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Montero-Tena JA, Abdollahi Sisi N, Kox T, Abbadi A, Snowdon RJ, Golicz AA. haploMAGIC: accurate phasing and detection of recombination in multiparental populations despite genotyping errors. G3 (BETHESDA, MD.) 2024; 14:jkae109. [PMID: 38808682 PMCID: PMC11304941 DOI: 10.1093/g3journal/jkae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 02/12/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024]
Abstract
Recombination is a key mechanism in breeding for promoting genetic variability. Multiparental populations (MPPs) constitute an excellent platform for precise genotype phasing, identification of genome-wide crossovers (COs), estimation of recombination frequencies, and construction of recombination maps. Here, we introduce haploMAGIC, a pipeline to detect COs in MPPs with single-nucleotide polymorphism (SNP) data by exploiting the pedigree relationships for accurate genotype phasing and inference of grandparental haplotypes. haploMAGIC applies filtering to prevent false-positive COs due to genotyping errors (GEs), a common problem in high-throughput SNP analysis of complex plant genomes. Hence, it discards haploblocks not reaching a specified minimum number of informative alleles. A performance analysis using populations simulated with AlphaSimR revealed that haploMAGIC improves upon existing methods of CO detection in terms of recall and precision, most notably when GE rates are high. Furthermore, we constructed recombination maps using haploMAGIC with high-resolution genotype data from 2 large multiparental populations of winter rapeseed (Brassica napus). The results demonstrate the applicability of the pipeline in real-world scenarios and showed good correlations in recombination frequency compared with alternative software. Therefore, we propose haploMAGIC as an accurate tool at CO detection with MPPs that shows robustness against GEs.
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Affiliation(s)
- Jose A Montero-Tena
- Department of Agrobioinformatics, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany
| | - Nayyer Abdollahi Sisi
- Department of Plant Breeding, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany
| | - Tobias Kox
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363 Holtsee, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363 Holtsee, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany
| | - Agnieszka A Golicz
- Department of Agrobioinformatics, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany
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2
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Rhaman MS, Ali M, Ye W, Li B. Opportunities and Challenges in Advancing Plant Research with Single-cell Omics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae026. [PMID: 38996445 DOI: 10.1093/gpbjnl/qzae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 07/14/2024]
Abstract
Plants possess diverse cell types and intricate regulatory mechanisms to adapt to the ever-changing environment of nature. Various strategies have been employed to study cell types and their developmental progressions, including single-cell sequencing methods which provide high-dimensional catalogs to address biological concerns. In recent years, single-cell sequencing technologies in transcriptomics, epigenomics, proteomics, metabolomics, and spatial transcriptomics have been increasingly used in plant science to reveal intricate biological relationships at the single-cell level. However, the application of single-cell technologies to plants is more limited due to the challenges posed by cell structure. This review outlines the advancements in single-cell omics technologies, their implications in plant systems, future research applications, and the challenges of single-cell omics in plant systems.
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Affiliation(s)
- Mohammad Saidur Rhaman
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Muhammad Ali
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Wenxiu Ye
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
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3
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Zou M, Shabala S, Zhao C, Zhou M. Molecular mechanisms and regulation of recombination frequency and distribution in plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:86. [PMID: 38512498 PMCID: PMC10957645 DOI: 10.1007/s00122-024-04590-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
KEY MESSAGE Recent developments in understanding the distribution and distinctive features of recombination hotspots are reviewed and approaches are proposed to increase recombination frequency in coldspot regions. Recombination events during meiosis provide the foundation and premise for creating new varieties of crops. The frequency of recombination in different genomic regions differs across eukaryote species, with recombination generally occurring more frequently at the ends of chromosomes. In most crop species, recombination is rare in centromeric regions. If a desired gene variant is linked in repulsion with an undesired variant of a second gene in a region with a low recombination rate, obtaining a recombinant plant combining two favorable alleles will be challenging. Traditional crop breeding involves combining desirable genes from parental plants into offspring. Therefore, understanding the mechanisms of recombination and factors affecting the occurrence of meiotic recombination is important for crop breeding. Here, we review chromosome recombination types, recombination mechanisms, genes and proteins involved in the meiotic recombination process, recombination hotspots and their regulation systems and discuss how to increase recombination frequency in recombination coldspot regions.
