituteKiryat ShmonaIsrael
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCCanada
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66
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Owens GL, Baute GJ, Hubner S, Rieseberg LH. Genomic sequence and copy number evolution during hybrid crop development in sunflowers. Evol Appl 2019. [PMID: 30622635 DOI: 10.111/eva.12603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Hybrid crops, an important part of modern agriculture, rely on the development of male and female heterotic gene pools. In sunflowers, heterotic gene pools were developed through the use of crop-wild relatives to produce cytoplasmic male sterile female and branching, fertility restoring male lines. Here, we use genomic data from a diversity panel of male, female, and open-pollinated lines to explore the genetic changes brought during modern improvement. We find the male lines have diverged most from their open-pollinated progenitors and that genetic differentiation is concentrated in chromosomes, 8, 10 and 13, due to introgressions from wild relatives. Ancestral variation from open-pollinated varieties almost universally evolved in parallel for both male and female lines suggesting little or no selection for heterotic overdominance. Furthermore, we show that gene content differs between the male and female lines and that differentiation in gene content is concentrated in high FST regions. This means that the introgressions that brought branching and fertility restoration to the male lines, brought with them different gene content from the ancestral haplotypes, including the removal of some genes. Although we find no evidence that gene complementation genomewide is responsible for heterosis between male and female lines, several of the genes that are largely absent in either the male or female lines are associated with pathogen defense, suggesting complementation may be functionally relevant for crop breeders.
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Affiliation(s)
- Gregory L Owens
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Gregory J Baute
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Sariel Hubner
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
- Department of Biotechnology Tel-Hai Academic College Upper Galilee Israel
- MIGAL - Galilee Research Institute Kiryat Shmona Israel
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre University of British Columbia Vancouver BC Canada
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Razali R, Bougouffa S, Morton MJL, Lightfoot DJ, Alam I, Essack M, Arold ST, Kamau AA, Schmöckel SM, Pailles Y, Shahid M, Michell CT, Al-Babili S, Ho YS, Tester M, Bajic VB, Negrão S. The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance. FRONTIERS IN PLANT SCIENCE 2018; 9:1402. [PMID: 30349549 PMCID: PMC6186997 DOI: 10.3389/fpls.2018.01402] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 09/04/2018] [Indexed: 05/19/2023]
Abstract
Solanum pimpinellifolium, a wild relative of cultivated tomato, offers a wealth of breeding potential for desirable traits such as tolerance to abiotic and biotic stresses. Here, we report the genome assembly and annotation of S. pimpinellifolium 'LA0480.' Moreover, we present phenotypic data from one field experiment that demonstrate a greater salinity tolerance for fruit- and yield-related traits in S. pimpinellifolium compared with cultivated tomato. The 'LA0480' genome assembly size (811 Mb) and the number of annotated genes (25,970) are within the range observed for other sequenced tomato species. We developed and utilized the Dragon Eukaryotic Analyses Platform (DEAP) to functionally annotate the 'LA0480' protein-coding genes. Additionally, we used DEAP to compare protein function between S. pimpinellifolium and cultivated tomato. Our data suggest enrichment in genes involved in biotic and abiotic stress responses. To understand the genomic basis for these differences in S. pimpinellifolium and S. lycopersicum, we analyzed 15 genes that have previously been shown to mediate salinity tolerance in plants. We show that S. pimpinellifolium has a higher copy number of the inositol-3-phosphate synthase and phosphatase genes, which are both key enzymes in the production of inositol and its derivatives. Moreover, our analysis indicates that changes occurring in the inositol phosphate pathway may contribute to the observed higher salinity tolerance in 'LA0480.' Altogether, our work provides essential resources to understand and unlock the genetic and breeding potential of S. pimpinellifolium, and to discover the genomic basis underlying its environmental robustness.
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Affiliation(s)
- Rozaimi Razali
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Salim Bougouffa
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mitchell J. L. Morton
- Division of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Damien J. Lightfoot
- Division of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Division of Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Stefan T. Arold
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Division of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Allan A. Kamau
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Division of Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sandra M. Schmöckel
- Division of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Yveline Pailles
- Division of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohammed Shahid
- International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Craig T. Michell
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Salim Al-Babili
- Division of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Yung Shwen Ho
- Division of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Vladimir B. Bajic
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Division of Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sónia Negrão
- Division of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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68
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Stitzer MC, Ross-Ibarra J. Maize domestication and gene interaction. THE NEW PHYTOLOGIST 2018; 220:395-408. [PMID: 30035321 DOI: 10.1111/nph.15350] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/05/2018] [Indexed: 05/24/2023]
Abstract
Contents Summary 395 I. Introduction 395 II. The genetic basis of maize domestication 396 III. The tempo of maize domestication 401 IV. Genetic interactions and selection during maize domestication 401 V. Gene networks of maize domestication alleles 404 VI. Implications of gene interactions on evolution and selection404 VII. Conclusions 405 Acknowledgements 405 References 405 SUMMARY: Domestication is a tractable system for following evolutionary change. Under domestication, wild populations respond to shifting selective pressures, resulting in adaptation to the new ecological niche of cultivation. Owing to the important role of domesticated crops in human nutrition and agriculture, the ancestry and selection pressures transforming a wild plant into a domesticate have been extensively studied. In Zea mays, morphological, genetic and genomic studies have elucidated how a wild plant, the teosinte Z. mays subsp. parviglumis, was transformed into the domesticate Z. mays subsp. mays. Five major morphological differences distinguish these two subspecies, and careful genetic dissection has pinpointed the molecular changes responsible for several of these traits. But maize domestication was a consequence of more than just five genes, and regions throughout the genome contribute. The impacts of these additional regions are contingent on genetic background, both the interactions between alleles of a single gene and among alleles of the multiple genes that modulate phenotypes. Key genetic interactions include dominance relationships, epistatic interactions and pleiotropic constraint, including how these variants are connected in gene networks. Here, we review the role of gene interactions in generating the dramatic phenotypic evolution seen in the transition from teosinte to maize.
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Affiliation(s)
- Michelle C Stitzer
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
- Center for Population Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
- Center for Population Biology, University of California, Davis, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, Davis, CA, 95616, USA
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69
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Prunier J, Giguère I, Ryan N, Guy R, Soolanayakanahally R, Isabel N, MacKay J, Porth I. Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations. Mol Ecol 2018; 28:1476-1490. [PMID: 30270494 DOI: 10.1111/mec.14836] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022]
Abstract
Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genomewide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F1 progenies of an intraprovenance cross (north-north cross, 58th parallel) and an interprovenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a widespread North American forest tree. A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar's 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the interprovenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar's distribution, and higher photosynthetic assimilation rates and water-use efficiency at high latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs may in fact represent efficient adaptive variations against fast-evolving pathogens.
