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Boschiero C, Neupane M, Yang L, Schroeder SG, Tuo W, Ma L, Baldwin RL, Van Tassell CP, Liu GE. A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle. Animals (Basel) 2024; 14:1921. [PMID: 38998033 PMCID: PMC11240624 DOI: 10.3390/ani14131921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/18/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024] Open
Abstract
Presence-absence variations (PAVs) are important structural variations, wherein a genomic segment containing one or more genes is present in some individuals but absent in others. While PAVs have been extensively studied in plants, research in cattle remains limited. This study identified PAVs in 173 Holstein bulls using whole-genome sequencing data and assessed their associations with 46 economically important traits. Out of 28,772 cattle genes (from the longest transcripts), a total of 26,979 (93.77%) core genes were identified (present in all individuals), while variable genes included 928 softcore (present in 95-99% of individuals), 494 shell (present in 5-94%), and 371 cloud genes (present in <5%). Cloud genes were enriched in functions associated with hormonal and antimicrobial activities, while shell genes were enriched in immune functions. PAV-based genome-wide association studies identified associations between gene PAVs and 16 traits including milk, fat, and protein yields, as well as traits related to health and reproduction. Associations were found on multiple chromosomes, illustrating important associations on cattle chromosomes 7 and 15, involving olfactory receptor and immune-related genes, respectively. By examining the PAVs at the population level, the results of this research provided crucial insights into the genetic structures underlying the complex traits of Holstein cattle.
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Affiliation(s)
- Clarissa Boschiero
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Mahesh Neupane
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Liu Yang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Wenbin Tuo
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
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2
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Munasinghe M, Read A, Stitzer MC, Song B, Menard CC, Ma KY, Brandvain Y, Hirsch CN, Springer N. Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PLoS Genet 2023; 19:e1011086. [PMID: 38134220 PMCID: PMC10773942 DOI: 10.1371/journal.pgen.1011086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 01/08/2024] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de novo genome assemblies of 26 diverse inbred maize lines. We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both simple and complex connections between TEs and structural variants. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that within these recently diverged genomic regions, deletions of transposable elements likely account for more structural variation events and base pairs than insertions. These deletions are often large structural variants containing multiple transposable elements. Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.
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Affiliation(s)
- Manisha Munasinghe
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Andrew Read
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Michelle C. Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Claire C. Menard
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Kristy Yubo Ma
- Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, Minnesota, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nathan Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
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3
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Macholán M, Daniszová K, Hiadlovská Z. The Expansion of House Mouse Major Urinary Protein Genes Likely Did Not Facilitate Commensalism with Humans. Genes (Basel) 2023; 14:2090. [PMID: 38003032 PMCID: PMC10671799 DOI: 10.3390/genes14112090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Mouse wild-derived strains (WDSs) combine the advantages of classical laboratory stocks and wild animals, and thus appear to be promising tools for diverse biomedical and evolutionary studies. We employed 18 WDSs representing three non-synanthropic species (Mus spretus, Mus spicilegus, and M. macedonicus) and three house mouse subspecies (Mus musculus musculus, M. m. domesticus, M. m. castaneus), which are all important human commensals to explore whether the number of major urinary protein (MUP) genes and their final protein levels in urine are correlated with the level of commensalism. Contrary to expectations, the MUP copy number (CN) and protein excretion in the strains derived from M. m. castaneus, which is supposed to be the strongest commensal, were not significantly different from the non-commensal species. Regardless of an overall tendency for higher MUP amounts in taxa with a higher CN, there was no significant correlation at the strain level. Our study thus suggests that expansion of the Mup cluster, which appeared before the house mouse diversification, is unlikely to facilitate commensalism with humans in three house mouse subspecies. Finally, we found considerable variation among con(sub)specific WDSs, warning against generalisations of results based on a few strains.
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Affiliation(s)
- Miloš Macholán
- Institute of Animal Physiology and Genetics, Laboratory of Mammalian Evolutionary Genetics, Czech Academy of Sciences, 602 00 Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 601 77 Brno, Czech Republic
| | - Kristina Daniszová
- Institute of Animal Physiology and Genetics, Laboratory of Mammalian Evolutionary Genetics, Czech Academy of Sciences, 602 00 Brno, Czech Republic
| | - Zuzana Hiadlovská
- Institute of Animal Physiology and Genetics, Laboratory of Mammalian Evolutionary Genetics, Czech Academy of Sciences, 602 00 Brno, Czech Republic
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4
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Weber SE, Chawla HS, Ehrig L, Hickey LT, Frisch M, Snowdon RJ. Accurate prediction of quantitative traits with failed SNP calls in canola and maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1221750. [PMID: 37936929 PMCID: PMC10627008 DOI: 10.3389/fpls.2023.1221750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023]
Abstract
In modern plant breeding, genomic selection is becoming the gold standard to select superior genotypes in large breeding populations that are only partially phenotyped. Many breeding programs commonly rely on single-nucleotide polymorphism (SNP) markers to capture genome-wide data for selection candidates. For this purpose, SNP arrays with moderate to high marker density represent a robust and cost-effective tool to generate reproducible, easy-to-handle, high-throughput genotype data from large-scale breeding populations. However, SNP arrays are prone to technical errors that lead to failed allele calls. To overcome this problem, failed calls are often imputed, based on the assumption that failed SNP calls are purely technical. However, this ignores the biological causes for failed calls-for example: deletions-and there is increasing evidence that gene presence-absence and other kinds of genome structural variants can play a role in phenotypic expression. Because deletions are frequently not in linkage disequilibrium with their flanking SNPs, permutation of missing SNP calls can potentially obscure valuable marker-trait associations. In this study, we analyze published datasets for canola and maize using four parametric and two machine learning models and demonstrate that failed allele calls in genomic prediction are highly predictive for important agronomic traits. We present two statistical pipelines, based on population structure and linkage disequilibrium, that enable the filtering of failed SNP calls that are likely caused by biological reasons. For the population and trait examined, prediction accuracy based on these filtered failed allele calls was competitive to standard SNP-based prediction, underlying the potential value of missing data in genomic prediction approaches. The combination of SNPs with all failed allele calls or the filtered allele calls did not outperform predictions with only SNP-based prediction due to redundancy in genomic relationship estimates.
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Affiliation(s)
- Sven E. Weber
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | | | - Lennard Ehrig
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Lee T. Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Matthias Frisch
- Department of Biometry and Population Genetics, Justus Liebig University, Giessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
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5
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Zhang J, Xie Y, Zhang H, He C, Wang X, Cui Y, Heng Y, Lin Y, Gu R, Wang J, Fu J. Integrated Multi-Omics Reveals Significant Roles of Non-Additively Expressed Small RNAs in Heterosis for Maize Plant Height. Int J Mol Sci 2023; 24:ijms24119150. [PMID: 37298102 DOI: 10.3390/ijms24119150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/12/2023] Open
Abstract
Heterosis is a complex biological phenomenon regulated by genetic variations and epigenetic changes. However, the roles of small RNAs (sRNAs), an important epigenetic regulatory element, on plant heterosis are still poorly understood. Here, an integrative analysis was performed with sequencing data from multi-omics layers of maize hybrids and their two homologous parental lines to explore the potential underlying mechanisms of sRNAs in plant height (PH) heterosis. sRNAome analysis revealed that 59 (18.61%) microRNAs (miRNAs) and 64,534 (54.00%) 24-nt small interfering RNAs (siRNAs) clusters were non-additively expressed in hybrids. Transcriptome profiles showed that these non-additively expressed miRNAs regulated PH heterosis through activating genes involved in vegetative growth-related pathways while suppressing those related to reproductive and stress response pathways. DNA methylome profiles showed that non-additive methylation events were more likely to be induced by non-additively expressed siRNA clusters. Genes associated with low-parental expression (LPE) siRNAs and trans-chromosomal demethylation (TCdM) events were enriched in developmental processes as well as nutrients and energy metabolism, whereas genes associated with high-parental expression (HPE) siRNAs and trans-chromosomal methylation (TCM) events were gathered in stress response and organelle organization pathways. Our results provide insights into the expression and regulation patterns of sRNAs in hybrids and help to elucidate their potential targeting pathways contributing to PH heterosis.
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Affiliation(s)
- Jie Zhang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Molecular Genetics, Guizhou Institute of Tobacco Science, Guiyang 550081, China
| | - Yuxin Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, USA
| | - Xiaoli Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanfang Heng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingchao Lin
- Key Laboratory of Molecular Genetics, Guizhou Institute of Tobacco Science, Guiyang 550081, China
| | - Riliang Gu
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jianhua Wang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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6
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Grzybowski MW, Mural RV, Xu G, Turkus J, Yang J, Schnable JC. A common resequencing-based genetic marker data set for global maize diversity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1109-1121. [PMID: 36705476 DOI: 10.1111/tpj.16123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Maize (Zea mays ssp. mays) populations exhibit vast ranges of genetic and phenotypic diversity. As sequencing costs have declined, an increasing number of projects have sought to measure genetic differences between and within maize populations using whole-genome resequencing strategies, identifying millions of segregating single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Unlike older genotyping strategies like microarrays and genotyping by sequencing, resequencing should, in principle, frequently identify and score common genetic variants. However, in practice, different projects frequently employ different analytical pipelines, often employ different reference genome assemblies and consistently filter for minor allele frequency within the study population. This constrains the potential to reuse and remix data on genetic diversity generated from different projects to address new biological questions in new ways. Here, we employ resequencing data from 1276 previously published maize samples and 239 newly resequenced maize samples to generate a single unified marker set of approximately 366 million segregating variants and approximately 46 million high-confidence variants scored across crop wild relatives, landraces as well as tropical and temperate lines from different breeding eras. We demonstrate that the new variant set provides increased power to identify known causal flowering-time genes using previously published trait data sets, as well as the potential to track changes in the frequency of functionally distinct alleles across the global distribution of modern maize.
