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Shi TL, Jia KH, Bao YT, Nie S, Tian XC, Yan XM, Chen ZY, Li ZC, Zhao SW, Ma HY, Zhao Y, Li X, Zhang RG, Guo J, Zhao W, El-Kassaby YA, Müller N, Van de Peer Y, Wang XR, Street NR, Porth I, An X, Mao JF. High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar. PLANT PHYSIOLOGY 2024; 195:652-670. [PMID: 38412470 PMCID: PMC11060683 DOI: 10.1093/plphys/kiae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/29/2024]
Abstract
Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
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Affiliation(s)
- Tian-Le Shi
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Kai-Hua Jia
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan 250100, China
| | - Yu-Tao Bao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Xue-Chan Tian
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xue-Mei Yan
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhao-Yang Chen
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhi-Chao Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shi-Wei Zhao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hai-Yao Ma
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ye Zhao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiang Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Ren-Gang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Jing Guo
- College of Forestry, Shandong Agricultural University, Tai’an 271000, China
| | - Wei Zhao
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - Yousry Aly El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Bc, V6T 1Z4, Canada
| | - Niels Müller
- Thünen-Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao-Ru Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - Nathaniel Robert Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Xinmin An
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jian-Feng Mao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
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2
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Hyden B, Carper DL, Abraham PE, Yuan G, Yao T, Baumgart L, Zhang Y, Chen C, O'Malley R, Chen J, Yang X, Hettich RL, Tuskan GA, Smart LB. Functional analysis of Salix purpurea genes support roles for ARR17 and GATA15 as master regulators of sex determination. PLANT DIRECT 2023; 7:e3546. [PMID: 38028649 PMCID: PMC10651977 DOI: 10.1002/pld3.546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
The Salicaceae family is of growing interest in the study of dioecy in plants because the sex determination region (SDR) has been shown to be highly dynamic, with differing locations and heterogametic systems between species. Without the ability to transform and regenerate Salix in tissue culture, previous studies investigating the mechanisms regulating sex in the genus Salix have been limited to genome resequencing and differential gene expression, which are mostly descriptive in nature, and functional validation of candidate sex determination genes has not yet been conducted. Here, we used Arabidopsis to functionally characterize a suite of previously identified candidate genes involved in sex determination and sex dimorphism in the bioenergy shrub willow Salix purpurea. Six candidate master regulator genes for sex determination were heterologously expressed in Arabidopsis, followed by floral proteome analysis. In addition, 11 transcription factors with predicted roles in mediating sex dimorphism downstream of the SDR were tested using DAP-Seq in both male and female S. purpurea DNA. The results of this study provide further evidence to support models for the roles of ARR17 and GATA15 as master regulator genes of sex determination in S. purpurea, contributing to a regulatory system that is notably different from that of its sister genus Populus. Evidence was also obtained for the roles of two transcription factors, an AP2/ERF family gene and a homeodomain-like transcription factor, in downstream regulation of sex dimorphism.
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Affiliation(s)
- Brennan Hyden
- Horticulture Section, School of Integrative Plant ScienceCornell University, Cornell AgriTechGenevaNew YorkUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Dana L. Carper
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Paul E. Abraham
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Guoliang Yuan
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Tao Yao
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Leo Baumgart
- Lawrence Berkeley National LaboratoryUS Department of Energy Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Yu Zhang
- Lawrence Berkeley National LaboratoryUS Department of Energy Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Cindy Chen
- Lawrence Berkeley National LaboratoryUS Department of Energy Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Ronan O'Malley
- Lawrence Berkeley National LaboratoryUS Department of Energy Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Jin‐Gui Chen
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Xiaohan Yang
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Robert L. Hettich
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Gerald A. Tuskan
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant ScienceCornell University, Cornell AgriTechGenevaNew YorkUSA
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3
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Gao Z, Yang X, Chen J, Rausher MD, Shi T. Expression inheritance and constraints on cis- and trans-regulatory mutations underlying lotus color variation. PLANT PHYSIOLOGY 2023; 191:1662-1683. [PMID: 36417237 PMCID: PMC10022630 DOI: 10.1093/plphys/kiac522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Both cis- and trans-regulatory mutations drive changes in gene expression that underpin plant phenotypic evolution. However, how and why these two major types of regulatory mutations arise in different genes and how gene expression is inherited and associated with these regulatory changes are unclear. Here, by studying allele-specific expression in F1 hybrids of pink-flowered sacred lotus (Nelumbo nucifera) and yellow-flowered American lotus (N. lutea), we reveal the relative contributions of cis- and trans-regulatory changes to interspecific expression rewiring underlying petal color change and how the expression is inherited in hybrids. Although cis-only variants influenced slightly more genes, trans-only variants had a stronger impact on expression differences between species. In F1 hybrids, genes under cis-only and trans-only regulatory effects showed a propensity toward additive and dominant inheritance, respectively, whereas transgressive inheritance was observed in genes carrying both cis- and trans-variants acting in opposite directions. By investigating anthocyanin and carotenoid coexpression networks in petals, we found that the same category of regulatory mutations, particularly trans-variants, tend to rewire hub genes in coexpression modules underpinning flower color differentiation between species; we identified 45 known genes with cis- and trans-regulatory variants significantly correlated with flower coloration, such as ANTHOCYANIN 5-AROMATIC ACYLTRANSFERASE (ACT), GLUTATHIONE S-TRANSFERASE F11 (GSTF11), and LYCOPENE Ε-CYCLASE (LCYE). Notably, the relative abundance of genes in different categories of regulatory divergence was associated with the inferred magnitude of constraints like expression level and breadth. Overall, our study suggests distinct selective constraints and modes of gene expression inheritance among different regulatory mutations underlying lotus petal color divergence.