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Affiliation(s)
- Julien Prunier
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.,Centre for Forest Research, Université Laval, Québec, Quebec, Canada
| | - Isabelle Giguère
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.,Centre for Forest Research, Université Laval, Québec, Quebec, Canada
| | - Natalie Ryan
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert Guy
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Raju Soolanayakanahally
- Indian Head Research Farm, Agriculture and Agri-Food Canada, Indian Head, Saskatchewan, Canada
| | - Nathalie Isabel
- Laurentian Forest Centre, Canadian Forest Service, Natural Resources Canada, Québec, Quebec, Canada
| | - John MacKay
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Ilga Porth
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.,Centre for Forest Research, Université Laval, Québec, Quebec, Canada
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70
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Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time. G3-GENES GENOMES GENETICS 2018; 8:3049-3058. [PMID: 30030405 PMCID: PMC6118310 DOI: 10.1534/g3.118.200580] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tandem duplicate genes are proximally duplicated and as such occur in similar genomic neighborhoods. Using the maize B73 and PH207 de novo genome assemblies, we identified thousands of tandem gene duplicates that account for ∼10% of the annotated genes. These tandem duplicates have a bimodal distribution of ages, which coincide with ancient allopolyploidization and more recent domestication. Tandem duplicates are smaller on average and have a higher probability of containing LTR elements than other genes, suggesting origins in nonhomologous recombination. Within relatively recent tandem duplicate genes, ∼26% appear to be undergoing degeneration or divergence in function from the ancestral copy. Our results show that tandem duplicates are abundant in maize, arose in bursts throughout maize evolutionary history under multiple potential mechanisms, and may provide a substrate for novel phenotypic variation.
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71
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Gaut BS, Seymour DK, Liu Q, Zhou Y. Demography and its effects on genomic variation in crop domestication. NATURE PLANTS 2018; 4:512-520. [PMID: 30061748 DOI: 10.1038/s41477-018-0210-1] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 05/20/2023]
Abstract
Over two thousand plant species have been modified morphologically through cultivation and human use. Here, we review three aspects of crop domestication that are currently undergoing marked revisions, due to analytical advancements and their application to whole genome resequencing (WGS) data. We begin by discussing the duration and demographic history of domestication. There has been debate as to whether domestication occurred quickly or slowly. The latter is tentatively supported both by fossil data and application of WGS data to sequentially Markovian coalescent methods that infer the history of effective population size. This history suggests the possibility of extended human impacts on domesticated lineages prior to their purposeful cultivation. We also make the point that demographic history matters, because it shapes patterns and levels of extant genetic diversity. We illustrate this point by discussing the evolutionary processes that contribute to the empirical observation that most crops examined to date have more putatively deleterious alleles than their wild relatives. These deleterious alleles may contribute to genetic load within crops and may be fitting targets for crop improvement. Finally, the same demographic factors are likely to shape the spectrum of structural variants (SVs) within crops. SVs are known to underlie many of the phenotypic changes associated with domestication and crop improvement, but we currently lack sufficient knowledge about the mechanisms that create SVs, their rates of origin, their population frequencies and their phenotypic effects.
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Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Danelle K Seymour
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Qingpo Liu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, China
| | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA.
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72
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Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet 2018; 50:1289-1295. [PMID: 30061735 DOI: 10.1038/s41588-018-0182-0] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 06/05/2018] [Indexed: 12/24/2022]
Abstract
Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.
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73
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The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet 2018; 50:1282-1288. [PMID: 30061736 DOI: 10.1038/s41588-018-0158-0] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/17/2018] [Indexed: 11/08/2022]
Abstract
The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.
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74
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Iqbal MZ, Cheng M, Zhao Y, Wen X, Ping Zhang, Zhang L, Ali A, Rong T, Tang QL. Mysterious meiotic behavior of autopolyploid and allopolyploid maize. COMPARATIVE CYTOGENETICS 2018; 12:247-265. [PMID: 30061981 PMCID: PMC6063980 DOI: 10.3897/compcytogen.v12i2.24907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/05/2018] [Indexed: 06/29/2024]
Abstract
This study was aimed to investigate the stability of chromosomes during meiosis in autopolyploid and allopolyploid maize, as well as to determine an association of chromosomes between maize (Zea mays ssp. mays Linnaeus, 1753) and Z. perennis (Hitchcock, 1922) Reeves & Mangelsdor, 1942, by producing a series of autopolyploid and allopolyploid maize hybrids. The intra-genomic and inter-genomic meiotic pairings in these polyploids were quantified and compared using dual-color genomic in-situ hybridization. The results demonstrated higher level of chromosome stability in allopolyploid maize during meiosis as compared to autopolyploid maize. In addition, the meiotic behavior of Z. perennis was relatively more stable as compared to the allopolyploid maize. Moreover, ten chromosomes of "A" subgenome in maize were homologous to twenty chromosomes of Z. perennis genome with a higher pairing frequency and little evolutionary differentiation. At the same time, little evolutionary differentiation has been shown by chromosomes of "A" subgenome in maize, while chromosomes of "B" subgenome, had a lower pairing frequency and higher evolutionary differentiation. Furthermore, 5IM + 5IIPP + 5IIIMPP and 5IIMM + 5IIPP + 5IVMMPP were observed in allotriploids and allotetraploids respectively, whereas homoeologous chromosomes were found between the "A" and "B" genome of maize and Z. perennis.
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Affiliation(s)
- Muhammad Zafar Iqbal
- Sichuan Agricultural University, Maize Research Institute, Wenjiang 611130, Sichuan, China
| | - Mingjun Cheng
- Sichuan Agricultural University, Maize Research Institute, Wenjiang 611130, Sichuan, China
- Sichuan Provincial Grassland Work Station, Chengdu 610041, China
| | - Yanli Zhao
- Sichuan Agricultural University, Maize Research Institute, Wenjiang 611130, Sichuan, China
| | - Xiaodong Wen
- Sichuan Agricultural University, Maize Research Institute, Wenjiang 611130, Sichuan, China
| | - Ping Zhang
- Sichuan Agricultural University, Maize Research Institute, Wenjiang 611130, Sichuan, China
| | - Lei Zhang
- Sichuan Agricultural University, Maize Research Institute, Wenjiang 611130, Sichuan, China
| | - Asif Ali
- Sichuan Agricultural University, Maize Research Institute, Wenjiang 611130, Sichuan, China
| | - Tingzhao Rong
- Sichuan Agricultural University, Maize Research Institute, Wenjiang 611130, Sichuan, China
| | - Qi Lin Tang
- Sichuan Agricultural University, Maize Research Institute, Wenjiang 611130, Sichuan, China
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75
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Liu N, Liu J, Li W, Pan Q, Liu J, Yang X, Yan J, Xiao Y. Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize. BMC PLANT BIOLOGY 2018; 18:66. [PMID: 29673320 PMCID: PMC5909218 DOI: 10.1186/s12870-018-1287-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 04/11/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Residual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies. However, knowledge of factors affecting the genome-wide distribution of RH remains limited. RESULTS A set of 2196 heterogeneous inbred family (HIF) maize lines derived from 12 recombinant inbred line (RIL) populations was genotyped using the Maize50K SNP chip. A total of 18,615 unique RH intervals were identified, ranging from 505 to 2095 intervals per population, with average maize genome coverage of 94.8%. Across all populations, there were 8.6 RH intervals per HIF line on average, ranging from 1.8 to 14 intervals; the average size of an RH interval was approximately 58.7 Mb, ranging from 7.2 to 74.1 Mb. A given RH region was present in an average of 5 different individuals within a population. Seven RH hotspots, where RH segments were enriched in the genome, were found to be subject to selection during population development. The RH patterns varied significantly across populations, presumably reflecting differences in the genetic background of each population, and 8 QTLs were found to affect heterozygosity levels in the RH hotspots. The potential use of this HIF library for the fine mapping of QTLs was assessed based on publicly available QTL information, achieving a ≤ 1 Mb resolution on average. CONCLUSION The examined library of HIF lines offers insight into the RH landscape and its intraspecific variation and provides a useful resource for the QTL cloning of important agronomic traits in maize.