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Affiliation(s)
- Marcin W Grzybowski
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Ravi V Mural
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Gen Xu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jonathan Turkus
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jinliang Yang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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7
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Guerra‐Garcia A, Haile T, Ogutcen E, Bett KE, von Wettberg EJ. An evolutionary look into the history of lentil reveals unexpected diversity. Evol Appl 2022; 15:1313-1325. [PMID: 36051460 PMCID: PMC9423085 DOI: 10.1111/eva.13467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 07/12/2022] [Accepted: 08/01/2022] [Indexed: 11/29/2022] Open
Abstract
The characterization and preservation of genetic variation in crops is critical to meeting the challenges of breeding in the face of changing climates and markets. In recent years, the use of single nucleotide polymorphisms (SNPs) has become routine, allowing us to understand the population structure, find divergent lines for crosses, and illuminate the origin of crops. However, the focus on SNPs overlooks other forms of variation, such as copy number variation (CNVs). Lentil is the third most important cold‐season legume and was domesticated in the Fertile Crescent. We genotyped 324 accessions that represent its global diversity, and using both SNPs and CNVs, we dissected the population structure and genetic variation, and identified candidate genes. Eight clusters were detected, most of them located in or near the Fertile Crescent, even though different clusters were present in distinct regions. The cluster from South Asia was particularly differentiated and presented low diversity, contrasting with the clusters from the Mediterranean and the northern temperate. Accessions from North America were mainly assigned to one cluster and were highly diverse, reflecting the efforts of breeding programs to integrate variation. Thirty‐three genes were identified as candidates under selection and among their functions were sporopollenin synthesis in pollen, a component of chlorophyll B reductase that partially determines the antenna size, and two genes related to the import system of chloroplasts. Eleven percent of all lentil genes and 21% of lentil disease resistance genes were affected by CNVs. The gene categories overrepresented in these genes were “enzymes,” “Cell Wall Organization,” and “external stimuli response.” All the genes found in the latter were associated with pathogen response. CNVs provided information about population structure and might have played a role in adaptation. The incorporation of CNVs in diversity studies is needed for a broader understanding of how they evolve and contribute to domestication.
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Affiliation(s)
| | - Teketel Haile
- Department of Plant Sciences University of Saskatchewan Saskatoon SK Canada
| | - Ezgi Ogutcen
- Conservatoire et Jardin Botaniques de la Ville de Genève Geneva Switzerland
| | - Kirstin E. Bett
- Department of Plant Sciences University of Saskatchewan Saskatoon SK Canada
| | - Eric J. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment University of Vermont Burlington VT USA
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8
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Lee MB, Shekasteband R, Hutton SF, Lee TG. A mutant allele of the flowering promoting factor 1 gene at the tomato BRACHYTIC locus reduces plant height with high quality fruit. PLANT DIRECT 2022; 6:e422. [PMID: 35949955 PMCID: PMC9352537 DOI: 10.1002/pld3.422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 05/07/2023]
Abstract
Reduced plant height due to shortened stems is beneficial for improving crop yield potential, better resilience to biotic/abiotic stresses, and rapid crop producer adoption of the agronomic and management practices. Breeding tomato plants with a reduced height, however, poses a particular challenge because this trait is often associated with a significant fruit size (weight) reduction. The tomato BRACHYTIC (BR) locus controls plant height. Genetic mapping and genome assembly revealed three flowering promoting factor 1 (FPF1) genes located within the BR mapping interval, and a complete coding sequence deletion of the telomere proximal FPF1 (Solyc01g066980) was found in the br allele but not in BR. The knock-out of Solyc01g066980 in BR large-fruited fresh-market tomato reduced the height and fruit yield, but the ability to produce large size fruits was retained. However, concurrent yield evaluation of a pair of sister lines with or without the br allele revealed that artificial selection contributes to commercially acceptable yield potential in br tomatoes. A network analysis of gene-expression patterns across genotypes, tissues, and the gibberellic acid (GA) treatment revealed that member(s) of the FPF1 family may play a role in the suppression of the GA biosynthesis in roots and provided a framework for identifying the responsible molecular signaling pathways in br-mediated phenotypic changes. Lastly, mutations of br homologs also resulted in reduced height. These results shed light on the genetic and physiological mechanisms by which the br allele alters tomato architecture.
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Affiliation(s)
- Man Bo Lee
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
| | - Reza Shekasteband
- Department of Horticultural ScienceNorth Carolina State University, Mountain Horticultural Crops Research & Extension CenterMills RiverNorth CarolinaUSA
| | - Samuel F. Hutton
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
- Horticultural Sciences DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Plant Breeders Working GroupUniversity of FloridaGainesvilleFloridaUSA
| | - Tong Geon Lee
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
- Horticultural Sciences DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Plant Breeders Working GroupUniversity of FloridaGainesvilleFloridaUSA
- Plant Molecular and Cellular Biology Graduate ProgramUniversity of FloridaGainesvilleFloridaUSA
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9
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Baldauf JA, Liu M, Vedder L, Yu P, Piepho HP, Schoof H, Nettleton D, Hochholdinger F. Single-parent expression complementation contributes to phenotypic heterosis in maize hybrids. PLANT PHYSIOLOGY 2022; 189:1625-1638. [PMID: 35522211 PMCID: PMC9237695 DOI: 10.1093/plphys/kiac180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
The dominance model of heterosis explains the superior performance of F1-hybrids via the complementation of deleterious alleles by beneficial alleles in many genes. Genes active in one parent but inactive in the second lead to single-parent expression (SPE) complementation in maize (Zea mays L.) hybrids. In this study, SPE complementation resulted in approximately 700 additionally active genes in different tissues of genetically diverse maize hybrids on average. We established that the number of SPE genes is significantly associated with mid-parent heterosis (MPH) for all surveyed phenotypic traits. In addition, we highlighted that maternally (SPE_B) and paternally (SPE_X) active SPE genes enriched in gene co-expression modules are highly correlated within each SPE type but separated between these two SPE types. While SPE_B-enriched co-expression modules are positively correlated with phenotypic traits, SPE_X-enriched modules displayed a negative correlation. Gene ontology term enrichment analyses indicated that SPE_B patterns are associated with growth and development, whereas SPE_X patterns are enriched in defense and stress response. In summary, these results link the degree of phenotypic MPH to the prevalence of gene expression complementation observed by SPE, supporting the notion that hybrids benefit from SPE complementation via its role in coordinating maize development in fluctuating environments.
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Affiliation(s)
- Jutta A Baldauf
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | | | - Lucia Vedder
- Institute of Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, 53115 Bonn, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
| | - Hans-Peter Piepho
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany
| | - Heiko Schoof
- Institute of Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, 53115 Bonn, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011-1210, USA
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10
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Mo Y, Jiao Y. Advances and applications of single-cell omics technologies in plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1551-1563. [PMID: 35426954 DOI: 10.1111/tpj.15772] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Single-cell sequencing approaches reveal the intracellular dynamics of individual cells and answer biological questions with high-dimensional catalogs of millions of cells, including genomics, transcriptomics, chromatin accessibility, epigenomics, and proteomics data across species. These emerging yet thriving technologies have been fully embraced by the field of plant biology, with a constantly expanding portfolio of applications. Here, we introduce the current technical advances used for single-cell omics, especially single-cell genome and transcriptome sequencing. Firstly, we overview methods for protoplast and nucleus isolation and genome and transcriptome amplification. Subsequently, we use well-executed benchmarking studies to highlight advances made through the application of single-cell omics techniques. Looking forward, we offer a glimpse of additional hurdles and future opportunities that will introduce broad adoption of single-cell sequencing with revolutionary perspectives in plant biology.
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Affiliation(s)
- Yajin Mo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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11
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Nanni AV, Morse AM, Newman JRB, Choquette NE, Wedow JM, Liu Z, Leakey ADB, Conesa A, Ainsworth EA, McIntyre LM. Variation in leaf transcriptome responses to elevated ozone corresponds with physiological sensitivity to ozone across maize inbred lines. Genetics 2022; 221:6586798. [PMID: 35579358 DOI: 10.1093/genetics/iyac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
We examine the impact of sustained elevated ozone concentration on the leaf transcriptome of 5 diverse maize inbred genotypes, which vary in physiological sensitivity to ozone (B73, Mo17, Hp301, C123, NC338), using long reads to assemble transcripts and short reads to quantify expression of these transcripts. More than 99% of the long reads, 99% of the assembled transcripts, and 97% of the short reads map to both B73 and Mo17 reference genomes. Approximately 95% of the genes with assembled transcripts belong to known B73-Mo17 syntenic loci and 94% of genes with assembled transcripts are present in all temperate lines in the NAM pan-genome. While there is limited evidence for alternative splicing in response to ozone stress, there is a difference in the magnitude of differential expression among the 5 genotypes. The transcriptional response to sustained ozone stress in the ozone resistant B73 genotype (151 genes) was modest, while more than 3,300 genes were significantly differentially expressed in the more sensitive NC338 genotype. There is the potential for tandem duplication in 30% of genes with assembled transcripts, but there is no obvious association between potential tandem duplication and differential expression. Genes with a common response across the 5 genotypes (83 genes) were associated with photosynthesis, in particular photosystem I. The functional annotation of genes not differentially expressed in B73 but responsive in the other 4 genotypes (789) identifies reactive oxygen species. This suggests that B73 has a different response to long term ozone exposure than the other 4 genotypes. The relative magnitude of the genotypic response to ozone, and the enrichment analyses are consistent regardless of whether aligning short reads to: long read assembled transcripts; the B73 reference; the Mo17 reference. We find that prolonged ozone exposure directly impacts the photosynthetic machinery of the leaf.