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Affiliation(s)
- Zhiyan Gao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan 430081, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
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4
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Wang Y, Cai X, Zhang Y, Hörandl E, Zhang Z, He L. The male-heterogametic sex determination system on chromosome 15 of Salix triandra and Salix arbutifolia reveals ancestral male heterogamety and subsequent turnover events in the genus Salix. Heredity (Edinb) 2023; 130:122-134. [PMID: 36593355 PMCID: PMC9981616 DOI: 10.1038/s41437-022-00586-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 01/03/2023] Open
Abstract
Dioecious Salix evolved more than 45 million years ago, but have homomorphic sex chromosomes, suggesting that turnover event(s) prevented major differentiation. Sex chromosome turnover events have been inferred in the sister genus Populus. The genus Salix includes two main clades, Salix and Vetrix, with several previously studied Vetrix clade species having female-heterogametic (ZW) or male-heterogametic (XY) sex-determining systems (SDSs) on chromosome 15, while three Salix clade species have XY SDSs on chromosome 7. We here studied two basal taxa of the Vetrix clade, S. arbutifolia and S. triandra using S. purpurea as the reference genome. Analyses of whole genome resequencing data for genome-wide associations (GWAS) with the sexes and genetic differentiation between the sexes (FST values) showed that both species have male heterogamety with a sex-determining locus on chromosome 15, suggesting an early turnover event within the Vetrix clade, perhaps promoted by sexually antagonistic or (and) sex-ratio selection. Changepoint analysis based on FST values identified small sex-linked regions of ~3.33 Mb and ~2.80 Mb in S. arbutifolia and S. triandra, respectively. The SDS of S. arbutifolia was consistent with recent results that used its own genome as reference. Ancestral state reconstruction of SDS suggests that at least two turnover events occurred in Salix.
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Affiliation(s)
- Yi Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Xinjie Cai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yue Zhang
- Shenyang Arboretum, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
| | - Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
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5
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Keefover-Ring K, Carlson CH, Hyden B, Azeem M, Smart LB. Genetic mapping of sexually dimorphic volatile and non-volatile floral secondary chemistry of a dioecious willow. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6352-6366. [PMID: 35710312 DOI: 10.1093/jxb/erac260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Secondary chemistry often differs between sexes in dioecious plant species, a pattern attributed to its possible role in the evolution and/or maintenance of dioecy. We used GC-MS to measure floral volatiles emitted from, and LC-MS to quantitate non-volatile secondary compounds contained in, female and male Salix purpurea willow catkins from an F2 family. Using the abundance of these chemicals, we then performed quantitative trait locus (QTL) mapping to locate them on the genome, identified biosynthetic candidate genes in the QTL intervals, and examined expression patterns of candidate genes using RNA-seq. Male flowers emitted more total terpenoids than females, but females produced more benzenoids. Male tissue contained greater amounts of phenolic glycosides, but females had more chalcones and flavonoids. A flavonoid pigment and a spermidine derivative were found only in males. Male catkins were almost twice the mass of females. Forty-two QTL were mapped for 25 chemical traits and catkin mass across 16 of the 19 S. purpurea chromosomes. Several candidate genes were identified, including a chalcone isomerase associated with seven compounds. A better understanding of the genetic basis of the sexually dimorphic chemistry of a dioecious species may shed light on how chemically mediated ecological interactions may have helped in the evolution and maintenance of dioecy.
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Affiliation(s)
- Ken Keefover-Ring
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Department of Geography, University of Wisconsin-Madison, Madison, WI, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Brennan Hyden
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Muhammad Azeem
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
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6
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Carlson CH, Choi Y, Chan AP, Town CD, Smart LB. Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.). G3 (BETHESDA, MD.) 2022; 12:6472355. [PMID: 35100357 PMCID: PMC9210313 DOI: 10.1093/g3journal/jkab436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022]
Abstract
Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polyploid species, such as willow (Salix spp.). Shrub willow is a dedicated energy crop bred to be fast-growing and high yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploids produced from crosses between diploid and tetraploid species. Here, we test whether differentially expressed genes are associated with heterosis in triploid families derived from diploid Salix purpurea, diploid Salix viminalis, and tetraploid Salix miyabeana parents. Three biological replicates of shoot tips from all family progeny and parents were collected after 12 weeks in the greenhouse and RNA extracted for RNA-Seq analysis. This study provides evidence that nonadditive patterns of gene expression are correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow. Expression-level dominance was most correlated with heterosis for biomass yield traits and was highly enriched for processes involved in starch and sucrose metabolism. In addition, there was a global dosage effect of parent alleles in triploid hybrids, with expression proportional to copy number variation. Importantly, differentially expressed genes between family parents were most predictive of heterosis for both field and greenhouse collected traits. Altogether, these data will be used to progress models of heterosis to complement the growing genomic resources available for the improvement of heterozygous perennial bioenergy crops.