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Affiliation(s)
- Nannan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jianxiao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
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76
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Lai X, Yan L, Lu Y, Schnable JC. Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:843-855. [PMID: 29265526 DOI: 10.1111/tpj.13806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/27/2017] [Accepted: 12/04/2017] [Indexed: 05/14/2023]
Abstract
The domestication of diverse grain crops from wild grasses was a result of artificial selection for a suite of overlapping traits producing changes referred to in aggregate as 'domestication syndrome'. Parallel phenotypic change can be accomplished by either selection on orthologous genes or selection on non-orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many 'classic' domestication genes identified through quantitative trait locus mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization part of domestication targeted small and largely non-overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.
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Affiliation(s)
- Xianjun Lai
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lang Yan
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
- Laboratory of Functional Genome and Application of Potato, Xichang College, Liangshan, 615000, China
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - James C Schnable
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
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77
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Steenwyk JL, Rokas A. Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation. Front Microbiol 2018; 9:288. [PMID: 29520259 PMCID: PMC5826948 DOI: 10.3389/fmicb.2018.00288] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/07/2018] [Indexed: 11/13/2022] Open
Abstract
In recent years, copy number (CN) variation has emerged as a new and significant source of genetic polymorphisms contributing to the phenotypic diversity of populations. CN variants are defined as genetic loci that, due to duplication and deletion, vary in their number of copies across individuals in a population. CN variants range in size from 50 base pairs to whole chromosomes, can influence gene activity, and are associated with a wide range of phenotypes in diverse organisms, including the budding yeast Saccharomyces cerevisiae. In this review, we introduce CN variation, discuss the genetic and molecular mechanisms implicated in its generation, how they can contribute to genetic and phenotypic diversity in fungal populations, and consider how CN variants may influence wine yeast adaptation in fermentation-related processes. In particular, we focus on reviewing recent work investigating the contribution of changes in CN of fermentation-related genes in yeast wine strains and offer notable illustrations of such changes, including the high levels of CN variation among the CUP genes, which confer resistance to copper, a metal with fungicidal properties, and the preferential deletion and duplication of the MAL1 and MAL3 loci, respectively, which are responsible for metabolizing maltose and sucrose. Based on the available data, we propose that CN variation is a substantial dimension of yeast genetic diversity that occurs largely independent of single nucleotide polymorphisms. As such, CN variation harbors considerable potential for understanding and manipulating yeast strains in the wine fermentation environment and beyond.
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Affiliation(s)
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
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78
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Hu Y, Ren J, Peng Z, Umana AA, Le H, Danilova T, Fu J, Wang H, Robertson A, Hulbert SH, White FF, Liu S. Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize. FRONTIERS IN PLANT SCIENCE 2018; 9:110. [PMID: 29479358 PMCID: PMC5812337 DOI: 10.3389/fpls.2018.00110] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/19/2018] [Indexed: 05/19/2023]
Abstract
Goss's wilt (GW) of maize is caused by the Gram-positive bacterium Clavibacter michiganensis subsp. nebraskensis (Cmn) and has spread in recent years throughout the Great Plains, posing a threat to production. The genetic basis of plant resistance is unknown. Here, a simple method for quantifying disease symptoms was developed and used to select cohorts of highly resistant and highly susceptible lines known as extreme phenotypes (XP). Copy number variation (CNV) analyses using whole genome sequences of bulked XP revealed 141 genes containing CNV between the two XP groups. The CNV genes include the previously identified common rust resistant locus rp1. Multiple Rp1 accessions with distinct rp1 haplotypes in an otherwise susceptible accession exhibited hypersensitive responses upon inoculation. GW provides an excellent system for the genetic dissection of diseases caused by closely related subspecies of C. michiganesis. Further work will facilitate breeding strategies to control GW and provide needed insight into the resistance mechanism of important related diseases such as bacterial canker of tomato and bacterial ring rot of potato.
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Affiliation(s)
- Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Zhao Peng
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Arnoldo A. Umana
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Ha Le
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Tatiana Danilova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiyan Wang
- Department of Statistics, Kansas State University, Manhattan, KS, United States
| | - Alison Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
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79
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Darracq A, Vitte C, Nicolas S, Duarte J, Pichon JP, Mary-Huard T, Chevalier C, Bérard A, Le Paslier MC, Rogowsky P, Charcosset A, Joets J. Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics 2018; 19:119. [PMID: 29402214 PMCID: PMC5800051 DOI: 10.1186/s12864-018-4490-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, they have been only scarcely characterized at the sequence level and the extent of presence/absence variation and relative chromosomal landscape of inbred-specific regions remain to be elucidated. RESULTS De novo genome sequencing of the French F2 maize inbred line revealed 10,044 novel genomic regions larger than 1 kb, making up 88 Mb of DNA, that are present in F2 but not in B73 (PAV). This set of maize PAV sequences allowed us to annotate PAV content and to analyze sequence breakpoints. Using PAV genotyping on a collection of 25 temperate lines, we also analyzed Linkage Disequilibrium in PAVs and flanking regions, and PAV frequencies within maize genetic groups. CONCLUSIONS We highlight the possible role of MMEJ-type double strand break repair in maize PAV formation and discover 395 new genes with transcriptional support. Pattern of linkage disequilibrium within PAVs strikingly differs from this of flanking regions and is in accordance with the intuition that PAVs may recombine less than other genomic regions. We show that most PAVs are ancient, while some are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Characterization of such PAVs will provide useful material for further association genetic studies in European and temperate maize.