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Affiliation(s)
- Adalena V Nanni
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611, USA.,Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Alison M Morse
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611, USA.,Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Jeremy R B Newman
- Department of Pathology, University of Florida, Gainesville, Florida 32611, USA.,Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Nicole E Choquette
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jessica M Wedow
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Zihao Liu
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611, USA.,Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Andrew D B Leakey
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ana Conesa
- Department of Cell and Microbial Sciences, University of Florida, Gainesville, Florida 32611, USA.,Institute for Integrative Systems Biology, Spanish National Research Council, 46980 Paterna, Spain
| | - Elizabeth A Ainsworth
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL 61801, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611, USA.,Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
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12
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Canaguier A, Guilbaud R, Denis E, Magdelenat G, Belser C, Istace B, Cruaud C, Wincker P, Le Paslier MC, Faivre-Rampant P, Barbe V. Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection. BMC Genomics 2022; 23:317. [PMID: 35448948 PMCID: PMC9026655 DOI: 10.1186/s12864-022-08499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 03/17/2022] [Indexed: 11/10/2022] Open
Abstract
Background Structural Variations (SVs) are genomic rearrangements derived from duplication, deletion, insertion, inversion, and translocation events. In the past, SVs detection was limited to cytological approaches, then to Next-Generation Sequencing (NGS) short reads and partitioned assemblies. Nowadays, technologies such as DNA long read sequencing and optical mapping have revolutionized the understanding of SVs in genomes, due to the enhancement of the power of SVs detection. This study aims to investigate performance of two techniques, 1) long-read sequencing obtained with the MinION device (Oxford Nanopore Technologies) and 2) optical mapping obtained with Saphyr device (Bionano Genomics) to detect and characterize SVs in the genomes of the two ecotypes of Arabidopsis thaliana, Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1). Results We described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 against the public reference genome Col-0 TAIR10.1. After filtering (SV > 1 kb), 1184 and 591 Ler-1 SVs were retained from ONT and Bionano technologies respectively. A total of 948 Ler-1 ONT SVs (80.1%) corresponded to 563 Bionano SVs (95.3%) leading to 563 common locations. The specific locations were scrutinized to assess improvement in SV detection by either technology. The ONT SVs were mostly detected near TE and gene features, and resistance genes seemed particularly impacted. Conclusions Structural variations linked to ONT sequencing error were removed and false positives limited, with high quality Bionano SVs being conserved. When compared with the Col-0 TAIR10.1 reference genome, most of the detected SVs discovered by both technologies were found in the same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the latter being more efficient to characterize large SVs. Even if both technologies are complementary approaches, ONT data appears to be more adapted to large scale populations studies, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08499-4.
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Affiliation(s)
- Aurélie Canaguier
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000, Evry-Courcouronnes, France
| | - Romane Guilbaud
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000, Evry-Courcouronnes, France
| | - Erwan Denis
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Ghislaine Magdelenat
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Corinne Cruaud
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Marie-Christine Le Paslier
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000, Evry-Courcouronnes, France
| | - Patricia Faivre-Rampant
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000, Evry-Courcouronnes, France.
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
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13
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Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives. Genes (Basel) 2022; 13:genes13040598. [PMID: 35456404 PMCID: PMC9031676 DOI: 10.3390/genes13040598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 01/25/2023] Open
Abstract
Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species diversity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host–pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems.
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14
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Sun G, Mural RV, Turkus JD, Schnable JC. Quantitative Resistance Loci to Southern Rust Mapped in a Temperate Maize Diversity Panel. PHYTOPATHOLOGY 2022; 112:579-587. [PMID: 34282952 DOI: 10.1094/phyto-04-21-0160-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Southern rust is a severe foliar disease of maize (Zea mays) resulting from infection with the obligate biotrophic fungus Puccinia polysora. This disease reduces photosynthetic productivity, which in turn reduces yields, with the greatest yield losses (up to 50%) associated with earlier onset infections. P. polysora urediniospores overwinter only in tropical and subtropical regions but cause outbreaks when environmental conditions favor initial infection. Increased temperatures and humidity during the growing season combined with an increased frequency of moderate winters are likely to increase the frequency of severe southern rust outbreaks in the U.S. Corn Belt. In summer 2020, a severe outbreak of southern rust was observed in eastern Nebraska, United States. We scored a replicated maize association panel planted in Lincoln, NE for disease severity and found that disease incidence and severity showed significant variation among maize genotypes. Genome-wide association studies identified four loci associated with significant quantitative variation in disease severity. These loci were associated with candidate genes with plausible links to quantitative disease resistance. A transcriptome-wide association study identified additional genes associated with disease severity. Together, these results indicate that substantial diversity in resistance to southern rust exists among current temperate-adapted maize germplasm, including several candidate loci that may explain the observed variation in resistance to southern rust.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Guangchao Sun
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE 68588
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Ravi V Mural
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE 68588
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Jonathan D Turkus
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE 68588
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - James C Schnable
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE 68588
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588
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15
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Zhang X, Zhu Y, Kremling KAG, Romay MC, Bukowski R, Sun Q, Gao S, Buckler ES, Lu F. Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:273-290. [PMID: 34661697 DOI: 10.1007/s00122-021-03965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Two read depth methods were jointly used in next-generation sequencing data to identify deletions in maize population. GWAS by deletions were analyzed for gene expression pattern and classical traits, respectively. Many studies have confirmed that structural variation (SV) is pervasive throughout the maize genome. Deletion is one type of SV that may impact gene expression and cause phenotypic changes in quantitative traits. In this study, two read count approaches were used to analyze the deletions in the whole-genome sequencing data of 270 maize inbred lines. A total of 19,754 deletion windows overlapped 12,751 genes, which were unevenly distributed across the genome. The deletions explained population structure well and correlated with genomic features. The deletion proportion of genes was determined to be negatively correlated with its expression. The detection of gene expression quantitative trait loci (eQTL) indicated that local eQTL were fewer but had larger effects than distant ones. The common associated genes were related to basic metabolic processes, whereas unique associated genes with eQTL played a role in the stress or stimulus responses in multiple tissues. Compared with the eQTL detected by SNPs derived from the same sequencing data, 89.4% of the associated genes could be detected by both markers. The effect of top eQTL detected by SNPs was usually larger than that detected by deletions for the same gene. A genome-wide association study (GWAS) on flowering time and plant height illustrated that only a few loci could be consistently captured by SNPs, suggesting that combining deletion and SNP for GWAS was an excellent strategy to dissect trait architecture. Our findings will provide insights into characteristic and biological function of genome-wide deletions in maize.
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Affiliation(s)
- Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China.
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA.
| | - Yonghui Zhu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Karl A G Kremling
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
| | - Robert Bukowski
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Qi Sun
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
- USDA-ARS, R. W. Holley Center, Cornell University, Ithaca, NY, USA
| | - Fei Lu
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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16
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Prunier J, Carrier A, Gilbert I, Poisson W, Albert V, Taillon J, Bourret V, Côté SD, Droit A, Robert C. CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly. Life Sci Alliance 2021; 5:5/3/e202101207. [PMID: 34911809 PMCID: PMC8711850 DOI: 10.26508/lsa.202101207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 01/13/2023] Open
Abstract
Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length > 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here.
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Affiliation(s)
- Julien Prunier
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Quebec City, Canada
| | - Alexandra Carrier
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - William Poisson
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Steeve D Côté
- Caribou Ungava, département de biologie, Faculté des Sciences et de Génie, Université Laval, Quebec City, Canada
| | - Arnaud Droit
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Quebec City, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
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17
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Comai L, Amundson KR, Ordoñez B, Zhao X, Braz GT, Jiang J, Henry IM. LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci. Genetics 2021; 219:6357040. [PMID: 34740239 DOI: 10.1093/genetics/iyab137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/13/2021] [Indexed: 12/30/2022] Open
Abstract
Large-scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1 Mb bin, we tested independence, effectively an apparent linkage disequilibrium (LD), with other variable bins. In nine potato (Solanum tuberosum) dihaploid families translocations affecting pericentromeric regions were common and in two cases were due to genomic misassembly. In two populations, we found evidence for translocation affecting euchromatic arms. In cv. PI 310467, a nonreciprocal translocation between chromosomes (chr.) 7 and 8 resulted in a 5-3 copy number change affecting several Mb at the respective chromosome tips. In cv. "Alca Tarma," the terminal arm of chr. 4 translocated to the tip of chr. 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, while apparent LD between pericentromeric regions suggested the effect of repeats. This method, LD-CNV, should be useful in species where translocations are suspected because it tests linkage without the need for genotyping.
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Affiliation(s)
- Luca Comai
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Kirk R Amundson
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Benny Ordoñez
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Xin Zhao
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Guilherme Tomaz Braz
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
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18
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Dong MY, Lei L, Fan XW, Li YZ. Analyses of open-access multi-omics data sets reveal genetic and expression characteristics of maize ZmCCT family genes. AOB PLANTS 2021; 13:plab048. [PMID: 34567492 PMCID: PMC8459886 DOI: 10.1093/aobpla/plab048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Flowering in maize (Zea mays) is influenced by photoperiod. The CO, CO-like/COL and TOC1 (CCT) domain protein-encoding genes in maize, ZmCCTs, are particularly important for photoperiod sensitivity. However, little is known about CCT protein-encoding gene number across plant species or among maize inbred lines. Therefore, we analysed CCT protein-encoding gene number across plant species, and characterized ZmCCTs in different inbred lines, including structural variations (SVs), copy number variations (CNVs), expression under stresses, dark-dark (DD) and dark-light (DL) cycles, interaction network and associations with maize quantitative trait loci (QTLs) by referring to the latest v4 genome data of B73. Gene number varied greatly across plant species, more in polyploids than in diploids. The numbers of ZmCCTs identified were 58 in B73, 59 in W22, 48 in Mo17, and 57 in Huangzao4 for temperate maize inbred lines, and 68 in tropical maize inbred line SK. Some ZmCCTs underwent duplications and presented chromosome collinearity. Structural variations and CNVs were found but they had no germplasm specificity. Forty-two ZmCCTs responded to stresses. Expression of 37 ZmCCTs in embryonic leaves during seed germination of maize under DD and DL cycles was roughly divided into five patterns of uphill pattern, downhill-pattern, zigzag-pattern, └-pattern and ⅃-pattern, indicating some of them have a potential to perceive dark and/or dark-light transition. Thirty-three ZmCCTs were co-expressed with 218 other maize genes; and 24 ZmCCTs were associated with known QTLs. The data presented in this study will help inform further functions of ZmCCTs.