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Affiliation(s)
- Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Yongwook Choi
- Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Agnes P Chan
- Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | | | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
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7
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Ye X, Zhao X, Sun Y, Zhang M, Feng S, Zhou A, Wu W, Ma S, Liu S. The underlying molecular conservation and diversification of dioecious flower and leaf buds provide insights into the development, dormancy breaking, flowering, and sex association of willows. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:651-664. [PMID: 34488151 DOI: 10.1016/j.plaphy.2021.08.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/07/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
As harbingers of bursting growth, flower buds and leaf buds generally show similar surface morphologies but different structural and functional changes. Dioecious plants further generate four types of Female/Male Flower/Leaf Buds (FFB, FLB, MFB, and MLB), showing a complex regulation. However, little is known about their underlying molecular mechanisms. Here, we exemplify the woody dioecious Salix linearistipularis to investigate their morphological characteristics and potential molecular mechanisms by combining cytological, physiological, phenological, and transcriptomic datasets. First, FFB and MFB have simultaneous development dynamics and so do FLB and MLB. Interestingly, FLB and MLB show very similar expression profiles preparing for photosynthesis and stress-tolerance, whereas FFB and MFB show great similarities but also striking sexual differences. Comparing flower buds and leaf buds after their revival from dormancy shows different cold- and vernalization-responsive genes (e.g. SliVRN1, SliAGL19, and SliAGL24), implying different programming processes for dormancy breaking between the buds. Moreover, except SliAP3, the expression of ABCDE model genes is consistent with their roles in the buds, suggesting a conserved mechanism of flower development between dioecious Salix and hermaphrodite Arabidopsis. Finally, considering sex-associated genes (e.g. SliCLE25, SliTPS21, and SliARR9) on Salix chromosomes and other reports, we hypothesize a dynamic model of sex determination on chromosomes 15 and 19 in the last ancestor of Salix and Populus but evolutionarily on 15 in Salix after their divergence. Together, our study provides new insights into the molecular mechanisms of dioecious four-type buds by showing the genes involved in their development, dormancy breaking, flowering, and sexual association.
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Affiliation(s)
- Xiaoxue Ye
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China; Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China.
| | - Yajun Sun
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China; Qiqihar Eco-environmental Monitoring Center of Heilongjiang Province, Qiqihar, 161005, China.
| | - Meijiao Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
| | - Shuang Feng
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
| | - Aimin Zhou
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China.
| | - Shurong Ma
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China.
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8
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Hyden B, Carlson CH, Gouker FE, Schmutz J, Barry K, Lipzen A, Sharma A, Sandor L, Tuskan GA, Feng G, Olson MS, DiFazio SP, Smart LB. Integrative genomics reveals paths to sex dimorphism in Salix purpurea L. HORTICULTURE RESEARCH 2021; 8:170. [PMID: 34333534 PMCID: PMC8325687 DOI: 10.1038/s41438-021-00606-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/23/2021] [Accepted: 06/01/2021] [Indexed: 05/16/2023]
Abstract
Sex dimorphism and gene expression were studied in developing catkins in 159 F2 individuals from the bioenergy crop Salix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.
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Affiliation(s)
- Brennan Hyden
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
- Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Anna Lipzen
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Aditi Sharma
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Laura Sandor
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Guanqiao Feng
- Department of Biology, Texas Tech University, Lubbock, TX, USA
| | - Matthew S Olson
- Department of Biology, Texas Tech University, Lubbock, TX, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA.
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9
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Florez-Rueda AM, Fiscalini F, Roth M, Grossniklaus U, Städler T. Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure. Genome Biol Evol 2021; 13:6278300. [PMID: 34009298 PMCID: PMC8358227 DOI: 10.1093/gbe/evab107] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 01/10/2023] Open
Abstract
Crosses between the wild tomato species Solanum peruvianum and Solanum chilense result in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent-of-origin–dependent expression of alleles, is perturbed in the hybrid endosperm, with many of the normally paternally expressed genes losing their imprinted status. Here, we report transcriptome-based analyses of gene and small RNA (sRNA) expression levels. We identified 2,295 genes and 387 sRNA clusters as differentially expressed when comparing reciprocal hybrid seed to seeds and endosperms from the two within-species crosses. Our analyses uncovered a pattern of overdominance in endosperm gene expression in both hybrid cross directions, in marked contrast to the patterns of sRNA expression in whole seeds. Intriguingly, patterns of increased gene expression resemble the previously reported increased maternal expression proportions in hybrid endosperms. We identified physical clusters of sRNAs; differentially expressed sRNAs exhibit reduced transcript abundance in hybrid seeds of both cross directions. Moreover, sRNAs map to genes coding for key proteins involved in epigenetic regulation of gene expression, suggesting a regulatory feedback mechanism. We describe examples of genes that appear to be targets of sRNA-mediated gene silencing; in these cases, reduced sRNA abundance is concomitant with increased gene expression in hybrid seeds. Our analyses also show that S. peruvianum dominance impacts gene and sRNA expression in hybrid seeds. Overall, our study indicates roles for sRNA-mediated epigenetic regulation in HSF between closely related wild tomato species.