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Affiliation(s)
- Aude Darracq
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Clémentine Vitte
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stéphane Nicolas
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | | | - Tristan Mary-Huard
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- MIA, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Céline Chevalier
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélie Bérard
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, Evry, France
| | | | - Peter Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Alain Charcosset
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Johann Joets
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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80
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Yin J, Gosney MJ, Dilkes BP, Mickelbart MV. Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions. PLANT DIRECT 2018; 2:e00032. [PMID: 31245703 PMCID: PMC6508522 DOI: 10.1002/pld3.32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/01/2017] [Accepted: 12/08/2017] [Indexed: 05/16/2023]
Abstract
Eutrema salsugineum is a model species for the study of plant adaptation to abiotic stresses. Two accessions of E. salsugineum, Shandong (SH) and Yukon (YK), exhibit contrasting morphology and biotic and abiotic stress tolerance. Transcriptome profiling and metabolic profiling from tissue samples collected during the dark period were used to investigate the molecular and metabolic bases of these contrasting phenotypes. RNA sequencing identified 17,888 expressed genes, of which 157 were not in the published reference genome, and 65 of which were detected for the first time. Differential expression was detected for only 31 genes. The RNA sequencing data contained 14,808 single nucleotide polymorphisms (SNPs) in transcripts, 3,925 of which are newly identified. Among the differentially expressed genes, there were no obvious candidates for the physiological or morphological differences between SH and YK. Metabolic profiling indicated that YK accumulates free fatty acids and long-chain fatty acid derivatives as compared to SH, whereas sugars are more abundant in SH. Metabolite levels suggest that carbohydrate and respiratory metabolism, including starch degradation, is more active during the first half of the dark period in SH. These metabolic differences may explain the greater biomass accumulation in YK over SH. The accumulation of 56% of the identified metabolites was lower in F1 hybrids than the mid-parent averages and the accumulation of 17% of the metabolites in F1 plants transgressed the level in both parents. Concentrations of several metabolites in F1 hybrids agree with previous studies and suggest a role for primary metabolism in heterosis. The improved annotation of the E. salsugineum genome and newly identified high-quality SNPs will permit accelerated studies using the standing variation in this species to elucidate the mechanisms of its diverse adaptations to the environment.
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Affiliation(s)
- Jie Yin
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteINUSA
| | - Michael J. Gosney
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteINUSA
| | - Brian P. Dilkes
- Department of BiochemistryPurdue UniversityWest LafayetteINUSA
| | - Michael V. Mickelbart
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteINUSA
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteINUSA
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81
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Chen L, Zhang P, Fan Y, Lu Q, Li Q, Yan J, Muehlbauer GJ, Schnable PS, Dai M, Li L. Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize. THE NEW PHYTOLOGIST 2018; 217:1292-1306. [PMID: 29155438 DOI: 10.1111/nph.14901] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/18/2017] [Indexed: 05/21/2023]
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules. Recent studies have shown that circRNAs can arise from the transcripts of transposons. Given the prevalence of transposons in the maize genome and dramatic genomic variation driven by transposons, we hypothesize that transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. We performed circRNA-Seq on B73 seedling leaves and uncovered 2804 high-confidence maize circRNAs, which show distinct genomic features. Comprehensive analyses demonstrated that sequences related to LINE1-like elements (LLEs) and their Reverse Complementary Pairs (LLERCPs) are significantly enriched in the flanking regions of circRNAs. Interestingly, as the number of LLERCPs increase, the accumulation of circRNAs varies, whereas that of linear transcripts decreases. Furthermore, genes with LLERCP-mediated circRNAs are enriched among loci that are associated with phenotypic variation. These results suggest that circRNAs are likely to be involved in the modulation of phenotypic variation by LLERCPs. Further, we showed that the presence/absence variation of LLERCPs was associated with expression variation of circRNA-circ1690 and was related to ear height, potentially through the interplay between circRNAs and functional linear transcripts. Our first study of maize circRNAs uncovers a potential new way for transposons to modulate transcriptomic and phenotypic variations.
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Affiliation(s)
- Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiong Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | | | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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82
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Baldauf JA, Marcon C, Lithio A, Vedder L, Altrogge L, Piepho HP, Schoof H, Nettleton D, Hochholdinger F. Single-Parent Expression Is a General Mechanism Driving Extensive Complementation of Non-syntenic Genes in Maize Hybrids. Curr Biol 2018; 28:431-437.e4. [PMID: 29358068 DOI: 10.1016/j.cub.2017.12.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 12/11/2022]
Abstract
Maize (Zea mays L.) displays an exceptional degree of structural genomic diversity [1, 2]. In addition, variation in gene expression further contributes to the extraordinary phenotypic diversity and plasticity of maize. This study provides a systematic investigation on how distantly related homozygous maize inbred lines affect the transcriptomic plasticity of their highly heterozygous F1 hybrids. The classical dominance model of heterosis explains the superiority of hybrid plants by the complementation of deleterious parental alleles by superior alleles of the second parent at many loci [3]. Genes active in one inbred line but inactive in another represent an extreme instance of allelic diversity defined as single-parent expression [4]. We observed on average ∼1,000 such genes in all inbred line combinations during primary root development. These genes consistently displayed expression complementation (i.e., activity) in their hybrid progeny. Consequently, extreme expression complementation is a general mechanism that results on average in ∼600 additionally active genes and their encoded biological functions in hybrids. The modern maize genome is complemented by a set of non-syntenic genes, which emerged after the separation of the maize and sorghum lineages and lack syntenic orthologs in any other grass species [5]. We demonstrated that non-syntenic genes are the driving force of gene expression complementation in hybrids. Among those, the highly diversified families of bZIP and bHLH transcription factors [6] are systematically overrepresented. In summary, extreme gene expression complementation extensively shapes the transcriptomic plasticity of maize hybrids and might therefore be one factor controlling the developmental plasticity of hybrids.
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Affiliation(s)
- Jutta A Baldauf
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Caroline Marcon
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, 2438 Osborne Dr., Ames, IA 50011-1210, USA
| | - Lucia Vedder
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115 Bonn, Germany
| | - Lena Altrogge
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115 Bonn, Germany
| | - Hans-Peter Piepho
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstraße 23, 70599 Stuttgart, Germany
| | - Heiko Schoof
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115 Bonn, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, 2438 Osborne Dr., Ames, IA 50011-1210, USA
| | - Frank Hochholdinger
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany.
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83
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Brohammer AB, Kono TJY, Springer NM, McGaugh SE, Hirsch CN. The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:131-141. [PMID: 29124819 DOI: 10.1111/tpj.13765] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/14/2017] [Accepted: 10/27/2017] [Indexed: 05/22/2023]
Abstract
Maize is a diverse paleotetraploid species with considerable presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization. Differential fractionation refers to non-shared gene loss events between individuals following a whole-genome duplication event. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole-genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variably fractionated syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non-syntenic genes were six times more likely to be variable than syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large-scale presence/absence variation among syntenic genes.