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Affiliation(s)
- Ming-You Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - Ling Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - Xian-Wei Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - You-Zhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
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19
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Nie S, Wang B, Ding H, Lin H, Zhang L, Li Q, Wang Y, Zhang B, Liang A, Zheng Q, Wang H, Lv H, Zhu K, Jia M, Wang X, Du J, Zhao R, Jiang Z, Xia C, Qiao Z, Li X, Liu B, Zhu H, An R, Li Y, Jiang Q, Chen B, Zhang H, Wang D, Tang C, Yuan Y, Dai J, Zhan J, He W, Wang X, Shi J, Wang B, Gong M, He X, Li P, Huang L, Li H, Pan C, Huang H, Yuan G, Lan H, Nie Y, Li X, Zhao X, Zhang X, Pan G, Wu Q, Xu F, Zhang Z. Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:40-54. [PMID: 34252236 DOI: 10.1111/tpj.15421] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Maize is an important crop worldwide, as well as a valuable model with vast genetic diversity. Accurate genome and annotation information for a wide range of inbred lines would provide valuable resources for crop improvement and pan-genome characterization. In this study, we generated a high-quality de novo genome assembly (contig N50 of 15.43 Mb) of the Chinese elite inbred line RP125 using Nanopore long-read sequencing and Hi-C scaffolding, which yield highly contiguous, chromosome-length scaffolds. Global comparison of the RP125 genome with those of B73, W22, and Mo17 revealed a large number of structural variations. To create new germplasm for maize research and crop improvement, we carried out an EMS mutagenesis screen on RP125. In total, we obtained 5818 independent M2 families, with 946 mutants showing heritable phenotypes. Taking advantage of the high-quality RP125 genome, we successfully cloned 10 mutants from the EMS library, including the novel kernel mutant qk1 (quekou: "missing a small part" in Chinese), which exhibited partial loss of endosperm and a starch accumulation defect. QK1 encodes a predicted metal tolerance protein, which is specifically required for Fe transport. Increased accumulation of Fe and reactive oxygen species as well as ferroptosis-like cell death were detected in qk1 endosperm. Our study provides the community with a high-quality genome sequence and a large collection of mutant germplasm.
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Affiliation(s)
- Shujun Nie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Haiping Ding
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Haijian Lin
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Li Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Qigui Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Yujiao Wang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Bin Zhang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Anping Liang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Qi Zheng
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
- The Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Hui Wang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Huayang Lv
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Kun Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Minghui Jia
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xiaotong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Jiyuan Du
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Runtai Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Zhenzhen Jiang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Caina Xia
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Zhenghao Qiao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xiaohu Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Boyan Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Hongbo Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Rong An
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Yucui Li
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Qian Jiang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Benfang Chen
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Hongkai Zhang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Dening Wang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Changxiao Tang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Yang Yuan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Jie Dai
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Jing Zhan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Weiqiang He
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Xuebo Wang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Jian Shi
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Bin Wang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Min Gong
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Xiujing He
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Peng Li
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Li Huang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Hui Li
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Chao Pan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Hong Huang
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Guangsheng Yuan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Yongxin Nie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xinzheng Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xiangyu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Xiansheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Guangtang Pan
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
| | - Qingyu Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fang Xu
- The Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zhiming Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
- Maize Research Institute, Sichuan Agricultural University, ChengDu, 611130, China
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20
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Qiu Y, O’Connor CH, Della Coletta R, Renk JS, Monnahan PJ, Noshay JM, Liang Z, Gilbert A, Anderson SN, McGaugh SE, Springer NM, Hirsch CN. Whole-genome variation of transposable element insertions in a maize diversity panel. G3 (BETHESDA, MD.) 2021; 11:jkab238. [PMID: 34568911 PMCID: PMC8473971 DOI: 10.1093/g3journal/jkab238] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023]
Abstract
Intact transposable elements (TEs) account for 65% of the maize genome and can impact gene function and regulation. Although TEs comprise the majority of the maize genome and affect important phenotypes, genome-wide patterns of TE polymorphisms in maize have only been studied in a handful of maize genotypes, due to the challenging nature of assessing highly repetitive sequences. We implemented a method to use short-read sequencing data from 509 diverse inbred lines to classify the presence/absence of 445,418 nonredundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e., LTRs, Helitrons, and TIRs) had different frequency distributions within the population. LTRs with lower LTR similarity were generally more frequent in the population than LTRs with higher LTR similarity, though high-frequency insertions with very high LTR similarity were observed. LTR similarity and frequency estimates of nested elements and the outer elements in which they insert revealed that most nesting events occurred very near the timing of the outer element insertion. TEs within genes were at higher frequency than those that were outside of genes and this is particularly true for those not inserted into introns. Many TE insertional polymorphisms observed in this population were tagged by SNP markers. However, there were also 19.9% of the TE polymorphisms that were not well tagged by SNPs (R2 < 0.5) that potentially represent information that has not been well captured in previous SNP-based marker-trait association studies. This study provides a population scale genome-wide assessment of TE variation in maize and provides valuable insight on variation in TEs in maize and factors that contribute to this variation.
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Affiliation(s)
- Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Christine H O’Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Jonathan S Renk
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Patrick J Monnahan
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Zhikai Liang
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Amanda Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sarah N Anderson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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21
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Huang Y, Huang W, Meng Z, Braz GT, Li Y, Wang K, Wang H, Lai J, Jiang J, Dong Z, Jin W. Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation. Genome Biol 2021; 22:237. [PMID: 34416918 PMCID: PMC8377971 DOI: 10.1186/s13059-021-02448-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/02/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation. RESULTS In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement. CONCLUSIONS These findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the "fossil" structure variations during genome evolution and speciation.
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Affiliation(s)
- Yumin Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Wei Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Zhuang Meng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Guilherme Tomaz Braz
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yunfei Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Kai Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hai Wang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Zhaobin Dong
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China.
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China.
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22
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Noshay JM, Liang Z, Zhou P, Crisp PA, Marand AP, Hirsch CN, Schmitz RJ, Springer NM. Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3 (BETHESDA, MD.) 2021; 11:6288454. [PMID: 34849810 PMCID: PMC8496265 DOI: 10.1093/g3journal/jkab190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Accessible chromatin and unmethylated DNA are associated with many genes and cis-regulatory elements. Attempts to understand natural variation for accessible chromatin regions (ACRs) and unmethylated regions (UMRs) often rely upon alignments to a single reference genome. This limits the ability to assess regions that are absent in the reference genome assembly and monitor how nearby structural variants influence variation in chromatin state. In this study, de novo genome assemblies for four maize inbreds (B73, Mo17, Oh43, and W22) are utilized to assess chromatin accessibility and DNA methylation patterns in a pan-genome context. A more complete set of UMRs and ACRs can be identified when chromatin data are aligned to the matched genome rather than a single reference genome. While there are UMRs and ACRs present within genomic regions that are not shared between genotypes, these features are 6- to 12-fold enriched within regions between genomes. Characterization of UMRs present within shared genomic regions reveals that most UMRs maintain the unmethylated state in other genotypes with only ∼5% being polymorphic between genotypes. However, the majority (71%) of UMRs that are shared between genotypes only exhibit partial overlaps suggesting that the boundaries between methylated and unmethylated DNA are dynamic. This instability is not solely due to sequence variation as these partially overlapping UMRs are frequently found within genomic regions that lack sequence variation. The ability to compare chromatin properties among individuals with structural variation enables pan-epigenome analyses to study the sources of variation for accessible chromatin and unmethylated DNA.
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Affiliation(s)
- Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Zhikai Liang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Peter A Crisp
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | | | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
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23
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Tao Y, Luo H, Xu J, Cruickshank A, Zhao X, Teng F, Hathorn A, Wu X, Liu Y, Shatte T, Jordan D, Jing H, Mace E. Extensive variation within the pan-genome of cultivated and wild sorghum. NATURE PLANTS 2021; 7:766-773. [PMID: 34017083 DOI: 10.1038/s41477-021-00925-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 04/21/2021] [Indexed: 05/18/2023]
Abstract
Sorghum is a drought-tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importance. Cultivated sorghum and its inter-fertile wild relatives constitute the primary gene pool for sorghum. Understanding and characterizing the diversity within this valuable resource is fundamental for its effective utilization in crop improvement. Here, we report analysis of a sorghum pan-genome to explore genetic diversity within the sorghum primary gene pool. We assembled 13 genomes representing cultivated sorghum and its wild relatives, and integrated them with 3 other published genomes to generate a pan-genome of 44,079 gene families with 222.6 Mb of new sequence identified. The pan-genome displays substantial gene-content variation, with 64% of gene families showing presence/absence variation among genomes. Comparisons between core genes and dispensable genes suggest that dispensable genes are important for sorghum adaptation. Extensive genetic variation was uncovered within the pan-genome, and the distribution of these variations was influenced by variation of recombination rate and transposable element content across the genome. We identified presence/absence variants that were under selection during sorghum domestication and improvement, and demonstrated that such variation had important phenotypic outcomes that could contribute to crop improvement. The constructed sorghum pan-genome represents an important resource for sorghum improvement and gene discovery.
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Affiliation(s)
- Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, Australia
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Alan Cruickshank
- Hermitage Research Facility, Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Warwick, Queensland, Australia
| | - Xianrong Zhao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, Australia
| | - Fei Teng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, Australia
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tracey Shatte
- Hermitage Research Facility, Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Warwick, Queensland, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, Australia.
| | - Haichun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Queensland, Australia.
- Hermitage Research Facility, Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Warwick, Queensland, Australia.
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24
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Bastiaanse H, Henry IM, Tsai H, Lieberman M, Canning C, Comai L, Groover A. A systems genetics approach to deciphering the effect of dosage variation on leaf morphology in Populus. THE PLANT CELL 2021; 33:940-960. [PMID: 33793772 PMCID: PMC8226299 DOI: 10.1093/plcell/koaa016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/30/2020] [Indexed: 05/05/2023]
Abstract
Gene copy number variation is frequent in plant genomes of various species, but the impact of such gene dosage variation on morphological traits is poorly understood. We used a large population of Populus carrying genomically characterized insertions and deletions across the genome to systematically assay the effect of gene dosage variation on a suite of leaf morphology traits. A systems genetics approach was used to integrate insertion and deletion locations, leaf morphology phenotypes, gene expression, and transcriptional network data, to provide an overview of how gene dosage influences morphology. Dosage-sensitive genomic regions were identified that influenced individual or pleiotropic morphological traits. We also identified cis-expression quantitative trait loci (QTL) within these dosage QTL regions, a subset of which modulated trans-expression QTL as well. Integration of data types within a gene co-expression framework identified co-expressed gene modules that are dosage sensitive, enriched for dosage expression QTL, and associated with morphological traits. Functional description of these modules linked dosage-sensitive morphological variation to specific cellular processes, as well as candidate regulatory genes. Together, these results show that gene dosage variation can influence morphological variation through complex changes in gene expression, and suggest that frequently occurring gene dosage variation has the potential to likewise influence quantitative traits in nature.