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Affiliation(s)
- Ana Marcela Florez-Rueda
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland.,Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
| | - Flurin Fiscalini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Morgane Roth
- Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Thomas Städler
- Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
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10
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Gao Z, Li H, Yang X, Yang P, Chen J, Shi T. Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera). PLANT MOLECULAR BIOLOGY 2021; 106:207-220. [PMID: 33738679 DOI: 10.1007/s11103-021-01138-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
The genome-wide allele-specific expression in F1 hybrids from the cross of tropical and temperate lotus unveils how cis-regulatory divergences affect genes in key pathways related to ecotypic divergence. Genetic variation, particularly cis-regulatory variation, plays a crucial role in phenotypic variation and adaptive evolution in plants. Temperate and tropical lotus, the two ecotypes of Nelumbo nucifera, show distinction in the degree of rhizome enlargement, which is associated with winter dormancy. To understand the roles of genome-wide cis-regulatory divergences on adaptive evolution of temperate and tropical lotus (Nelumbo nucifera), here we performed allele-specific expression (ASE) analyses on the tissues including flowers, leaves and rhizome from F1 hybrids of tropical and temperate lotus. For all investigated tissues in F1s, about 36% of genes showed ASE and about 3% of genes showed strong consistent ASE. Most of ASEs were biased towards the tropical parent in all surveyed samples, indicating that the tropical genome might be dominant over the temperate genome in gene expression of tissues from their F1 hybrids. We found that promoter sequences with similar allelic expression are more conserved than genes with significant or conditional ASE, suggesting the cis-regulatory sequence divergence underlie the allelic expression bias. We further uncovered biased genes being related to phenotypic differentiation between two lotus ecotypes, especially metabolic and phytohormone-related pathways in the rhizome. Overall, our study provides a global landscape of cis-regulatory variations between two lotus ecotypes and highlights their roles in rhizome growth variation for the climatic adaptation.
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Affiliation(s)
- Zhiyan Gao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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11
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Sanderson BJ, Feng G, Hu N, Carlson CH, Smart LB, Keefover-Ring K, Yin T, Ma T, Liu J, DiFazio SP, Olson MS. Sex determination through X-Y heterogamety in Salix nigra. Heredity (Edinb) 2021; 126:630-639. [PMID: 33510464 PMCID: PMC8115673 DOI: 10.1038/s41437-020-00397-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
The development of non-recombining sex chromosomes has radical effects on the evolution of discrete sexes and sexual dimorphism. Although dioecy is rare in plants, sex chromosomes have evolved repeatedly throughout the diversification of angiosperms, and many of these sex chromosomes are relatively young compared to those found in vertebrates. In this study, we designed and used a sequence capture array to identify a novel sex-linked region (SLR) in Salix nigra, a basal species in the willow clade, and demonstrated that this species has XY heterogamety. We did not detect any genetic overlap with the previously characterized ZW SLRs in willows, which map to a different chromosome. The S. nigra SLR is characterized by strong recombination suppression across a 2 MB region and an excess of low-frequency alleles, resulting in a low Tajima's D compared to the remainder of the genome. We speculate that either a recent bottleneck in population size or factors related to positive or background selection generated this differential pattern of Tajima's D on the X and autosomes. This discovery provides insights into factors that may influence the evolution of sex chromosomes in plants and contributes to a large number of recent observations that underscore their dynamic nature.
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Affiliation(s)
- Brian J. Sanderson
- grid.264784.b0000 0001 2186 7496Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131 USA ,grid.268154.c0000 0001 2156 6140Present Address: Department of Biology, West Virginia University, Morgantown, WV 26506-6057 USA
| | - Guanqiao Feng
- grid.264784.b0000 0001 2186 7496Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131 USA
| | - Nan Hu
- grid.264784.b0000 0001 2186 7496Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131 USA
| | - Craig H. Carlson
- grid.5386.8000000041936877XHorticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456 USA
| | - Lawrence B. Smart
- grid.5386.8000000041936877XHorticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456 USA
| | - Ken Keefover-Ring
- grid.14003.360000 0001 2167 3675Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Tongming Yin
- grid.410625.40000 0001 2293 4910Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Tao Ma
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Jianquan Liu
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu, 610065 China ,grid.32566.340000 0000 8571 0482State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Stephen P. DiFazio
- grid.268154.c0000 0001 2156 6140Department of Biology, West Virginia University, Morgantown, WV 26506-6057 USA
| | - Matthew S. Olson
- grid.264784.b0000 0001 2186 7496Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131 USA
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12
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Sanderson BJ, DiFazio SP, Cronk QCB, Ma T, Olson MS. A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11394. [PMID: 33163293 PMCID: PMC7598885 DOI: 10.1002/aps3.11394] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/12/2020] [Indexed: 05/03/2023]
Abstract
PREMISE The family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus. METHODS We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 bp of exonic regions of 972 genes. RESULTS We recovered sequence data for nearly all of the targeted genes in three species of Populus and three species of Salix. We present a species tree, discuss concordance among gene trees, and present population genomic summary statistics for these loci. CONCLUSIONS Our sequence capture array has extremely high capture efficiency within the genera Populus and Salix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.