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Affiliation(s)
- Meilin Zou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, 6009, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia.
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Peñuela M, Finke J, Rocha C. Methylomes as key features for predicting recombination in some plant species. PLANT MOLECULAR BIOLOGY 2024; 114:25. [PMID: 38457042 PMCID: PMC10924001 DOI: 10.1007/s11103-023-01396-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/27/2023] [Indexed: 03/09/2024]
Abstract
Knowing how chromosome recombination works is essential for plant breeding. It enables the design of crosses between different varieties to combine desirable traits and create new ones. This is because the meiotic crossovers between homologous chromatids are not purely random, and various strategies have been developed to describe and predict such exchange events. Recent studies have used methylation data to predict chromosomal recombination in rice using machine learning models. This approach proved successful due to the presence of a positive correlation between the CHH context cytosine methylation and recombination rates in rice chromosomes. This paper assesses the question if methylation can be used to predict recombination in four plant species: Arabidopsis, maize, sorghum, and tomato. The results indicate a positive association between CHH context methylation and recombination rates in certain plant species, with varying degrees of strength in their relationships. The CG and CHG methylation contexts show negative correlation with recombination. Methylation data was key effectively in predicting recombination in sorghum and tomato, with a mean determination coefficient of 0.65 ± 0.11 and 0.76 ± 0.05, respectively. In addition, the mean correlation values between predicted and experimental recombination rates were 0.83 ± 0.06 for sorghum and 0.90 ± 0.05 for tomato, confirming the significance of methylomes in both monocotyledonous and dicotyledonous species. The predictions for Arabidopsis and maize were not as accurate, likely due to the comparatively weaker relationships between methylation contexts and recombination, in contrast to sorghum and tomato, where stronger associations were observed. To enhance the accuracy of predictions, further evaluations using data sets closely related to each other might prove beneficial. In general, this methylome-based method holds great potential as a reliable strategy for predicting recombination rates in various plant species, offering valuable insights to breeders in their quest to develop novel and improved varieties.
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Affiliation(s)
- Mauricio Peñuela
- iÓMICAS, Facultad de Ingeniería y Ciencias, Pontificia Universidad Javeriana, 760031, Cali, Colombia.
| | - Jorge Finke
- iÓMICAS, Facultad de Ingeniería y Ciencias, Pontificia Universidad Javeriana, 760031, Cali, Colombia
| | - Camilo Rocha
- iÓMICAS, Facultad de Ingeniería y Ciencias, Pontificia Universidad Javeriana, 760031, Cali, Colombia
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Washburn M, Alaniz-Fabián J, Scroggs T, Nelms B. Single-cell RNA-seq of maize meiocytes and pollen grains. Nat Protoc 2023; 18:3512-3533. [PMID: 37783945 DOI: 10.1038/s41596-023-00889-6] [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: 12/23/2022] [Accepted: 07/11/2023] [Indexed: 10/04/2023]
Abstract
RNA-sequencing (RNA-seq) provides invaluable knowledge on developmental pathways and the effects of mutant phenotypes. Plant reproductive cells have traditionally been difficult to isolate for genomics because they are rare and often deeply embedded within somatic tissues. Here, we present a protocol to isolate single maize meiocytes and pollen grains for RNA-seq. We discuss how to identify and isolate each sample type under a microscope, prepare RNA-seq libraries and analyze the data. This technique has several advantages over alternative methods, combining the ability to target specific rare cell types while resolving cell-to-cell heterogeneity with single-cell RNA-seq. The technique is compatible with minute amounts of starting material (e.g., a single anther), making it possible to collect dense time courses. Furthermore, developmentally synchronized anthers are saved for microscopy, allowing staging to be performed in parallel with expression analysis. Up to 200 cells can be collected in 4-5 h by someone proficient in tissue dissection, and library preparation can be completed in 2 d by researchers experienced in molecular biology and genomics. This protocol will facilitate research on plant reproduction, providing insights critical to plant breeding, genetics and agriculture.