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Affiliation(s)
- Héloïse Bastiaanse
- Present address: VIB Center for Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
| | - Isabelle M Henry
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
| | - Helen Tsai
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
| | - Meric Lieberman
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
| | - Courtney Canning
- Pacific Southwest Research Station, US Forest Service, Davis, California 95618
| | - Luca Comai
- Genome Center, University of California Davis, Davis 95616
- Department of Plant Biology, University of California Davis, Davis 95616
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25
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Songsomboon K, Brenton Z, Heuser J, Kresovich S, Shakoor N, Mockler T, Cooper EA. Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation. G3-GENES GENOMES GENETICS 2021; 11:6265466. [PMID: 33950177 PMCID: PMC8495935 DOI: 10.1093/g3journal/jkab154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/23/2021] [Indexed: 12/04/2022]
Abstract
Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum [Sorghum bicolor (L.) Moench] is one of the most widely grown cereal crops in the world. It has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity. In this study, we identified genome-wide SVs in the Biomass Association Panel, a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole-genome resequencing data from every genotype, we found a total of 24,648 SVs, including 22,359 deletions. The global site frequency spectrum of deletions and other types of SVs fit a model of neutral evolution, suggesting that the majority of these mutations were not under any types of selection. Clustering results based on single nucleotide polymorphisms separated the genotypes into eight clusters which largely corresponded with geographic origins, with many of the large deletions we uncovered being unique to a single cluster. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic and abiotic stress responses, supporting the possibility that at least some of these deletions contribute to local adaptation in sorghum.
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Affiliation(s)
- Kittikun Songsomboon
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223 USA.,North Carolina Research Campus, Kannapolis, NC 28081 USA
| | - Zachary Brenton
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634 USA
| | - James Heuser
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223 USA.,North Carolina Research Campus, Kannapolis, NC 28081 USA
| | - Stephen Kresovich
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634 USA
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, St. Louis, MO, 63132 USA
| | - Todd Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132 USA
| | - Elizabeth A Cooper
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223 USA.,North Carolina Research Campus, Kannapolis, NC 28081 USA
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26
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Pang H, Chen Q, Li Y, Wang Z, Wu L, Yang Q, Zheng X. Comparative analysis of the transcriptomes of two rice subspecies during domestication. Sci Rep 2021; 11:3660. [PMID: 33574456 PMCID: PMC7878495 DOI: 10.1038/s41598-021-83162-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/28/2021] [Indexed: 11/11/2022] Open
Abstract
Two subspecies of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica accessions, and identified 97,005 transcribed fragments and 4579 novel transcriptionally active regions. The two rice subspecies had significantly different gene expression profiles, we identified 1,357 (3.3% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. Combining existing gene function studies, it is found that some of these differential genes are related to the differentiation of the two subspecies, such as grain shape and cold tolerance, etc. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5'flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs. This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs those may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.
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Affiliation(s)
- Hongbo Pang
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Qiang Chen
- Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Yueying Li
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Ze Wang
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Longkun Wu
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Qingwen Yang
- Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoming Zheng
- Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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27
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Sielemann K, Weisshaar B, Pucker B. Reference-based QUantification Of gene Dispensability (QUOD). PLANT METHODS 2021; 17:18. [PMID: 33563309 PMCID: PMC7871624 DOI: 10.1186/s13007-021-00718-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 02/03/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a few investigated genomes. The binary classification as 'core' or 'dispensable' is often based on arbitrary cutoffs of presence/absence in the analysed genomes. Even when extended to 'conditionally dispensable', this concept still requires the assignment of genes to distinct groups. RESULTS Here, we present a new method which overcomes this distinct classification by quantifying gene dispensability and present a dedicated tool for reference-based QUantification Of gene Dispensability (QUOD). As a proof of concept, sequence data of 966 Arabidopsis thaliana accessions (Ath-966) were processed to calculate a gene-specific dispensability score for each gene based on normalised coverage in read mappings. We validated this score by comparison of highly conserved Benchmarking Universal Single Copy Orthologs (BUSCOs) to all other genes. The average scores of BUSCOs were significantly lower than the scores of non-BUSCOs. Analysis of variation demonstrated lower variation values between replicates of a single accession than between iteratively, randomly selected accessions from the whole dataset Ath-966. Functional investigations revealed defense and antimicrobial response genes among the genes with high-dispensability scores. CONCLUSIONS Instead of classifying a gene as core or dispensable, QUOD assigns a dispensability score to each gene. Hence, QUOD facilitates the identification of candidate dispensable genes, associated with high dispensability scores, which often underlie lineage-specific adaptation to varying environmental conditions.
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Affiliation(s)
- Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615 Bielefeld, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
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28
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Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson SA, Close TJ, Shubo W, Varshney RK. Genomic resources in plant breeding for sustainable agriculture. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153351. [PMID: 33412425 PMCID: PMC7903322 DOI: 10.1016/j.jplph.2020.153351] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 05/19/2023]
Abstract
Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; University of Southern Queensland, Toowoomba, Australia
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Emma Mace
- Agri-Science Queensland, Department of Agriculture & Fisheries (DAF), Warwick, Australia
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | | | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Bin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Vikas K Singh
- South Asia Hub, International Rice Research Institute (IRRI), Hyderabad, India
| | - Guowei Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CYMMIT), Mexico DF, Mexico; Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sanjay Kaila
- Department of Biotechnology, Ministry of Science and Technology, Government of India, India
| | - Henry Nguyen
- National Centre for Soybean Research, University of Missouri, Columbia, USA
| | - Sobhana Sivasankar
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | | | | | - Wan Shubo
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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29
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Li Z, Zhou P, Della Coletta R, Zhang T, Brohammer AB, H O'Connor C, Vaillancourt B, Lipzen A, Daum C, Barry K, de Leon N, Hirsch CD, Buell CR, Kaeppler SM, Springer NM, Hirsch CN. Single-parent expression drives dynamic gene expression complementation in maize hybrids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:93-107. [PMID: 33098691 DOI: 10.1111/tpj.15042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Single-parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non-presence/absence (non-PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverse Zea mays (maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non-PAV SPE genes are mainly regulated by cis effects, with a small fraction under trans regulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level of cis regulation for PAV SPE and non-PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non-PAV SPE genes. The expression of parentally silent alleles in hybrids of non-PAV SPE genes was relatively rare but occurred in most hybrids. Non-PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non-additive expression. This study provides a comprehensive understanding of the nature of non-PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids.
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Affiliation(s)
- Zhi Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Tifu Zhang
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Nathan M Springer
- 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
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30
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Han X, Qin Y, Sandrine AMN, Qiu F. Fine mapping of qKRN8, a QTL for maize kernel row number, and prediction of the candidate gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3139-3150. [PMID: 32857170 DOI: 10.1007/s00122-020-03660-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE: qKRN8, a major QTL for kernel row number in maize, was fine mapped to an interval of ~ 520 kb on chromosome 8 and the key candidate gene was identified via expression analysis. Kernel row number (KRN) is one of the most important yield-influencing traits and is closely associated with female inflorescence development in maize (Zea mays L.). In this study, an F2:3 population derived from a cross between V54 (low KRN line) and Lian87 (high KRN line) was used to map quantitative trait loci (QTLs) conferring KRN in maize. We identified 12 QTLs for KRN in four environments, each explaining 1.40-14.95% of phenotypic variance. Among these, one novel major QTL (named qKRN8) was mapped to bin 8.03 in all four environments, explaining 8.79-14.95% of phenotypic variation. By combining map-based cloning with progeny testing of recombinants, we ultimately mapped qKRN8 to an ~ 520 kb genomic interval, harboring six putative candidate genes. Among them, one candidate gene showed contrasted expression level in immature ears of the near-isogenic lines qKRN8Lian87 and qKRN8V54. These findings should facilitate molecular breeding for KRN and the further identification of the polymorphism underlying this QTL.
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Affiliation(s)
- Xuesong Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Yao Qin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Ada Menie Nelly Sandrine
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China.
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31
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Schnable JC. Genes and gene models, an important distinction. THE NEW PHYTOLOGIST 2020; 228:50-55. [PMID: 31241760 DOI: 10.1111/nph.16011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/07/2019] [Indexed: 05/22/2023]
Abstract
Genome sequencing has fundamentally changed how plant biologists think about genes. All or nearly all genes can ultimately be associated with a gene model. However, many gene models appear to play little or no role in the traits of an organism. A range of structural, molecular, population and evolutionary features all show a separation between genes with known phenotypes and the overall set of annotated gene models. These different features could be combined to develop models to distinguish the genes that determine the traits of plants from the subset gene other annotated gene models which are unlikely to play a role in doing so. Efforts to identify the subset of annotated gene models likely involved in specifying the characteristics of plants would help aid a wide range of researchers.
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Affiliation(s)
- James C Schnable
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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32
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Bruggeman SA, Horvath DP, Fennell AY, Gonzalez-Hernandez JL, Clay SA. Teosinte (Zea mays ssp parviglumis) growth and transcriptomic response to weed stress identifies similarities and differences between varieties and with modern maize varieties. PLoS One 2020; 15:e0237715. [PMID: 32822374 PMCID: PMC7444550 DOI: 10.1371/journal.pone.0237715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 07/31/2020] [Indexed: 12/22/2022] Open
Abstract
Transcriptomic responses of plants to weed presence gives insight on the physiological and molecular mechanisms involved in the stress response. This study evaluated transcriptomic and morphological responses of two teosinte (Zea mays ssp parviglumis) (an ancestor of domesticated maize) lines (Ames 21812 and Ames 21789) to weed presence and absence during two growing seasons. Responses were compared after 6 weeks of growth in Aurora, South Dakota, USA. Plant heights between treatments were similar in Ames 21812, whereas branch number decreased when weeds were present. Ames 21789 was 45% shorter in weedy vs weed-free plots, but branch numbers were similar between treatments. Season-long biomass was reduced in response to weed stress in both lines. Common down-regulated subnetworks in weed-stressed plants were related to light, photosynthesis, and carbon cycles. Several unique response networks (e.g. aging, response to chitin) and gene sets were present in each line. Comparing transcriptomic responses of maize (determined in an adjacent study) and teosinte lines indicated three common gene ontologies up-regulated when weed-stressed: jasmonic acid response/signaling, UDP-glucosyl and glucuronyltransferases, and quercetin glucosyltransferase (3-O and 7-O). Overall, morphologic and transcriptomic differences suggest a greater varietal (rather than a conserved) response to weed stress, and implies multiple responses are possible. These findings offer insights into opportunities to define and manipulate gene expression of several different pathways of modern maize varieties to improve performance under weedy conditions.