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Affiliation(s)
- Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, 1445 Gortner Avenue, St Paul, MN, 55108, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
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84
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85
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Dolatabadian A, Patel DA, Edwards D, Batley J. Copy number variation and disease resistance in plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2479-2490. [PMID: 29043379 DOI: 10.1007/s00122-017-2993-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 09/27/2017] [Indexed: 05/06/2023]
Abstract
Plant genome diversity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype; in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning. Since CNVs are likely to be associated with disease resistance in plants, an understanding of the distribution of CNVs could assist in the identification of novel plant disease-resistance genes. In this paper, we review existing information about CNVs; their importance, role and function, as well as their association with disease resistance in plants.
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Affiliation(s)
- Aria Dolatabadian
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Dhwani Apurva Patel
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia.
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86
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Grover CE, Arick MA, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, Wendel JF. Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing. Genome Biol Evol 2017; 9:3328-3344. [PMID: 29194487 PMCID: PMC5737505 DOI: 10.1093/gbe/evx248] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2017] [Indexed: 12/19/2022] Open
Abstract
Long-distance insular dispersal is associated with divergence and speciation because of founder effects and strong genetic drift. The cotton tribe (Gossypieae) has experienced multiple transoceanic dispersals, generating an aggregate geographic range that encompasses much of the tropics and subtropics worldwide. Two genera in the Gossypieae, Kokia and Gossypioides, exhibit a remarkable geographic disjunction, being restricted to the Hawaiian Islands and Madagascar/East Africa, respectively. We assembled and use de novo genome sequences to address questions regarding the divergence of these two genera from each other and from their sister-group, Gossypium. In addition, we explore processes underlying the genome downsizing that characterizes Kokia and Gossypioides relative to other genera in the tribe. Using 13,000 gene orthologs and synonymous substitution rates, we show that the two disjuncts last shared a common ancestor ∼5 Ma, or half as long ago as their divergence from Gossypium. We report relative stasis in the transposable element fraction. In comparison to Gossypium, there is loss of ∼30% of the gene content in the two disjunct genera and a history of genome-wide accumulation of deletions. In both genera, there is a genome-wide bias toward deletions over insertions, and the number of gene losses exceeds the number of gains by ∼2- to 4-fold. The genomic analyses presented here elucidate genomic consequences of the demographic and biogeographic history of these closest relatives of Gossypium, and enhance their value as phylogenetic outgroups.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Mark A Arick
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Adam Thrash
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - William S Sanders
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
- Department of Computer Science & Engineering, Mississippi State University, Mississippi State, MS
- The Jackson Laboratory, Connecticut, Farmington, CT
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Punjab, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Punjab, Pakistan
| | - Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, P.R. China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, P.R. China
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico
| | | | - Joshua A Udall
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
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87
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Hu X, Wang H, Li K, Wu Y, Liu Z, Huang C. Genome-wide proteomic profiling reveals the role of dominance protein expression in heterosis in immature maize ears. Sci Rep 2017; 7:16130. [PMID: 29170427 PMCID: PMC5700959 DOI: 10.1038/s41598-017-15985-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/06/2017] [Indexed: 01/02/2023] Open
Abstract
Heterosis refers to the phenomenon in which hybrid progeny show superior performance relative to their parents. Early maize ear development shows strong heterosis in ear architecture traits and greatly affects grain yield. To explore the underlying molecular mechanisms, genome-wide proteomics of immature ears of maize hybrid ZD909 and its parents were analyzed using tandem mass tag (TMT) technology. A total of 9,713 proteins were identified in all three genotypes. Among them, 3,752 (38.6%) proteins were differentially expressed between ZD909 and its parents. Multiple modes of protein action were discovered in the hybrid, while dominance expression patterns accounted for 63.6% of the total differentially expressed proteins (DEPs). Protein pathway enrichment analysis revealed that high parent dominance proteins mainly participated in carbon metabolism and nitrogen assimilation processes. Our results suggested that the dominant expression of favorable alleles related to C/N metabolism in the hybrid may be essential for ZD909 ear growth and heterosis formation. Integrated analysis of proteomic and quantitative trait locus (QTL) data further support our DEP identification and provide useful information for the discovery of genes associated with ear development. Our study provides comprehensive insight into the molecular mechanisms underlying heterosis in immature maize ears from a proteomic perspective.
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Affiliation(s)
- Xiaojiao Hu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Hongwu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Kun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Yujin Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China
| | - Zhifang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China.
| | - Changling Huang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Engineering Laboratory for Crop Molecular Breeding, Beijing, 100081, China.
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88
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Prunier J, Caron S, Lamothe M, Blais S, Bousquet J, Isabel N, MacKay J. Gene copy number variations in adaptive evolution: The genomic distribution of gene copy number variations revealed by genetic mapping and their adaptive role in an undomesticated species, white spruce (Picea glauca). Mol Ecol 2017; 26:5989-6001. [PMID: 28833771 DOI: 10.1111/mec.14337] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/26/2017] [Accepted: 08/05/2017] [Indexed: 01/09/2023]
Abstract
Gene copy number variation (CNV) has been associated with phenotypic variability in animals and plants, but a genomewide understanding of their impacts on phenotypes is largely restricted to human and agricultural systems. As such, CNVs have rarely been considered in investigations of the genomic architecture of adaptation in wild species. Here, we report on the genetic mapping of gene CNVs in white spruce, which lacks a contiguous assembly of its large genome (~20 Gb), and their relationships with adaptive phenotypic variation. We detected 3,911 gene CNVs including de novo structural variations using comparative genome hybridization on arrays (aCGH) in a large progeny set. We inferred the heterozygosity at CNV loci within parents by comparing haploid and diploid tissues and genetically mapped 82 gene CNVs. Our analysis showed that CNVs were distributed over 10 linkage groups and identified four CNV hotspots that we predict to occur in other species of the Pinaceae. Significant relationships were found between 29 of the gene CNVs and adaptive traits based on regression analyses with timings of bud set and bud flush, and height growth, suggesting a role for CNVs in climate adaptation. The importance of CNVs in adaptive evolution of white spruce was also indicated by functional gene annotations and the clustering of 31% of the mapped adaptive gene CNVs in CNV hotspots. Taken together, these results illustrate the feasibility of studying CNVs in undomesticated species and represent a major step towards a better understanding of the roles of CNVs in adaptive evolution.
