151
|
Pass DA, Sornay E, Marchbank A, Crawford MR, Paszkiewicz K, Kent NA, Murray JAH. Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet 2017; 13:e1006988. [PMID: 28902852 PMCID: PMC5597176 DOI: 10.1371/journal.pgen.1006988] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes. The genome-wide profile of these subNSPs has not been previously analysed in plants and this study investigates the relationship of dynamic bound particles with transcriptional control. Here we combine differential micrococcal nuclease (MNase) digestion and a modified paired-end sequencing protocol to reveal the chromatin structure landscape of Arabidopsis cells across a wide particle size range. Linking this data to RNAseq expression analysis provides detailed insight into the relationship of identified DNA-bound particles with transcriptional activity. The use of differential digestion reveals sensitive positions, including a labile -1 nucleosome positioned upstream of the transcription start site (TSS) of active genes. We investigated the response of the chromatin landscape to changes in environmental conditions using light and dark growth, given the large transcriptional changes resulting from this simple alteration. The resulting shifts in the suites of expressed and repressed genes show little correspondence to changes in nucleosome positioning, but led to significant alterations in the profile of subNSPs upstream of TSS both globally and locally. We examined previously mapped positions for the TFs PIF3, PIF4 and CCA1, which regulate light responses, and found that changes in subNSPs co-localized with these binding sites. This small particle structure is detected only under low levels of MNase digestion and is lost on more complete digestion of chromatin to nucleosomes. We conclude that wide-spectrum analysis of the Arabidopsis genome by differential MNase digestion allows detection of sensitive features hereto obscured, and the comparisons between genome-wide subNSP profiles reveals dynamic changes in their distribution, particularly at distinct genomic locations (i.e. 5'UTRs). The method here employed allows insight into the complex influence of genetic and extrinsic factors in modifying the sub-nucleosomal landscape in association with transcriptional changes.
Collapse
Affiliation(s)
- Daniel Antony Pass
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Emily Sornay
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Angela Marchbank
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Margaret R. Crawford
- Genome Centre, University of Sussex, Sussex House, Falmer, Brighton, United Kingdom
| | - Konrad Paszkiewicz
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, United Kingdom
| | - Nicholas A. Kent
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - James A. H. Murray
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| |
Collapse
|
152
|
Wear EE, Song J, Zynda GJ, LeBlanc C, Lee TJ, Mickelson-Young L, Concia L, Mulvaney P, Szymanski ES, Allen GC, Martienssen RA, Vaughn MW, Hanley-Bowdoin L, Thompson WF. Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize ( Zea mays) Root Tips. THE PLANT CELL 2017; 29:2126-2149. [PMID: 28842533 PMCID: PMC5635974 DOI: 10.1105/tpc.17.00037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/31/2017] [Accepted: 08/24/2017] [Indexed: 05/19/2023]
Abstract
All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ∼32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.
Collapse
Affiliation(s)
- Emily E Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Gregory J Zynda
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Chantal LeBlanc
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Lorenzo Concia
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Patrick Mulvaney
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Eric S Szymanski
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - George C Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - William F Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| |
Collapse
|
153
|
Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, Mumm RH, Ross-Ibarra J. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genet 2017; 13:e1007019. [PMID: 28953891 PMCID: PMC5633198 DOI: 10.1371/journal.pgen.1007019] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 10/09/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.
Collapse
Affiliation(s)
- Jinliang Yang
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Sofiane Mezmouk
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | | | - Edward S. Buckler
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
- Institute for Genomic Diversity, Ithaca, New York, United States of America
- US Department of Agriculture–Agricultural Research Service, Ithaca, New York, United States of America
| | - Katherine E. Guill
- US Department of Agriculture, Agricultural Research Service, Columbia, Missouri, United States of America
| | - Michael D. McMullen
- US Department of Agriculture, Agricultural Research Service, Columbia, Missouri, United States of America
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Rita H. Mumm
- Department of Crop Sciences and the Illinois Plant Breeding Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Center for Population Biology and Genome Center, University of California, Davis, California, United States of America
| |
Collapse
|
154
|
Kusmec A, Srinivasan S, Nettleton D, Schnable PS. Distinct genetic architectures for phenotype means and plasticities in Zea mays. NATURE PLANTS 2017; 3:715-723. [PMID: 29150689 PMCID: PMC6209453 DOI: 10.1038/s41477-017-0007-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 07/25/2017] [Indexed: 05/02/2023]
Abstract
Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of paramount importance for maintaining and increasing yields in a world experiencing climate change. Here, we report the results of genome-wide association analyses of multiple phenotypes and two measures of phenotypic plasticity in a maize nested association mapping (US-NAM) population grown in multiple environments and genotyped with ~2.5 million single-nucleotide polymorphisms. We show that across all traits the candidate genes for mean phenotype values and plasticity measures form structurally and functionally distinct groups. Such independent genetic control suggests that breeders will be able to select semi-independently for mean phenotype values and plasticity, thereby generating varieties with both high mean phenotype values and levels of plasticity that are appropriate for the target performance environments.