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Affiliation(s)
| | - Jaime Alaniz-Fabián
- National Laboratory of Genomics for Biodiversity, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-LANGEBIO), Irapuato, Mexico
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Wang Y, Dong Z, Ma Y, Zheng Y, Huang S, Yang X. Comprehensive dissection of meiotic DNA double-strand breaks and crossovers in cucumber. PLANT PHYSIOLOGY 2023; 193:1913-1932. [PMID: 37530486 PMCID: PMC10602612 DOI: 10.1093/plphys/kiad432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/21/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Meiotic recombination drives genetic diversity and crop genome optimization. In plant breeding, parents with favorable traits are crossed to create elite varieties. Different hybridizations produce diverse types of segment reshuffling between homologous chromosomes. However, little is known about the factors that cause hybrid-specific changes in crossovers (COs). Here, we constructed 2 F2 populations from crosses between a semiwild and 2 domesticated cucumber (Cucumis sativus) accessions and examined CO events. COs mainly occurred around genes and differed unevenly along chromosomes between the 2 hybrids. Fine-scale CO distributions were suppressed in regions of heterozygous structural variations (SVs) and were accelerated by high sequence polymorphism. C. sativus RADiation sensitive 51A (CsRAD51A) binding, histone H3 lysine 4 trimethylation (H3K4me3) modification, chromatin accessibility, and hypomethylation were positively associated with global CO landscapes and in local DNA double-strand break (DSB) hotspots and genes. The frequency and suppression of COs could be roughly predicted based on multiomic information. Differences in CO events between hybrids could be partially traced to distinct genetic and epigenetic features and were significantly associated with specific DSB hotspots and heterozygous SVs. Our findings identify the genomic and epigenetic features that contribute to CO formation and hybrid-specific divergence in cucumber and provide theoretical support for selecting parental combinations and manipulating recombination events at target genomic regions during plant breeding.
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Affiliation(s)
- Yanling Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhaonian Dong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yalin Ma
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yi Zheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xueyong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Somers J, Nelms B. The sporophyte-to-gametophyte transition: The haploid generation comes of age. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102416. [PMID: 37441836 DOI: 10.1016/j.pbi.2023.102416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Flowering plants alternate between two multicellular generations: the diploid sporophyte and haploid gametophyte. Despite its small size, the gametophyte has significant impacts on plant genetics, evolution, and breeding. Each male pollen grain and female embryo sac is a multicellular organism with independent gene expression, a functioning metabolism, and specialized cell types. In this review, we describe recent progress in understanding the process in which the haploid genome takes over expression from its diploid parent - the sporophyte-to-gametophyte transition. The focus is on pollen, but similar concepts may also apply to the female gametophyte. Technological advances in single-cell genomics offer the opportunity to characterize haploid gene expression in unprecedented detail, positioning the field to make rapid progress.
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Affiliation(s)
- Julian Somers
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Brad Nelms
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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8
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Chen C, Ge Y, Lu L. Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1185377. [PMID: 37636094 PMCID: PMC10453814 DOI: 10.3389/fpls.2023.1185377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023]
Abstract
Single-cell and spatial transcriptomics have diverted researchers' attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research.
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Affiliation(s)
- Ce Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yining Ge
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lingli Lu
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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9
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Ziolkowski PA. Why do plants need the ZMM crossover pathway? A snapshot of meiotic recombination from the perspective of interhomolog polymorphism. PLANT REPRODUCTION 2023; 36:43-54. [PMID: 35819509 PMCID: PMC9958190 DOI: 10.1007/s00497-022-00446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/20/2022] [Indexed: 06/06/2023]
Abstract
At the heart of meiosis is crossover recombination, i.e., reciprocal exchange of chromosome fragments between parental genomes. Surprisingly, in most eukaryotes, including plants, several recombination pathways that can result in crossover event operate in parallel during meiosis. These pathways emerged independently in the course of evolution and perform separate functions, which directly translate into their roles in meiosis. The formation of one crossover per chromosome pair is required for proper chromosome segregation. This "obligate" crossover is ensured by the major crossover pathway in plants, and in many other eukaryotes, known as the ZMM pathway. The secondary pathways play important roles also in somatic cells and function mainly as repair mechanisms for DNA double-strand breaks (DSBs) not used for crossover formation. One of the consequences of the functional differences between ZMM and other DSB repair pathways is their distinct sensitivities to polymorphisms between homologous chromosomes. From a population genetics perspective, these differences may affect the maintenance of genetic variability. This might be of special importance when considering that a significant portion of plants uses inbreeding as a predominant reproductive strategy, which results in loss of interhomolog polymorphism. While we are still far from fully understanding the relationship between meiotic recombination pathways and genetic variation in populations, recent studies of crossovers in plants offer a new perspective.