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Affiliation(s)
- Julien Prunier
- Institute for System and Integrative Biology (IBIS), Université Laval, Québec, QC, Canada.,Centre for Forest Research, Université Laval, Québec, QC, Canada
| | - Sébastien Caron
- Institute for System and Integrative Biology (IBIS), Université Laval, Québec, QC, Canada.,Centre for Forest Research, Université Laval, Québec, QC, Canada
| | - Manuel Lamothe
- Laurentian Forest Centre, Canadian Forest Service, Natural Resources Canada, Quebec, QC, Canada.,Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC, Canada
| | - Sylvie Blais
- Institute for System and Integrative Biology (IBIS), Université Laval, Québec, QC, Canada.,Centre for Forest Research, Université Laval, Québec, QC, Canada.,Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC, Canada
| | - Jean Bousquet
- Institute for System and Integrative Biology (IBIS), Université Laval, Québec, QC, Canada.,Centre for Forest Research, Université Laval, Québec, QC, Canada.,Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC, Canada
| | - Nathalie Isabel
- Laurentian Forest Centre, Canadian Forest Service, Natural Resources Canada, Quebec, QC, Canada.,Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC, Canada
| | - John MacKay
- Centre for Forest Research, Université Laval, Québec, QC, Canada.,Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC, Canada.,Department of Plant Sciences, University of Oxford, Oxford, UK
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89
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Liu J, Sniezko RA, Zamany A, Williams H, Wang N, Kegley A, Savin DP, Chen H, Sturrock RN. Saturated genic SNP mapping identified functional candidates and selection tools for the Pinus monticola Cr2 locus controlling resistance to white pine blister rust. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1149-1162. [PMID: 28176454 PMCID: PMC5552481 DOI: 10.1111/pbi.12705] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 01/11/2017] [Accepted: 02/02/2017] [Indexed: 05/17/2023]
Abstract
Molecular breeding incorporates efficient tools to increase rust resistance in five-needle pines. Susceptibility of native five-needle pines to white pine blister rust (WPBR), caused by the non-native invasive fungus Cronartium ribicola (J.C. Fisch.), has significantly reduced wild populations of these conifers in North America. Major resistance (R) genes against specific avirulent pathotypes have been found in several five-needle pine species. In this study, we screened genic SNP markers by comparative transcriptome and genetic association analyses and constructed saturated linkage maps for the western white pine (Pinus monticola) R locus (Cr2). Phenotypic segregation was measured by a hypersensitive reaction (HR)-like response on the needles and disease symptoms of cankered stems post inoculation by the C. ribicola avcr2 race. SNP genotypes were determined by HRM- and TaqMan-based SNP genotyping. Saturated maps of the Cr2-linkage group (LG) were constructed in three seed families using a total of 34 SNP markers within 21 unique genes. Cr2 was consistently flanked by contig_2142 (encoding a ruvb-like protein) and contig_3772 (encoding a delta-fatty acid desaturase) across the three seed families. Cr2 was anchored to the Pinus consensus LG-1, which differs from LGs where other R loci of Pinus species were mapped. GO annotation identified a set of NBS-LRR and other resistance-related genes as R candidates in the Cr2 region. Association of one nonsynonymous SNP locus of an NBS-LRR gene with Cr2-mediated phenotypes provides a valuable tool for marker-assisted selection (MAS), which will shorten the breeding cycle of resistance screening and aid in the restoration of WPBR-disturbed forest ecosystems.
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Affiliation(s)
- Jun‐Jun Liu
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
| | | | - Arezoo Zamany
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
| | - Holly Williams
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
| | - Ning Wang
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
- Academy of Agriculture and Forestry ScienceQinghai UniversityXiningChina
| | - Angelia Kegley
- Dorena Genetic Resource CenterUSDA Forest ServiceCottage GroveORUSA
| | - Douglas P. Savin
- Dorena Genetic Resource CenterUSDA Forest ServiceCottage GroveORUSA
| | - Hao Chen
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
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90
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Yurkevich OY, Kirov IV, Bolsheva NL, Rachinskaya OA, Grushetskaya ZE, Zoschuk SA, Samatadze TE, Bogdanova MV, Lemesh VA, Amosova AV, Muravenko OV. Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase ( CesA) Genes in Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1467. [PMID: 28878799 PMCID: PMC5572355 DOI: 10.3389/fpls.2017.01467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 08/07/2017] [Indexed: 05/07/2023]
Abstract
Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase (CesA) multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH)-based chromosomal localization of the CesA conserved fragment (KF011584.1), 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum. Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG) 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.
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Affiliation(s)
- Olga Y. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Ilya V. Kirov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga A. Rachinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Zoya E. Grushetskaya
- Institute of Genetics and Cytology, National Academy of Sciences of BelarusMinsk, Belarus
| | - Svyatoslav A. Zoschuk
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Marina V. Bogdanova
- Institute of Genetics and Cytology, National Academy of Sciences of BelarusMinsk, Belarus
| | - Valentina A. Lemesh
- Institute of Genetics and Cytology, National Academy of Sciences of BelarusMinsk, Belarus
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
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91
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Feenstra AD, Alexander LE, Song Z, Korte AR, Yandeau-Nelson MD, Nikolau BJ, Lee YJ. Spatial Mapping and Profiling of Metabolite Distributions during Germination. PLANT PHYSIOLOGY 2017; 174:2532-2548. [PMID: 28634228 PMCID: PMC5543969 DOI: 10.1104/pp.17.00652] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/15/2017] [Indexed: 05/18/2023]
Abstract
Germination is a highly complex process by which seeds begin to develop and establish themselves as viable organisms. In this study, we utilize a combination of gas chromatography-mass spectrometry, liquid chromatography-fluorescence, and mass spectrometry imaging approaches to profile and visualize the metabolic distributions of germinating seeds from two different inbreds of maize (Zea mays) seeds, B73 and Mo17. Gas chromatography and liquid chromatography analyses demonstrate that the two inbreds are highly differentiated in their metabolite profiles throughout the course of germination, especially with regard to amino acids, sugar alcohols, and small organic acids. Crude dissection of the seed followed by gas chromatography-mass spectrometry analysis of polar metabolites also revealed that many compounds were highly sequestered among the various seed tissue types. To further localize compounds, matrix-assisted laser desorption/ionization mass spectrometry imaging was utilized to visualize compounds in fine detail in their native environments over the course of germination. Most notably, the fatty acyl chain-dependent differential localization of phospholipids and triacylglycerols was observed within the embryo and radicle, showing correlation with the heterogeneous distribution of fatty acids. Other interesting observations include unusual localization of ceramides on the endosperm/scutellum boundary and subcellular localization of ferulate in the aleurone.
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Affiliation(s)
- Adam D Feenstra
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
- Ames Laboratory-United States Department of Energy, Ames, Iowa 50011
| | - Liza E Alexander
- Ames Laboratory-United States Department of Energy, Ames, Iowa 50011
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Zhihong Song
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Andrew R Korte
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
- Ames Laboratory-United States Department of Energy, Ames, Iowa 50011
| | - Marna D Yandeau-Nelson
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Basil J Nikolau
- Ames Laboratory-United States Department of Energy, Ames, Iowa 50011
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
- Ames Laboratory-United States Department of Energy, Ames, Iowa 50011
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92
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Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D. Improved maize reference genome with single-molecule technologies. Nature 2017; 546:524-527. [PMID: 28605751 DOI: 10.1101/079004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 05/14/2017] [Indexed: 05/21/2023]
Abstract
Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.