Collapse
Affiliation(s)
- Aaron Kusmec
- Department of Agronomy, Iowa State University, Ames, IA, 50010-3650, USA
| | - Srikant Srinivasan
- Plant Sciences Institute, Iowa State University, Ames, IA, 50010-3650, USA
- School of Computing and Electrical Engineering, IIT Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Dan Nettleton
- Plant Sciences Institute, Iowa State University, Ames, IA, 50010-3650, USA
- Department of Statistics, Iowa State University, Ames, IA, 50010-3650, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA, 50010-3650, USA.
- Plant Sciences Institute, Iowa State University, Ames, IA, 50010-3650, USA.
| |
Collapse
|
155
|
Hsu FM, Yen MR, Wang CT, Lin CY, Wang CJR, Chen PY. Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize. Epigenetics Chromatin 2017; 10:42. [PMID: 28854962 PMCID: PMC5577757 DOI: 10.1186/s13072-017-0148-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/08/2017] [Indexed: 11/11/2022] Open
Abstract
Background
DNA methylation plays important roles in many regulatory processes in plants. It is economically infeasible to profile genome-wide DNA methylation at a single-base resolution in maize, given its genome size of ~2.5 Gb. As an alternative, we adapted region of interest (ROI)-directed reduced representation bisulfite sequencing (RRBS) to survey genome-wide methylation in maize. Results We developed a pipeline for selecting restriction enzymes in silico and experimentally showed that, in the maize genome, MseI- and CviQI-digested fragments are precisely enriched in promoters and gene bodies, respectively. We proceeded with comparisons of epigenomes and transcriptomes between shoots and tassels and found that the occurrences of highly methylated, tissue-specific, mCHH islands upstream of transcription start sites (TSSs) were positively correlated with differential gene expression. Furthermore, 5′ regulatory regions between TSS and mCHH islands often contain putative binding sites of known transcription factors (TFs) that regulate the flowering process and the timing of the transition from the vegetative to the reproductive phase. By integrating MNase-seq and siRNA-seq data, we found that regions of mCHH islands accumulate 21nt-siRNAs in a tissue-specific manner, marking the transition to open chromatin, thereby ensuring the accessibility of TFs for tissue-specific gene regulation. Conclusions Our ROI-directed RRBS pipeline is eminently applicable to DNA methylation profiling of large genomes. Our results provide novel insights into the tissue-specific epigenomic landscapes in maize, demonstrating that DNA methylation and siRNA and chromatin accessibility constitute a critical, interdependent component that orchestrates the transition from the vegetative to the reproductive phase. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0148-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Fei-Man Hsu
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chi-Ting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chien-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chung-Ju Rachel Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
| |
Collapse
|
156
|
Lu Z, Hofmeister BT, Vollmers C, DuBois RM, Schmitz RJ. Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Res 2017; 45:e41. [PMID: 27903897 PMCID: PMC5389718 DOI: 10.1093/nar/gkw1179] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/15/2016] [Indexed: 12/27/2022] Open
Abstract
Chromatin structure plays a pivotal role in facilitating proper control of gene expression. Transcription factor (TF) binding of cis-elements is often associated with accessible chromatin regions. Therefore, the ability to identify these accessible regions throughout plant genomes will advance understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is a recently developed technique used to map open chromatin zones in animal genomes. However, in plants, the existence of cell walls, subcellular organelles and the lack of stable cell lines have prevented routine application of this technique. Here, we describe an assay combining ATAC-seq with fluorescence-activated nuclei sorting (FANS) to identify and map open chromatin and TF-binding sites in plant genomes. FANS-ATAC-seq compares favorably with published DNaseI sequencing (DNase-seq) results and it requires less than 50 000 nuclei for accurate identification of accessible genomic regions. Summary: Application of ATAC-seq to sorted nuclei identifies accessible regions genome-wide.