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Affiliation(s)
- Brian J. Sanderson
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409‐3131USA
- Department of BiologyWest Virginia UniversityMorgantownWest Virginia26506USA
| | - Stephen P. DiFazio
- Department of BiologyWest Virginia UniversityMorgantownWest Virginia26506USA
| | - Quentin C. B. Cronk
- Department of BotanyUniversity of British ColumbiaVancouverBritish ColumbiaV6T 1Z4Canada
| | - Tao Ma
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengdu610065People’s Republic of China
| | - Matthew S. Olson
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409‐3131USA
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13
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Wang W, Carlson CH, Smart LB, Carlson JE. Transcriptome analysis of contrasting resistance to herbivory by Empoasca fabae in two shrub willow species and their hybrid progeny. PLoS One 2020; 15:e0236586. [PMID: 32726362 PMCID: PMC7390382 DOI: 10.1371/journal.pone.0236586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/08/2020] [Indexed: 11/18/2022] Open
Abstract
Short rotation woody biomass cultivars developed from fast-growing shrub species of willow (Salix spp.) have superior properties as perennial energy crops for the Northeast and Midwest US. However, the insect pest potato leafhopper (PLH) Empoasca fabae (Harris) can cause serious damage and reduce yield of susceptible genotypes. Currently, the willow cultivars in use display varying levels of susceptibility under PLH infestation. However, genes and markers for resistance to PLH are not yet available for marker-assisted selection in breeding. In this study, transcriptome differences between a resistant genotype 94006 (S. purpurea) and a susceptible cultivar ‘Jorr’ (S. viminalis), and their hybrid progeny were determined. Over 600 million RNA-Seq reads were generated and mapped to the Salix purpurea reference transcriptome. Gene expression analyses revealed the unique defense mechanism in resistant genotype 94006 that involves PLH-induced secondary cell wall modification. In the susceptible genotypes, genes involved in programed cell death were highly expressed, explaining the necrosis symptoms after PLH feeding. Overall, the discovery of resistance genes and defense mechanisms provides new resources for shrub willow breeding and research in the future.
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Affiliation(s)
- Wanyan Wang
- Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Craig H. Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York, United States of America
| | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York, United States of America
| | - John E. Carlson
- Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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14
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Characterization and Expression of KT/HAK/KUP Transporter Family Genes in Willow under Potassium Deficiency, Drought, and Salt Stresses. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2690760. [PMID: 32596286 PMCID: PMC7303730 DOI: 10.1155/2020/2690760] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022]
Abstract
The K+ transporter/high-affinity K+/K+ uptake (KT/HAK/KUP) transporters dominate K+ uptake, transport, and allocation that play a pivotal role in mineral homeostasis and plant adaptation to adverse abiotic stresses. However, molecular mechanisms towards K+ nutrition in forest trees are extremely rare, especially in willow. In this study, we identified 22 KT/HAK/KUP transporter genes in purple osier willow (designated as SpuHAK1 to SpuHAK22) and examined their expression under K+ deficiency, drought, and salt stress conditions. Both transcriptomic and quantitative real-time PCR (qRT-PCR) analyses demonstrated that SpuHAKs were predominantly expressed in stems, and the expression levels of SpuHAK1, SpuHAK2, SpuHAK3, SpuHAK7, and SpuHAK8 were higher at the whole plant level, whereas SpuHAK9, SpuHAK11, SpuHAK20, and SpuHAK22 were hardly detected in tested tissues. In addition, both K+ deficiency and salt stress decreased the tissue K+ content, while drought increased the tissue K+ content in purple osier plant. Moreover, SpuHAK genes were differentially responsive to K+ deficiency, drought, and salt stresses in roots. K+ deficiency and salt stress mainly enhanced the expression level of responsive SpuHAK genes. Fifteen putative cis-acting regulatory elements, including the stress response, hormone response, circadian regulation, and nutrition and development, were identified in the promoter region of SpuHAK genes. Our findings provide a foundation for further functional characterization of KT/HAK/KUP transporters in forest trees and may be useful for breeding willow rootstocks that utilize potassium more efficiently.
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15
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Zhou R, Macaya-Sanz D, Carlson CH, Schmutz J, Jenkins JW, Kudrna D, Sharma A, Sandor L, Shu S, Barry K, Tuskan GA, Ma T, Liu J, Olson M, Smart LB, DiFazio SP. A willow sex chromosome reveals convergent evolution of complex palindromic repeats. Genome Biol 2020; 21:38. [PMID: 32059685 PMCID: PMC7023750 DOI: 10.1186/s13059-020-1952-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
Background Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination. Results Here we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea. The W chromosome has an expanded number of genes due to transpositions from autosomes. It also contains two consecutive palindromes that span a region of 200 kb, with conspicuous 20-kb stretches of highly conserved sequences among the four arms that show evidence of gene conversion. Four genes in the palindrome are homologous to genes in the sex determination regions of the closely related genus Populus, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes. Conclusion The presence of palindromes in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.