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Affiliation(s)
- Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Paul Peluso
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Jinghua Shi
- BioNano Genomics, San Diego, California 92121, USA
| | | | - Michelle C Stitzer
- Department of Plant Sciences and Center for Population Biology, University of California, Davis, Davis, California 95616, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Joshua C Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Xuehong Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Katherine Guill
- USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri 65211, USA
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Kevin L Schneider
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Thomas K Wolfgruber
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Michael R May
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA
| | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Eric Antoniou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Gernot G Presting
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Michael McMullen
- USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri 65211, USA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, Center for Population Biology, and Genome Center, University of California, Davis, California 95616, USA
| | - R Kelly Dawe
- University of Georgia, Athens, Georgia 30602, USA
| | - Alex Hastie
- BioNano Genomics, San Diego, California 92121, USA
| | - David R Rank
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- USDA-ARS, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York 14853, USA
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93
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Improved maize reference genome with single-molecule technologies. Nature 2017; 546:524-527. [PMID: 28605751 PMCID: PMC7052699 DOI: 10.1038/nature22971] [Citation(s) in RCA: 711] [Impact Index Per Article: 101.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 05/14/2017] [Indexed: 01/01/2023]
Abstract
An improved reference genome for maize, using single-molecule sequencing and high-resolution optical mapping, enables characterization of structural variation and repetitive regions, and identifies lineage expansions of transposable elements that are unique to maize. The maize genome was initially reported in 2009 but with some accuracy limitations. Doreen Ware and colleagues report a new reference genome for maize using single-molecule sequencing and high-resolution optical mapping. The technique shows improvements in the gene space including resolution of gaps and misassemblies and correction of order and orientation of genes. The authors characterize structural variation and repetitive regions, and identify transposable element lineage expansions unique to maize. Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation1. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions2. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome3, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing4. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.
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94
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Xu Y, Li P, Zou C, Lu Y, Xie C, Zhang X, Prasanna BM, Olsen MS. Enhancing genetic gain in the era of molecular breeding. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2641-2666. [PMID: 28830098 DOI: 10.1093/jxb/erx135] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/03/2017] [Indexed: 05/20/2023]
Abstract
As one of the important concepts in conventional quantitative genetics and breeding, genetic gain can be defined as the amount of increase in performance that is achieved annually through artificial selection. To develop pro ducts that meet the increasing demand of mankind, especially for food and feed, in addition to various industrial uses, breeders are challenged to enhance the potential of genetic gain continuously, at ever higher rates, while they close the gaps that remain between the yield potential in breeders' demonstration trials and the actual yield in farmers' fields. Factors affecting genetic gain include genetic variation available in breeding materials, heritability for traits of interest, selection intensity, and the time required to complete a breeding cycle. Genetic gain can be improved through enhancing the potential and closing the gaps, which has been evolving and complemented with modern breeding techniques and platforms, mainly driven by molecular and genomic tools, combined with improved agronomic practice. Several key strategies are reviewed in this article. Favorable genetic variation can be unlocked and created through molecular and genomic approaches including mutation, gene mapping and discovery, and transgene and genome editing. Estimation of heritability can be improved by refining field experiments through well-controlled and precisely assayed environmental factors or envirotyping, particularly for understanding and controlling spatial heterogeneity at the field level. Selection intensity can be significantly heightened through improvements in the scale and precision of genotyping and phenotyping. The breeding cycle time can be shortened by accelerating breeding procedures through integrated breeding approaches such as marker-assisted selection and doubled haploid development. All the strategies can be integrated with other widely used conventional approaches in breeding programs to enhance genetic gain. More transdisciplinary approaches, team breeding, will be required to address the challenge of maintaining a plentiful and safe food supply for future generations. New opportunities for enhancing genetic gain, a high efficiency breeding pipeline, and broad-sense genetic gain are also discussed prospectively.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, México
| | - Ping Li
- Nantong Xinhe Bio-Technology, Nantong 226019, PR China
| | - Cheng Zou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Chuanxiao Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, México
| | - Boddupalli M Prasanna
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF campus, United Nations Avenue, Nairobi, Kenya
| | - Michael S Olsen
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF campus, United Nations Avenue, Nairobi, Kenya
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95
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Ruggieri V, Anzar I, Paytuvi A, Calafiore R, Cigliano RA, Sanseverino W, Barone A. Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP. DNA Res 2017; 24:81-91. [PMID: 28011720 PMCID: PMC5381350 DOI: 10.1093/dnares/dsw050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/26/2016] [Indexed: 01/08/2023] Open
Abstract
The recent development of Sequence Capture methodology represents a powerful strategy for enhancing data generation to assess genetic variation of targeted genomic regions. Here, we present SUPER-CAP, a bioinformatics web tool aimed at handling Sequence Capture data, fine calculating the allele frequency of variations and building genotype-specific sequence of captured genes. The dataset used to develop this in silico strategy consists of 378 loci and related regulative regions in a collection of 44 tomato landraces. About 14,000 high-quality variants were identified. The high depth (>40×) of coverage and adopting the correct filtering criteria allowed identification of about 4,000 rare variants and 10 genes with a different copy number variation. We also show that the tool is capable to reconstruct genotype-specific sequences for each genotype by using the detected variants. This allows evaluating the combined effect of multiple variants in the same protein. The architecture and functionality of SUPER-CAP makes the software appropriate for a broad set of analyses including SNP discovery and mining. Its functionality, together with the capability to process large data sets and efficient detection of sequence variation, makes SUPER-CAP a valuable bioinformatics tool for genomics and breeding purposes.
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Affiliation(s)
- Valentino Ruggieri
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy.,Sequentia Biotech SL, Calle Compte d'Urgell, 240, 08035 Barcelona, Spain
| | - Irantzu Anzar
- Sequentia Biotech SL, Calle Compte d'Urgell, 240, 08035 Barcelona, Spain
| | - Andreu Paytuvi
- Sequentia Biotech SL, Calle Compte d'Urgell, 240, 08035 Barcelona, Spain
| | - Roberta Calafiore
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy
| | | | - Walter Sanseverino
- Sequentia Biotech SL, Calle Compte d'Urgell, 240, 08035 Barcelona, Spain
| | - Amalia Barone
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy
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96
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Sedivy EJ, Wu F, Hanzawa Y. Soybean domestication: the origin, genetic architecture and molecular bases. THE NEW PHYTOLOGIST 2017; 214:539-553. [PMID: 28134435 DOI: 10.1111/nph.14418] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/28/2016] [Indexed: 05/20/2023]
Abstract
Domestication provides an important model for the study of evolution, and information learned from domestication research aids in the continued improvement of crop species. Recent progress in de novo assembly and whole-genome resequencing of wild and cultivated soybean genomes, in addition to new archeological discoveries, sheds light on the origin of this important crop and provides a clearer view on the modes of artificial selection that drove soybean domestication and diversification. This novel genomic information enables the search for polymorphisms that underlie variation in agronomic traits and highlights genes that exhibit a signature of selection, leading to the identification of a number of candidate genes that may have played important roles in soybean domestication, diversification and improvement. These discoveries provide a novel point of comparison on the evolutionary bases of important agronomic traits among different crop species.