Collapse
Affiliation(s)
- Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | | | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rebecca M DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
157
|
Zhang Y, Ngu DW, Carvalho D, Liang Z, Qiu Y, Roston RL, Schnable JC. Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize. THE PLANT CELL 2017; 29:1938-1951. [PMID: 28733421 PMCID: PMC5590507 DOI: 10.1105/tpc.17.00354] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/05/2017] [Accepted: 07/18/2017] [Indexed: 05/19/2023]
Abstract
Identifying interspecies changes in gene regulation, one of the two primary sources of phenotypic variation, is challenging on a genome-wide scale. The use of paired time-course data on cold-responsive gene expression in maize (Zea mays) and sorghum (Sorghum bicolor) allowed us to identify differentially regulated orthologs. While the majority of cold-responsive transcriptional regulation of conserved gene pairs is species specific, the initial transcriptional responses to cold appear to be more conserved than later responses. In maize, the promoters of genes with conserved transcriptional responses to cold tend to contain more micrococcal nuclease hypersensitive sites in their promoters, a proxy for open chromatin. Genes with conserved patterns of transcriptional regulation between the two species show lower ratios of nonsynonymous to synonymous substitutions. Genes involved in lipid metabolism, known to be involved in cold acclimation, tended to show consistent regulation in both species. Genes with species-specific cold responses did not cluster in particular pathways nor were they enriched in particular functional categories. We propose that cold-responsive transcriptional regulation in individual species may not be a reliable marker for function, while a core set of genes involved in perceiving and responding to cold stress are subject to functionally constrained cold-responsive regulation across the grass tribe Andropogoneae.
Collapse
Affiliation(s)
- Yang Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Daniel W Ngu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Daniel Carvalho
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Zhikai Liang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Yumou Qiu
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Rebecca L Roston
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| |
Collapse
|
158
|
Lai X, Behera S, Liang Z, Lu Y, Deogun JS, Schnable JC. STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species. MOLECULAR PLANT 2017; 10:990-999. [PMID: 28602693 DOI: 10.1016/j.molp.2017.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
One method for identifying noncoding regulatory regions of a genome is to quantify rates of divergence between related species, as functional sequence will generally diverge more slowly. Most approaches to identifying these conserved noncoding sequences (CNSs) based on alignment have had relatively large minimum sequence lengths (≥15 bp) compared with the average length of known transcription factor binding sites. To circumvent this constraint, STAG-CNS that can simultaneously integrate the data from the promoters of conserved orthologous genes in three or more species was developed. Using the data from up to six grass species made it possible to identify conserved sequences as short as 9 bp with false discovery rate ≤0.05. These CNSs exhibit greater overlap with open chromatin regions identified using DNase I hypersensitivity assays, and are enriched in the promoters of genes involved in transcriptional regulation. STAG-CNS was further employed to characterize loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy. Genes with fewer retained CNSs show lower overall expression, although this bias is more apparent in samples of complex organ systems containing many cell types, suggesting that CNS loss may correspond to a reduced number of expression contexts rather than lower expression levels across the entire ancestral expression domain.
Collapse
Affiliation(s)
- Xianjun Lai
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Sairam Behera
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Zhikai Liang
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jitender S Deogun
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
| | - James C Schnable
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
| |
Collapse
|
159
|
Chen J, Li E, Zhang X, Dong X, Lei L, Song W, Zhao H, Lai J. Genome-wide Nucleosome Occupancy and Organization Modulates the Plasticity of Gene Transcriptional Status in Maize. MOLECULAR PLANT 2017; 10:962-974. [PMID: 28487258 DOI: 10.1016/j.molp.2017.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/28/2017] [Accepted: 05/01/2017] [Indexed: 05/16/2023]
Abstract
Nucleosomes are fundamental units of chromatin that play critical roles in gene regulation by modulating DNA accessibility. However, their roles in regulating tissue-specific gene transcription are poorly understood. Here, we present genome-wide nucleosome maps of maize shoot and endosperm generated by sequencing the micrococcal nuclease digested nucleosomal DNA. The changes of gene transcriptional status between shoot and endosperm were accompanied by preferential nucleosome loss from the promoters and shifts in the first nucleosome downstream of the transcriptional start sites (+1 nucleosome) and upstream of transcriptional termination sites (-1 nucleosome). Intrinsically DNA-encoded nucleosome organization was largely associated with the capacity of a gene to alter its transcriptional status among different tissues. Compared with tissue-specific genes, constitutively expressed genes showed more pronounced 5' and 3' nucleosome-depleted regions as well as further +1 nucleosome to transcriptional start sites and -1 nucleosome to transcriptional termination sites. Moreover, nucleosome organization was more highly correlated with the plasticity of gene transcriptional status than with its expression level when examined using in vivo and predicted nucleosome data. In addition, the translational efficiencies of tissue-specific genes appeared to be greater than those of constitutively expressed genes. Taken together, our results indicate that intrinsically DNA-encoded nucleosome organization is important, beyond its role in regulating gene expression levels, in determining the plasticity of gene transcriptional status.