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Affiliation(s)
- Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.,Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | | | - David Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Aditi Sharma
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.,State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA.
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16
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Charlesworth D. Young sex chromosomes in plants and animals. THE NEW PHYTOLOGIST 2019; 224:1095-1107. [PMID: 31222890 DOI: 10.1111/nph.16002] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/10/2019] [Indexed: 05/28/2023]
Abstract
A major reason for studying plant sex chromosomes is that they may often be 'young' systems. There is considerable evidence for the independent evolution of separate sexes within plant families or genera, in some cases showing that the maximum possible time during which their sex-determining genes have existed must be much shorter than those of several animal taxa. Consequently, their sex-linked regions could either have evolved soon after genetic sex determination arose or considerably later. Plants, therefore, include species with both young and old systems. I review several questions about the evolution of sex-determining systems and sex chromosomes that require studies of young systems, including: the kinds of mutations involved in the transition to unisexual reproduction from hermaphroditism or monoecy (a form of functional hermaphroditism); the times when they arose; and the extent to which the properties of sex-linked regions of genomes reflect responses to new selective situations created by the presence of a sex-determining locus. I also evaluate which questions are best studied in plants, vs other suitable candidate organisms. Studies of young plant systems can help understand general evolutionary processes that are shared with the sex chromosomes of other organisms.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3LF, UK
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17
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Carlson CH, Gouker FE, Crowell CR, Evans L, DiFazio SP, Smart CD, Smart LB. Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.). ANNALS OF BOTANY 2019; 124:701-716. [PMID: 31008500 PMCID: PMC6821232 DOI: 10.1093/aob/mcz047] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 03/08/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Increasing energy demands and the necessity to reduce greenhouse gas emissions are key motivating factors driving the development of lignocellulosic crops as an alternative to non-renewable energy sources. The effects of global climate change will require a better understanding of the genetic basis of complex adaptive traits to breed more resilient bioenergy feedstocks, like willow (Salix spp.). Shrub willow is a sustainable and dedicated bioenergy crop, bred to be fast-growing and high-yielding on marginal land without competing with food crops. In a rapidly changing climate, genomic advances will be vital for the sustained improvement of willow and other non-model bioenergy crops. Here, joint genetic mapping was used to exploit genetic variation garnered from both recent and historical recombination events in S. purpurea. METHODS A panel of North American naturalized S. purpurea accessions and full-sib F2S. purpurea population were genotyped and phenotyped for a suite of morphological, physiological, pest and disease resistance, and wood chemical composition traits, collected from multi-environment and multi-year replicated field trials. Controlling for population stratification and kinship in the association panel and spatial variation in the F2, a comprehensive mixed model analysis was used to dissect the complex genetic architecture and plasticity of these important traits. KEY RESULTS Individually, genome-wide association (GWAS) models differed in terms of power, but the combined approach, which corrects for yearly and environmental co-factors across datasets, improved the overall detection and resolution of associated loci. Although there were few significant GWAS hits located within support intervals of QTL for corresponding traits in the F2, many large-effect QTL were identified, as well as QTL hotspots. CONCLUSIONS This study provides the first comparison of linkage analysis and linkage disequilibrium mapping approaches in Salix, and highlights the complementarity and limits of these two methods for elucidating the genetic architecture of complex bioenergy-related traits of a woody perennial breeding programme.
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Affiliation(s)
- Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Chase R Crowell
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Luke Evans
- Institute for Behavioral Genetics and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
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18
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Gomes C, Dupas A, Pagano A, Grima-Pettenati J, Paiva JAP. Hairy Root Transformation: A Useful Tool to Explore Gene Function and Expression in Salix spp. Recalcitrant to Transformation. FRONTIERS IN PLANT SCIENCE 2019; 10:1427. [PMID: 31781143 PMCID: PMC6859806 DOI: 10.3389/fpls.2019.01427] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/15/2019] [Indexed: 05/22/2023]
Abstract
Willow (Salix spp. L.) species are fast-growing trees and shrubs that have attracted emergent attention for their potential as feedstocks for bioenergy and biofuel production, as well as for pharmaceutical and phytoremediation applications. This economic and environmental potential has propelled the creation of several genetic and genomic resources for Salix spp. Furthermore, the recent availability of an annotated genome for Salix purpurea has pinpointed novel candidate genes underlying economically relevant traits. However, functional studies have been stalled by the lack of rapid and efficient coupled regeneration-transformation systems for Salix purpurea and Salix spp. in general. In this report, we describe a fast and highly efficient hairy root transformation protocol for S. purpurea. It was effective for different explant sources and S. purpurea genotypes, with efficiencies between 63.4% and 98.7%, and the screening of the transformed hairy roots was easily carried out using the fluorescent marker DsRed. To test the applicability of this hairy root transformation system for gene functional analysis, we transformed hairy roots with the vector pGWAY-SpDRM2, where the gene SpDRM2 encoding a putative Domain Rearranged Methyltransferase (DRM) was placed under the control of the CaMV 35S constitutive promoter. Indeed, the transgenic hairy roots obtained exhibited significantly increased expression of SpDRM2 as compared to controls, demonstrating that this protocol is suitable for the medium/high-throughput functional characterization of candidate genes in S. purpurea and other recalcitrant Salix spp.