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Affiliation(s)
- Eric J Sedivy
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Faqiang Wu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yoshie Hanzawa
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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97
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Xiao Y, Liu H, Wu L, Warburton M, Yan J. Genome-wide Association Studies in Maize: Praise and Stargaze. MOLECULAR PLANT 2017; 10:359-374. [PMID: 28039028 DOI: 10.1016/j.molp.2016.12.008] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 12/02/2016] [Accepted: 12/20/2016] [Indexed: 05/18/2023]
Abstract
Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype-phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies. Maize is an ideal crop for GWAS and significant progress has been made in the last decade. This review summarizes current GWAS efforts in maize functional genomics research and discusses future prospects in the omics era. The general goal of GWAS is to link genotypic variations to corresponding differences in phenotype using the most appropriate statistical model in a given population. The current review also presents perspectives for optimizing GWAS design and analysis. GWAS analysis of data from RNA, protein, and metabolite-based omics studies is discussed, along with new models and new population designs that will identify causes of phenotypic variation that have been hidden to date. The joint and continuous efforts of the whole community will enhance our understanding of maize quantitative traits and boost crop molecular breeding designs.
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Affiliation(s)
- Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Liuji Wu
- Synergetic Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Marilyn Warburton
- United States of Department of Agriculture, Agricultural Research Service, Corn Host Plant Resistance Research Unit, Box 9555, MS 39762, Mississippi, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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98
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Samelak-Czajka A, Marszalek-Zenczak M, Marcinkowska-Swojak M, Kozlowski P, Figlerowicz M, Zmienko A. MLPA-Based Analysis of Copy Number Variation in Plant Populations. FRONTIERS IN PLANT SCIENCE 2017; 8:222. [PMID: 28270823 PMCID: PMC5318451 DOI: 10.3389/fpls.2017.00222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/06/2017] [Indexed: 05/18/2023]
Abstract
Copy number variants (CNVs) are intraspecies duplications/deletions of large DNA segments (>1 kb). A growing number of reports highlight the functional and evolutionary impact of CNV in plants, increasing the need for appropriate tools that enable locus-specific CNV genotyping on a population scale. Multiplex ligation-dependent probe amplification (MLPA) is considered a gold standard in genotyping CNV in humans. Consequently, numerous commercial MLPA assays for CNV-related human diseases have been created. We routinely genotype complex multiallelic CNVs in human and plant genomes using the modified MLPA procedure based on fully synthesized oligonucleotide probes (90-200 nt), which greatly simplifies the design process and allows for the development of custom assays. Here, we present a step-by-step protocol for gene-specific MLPA probe design, multiplexed assay setup and data analysis in a copy number genotyping experiment in plants. As a case study, we present the results of a custom assay designed to genotype the copy number status of 12 protein coding genes in a population of 80 Arabidopsis accessions. The genes were pre-selected based on whole genome sequencing data and are localized in the genomic regions that display different levels of population-scale variation (non-variable, biallelic, or multiallelic, as well as CNVs overlapping whole genes or their fragments). The presented approach is suitable for population-scale validation of the CNV regions inferred from whole genome sequencing data analysis and for focused analysis of selected genes of interest. It can also be very easily adopted for any plant species, following optimization of the template amount and design of the appropriate control probes, according to the general guidelines presented in this paper.
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Affiliation(s)
- Anna Samelak-Czajka
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
| | - Malgorzata Marszalek-Zenczak
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | | | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Marek Figlerowicz
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Agnieszka Zmienko
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
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99
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Liu S, Zheng J, Migeon P, Ren J, Hu Y, He C, Liu H, Fu J, White FF, Toomajian C, Wang G. Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement. Sci Rep 2017; 7:42444. [PMID: 28186206 PMCID: PMC5301235 DOI: 10.1038/srep42444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/10/2017] [Indexed: 12/15/2022] Open
Abstract
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.
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Affiliation(s)
- Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jun Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Cheng He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Hongjun Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Taian 271018, P.R. China.,College of Life Sciences, Shandong Agricultural University, Taian 271018, P.R. China
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
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100
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Marcon C, Paschold A, Malik WA, Lithio A, Baldauf JA, Altrogge L, Opitz N, Lanz C, Schoof H, Nettleton D, Piepho HP, Hochholdinger F. Stability of Single-Parent Gene Expression Complementation in Maize Hybrids upon Water Deficit Stress. PLANT PHYSIOLOGY 2017; 173:1247-1257. [PMID: 27999083 PMCID: PMC5291719 DOI: 10.1104/pp.16.01045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/18/2016] [Indexed: 05/24/2023]
Abstract
Heterosis is the superior performance of F1 hybrids compared with their homozygous, genetically distinct parents. In this study, we monitored the transcriptomic divergence of the maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrid progeny in primary roots under control and water deficit conditions simulated by polyethylene glycol treatment. Single-parent expression (SPE) of genes is an extreme instance of gene expression complementation, in which genes are active in only one of two parents but are expressed in both reciprocal hybrids. In this study, 1,997 genes only expressed in B73 and 2,024 genes only expressed in Mo17 displayed SPE complementation under control and water deficit conditions. As a consequence, the number of active genes in hybrids exceeded the number of active genes in the parental inbred lines significantly independent of treatment. SPE patterns were substantially more stable to expression changes by water deficit treatment than other genotype-specific expression profiles. While, on average, 75% of all SPE patterns were not altered in response to polyethylene glycol treatment, only 17% of the remaining genotype-specific expression patterns were not changed by water deficit. Nonsyntenic genes that lack syntenic orthologs in other grass species, and thus evolved late in the grass lineage, were significantly overrepresented among SPE genes. Hence, the significant overrepresentation of nonsyntenic genes among SPE patterns and their stability under water limitation might suggest a function of these genes during the early developmental manifestation of heterosis under fluctuating environmental conditions in hybrid progeny of the inbred lines B73 and Mo17.
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Affiliation(s)
- Caroline Marcon
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Anja Paschold
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Waqas Ahmed Malik
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Andrew Lithio
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Jutta A Baldauf
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Lena Altrogge
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Christa Lanz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Heiko Schoof
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Dan Nettleton
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Hans-Peter Piepho
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.)
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics (C.M., A.P., J.A.B., N.O., F.H.) and Crop Bioinformatics (L.A., H.S.), University of Bonn, 53113 Bonn, Germany;
- Institute for Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.);
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210 (A.L., D.N.); and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany (C.L.)
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