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Affiliation(s)
- Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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10
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Abstract
KEY MESSAGE Chromatin state, and dynamic loading of pro-crossover protein HEI10 at recombination intermediates shape meiotic chromosome patterning in plants. Meiosis is the basis of sexual reproduction, and its basic progression is conserved across eukaryote kingdoms. A key feature of meiosis is the formation of crossovers which result in the reciprocal exchange of segments of maternal and paternal chromosomes. This exchange generates chromosomes with new combinations of alleles, increasing the efficiency of both natural and artificial selection. Crossovers also form a physical link between homologous chromosomes at metaphase I which is critical for accurate chromosome segregation and fertility. The patterning of crossovers along the length of chromosomes is a highly regulated process, and our current understanding of its regulation forms the focus of this review. At the global scale, crossover patterning in plants is largely governed by the classically observed phenomena of crossover interference, crossover homeostasis and the obligatory crossover which regulate the total number of crossovers and their relative spacing. The molecular actors behind these phenomena have long remained obscure, but recent studies in plants implicate HEI10 and ZYP1 as key players in their coordination. In addition to these broad forces, a wealth of recent studies has highlighted how genomic and epigenomic features shape crossover formation at both chromosomal and local scales, revealing that crossovers are primarily located in open chromatin associated with gene promoters and terminators with low nucleosome occupancy.
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Affiliation(s)
- Andrew Lloyd
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, Ceredigion, UK.
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11
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Dissecting the Meiotic Recombination Patterns in a Brassica napus Double Haploid Population Using 60K SNP Array. Int J Mol Sci 2023; 24:ijms24054469. [PMID: 36901901 PMCID: PMC10003086 DOI: 10.3390/ijms24054469] [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: 01/13/2023] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Meiotic recombination not only maintains the stability of the chromosome structure but also creates genetic variations for adapting to changeable environments. A better understanding of the mechanism of crossover (CO) patterns at the population level is useful for crop improvement. However, there are limited cost-effective and universal methods to detect the recombination frequency at the population level in Brassica napus. Here, the Brassica 60K Illumina Infinium SNP array (Brassica 60K array) was used to systematically study the recombination landscape in a double haploid (DH) population of B. napus. It was found that COs were unevenly distributed across the whole genome, and a higher frequency of COs existed at the distal ends of each chromosome. A considerable number of genes (more than 30%) in the CO hot regions were associated with plant defense and regulation. In most tissues, the average gene expression level in the hot regions (CO frequency of greater than 2 cM/Mb) was significantly higher than that in the regions with a CO frequency of less than 1 cM/Mb. In addition, a bin map was constructed with 1995 recombination bins. For seed oil content, Bin 1131 to 1134, Bin 1308 to 1311, Bin 1864 to 1869, and Bin 2184 to 2230 were identified on chromosomes A08, A09, C03, and C06, respectively, which could explain 8.5%, 17.3%, 8.6%, and 3.9% of the phenotypic variation. These results could not only deepen our understanding of meiotic recombination in B. napus at the population level, and provide useful information for rapeseed breeding in the future, but also provided a reference for studying CO frequency in other species.
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Gui S, Martinez-Rivas FJ, Wen W, Meng M, Yan J, Usadel B, Fernie AR. Going broad and deep: sequencing-driven insights into plant physiology, evolution, and crop domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:446-459. [PMID: 36534120 DOI: 10.1111/tpj.16070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high-quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome-wide association and transcriptome-wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes.