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Affiliation(s)
- Carolina Gomes
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Annabelle Dupas
- LRSV, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université Toulouse 3, Castanet Tolosan, France
| | - Andrea Pagano
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Jacqueline Grima-Pettenati
- LRSV, Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université Toulouse 3, Castanet Tolosan, France
| | - Jorge Almiro P. Paiva
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
- *Correspondence: Jorge Almiro P. Paiva,
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19
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Hobza R, Hudzieczek V, Kubat Z, Cegan R, Vyskot B, Kejnovsky E, Janousek B. Sex and the flower - developmental aspects of sex chromosome evolution. ANNALS OF BOTANY 2018; 122:1085-1101. [PMID: 30032185 PMCID: PMC6324748 DOI: 10.1093/aob/mcy130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/13/2018] [Indexed: 05/07/2023]
Abstract
Background The evolution of dioecious plants is occasionally accompanied by the establishment of sex chromosomes: both XY and ZW systems have been found in plants. Structural studies of sex chromosomes are now being followed up by functional studies that are gradually shedding light on the specific genetic and epigenetic processes that shape the development of separate sexes in plants. Scope This review describes sex determination diversity in plants and the genetic background of dioecy, summarizes recent progress in the investigation of both classical and emerging model dioecious plants and discusses novel findings. The advantages of interspecies hybrids in studies focused on sex determination and the role of epigenetic processes in sexual development are also overviewed. Conclusions We integrate the genic, genomic and epigenetic levels of sex determination and stress the impact of sex chromosome evolution on structural and functional aspects of plant sexual development. We also discuss the impact of dioecy and sex chromosomes on genome structure and expression.
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Affiliation(s)
- Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Vojtech Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Zdenek Kubat
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Radim Cegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Bohuslav Janousek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
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20
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Tuskan GA, Groover AT, Schmutz J, DiFazio SP, Myburg A, Grattapaglia D, Smart LB, Yin T, Aury JM, Kremer A, Leroy T, Le Provost G, Plomion C, Carlson JE, Randall J, Westbrook J, Grimwood J, Muchero W, Jacobson D, Michener JK. Hardwood Tree Genomics: Unlocking Woody Plant Biology. FRONTIERS IN PLANT SCIENCE 2018; 9:1799. [PMID: 30619389 PMCID: PMC6304363 DOI: 10.3389/fpls.2018.01799] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/19/2018] [Indexed: 05/07/2023]
Abstract
Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative ("evo-devo") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.
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Affiliation(s)
- Gerald A. Tuskan
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States
| | - Andrew T. Groover
- Pacific Southwest Research Station, USDA Forest Service, Davis, CA, United States
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
- Joint Genome Institute, Walnut Creek, CA, United States
| | | | - Alexander Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Dario Grattapaglia
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Universidade Católica de Brasília, Brasília, Brazil
| | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States
| | - Tongming Yin
- The Key Laboratory for Poplar Improvement of Jiangsu Province, Nanjing Forestry University, Nanjing, China
| | - Jean-Marc Aury
- Commissariat à l’Energie Atomique, Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Thibault Leroy
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | | | | | - John E. Carlson
- Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, United States
| | - Jennifer Randall
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Jared Westbrook
- The American Chestnut Foundation, Asheville, NC, United States
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Wellington Muchero
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States
| | - Daniel Jacobson
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States
| | - Joshua K. Michener
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States
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21
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Fraser HB. Improving Estimates of Compensatory cis-trans Regulatory Divergence. Trends Genet 2018; 35:3-5. [PMID: 30270122 DOI: 10.1016/j.tig.2018.09.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/31/2018] [Accepted: 09/07/2018] [Indexed: 11/30/2022]
Abstract
Interspecific hybrids have played a key role in research on gene expression regulation. A growing number of studies have measured genome-wide allele-specific expression in hybrids and observed that cis-regulatory changes often oppose trans-acting changes affecting the same genes, suggesting stabilizing selection for compensatory changes. However, the most common method for estimating these effects is biased, producing artifactual patterns of compensatory evolution. Here I introduce a simple modification leveraging biological replicates that ameliorates the bias.
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Affiliation(s)
- Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, USA; Lab website: https://web.stanford.edu/group/fraserlab/.