Collapse
Affiliation(s)
- Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - En Li
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Xiangbo Zhang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Xiaomei Dong
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Lei Lei
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Haiming Zhao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China.
| |
Collapse
|
160
|
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.
Collapse
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
| |
Collapse
|
161
|
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: 693] [Impact Index Per Article: 99.0] [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.
Collapse
|
162
|
Evolutionary forces affecting synonymous variations in plant genomes. PLoS Genet 2017; 13:e1006799. [PMID: 28531201 PMCID: PMC5460877 DOI: 10.1371/journal.pgen.1006799] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 06/06/2017] [Accepted: 05/04/2017] [Indexed: 01/04/2023] Open
Abstract
Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones. In protein coding genes, base composition strongly varies within and among plant genomes, especially at positions where changes do not alter the coded protein (synonymous variations). Some species, such as the model plant Arabidopsis thaliana, are relatively GC-poor and homogeneous while others, such as grasses, are highly heterogeneous and GC-rich. The causes of these variations are still debated: are they mainly due to selective or neutral processes? Answering to this question is important to correctly infer whether variations in base composition may have functional roles or not. We extended a population genetics method to jointly estimate the different forces that may affect synonymous variations and applied it to genomic datasets in 11 flowering plant species. We found that GC-biased gene conversion, a neutral process associated with recombination that mimics selection by favouring G and C bases, is a widespread and stronger process than selection and that it could explain the large variation in base composition observed in plant genomes. Our results bear implications for analysing plant genomes and for correctly interpreting what could be functional or not.
Collapse
|
163
|
Prakadan SM, Shalek AK, Weitz DA. Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. Nat Rev Genet 2017; 18:345-361. [PMID: 28392571 DOI: 10.1038/nrg.2017.15] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent advances in cellular profiling have demonstrated substantial heterogeneity in the behaviour of cells once deemed 'identical', challenging fundamental notions of cell 'type' and 'state'. Not surprisingly, these findings have elicited substantial interest in deeply characterizing the diversity, interrelationships and plasticity among cellular phenotypes. To explore these questions, experimental platforms are needed that can extensively and controllably profile many individual cells. Here, microfluidic structures - whether valve-, droplet- or nanowell-based - have an important role because they can facilitate easy capture and processing of single cells and their components, reducing labour and costs relative to conventional plate-based methods while also improving consistency. In this article, we review the current state-of-the-art methodologies with respect to microfluidics for mammalian single-cell 'omics' and discuss challenges and future opportunities.
Collapse
Affiliation(s)
- Sanjay M Prakadan
- Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Alex K Shalek
- Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
164
|
Josephs EB, Stinchcombe JR, Wright SI. What can genome-wide association studies tell us about the evolutionary forces maintaining genetic variation for quantitative traits? THE NEW PHYTOLOGIST 2017; 214:21-33. [PMID: 28211582 DOI: 10.1111/nph.14410] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/14/2016] [Indexed: 05/27/2023]
Abstract
Contents 21 I. 21 II. 22 III. 24 IV. 25 V. 29 30 References 30 SUMMARY: Understanding the evolutionary forces that shape genetic variation within species has long been a goal of evolutionary biology. Integrating data for the genetic architecture of traits from genome-wide association mapping studies (GWAS) along with the development of new population genetic methods for identifying selection in sequence data may allow us to evaluate the roles of mutation-selection balance and balancing selection in shaping genetic variation at various scales. Here, we review the theoretical predictions for genetic architecture and additional signals of selection on genomic sequence for the loci that affect traits. Next, we review how plant GWAS have tested for the signatures of various selective scenarios. Limited evidence to date suggests that within-population variation is maintained primarily by mutation-selection balance while variation across the landscape is the result of local adaptation. However, there are a number of inherent biases in these interpretations. We highlight these challenges and suggest ways forward to further understanding of the maintenance of variation.