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Affiliation(s)
- Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minghui Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, BioSc, 52428, Jülich, Germany
- Institute for Biological Data Science, CEPLAS, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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Felts AM, Pokharel B, Yahya D, Aziz AN. Whole-genomic DNA amplifications from individually isolated sweet sorghum microspores. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11501. [PMID: 36518943 PMCID: PMC9742829 DOI: 10.1002/aps3.11501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/12/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Sorghum is a multi-use crop, the efficient breeding of which requires the development of new genetic tools. One such tool could be the genetic assessment of free microspores, which are released just after the tetrad stage of pollen development. Microspores are ideal for DNA isolation as they have underdeveloped cell walls and can be readily lysed as natural protoplasts. METHODS Four cultivars of Sorghum bicolor ('Achi Turi', 'Dale', 'Local', and 'Topper 76-6') were grown in a greenhouse until flowering (7.7-11.5 cm flag leaf internode length), after which 30 immature microspores were isolated from each line. Plant height, time to flowering, boot radius, and spikelet maturation were recorded for each cultivar. The exine development of the microspores was observed under an inverted Nikon microscope, and those with underdeveloped exine were subjected to whole-genome amplification and sequencing. RESULTS Microspores in the early uninucleate to early binucleate stages had underdeveloped exine, and were therefore ideal for DNA extraction. High-quality DNA was obtained from these single-cell gametophytes. The average DNA concentration was 2902 ng/µL, with fragment sizes comparable to those obtained from leaf tissue extractions. DISCUSSION Harvesting panicles with immature microspores means the entire gametic population is accessible for DNA analyses. This is the first amplification of whole-genome DNA fragments from sorghum single-cell microspores isolated during gametogenesis.
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Affiliation(s)
- Aron M. Felts
- Department of Agricultural and Environmental SciencesTennessee State University3500 John Merritt Blvd.NashvilleTennessee37209USA
| | - Bharat Pokharel
- Department of Agricultural and Environmental SciencesTennessee State University3500 John Merritt Blvd.NashvilleTennessee37209USA
| | - Dilovan Yahya
- Department of Agricultural and Environmental SciencesTennessee State University3500 John Merritt Blvd.NashvilleTennessee37209USA
| | - Ahmad N. Aziz
- Department of Agricultural and Environmental SciencesTennessee State University3500 John Merritt Blvd.NashvilleTennessee37209USA
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14
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Li Z, Chen X, Shi S, Zhang H, Wang X, Chen H, Li W, Li L. DeepBSA: A deep-learning algorithm improves bulked segregant analysis for dissecting complex traits. MOLECULAR PLANT 2022; 15:1418-1427. [PMID: 35996754 DOI: 10.1016/j.molp.2022.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/03/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Bulked segregant analysis (BSA) is a rapid, cost-effective method for mapping mutations and quantitative trait loci (QTLs) in animals and plants based on high-throughput sequencing. However, the algorithms currently used for BSA have not been systematically evaluated and are complex and fallible to operate. We developed a BSA method driven by deep learning, DeepBSA, for QTL mapping and functional gene cloning. DeepBSA is compatible with a variable number of bulked pools and performed well with various simulated and real datasets in both animals and plants. DeepBSA outperformed all other algorithms when comparing absolute bias and signal-to-noise ratio. Moreover, we applied DeepBSA to an F2 segregating maize population of 7160 individuals and uncovered five candidate QTLs, including three well-known plant-height genes. Finally, we developed a user-friendly graphical user interface for DeepBSA, by integrating five widely used BSA algorithms and our two newly developed algorithms, that is easy to operate and can quickly map QTLs and functional genes. The DeepBSA software is freely available to non-commercial users at http://zeasystemsbio.hzau.edu.cn/tools.html and https://github.com/lizhao007/DeepBSA.
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Affiliation(s)
- Zhao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hainan Yazhou Bay Seed Lab, Hainan, China
| | - Xiaoxuan Chen
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaoqiang Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Chen
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Weifu Li
- College of Science, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hainan Yazhou Bay Seed Lab, Hainan, China.
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15
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Chuang YC, Smith GR. Meiotic crossover interference: Methods of analysis and mechanisms of action. Curr Top Dev Biol 2022; 151:217-244. [PMID: 36681471 PMCID: PMC10063388 DOI: 10.1016/bs.ctdb.2022.04.006] [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] [Indexed: 01/25/2023]
Abstract
Segregation of chromosomes during meiosis, to form haploid gametes from diploid precursor cells, requires in most species formation of crossovers physically connecting homologous chromosomes. Along with sister chromatid cohesion, crossovers allow tension to be generated when chromosomes begin to segregate; tension signals that chromosome movement is proceeding properly. But crossovers too close to each other might result in less sister chromatid cohesion and tension and thus failed meiosis. Interference describes the non-random distribution of crossovers, which occur farther apart than expected from independence. We discuss both genetic and cytological methods of assaying crossover interference and models for interference, whose molecular mechanism remains to be elucidated. We note marked differences among species.