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Affiliation(s)
- S. A. Bruggeman
- Biology Department, St. Augustana University, Sioux Falls, SD, United States of America
| | - D. P. Horvath
- USDA-ARS-ETSARC, Sunflower and Plant Biology Research Unit, Fargo, ND, United States of America
| | - A. Y. Fennell
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States of America
| | - J. L. Gonzalez-Hernandez
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States of America
| | - S. A. Clay
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States of America
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33
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Bretani G, Rossini L, Ferrandi C, Russell J, Waugh R, Kilian B, Bagnaresi P, Cattivelli L, Fricano A. Segmental duplications are hot spots of copy number variants affecting barley gene content. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1073-1088. [PMID: 32338390 PMCID: PMC7496488 DOI: 10.1111/tpj.14784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 05/31/2023]
Abstract
Copy number variants (CNVs) are pervasive in several animal and plant genomes and contribute to shaping genetic diversity. In barley, there is evidence that changes in gene copy number underlie important agronomic traits. The recently released reference sequence of barley represents a valuable genomic resource for unveiling the incidence of CNVs that affect gene content and for identifying sequence features associated with CNV formation. Using exome sequencing and read count data, we detected 16 605 deletions and duplications that affect barley gene content by surveying a diverse panel of 172 cultivars, 171 landraces, 22 wild relatives and other 32 uncategorized domesticated accessions. The quest for segmental duplications (SDs) in the reference sequence revealed many low-copy repeats, most of which overlap predicted coding sequences. Statistical analyses revealed that the incidence of CNVs increases significantly in SD-rich regions, indicating that these sequence elements act as hot spots for the formation of CNVs. The present study delivers a comprehensive genome-wide study of CNVs affecting barley gene content and implicates SDs in the molecular mechanisms that lead to the formation of this class of CNVs.
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Affiliation(s)
- Gianluca Bretani
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Laura Rossini
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Chiara Ferrandi
- Parco Tecnologico PadanoLoc. C.na CodazzaVia Einstein26900LodiItaly
| | | | - Robbie Waugh
- James Hutton Institute, InvergowrieDundeeDD2 5DAUK
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 306466GaterslebenGermany
- Global Crop Diversity TrustPlatz der Vereinten Nationen 753113BonnGermany
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics – Research Centre for Genomics & BioinformaticsVia San Protaso 30229017Fiorenzuola d'Arda (PC)Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics – Research Centre for Genomics & BioinformaticsVia San Protaso 30229017Fiorenzuola d'Arda (PC)Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics – Research Centre for Genomics & BioinformaticsVia San Protaso 30229017Fiorenzuola d'Arda (PC)Italy
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34
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Nieto Feliner G, Casacuberta J, Wendel JF. Genomics of Evolutionary Novelty in Hybrids and Polyploids. Front Genet 2020; 11:792. [PMID: 32849797 PMCID: PMC7399645 DOI: 10.3389/fgene.2020.00792] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.
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Affiliation(s)
- Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Madrid, Spain
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
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35
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European maize genomes highlight intraspecies variation in repeat and gene content. Nat Genet 2020; 52:950-957. [PMID: 32719517 PMCID: PMC7467862 DOI: 10.1038/s41588-020-0671-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/25/2020] [Indexed: 12/22/2022]
Abstract
The diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today’s highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report de novo genome sequences of four European flint lines assembled to pseudomolecules with scaffold N50 ranging from 6.1 to 10.4 Mb. Comparative analyses with two US Corn Belt lines explains the pronounced differences between both germplasms. While overall syntenic order and consolidated gene annotations reveal only moderate pangenomic differences, whole-genome alignments delineating the core and dispensable genome, and the analysis of heterochromatic knobs and orthologous long terminal repeat retrotransposons unveil the dynamics of the maize genome. The high-quality genome sequences of the flint pool complement the maize pangenome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding. De novo genome assemblies of four European flint maize lines and comparison with two US Corn Belt genomes provide insights into the dynamics of intraspecies variation in repeat and gene content in maize genomes.
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36
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N'Diaye A, Byrns B, Cory AT, Nilsen KT, Walkowiak S, Sharpe A, Robinson SJ, Pozniak CJ. Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat. THE PLANT GENOME 2020; 13:e20027. [PMID: 33016606 DOI: 10.1002/tpg2.20027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/24/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is a mechanism of epigenetic modification in eukaryotic organisms. Generally, methylation within genes promoter inhibits regulatory protein binding and represses transcription, whereas gene body methylation is associated with actively transcribed genes. However, it remains unclear whether there is interaction between methylation levels across genic regions and which site has the biggest impact on gene regulation. We investigated and used the methylation patterns of the bread wheat cultivar Chinese Spring to uncover differentially expressed genes (DEGs) between roots and leaves, using six machine learning algorithms and a deep neural network. As anticipated, genes with higher expression in leaves were mainly involved in photosynthesis and pigment biosynthesis processes whereas genes that were not differentially expressed between roots and leaves were involved in protein processes and membrane structures. Methylation occurred preponderantly (60%) in the CG context, whereas 35 and 5% of methylation occurred in CHG and CHH contexts, respectively. Methylation levels were highly correlated (r = 0.7 to 0.9) between all genic regions, except within the promoter (r = 0.4 to 0.5). Machine learning models gave a high (0.81) prediction accuracy of DEGs. There was a strong correlation (p-value = 9.20×10-10 ) between all features and gene expression, suggesting that methylation across all genic regions contribute to gene regulation. However, the methylation of the promoter, the CDS and the exon in CG context was the most impactful. Our study provides more insights into the interplay between DNA methylation and gene expression and paves the way for identifying tissue-specific genes using methylation profiles.
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Affiliation(s)
- Amidou N'Diaye
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Brook Byrns
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Aron T Cory
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Kirby T Nilsen
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Sean Walkowiak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Andrew Sharpe
- Global Institute for Food Security, Saskatoon, SK, Canada, S7N 0W9
| | - Stephen J Robinson
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
| | - Curtis J Pozniak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
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37
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Zmienko A, Marszalek-Zenczak M, Wojciechowski P, Samelak-Czajka A, Luczak M, Kozlowski P, Karlowski WM, Figlerowicz M. AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. THE PLANT CELL 2020; 32:1797-1819. [PMID: 32265262 PMCID: PMC7268809 DOI: 10.1105/tpc.19.00640] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 03/09/2020] [Accepted: 03/30/2020] [Indexed: 05/13/2023]
Abstract
Copy number variations (CNVs) greatly contribute to intraspecies genetic polymorphism and phenotypic diversity. Recent analyses of sequencing data for >1000 Arabidopsis (Arabidopsis thaliana) accessions focused on small variations and did not include CNVs. Here, we performed genome-wide analysis and identified large indels (50 to 499 bp) and CNVs (500 bp and larger) in these accessions. The CNVs fully overlap with 18.3% of protein-coding genes, with enrichment for evolutionarily young genes and genes involved in stress and defense. By combining analysis of both genes and transposable elements (TEs) affected by CNVs, we revealed that the variation statuses of genes and TEs are tightly linked and jointly contribute to the unequal distribution of these elements in the genome. We also determined the gene copy numbers in a set of 1060 accessions and experimentally validated the accuracy of our predictions by multiplex ligation-dependent probe amplification assays. We then successfully used the CNVs as markers to analyze population structure and migration patterns. Finally, we examined the impact of gene dosage variation triggered by a CNV spanning the SEC10 gene on SEC10 expression at both the transcript and protein levels. The catalog of CNVs, CNV-overlapping genes, and their genotypes in a top model dicot will stimulate the exploration of the genetic basis of phenotypic variation.
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Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | | | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
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Early Drought-Responsive Genes Are Variable and Relevant to Drought Tolerance. G3-GENES GENOMES GENETICS 2020; 10:1657-1670. [PMID: 32161086 PMCID: PMC7202030 DOI: 10.1534/g3.120.401199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Drought stress is an important crop yield limiting factor worldwide. Plant physiological responses to drought stress are driven by changes in gene expression. While drought-responsive genes (DRGs) have been identified in maize, regulation patterns of gene expression during progressive water deficits remain to be elucidated. In this study, we generated time-series transcriptomic data from the maize inbred line B73 under well-watered and drought conditions. Comparisons between the two conditions identified 8,626 DRGs and the stages (early, middle, and late drought) at which DRGs occurred. Different functional groups of genes were regulated at the three stages. Specifically, early and middle DRGs display higher copy number variation among diverse Zea mays lines, and they exhibited stronger associations with drought tolerance as compared to late DRGs. In addition, correlation of expression between small RNAs (sRNAs) and DRGs from the same samples identified 201 negatively sRNA/DRG correlated pairs, including genes showing high levels of association with drought tolerance, such as two glutamine synthetase genes, gln2 and gln6 The characterization of dynamic gene responses to progressive drought stresses indicates important adaptive roles of early and middle DRGs, as well as roles played by sRNAs in gene expression regulation upon drought stress.
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39
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Baldauf JA, Vedder L, Schoof H, Hochholdinger F. Robust non-syntenic gene expression patterns in diverse maize hybrids during root development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:865-876. [PMID: 31638701 DOI: 10.1093/jxb/erz452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Distantly related maize (Zea mays L.) inbred lines exhibit an exceptional degree of structural genomic diversity, which is probably unique among plants. This study systematically investigated the developmental and genotype-dependent regulation of the primary root transcriptomes of a genetically diverse panel of maize F1-hybrids and their parental inbred lines. While we observed substantial transcriptomic changes during primary root development, we demonstrated that hybrid-associated gene expression patterns, including differential, non-additive, and allele-specific transcriptome profiles, are particularly robust to these developmental fluctuations. For instance, differentially expressed genes with preferential expression in hybrids were highly conserved during development in comparison to their parental counterparts. Similarly, in hybrids a major proportion of non-additively expressed genes with expression levels between the parental values were particularly conserved during development. Importantly, in these expression patterns non-syntenic genes that evolved after the separation of the maize and sorghum lineages were systemically enriched. Furthermore, non-syntenic genes were substantially linked to the conservation of all surveyed gene expression patterns during primary root development. Among all F1-hybrids, between ~40% of the non-syntenic genes with unexpected allelic expression ratios and ~60% of the non-syntenic differentially and non-additively expressed genes were conserved and therefore robust to developmental changes. Hence, the enrichment of non-syntenic genes during primary root development might be involved in the developmental adaptation of maize roots and thus the superior performance of hybrids.