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22
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Identification of a dioxin-responsive oxylipin signature in roots of date palm: involvement of a 9-hydroperoxide fatty acid reductase, caleosin/peroxygenase PdPXG2. Sci Rep 2018; 8:13181. [PMID: 30181584 PMCID: PMC6123484 DOI: 10.1038/s41598-018-31342-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 07/17/2018] [Indexed: 01/02/2023] Open
Abstract
Dioxins are highly hazardous pollutants that have well characterized impacts on both animal and human health. However, the biological effects of dioxins on plants have yet to be described in detail. Here we describe a dioxin-inducible caleosin/peroxygenase isoform, PdPXG2, that is mainly expressed in the apical zone of date palm roots and specifically reduces 9-hydroperoxide fatty acids. A characteristic spectrum of 18 dioxin-responsive oxylipin (DROXYL) congeners was also detected in date palm roots after exposure to dioxin. Of particular interest, six oxylipins, mostly hydroxy fatty acids, were exclusively formed in response to TCDD. The DROXYL signature was evaluated in planta and validated in vitro using a specific inhibitor of PdPXG2 in a root-protoplast system. Comparative analysis of root suberin showed that levels of certain monomers, especially the mono-epoxides and tri-hydroxides of C16:3 and C18:3, were significantly increased after exposure to TCDD. Specific inhibition of PdPXG2 activity revealed a positive linear relationship between deposition of suberin in roots and their permeability to TCDD. The results highlight the involvement of this peroxygenase in the plant response to dioxin and suggest the use of dioxin-responsive oxylipin signatures as biomarkers for plant exposure to this important class of xenobiotic contaminants.
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23
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Zemp N, Widmer A, Charlesworth D. Has adaptation occurred in males and females since separate sexes evolved in the plant Silene latifolia? Proc Biol Sci 2018; 285:rspb.2017.2824. [PMID: 30051860 DOI: 10.1098/rspb.2017.2824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 07/03/2018] [Indexed: 11/12/2022] Open
Abstract
The evolution of separate sexes may involve changed expression of many genes, as each sex adapts to its new state. Evidence is accumulating for sex differences in expression even in organisms that have recently evolved separate sexes from hermaphrodite or monoecious (cosexual) ancestors, such as some dioecious flowering plants. We describe evidence that a dioecious plant species with recently evolved dioecy, Silene latifolia, has undergone adaptive changes that improve functioning in females, in addition to changes that are probably pleiotropic effects of male sterility. The results suggest pervasive adaptations as soon as males and females evolve from their cosexual ancestor.
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Affiliation(s)
- Niklaus Zemp
- Institute of Integrative Biology, Universitätstrasse 16, 8092 Zürich, Switzerland.,Genetic Diversity Centre (GDC), ETH Zurich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, Midlothian, Scotland
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24
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Zhou R, Macaya-Sanz D, Rodgers-Melnick E, Carlson CH, Gouker FE, Evans LM, Schmutz J, Jenkins JW, Yan J, Tuskan GA, Smart LB, DiFazio SP. Characterization of a large sex determination region in Salix purpurea L. (Salicaceae). Mol Genet Genomics 2018; 293:1437-1452. [PMID: 30022352 DOI: 10.1007/s00438-018-1473-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/09/2018] [Indexed: 12/30/2022]
Abstract
Dioecy has evolved numerous times in plants, but heteromorphic sex chromosomes are apparently rare. Sex determination has been studied in multiple Salix and Populus (Salicaceae) species, and P. trichocarpa has an XY sex determination system on chromosome 19, while S. suchowensis and S. viminalis have a ZW system on chromosome 15. Here we use whole genome sequencing coupled with quantitative trait locus mapping and a genome-wide association study to characterize the genomic composition of the non-recombining portion of the sex determination region. We demonstrate that Salix purpurea also has a ZW system on chromosome 15. The sex determination region has reduced recombination, high structural polymorphism, an abundance of transposable elements, and contains genes that are involved in sex expression in other plants. We also show that chromosome 19 contains sex-associated markers in this S. purpurea assembly, along with other autosomes. This raises the intriguing possibility of a translocation of the sex determination region within the Salicaceae lineage, suggesting a common evolutionary origin of the Populus and Salix sex determination loci.
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Affiliation(s)
- Ran Zhou
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Eli Rodgers-Melnick
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Luke M Evans
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA.,Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Juying Yan
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Gerald A Tuskan
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.,Biosciences Division, Oak Ridge National Lab, Oak Ridge, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA.
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25
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Charlesworth D. The Guppy Sex Chromosome System and the Sexually Antagonistic Polymorphism Hypothesis for Y Chromosome Recombination Suppression. Genes (Basel) 2018; 9:genes9050264. [PMID: 29783761 PMCID: PMC5977204 DOI: 10.3390/genes9050264] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/11/2018] [Accepted: 05/16/2018] [Indexed: 02/06/2023] Open
Abstract
Sex chromosomes regularly evolve suppressed recombination, distinguishing them from other chromosomes, and the reason for this has been debated for many years. It is now clear that non-recombining sex-linked regions have arisen in different ways in different organisms. A major hypothesis is that a sex-determining gene arises on a chromosome and that sexually antagonistic (SA) selection (sometimes called intra-locus sexual conflict) acting at a linked gene has led to the evolution of recombination suppression in the region, to reduce the frequency of low fitness recombinant genotypes produced. The sex chromosome system of the guppy (Poecilia reticulata) is often cited as supporting this hypothesis because SA selection has been demonstrated to act on male coloration in natural populations of this fish, and probably contributes to maintaining polymorphisms for the genetic factors involved. I review classical genetic and new molecular genetic results from the guppy, and other fish, including approaches for identifying the genome regions carrying sex-determining loci, and suggest that the guppy may exemplify a recently proposed route to sex chromosome evolution.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
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