Collapse
Affiliation(s)
- Emily B Josephs
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| |
Collapse
|
165
|
Uauy C. Wheat genomics comes of age. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:142-148. [PMID: 28346895 DOI: 10.1016/j.pbi.2017.01.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/24/2017] [Accepted: 01/30/2017] [Indexed: 05/18/2023]
Abstract
Advances in wheat genomics have lagged behind other major cereals (e.g., rice and maize) due to its highly repetitive and large polyploid genome. Recent technological developments in sequencing and assembly methods, however, have largely overcome these barriers. The community now moves to an era centred on functional characterisation of the genome. This includes understanding sequence and structural variation as well as how information is integrated across multiple homoeologous genomes. This understanding promises to uncover variation previously hidden from natural and human selection due to the often observed functional redundancy between homoeologs. Key functional genomic resources will enable this, including sequenced mutant populations and gene editing technologies which are now available in wheat. Training the next-generation of genomics-enabled researchers will be essential to ensure these advances are quickly translated into farmers' fields.
Collapse
Affiliation(s)
- Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
| |
Collapse
|
166
|
Genomic innovation for crop improvement. Nature 2017; 543:346-354. [DOI: 10.1038/nature22011] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/01/2017] [Indexed: 12/24/2022]
|
167
|
Abstract
The last decade has seen rapid advances in our understanding of the proteins of the nuclear envelope, which have multiple roles including positioning the nucleus, maintaining its structural organization, and in events ranging from mitosis and meiosis to chromatin positioning and gene expression. Diverse new and stimulating results relating to nuclear organization and genome function from across kingdoms were presented in a session stream entitled “Dynamic Organization of the Nucleus” at this year's Society of Experimental Biology (SEB) meeting in Brighton, UK (July 2016). This was the first session stream run by the Nuclear Dynamics Special Interest Group, which was organized by David Evans, Katja Graumann (both Oxford Brookes University, UK) and Iris Meier (Ohio State University, USA). The session featured presentations on areas relating to nuclear organization across kingdoms including the nuclear envelope, chromatin organization, and genome function.
Collapse
Affiliation(s)
- Stephen D Thorpe
- a Institute of Bioengineering, School of Engineering and Materials Science , Queen Mary University of London , London , UK
| | | |
Collapse
|
168
|
Ingvarsson PK, Hvidsten TR, Street NR. Towards integration of population and comparative genomics in forest trees. THE NEW PHYTOLOGIST 2016; 212:338-44. [PMID: 27575589 DOI: 10.1111/nph.14153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/27/2016] [Indexed: 05/08/2023]
Abstract
Contents 338 I. 338 II. 339 III. 340 IV. 342 343 References 343 SUMMARY: The past decade saw the initiation of an ongoing revolution in sequencing technologies that is transforming all fields of biology. This has been driven by the advent and widespread availability of high-throughput, massively parallel short-read sequencing (MPS) platforms. These technologies have enabled previously unimaginable studies, including draft assemblies of the massive genomes of coniferous species and population-scale resequencing. Transcriptomics studies have likewise been transformed, with RNA-sequencing enabling studies in nonmodel organisms, the discovery of previously unannotated genes (novel transcripts), entirely new classes of RNAs and previously unknown regulatory mechanisms. Here we touch upon current developments in the areas of genome assembly, comparative regulomics and population genetics as they relate to studies of forest tree species.
Collapse
Affiliation(s)
- Pär K Ingvarsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, 901 87, Umeå, Sweden
| | - Torgeir R Hvidsten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden.
| |
Collapse
|
169
|
Liu H, Wang F, Xiao Y, Tian Z, Wen W, Zhang X, Chen X, Liu N, Li W, Liu L, Liu J, Yan J, Liu J. MODEM: multi-omics data envelopment and mining in maize. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw117. [PMID: 27504011 PMCID: PMC4976297 DOI: 10.1093/database/baw117] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/12/2016] [Indexed: 11/13/2022]
Abstract
MODEM is a comprehensive database of maize multidimensional omics data, including genomic, transcriptomic, metabolic and phenotypic information from the cellular to individual plant level. This initial release contains approximately 1.06 M high quality SNPs for 508 diverse inbred lines obtained by combining variations from RNA sequencing on whole kernels (15 days after pollination) of 368 lines and a 50 K array for all 508 individuals. As all of these data were derived from the same diverse panel of lines, the database also allows various types of genetic mapping (including characterization of phenotypic QTLs, pQTLs; expression QTLs, eQTLs and metabolic QTLs, mQTLs). MODEM is thus designed to promote a better understanding of maize genetic architecture and deep functional annotation of the complex maize genome (and potentially those of other crop plants) and to explore the genotype-phenotype relationships and regulation of maize kernel development at multiple scales, which is also comprehensive for developing novel methods. MODEM is additionally designed to link with other databases to make full use of current resources, and it provides visualization tools for easy browsing. All of the original data and the related mapping results are freely available for easy query and download. This platform also provides helpful tools for general analyses and will be continually updated with additional materials, features and public data related to maize genetics or regulation as they become available.Database URL: (http://modem.hzau.edu.cn).