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Affiliation(s)
- Jutta A Baldauf
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Lucia Vedder
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- Institute for Crop Science and Resource Conservation, Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Frank Hochholdinger
- Institute for Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
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Welgemoed T, Pierneef R, Sterck L, Van de Peer Y, Swart V, Scheepers KD, Berger DK. De novo Assembly of Transcriptomes From a B73 Maize Line Introgressed With a QTL for Resistance to Gray Leaf Spot Disease Reveals a Candidate Allele of a Lectin Receptor-Like Kinase. FRONTIERS IN PLANT SCIENCE 2020; 11:191. [PMID: 32231673 PMCID: PMC7083176 DOI: 10.3389/fpls.2020.00191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/07/2020] [Indexed: 05/03/2023]
Abstract
Gray leaf spot (GLS) disease in maize, caused by the fungus Cercospora zeina, is a threat to maize production globally. Understanding the molecular basis for quantitative resistance to GLS is therefore important for food security. We developed a de novo assembly pipeline to identify candidate maize resistance genes. Near-isogenic maize lines with and without a QTL for GLS resistance on chromosome 10 from inbred CML444 were produced in the inbred B73 background. The B73-QTL line showed a 20% reduction in GLS disease symptoms compared to B73 in the field (p = 0.01). B73-QTL leaf samples from this field experiment conducted under GLS disease pressure were RNA sequenced. The reads that did not map to the B73 or C. zeina genomes were expected to contain novel defense genes and were de novo assembled. A total of 141 protein-coding sequences with B73-like or plant annotations were identified from the B73-QTL plants exposed to C. zeina. To determine whether candidate gene expression was induced by C. zeina, the RNAseq reads from C. zeina-challenged and control leaves were mapped to a master assembly of all of the B73-QTL reads, and differential gene expression analysis was conducted. Combining results from both bioinformatics approaches led to the identification of a likely candidate gene, which was a novel allele of a lectin receptor-like kinase named L-RLK-CML that (i) was induced by C. zeina, (ii) was positioned in the QTL region, and (iii) had functional domains for pathogen perception and defense signal transduction. The 817AA L-RLK-CML protein had 53 amino acid differences from its 818AA counterpart in B73. A second "B73-like" allele of L-RLK was expressed at a low level in B73-QTL. Gene copy-specific RT-qPCR confirmed that the l-rlk-cml transcript was the major product induced four-fold by C. zeina. Several other expressed defense-related candidates were identified, including a wall-associated kinase, two glutathione s-transferases, a chitinase, a glucan beta-glucosidase, a plasmodesmata callose-binding protein, several other receptor-like kinases, and components of calcium signaling, vesicular trafficking, and ethylene biosynthesis. This work presents a bioinformatics protocol for gene discovery from de novo assembled transcriptomes and identifies candidate quantitative resistance genes.
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Affiliation(s)
- Tanya Welgemoed
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Rian Pierneef
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Plant Systems Biology, VIB, Ghent, Belgium
| | - Yves Van de Peer
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Pretoria, South Africa
| | - Velushka Swart
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Kevin Daniel Scheepers
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Dave K. Berger
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- *Correspondence: Dave K. Berger,
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Cuello C, Baldy A, Brunaud V, Joets J, Delannoy E, Jacquemot MP, Botran L, Griveau Y, Guichard C, Soubigou-Taconnat L, Martin-Magniette ML, Leroy P, Méchin V, Reymond M, Coursol S. A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize. PLoS One 2019; 14:e0227011. [PMID: 31891625 PMCID: PMC6938352 DOI: 10.1371/journal.pone.0227011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/09/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding the mechanisms triggering variation of cell wall degradability is a prerequisite to improving the energy value of lignocellulosic biomass for animal feed or biorefinery. Here, we implemented a multiscale systems approach to shed light on the genetic basis of cell wall degradability in maize. We demonstrated that allele replacement in two pairs of near-isogenic lines at a region encompassing a major quantitative trait locus (QTL) for cell wall degradability led to phenotypic variation of a similar magnitude and sign to that expected from a QTL analysis of cell wall degradability in the F271 × F288 recombinant inbred line progeny. Using DNA sequences within the QTL interval of both F271 and F288 inbred lines and Illumina RNA sequencing datasets from internodes of the selected near-isogenic lines, we annotated the genes present in the QTL interval and provided evidence that allelic variation at the introgressed QTL region gives rise to coordinated changes in gene expression. The identification of a gene co-expression network associated with cell wall-related trait variation revealed that the favorable F288 alleles exploit biological processes related to oxidation-reduction, regulation of hydrogen peroxide metabolism, protein folding and hormone responses. Nested in modules of co-expressed genes, potential new cell-wall regulators were identified, including two transcription factors of the group VII ethylene response factor family, that could be exploited to fine-tune cell wall degradability. Overall, these findings provide new insights into the regulatory mechanisms by which a major locus influences cell wall degradability, paving the way for its map-based cloning in maize.
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Affiliation(s)
- Clément Cuello
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Aurélie Baldy
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Johann Joets
- Génétique Quantitative et Evolution—Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Marie-Pierre Jacquemot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Lucy Botran
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Yves Griveau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Cécile Guichard
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | | | - Valérie Méchin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Matthieu Reymond
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Sylvie Coursol
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O'Connor CH, Hirsch CD, Ross-Ibarra J, Hirsch CN, Springer NM. Transposable elements contribute to dynamic genome content in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1052-1065. [PMID: 31381222 DOI: 10.1111/tpj.14489] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/15/2019] [Accepted: 07/26/2019] [Indexed: 05/05/2023]
Abstract
Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 and PH207) with uniform structural annotations of TEs. Among these genomes we identified approximately 400 000 TEs that are polymorphic, encompassing 1.6 Gb of variable TE sequence. These polymorphic TEs include a combination of recent transposition events as well as deletions of older TEs. There are examples of polymorphic TEs within each of the superfamilies of TEs and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphic TEs within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in annotated gene content among these genotypes. TEs are highly variable in our survey of four temperate maize genomes, highlighting the major contribution of TEs in driving variation in genome organization and gene content. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://github.com/SNAnderson/maizeTE_variation; https://mcstitzer.github.io/maize_TEs.
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Affiliation(s)
- Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Michelle C Stitzer
- Department of Plant Sciences and Center for Population Biology, University of California, Davis, CA, 95616, USA
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences and Center for Population Biology, University of California, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
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43
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Zheng XM, Chen J, Pang HB, Liu S, Gao Q, Wang JR, Qiao WH, Wang H, Liu J, Olsen KM, Yang QW. Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication. SCIENCE ADVANCES 2019; 5:eaax3619. [PMID: 32064312 PMCID: PMC6989341 DOI: 10.1126/sciadv.aax3619] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 10/30/2019] [Indexed: 05/17/2023]
Abstract
Genomes carry millions of noncoding variants, and identifying the tiny fraction with functional consequences is a major challenge for genomics. We assessed the role of selection on long noncoding RNAs (lncRNAs) for domestication-related changes in rice grains. Among 3363 lncRNA transcripts identified in early developing panicles, 95% of those with differential expression (329 lncRNAs) between Oryza sativa ssp. japonica and wild rice were significantly down-regulated in the domestication event. Joint genome and transcriptome analyses reveal that directional selection on lncRNAs altered the expression of energy metabolism genes during domestication. Transgenic experiments and population analyses with three focal lncRNAs illustrate that selection on these loci led to increased starch content and grain weight. Together, our findings indicate that genome-wide selection for lncRNA down-regulation was an important mechanism for the emergence of rice domestication traits.
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Affiliation(s)
- X. M. Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - J. Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - H. B. Pang
- College of Life Science, Shenyang Normal University, Shenyang 110034, China
| | - S. Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Q. Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - J. R. Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - W. H. Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - H. Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - J. Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Corresponding author. (Q.W.Y.); (K.M.O.); (J.L.)
| | - K. M. Olsen
- Biology Department, Campus Box 1137, Washington University, St. Louis, MO 63130, USA
- Corresponding author. (Q.W.Y.); (K.M.O.); (J.L.)
| | - Q. W. Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Corresponding author. (Q.W.Y.); (K.M.O.); (J.L.)
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44
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Vergara D, Huscher EL, Keepers KG, Givens RM, Cizek CG, Torres A, Gaudino R, Kane NC. Gene copy number is associated with phytochemistry in Cannabis sativa. AOB PLANTS 2019; 11:plz074. [PMID: 32010439 PMCID: PMC6986684 DOI: 10.1093/aobpla/plz074] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/19/2019] [Indexed: 05/22/2023]
Abstract
Gene copy number (CN) variation is known to be important in nearly every species where it has been examined. Alterations in gene CN may provide a fast way of acquiring diversity, allowing rapid adaptation under strong selective pressures, and may also be a key component of standing genetic variation within species. Cannabis sativa plants produce a distinguishing set of secondary metabolites, the cannabinoids, many of which have medicinal utility. Two major cannabinoids-THCA (delta-9-tetrahydrocannabinolic acid) and CBDA (cannabidiolic acid)-are products of a three-step biochemical pathway. Using whole-genome shotgun sequence data for 69 Cannabis cultivars from diverse lineages within the species, we found that genes encoding the synthases in this pathway vary in CN. Transcriptome sequence data show that the cannabinoid paralogs are differentially expressed among lineages within the species. We also found that CN partially explains variation in cannabinoid content levels among Cannabis plants. Our results demonstrate that biosynthetic genes found at multiple points in the pathway could be useful for breeding purposes, and suggest that natural and artificial selection have shaped CN variation. Truncations in specific paralogs are associated with lack of production of particular cannabinoids, showing how phytochemical diversity can evolve through a complex combination of processes.