Collapse
Affiliation(s)
- Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Wang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zonglin Tian
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuehai Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- School of Mechanical Engineering, Shandong University, Jinan 250061, China
| | - Nannan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Liu
- 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
| | - Jianbing Yan
- 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 School of Computer & software, Nanjing University of Information Science & Technology, Nanjing 210000, China
| |
Collapse
|
170
|
Genetic Architecture of Domestication-Related Traits in Maize. Genetics 2016; 204:99-113. [PMID: 27412713 DOI: 10.1534/genetics.116.191106] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/08/2016] [Indexed: 01/24/2023] Open
Abstract
Strong directional selection occurred during the domestication of maize from its wild ancestor teosinte, reducing its genetic diversity, particularly at genes controlling domestication-related traits. Nevertheless, variability for some domestication-related traits is maintained in maize. The genetic basis of this could be sequence variation at the same key genes controlling maize-teosinte differentiation (due to lack of fixation or arising as new mutations after domestication), distinct loci with large effects, or polygenic background variation. Previous studies permit annotation of maize genome regions associated with the major differences between maize and teosinte or that exhibit population genetic signals of selection during either domestication or postdomestication improvement. Genome-wide association studies and genetic variance partitioning analyses were performed in two diverse maize inbred line panels to compare the phenotypic effects and variances of sequence polymorphisms in regions involved in domestication and improvement to the rest of the genome. Additive polygenic models explained most of the genotypic variation for domestication-related traits; no large-effect loci were detected for any trait. Most trait variance was associated with background genomic regions lacking previous evidence for involvement in domestication. Improvement sweep regions were associated with more trait variation than expected based on the proportion of the genome they represent. Selection during domestication eliminated large-effect genetic variants that would revert maize toward a teosinte type. Small-effect polygenic variants (enriched in the improvement sweep regions of the genome) are responsible for most of the standing variation for domestication-related traits in maize.
Collapse
|
171
|
Liu H, Wang F, Xiao Y, Tian Z, Wen W, Zhang X, Chen X, Liu N, Li W, Liu L, Liu J, Yan J, Liu J. MODEM: multi-omics data envelopment and mining in maize. Database (Oxford) 2016. [PMID: 27504011 DOI: 10.1093/database/baw1117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
MODEM is a comprehensive database of maize multidimensional omics data, including genomic, transcriptomic, metabolic and phenotypic information from the cellular to individual plant level. This initial release contains approximately 1.06 M high quality SNPs for 508 diverse inbred lines obtained by combining variations from RNA sequencing on whole kernels (15 days after pollination) of 368 lines and a 50 K array for all 508 individuals. As all of these data were derived from the same diverse panel of lines, the database also allows various types of genetic mapping (including characterization of phenotypic QTLs, pQTLs; expression QTLs, eQTLs and metabolic QTLs, mQTLs). MODEM is thus designed to promote a better understanding of maize genetic architecture and deep functional annotation of the complex maize genome (and potentially those of other crop plants) and to explore the genotype-phenotype relationships and regulation of maize kernel development at multiple scales, which is also comprehensive for developing novel methods. MODEM is additionally designed to link with other databases to make full use of current resources, and it provides visualization tools for easy browsing. All of the original data and the related mapping results are freely available for easy query and download. This platform also provides helpful tools for general analyses and will be continually updated with additional materials, features and public data related to maize genetics or regulation as they become available.Database URL: (http://modem.hzau.edu.cn).
Collapse
Affiliation(s)
- Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Wang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zonglin Tian
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuehai Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- School of Mechanical Engineering, Shandong University, Jinan 250061, China
| | - Nannan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Liu
- 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
| | - Jianbing Yan
- 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 School of Computer & software, Nanjing University of Information Science & Technology, Nanjing 210000, China
| |
Collapse
|