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Affiliation(s)
- Daniela Vergara
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Ezra L Huscher
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Kyle G Keepers
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | | | | | | | | | - Nolan C Kane
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
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45
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Wang Z, Zhang Z, Tang H, Zhang Q, Zhou G, Li X. High-Density Genetic Map Construction and QTL Mapping of Leaf and Needling Traits in Ziziphus jujuba Mill. FRONTIERS IN PLANT SCIENCE 2019; 10:1424. [PMID: 31824522 PMCID: PMC6882864 DOI: 10.3389/fpls.2019.01424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 10/14/2019] [Indexed: 05/23/2023]
Abstract
The Chinese jujube (Ziziphus jujuba Mill., 2n = 2x = 24), one of the most popular fruit trees in Asia, is widely cultivated and utilized in China, where it is traditionally consumed as both a fresh and dried food resource. A high-density genetic map can provide the necessary framework for quantitative trait loci (QTL) analyses and map-based gene cloning and molecular breeding. In this study, we constructed a new high-density genetic linkage map via a genotyping-by-sequencing approach. For the consensus linkage map, a total of 3,792 markers spanning 2,167.5 cM were mapped onto 12 linkage groups, with an average marker interval distance of 0.358 cM. The genetic map anchored 301 Mb (85.7%) of scaffolds from the sequenced Z. jujuba "Junzao" genome. Based on this genetic map, 30 potential QTLs were detected, including 27 QTLs for leaf traits and 3 QTLs for needling length. This high-density genetic map and the identified QTLs for relevant agronomic traits lay the groundwork for functional genetic mapping, map-based cloning, and marker-assisted selection in jujube.
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Affiliation(s)
- Zhongtang Wang
- College of Forestry, Northwest A&F University, Yangling, China
- Country Shandong Institute of Pomology, Taian, China
| | - Zhong Zhang
- College of Forestry, Northwest A&F University, Yangling, China
- Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Northwest A&F University, Yangling, China
| | - Haixia Tang
- Country Shandong Institute of Pomology, Taian, China
| | - Qiong Zhang
- Country Shandong Institute of Pomology, Taian, China
| | | | - Xingang Li
- College of Forestry, Northwest A&F University, Yangling, China
- Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Northwest A&F University, Yangling, China
- Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, China
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46
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Mabire C, Duarte J, Darracq A, Pirani A, Rimbert H, Madur D, Combes V, Vitte C, Praud S, Rivière N, Joets J, Pichon JP, Nicolas SD. High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array. BMC Genomics 2019; 20:848. [PMID: 31722668 PMCID: PMC6854671 DOI: 10.1186/s12864-019-6136-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/23/2019] [Indexed: 12/19/2022] Open
Abstract
Background Insertions/deletions (InDels) and more specifically presence/absence variations (PAVs) are pervasive in several species and have strong functional and phenotypic effect by removing or drastically modifying genes. Genotyping of such variants on large panels remains poorly addressed, while necessary for approaches such as association mapping or genomic selection. Results We have developed, as a proof of concept, a new high-throughput and affordable approach to genotype InDels. We first identified 141,000 InDels by aligning reads from the B73 line against the genome of three temperate maize inbred lines (F2, PH207, and C103) and reciprocally. Next, we designed an Affymetrix® Axiom® array to target these InDels, with a combination of probes selected at breakpoint sites (13%) or within the InDel sequence, either at polymorphic (25%) or non-polymorphic sites (63%) sites. The final array design is composed of 662,772 probes and targets 105,927 InDels, including PAVs ranging from 35 bp to 129kbp. After Affymetrix® quality control, we successfully genotyped 86,648 polymorphic InDels (82% of all InDels interrogated by the array) on 445 maize DNA samples with 422,369 probes. Genotyping InDels using this approach produced a highly reliable dataset, with low genotyping error (~ 3%), high call rate (~ 98%), and high reproducibility (> 95%). This reliability can be further increased by combining genotyping of several probes calling the same InDels (< 0.1% error rate and > 99.9% of call rate for 5 probes). This “proof of concept” tool was used to estimate the kinship matrix between 362 maize lines with 57,824 polymorphic InDels. This InDels kinship matrix was highly correlated with kinship estimated using SNPs from Illumina 50 K SNP arrays. Conclusions We efficiently genotyped thousands of small to large InDels on a sizeable number of individuals using a new Affymetrix® Axiom® array. This powerful approach opens the way to studying the contribution of InDels to trait variation and heterosis in maize. The approach is easily extendable to other species and should contribute to decipher the biological impact of InDels at a larger scale.
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Affiliation(s)
- Clément Mabire
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Jorge Duarte
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France
| | - Aude Darracq
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Ali Pirani
- Thermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA, 95051, USA
| | - Hélène Rimbert
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France.,Present address: GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Delphine Madur
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Valérie Combes
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Clémentine Vitte
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Sébastien Praud
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France
| | - Nathalie Rivière
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France
| | - Johann Joets
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | | | - Stéphane D Nicolas
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France.
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47
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Penning BW, Shiga TM, Klimek JF, SanMiguel PJ, Shreve J, Thimmapuram J, Sykes RW, Davis MF, McCann MC, Carpita NC. Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development. BMC Genomics 2019; 20:785. [PMID: 31664907 PMCID: PMC6819468 DOI: 10.1186/s12864-019-6117-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/20/2019] [Indexed: 11/23/2022] Open
Abstract
Background The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families. Maize is both a genetic model for grass species and a potential source of lignocellulosic biomass from crop residues. Genetic improvement of maize for its utility as a bioenergy feedstock depends on identification of the specific gene family members expressed during secondary wall development in stems. Results High-throughput sequencing of transcripts expressed in developing rind tissues of stem internodes provided a comprehensive inventory of cell wall-related genes in maize (Zea mays, cultivar B73). Of 1239 of these genes, 854 were expressed among the internodes at ≥95 reads per 20 M, and 693 of them at ≥500 reads per 20 M. Grasses have cell wall compositions distinct from non-commelinid species; only one-quarter of maize cell wall-related genes expressed in stems were putatively orthologous with those of the eudicot Arabidopsis. Using a slope-metric algorithm, five distinct patterns for sub-sets of co-expressed genes were defined across a time course of stem development. For the subset of genes associated with secondary wall formation, fifteen sequence motifs were found in promoter regions. The same members of gene families were often expressed in two maize inbreds, B73 and Mo17, but levels of gene expression between them varied, with 30% of all genes exhibiting at least a 5-fold difference at any stage. Although presence-absence and copy-number variation might account for much of these differences, fold-changes of expression of a CADa and a FLA11 gene were attributed to polymorphisms in promoter response elements. Conclusions Large genetic variation in maize as a species precludes the extrapolation of cell wall-related gene expression networks even from one common inbred line to another. Elucidation of genotype-specific expression patterns and their regulatory controls will be needed for association panels of inbreds and landraces to fully exploit genetic variation in maize and other bioenergy grass species.
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Affiliation(s)
- Bryan W Penning
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,, Present Address: USDA-ARS, Wheat Quality Research Unit, 1680 Madison Avenue, Wooster, OH, 44691, USA
| | - Tânia M Shiga
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Present Address: Departamento de Alimentos e Nutrição Experimental, FCF-USP F, 3091-3647 / 3091-3007, Av. Prof. Lineu Prestes, 580 - BL-14 CEP 05508-000, Butantã, Sâo Paulo, SP, Brazil
| | - John F Klimek
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Philip J SanMiguel
- Genomics Core Facility, Purdue University, 170 South University Street, Purdue University, West Lafayette, IN, 47907, USA
| | - Jacob Shreve
- Bioinformatics Core Facility, Purdue University, 155 South Grant Street, West Lafayette, IN, 47907, USA.,, Present Address: Department of Internal Medicine, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Jyothi Thimmapuram
- Present Address: Departamento de Alimentos e Nutrição Experimental, FCF-USP F, 3091-3647 / 3091-3007, Av. Prof. Lineu Prestes, 580 - BL-14 CEP 05508-000, Butantã, Sâo Paulo, SP, Brazil.,Bioinformatics Core Facility, Purdue University, 155 South Grant Street, West Lafayette, IN, 47907, USA
| | - Robert W Sykes
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,, Present Address: Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, Los Alamos, NM, 87545, USA
| | - Mark F Davis
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, West Lafayette, USA
| | - Nicholas C Carpita
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. .,Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. .,Purdue Center for Plant Biology, West Lafayette, USA.
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48
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Yuan J, Wang J, Yu J, Meng F, Zhao Y, Li J, Sun P, Sun S, Zhang Z, Liu C, Wei C, Guo H, Li X, Duan X, Shen S, Xie Y, Hou Y, Zhang J, Shehzad T, Wang X. Alignment of Rutaceae Genomes Reveals Lower Genome Fractionation Level Than Eudicot Genomes Affected by Extra Polyploidization. FRONTIERS IN PLANT SCIENCE 2019; 10:986. [PMID: 31447866 PMCID: PMC6691040 DOI: 10.3389/fpls.2019.00986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Owing to their nutritional and commercial values, the genomes of several citrus plants have been sequenced, and the genome of one close relative in the Rutaceae family, atalantia (Atalantia buxifolia), has also been sequenced. Here, we show a family-level comparative analysis of Rutaceae genomes. By using grape as the outgroup and checking cross-genome gene collinearity, we systematically performed a hierarchical and event-related alignment of Rutaceae genomes, and produced a gene list defining homologous regions based on ancestral polyploidization or speciation. We characterized genome fractionation resulting from gene loss or relocation, and found that erosion of gene collinearity could largely be described by a geometric distribution. Moreover, we found that well-assembled Rutaceae genomes retained significantly more genes (65-82%) than other eudicots affected by recursive polyploidization. Additionally, we showed divergent evolutionary rates among Rutaceae plants, with sweet orange evolving faster than others, and by performing evolutionary rate correction, re-dated major evolutionary events during their evolution. We deduced that the divergence between the Rutaceae family and grape occurred about 81.15-91.74 million years ago (mya), while the split between citrus and atalantia plants occurred <10 mya. In addition, we showed that polyploidization led to a copy number expansion of key gene families contributing to the biosynthesis of vitamin C. Overall, the present effort provides an important comparative genomics resource and lays a foundation to understand the evolution and functional innovation of Rutaceae genomes.
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Affiliation(s)
- Jiaqing Yuan
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yuhao Zhao
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jing Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Pengchuan Sun
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Sangrong Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Zhikang Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chao Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xinyu Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xueqian Duan
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shaoqi Shen
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Yangqin Xie
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Yue Hou
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jin Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
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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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50
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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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