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Affiliation(s)
| | - Gerald R Smith
- Fred Hutchinson Cancer Center, Seattle, WA, United States.
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16
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Chen G, Zhang B, Ding J, Wang H, Deng C, Wang J, Yang Q, Pi Q, Zhang R, Zhai H, Dong J, Huang J, Hou J, Wu J, Que J, Zhang F, Li W, Min H, Tabor G, Li B, Liu X, Zhao J, Yan J, Lai Z. Cloning southern corn rust resistant gene RppK and its cognate gene AvrRppK from Puccinia polysora. Nat Commun 2022; 13:4392. [PMID: 35906218 PMCID: PMC9338322 DOI: 10.1038/s41467-022-32026-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/14/2022] [Indexed: 02/06/2023] Open
Abstract
Broad-spectrum resistance has great values for crop breeding. However, its mechanisms are largely unknown. Here, we report the cloning of a maize NLR gene, RppK, for resistance against southern corn rust (SCR) and its cognate Avr gene, AvrRppK, from Puccinia polysora (the causal pathogen of SCR). The AvrRppK gene has no sequence variation in all examined isolates. It has high expression level during infection and can suppress pattern-triggered immunity (PTI). Further, the introgression of RppK into maize inbred lines and hybrids enhances resistance against multiple isolates of P. polysora, thereby increasing yield in the presence of SCR. Together, we show that RppK is involved in resistance against multiple P. polysora isolates and it can recognize AvrRppK, which is broadly distributed and conserved in P. polysora isolates. Southern corn rust (SCR) caused by Puccinia polysora is a major maize disease that can result in major yield loss. Here, the authors report the expression of a CC-NB-LRR type of R gene RppK results in SCR resistance in susceptible maize lines and it can recognize the effector AvrRppK produced by P. polysora.
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Affiliation(s)
- Gengshen Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Bao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, Henan, China.,The Shennong Laboratory, 450002, Zhengzhou, Henan, China
| | - Hongze Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Ce Deng
- College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, Henan, China
| | - Jiali Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Qianhui Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Qianyu Pi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Ruyang Zhang
- Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
| | - Haoyu Zhai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Junfei Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Junshi Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Jiabao Hou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Junhua Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Jiamin Que
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Fan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Haoxuan Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Girma Tabor
- Corteva Agriscience, Johnston, IA, 50131, USA
| | - Bailin Li
- Corteva Agriscience, Johnston, IA, 50131, USA
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China
| | - Jiuran Zhao
- Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China. .,Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China.
| | - Zhibing Lai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China. .,Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China.
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17
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Calvo‐Baltanás V, De Jaeger‐Braet J, Cher WY, Schönbeck N, Chae E, Schnittger A, Wijnker E. Knock-down of gene expression throughout meiosis and pollen formation by virus-induced gene silencing in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:19-37. [PMID: 35340073 PMCID: PMC9543169 DOI: 10.1111/tpj.15733] [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: 04/22/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Through the inactivation of genes that act during meiosis it is possible to direct the genetic make-up of plants in subsequent generations and optimize breeding schemes. Offspring may show higher recombination of parental alleles resulting from elevated crossover (CO) incidence, or by omission of meiotic divisions, offspring may become polyploid. However, stable mutations in genes essential for recombination, or for either one of the two meiotic divisions, can have pleiotropic effects on plant morphology and line stability, for instance by causing lower fertility. Therefore, it is often favorable to temporarily change gene expression during meiosis rather than relying on stable null mutants. It was previously shown that virus-induced gene silencing (VIGS) can be used to transiently reduce CO frequencies. We asked if VIGS could also be used to modify other processes throughout meiosis and during pollen formation in Arabidopsis thaliana. Here, we show that VIGS-mediated knock-down of FIGL1, RECQ4A/B, OSD1 and QRT2 can induce (i) an increase in chiasma numbers, (ii) unreduced gametes and (iii) pollen tetrads. We further show that VIGS can target both sexes and different genetic backgrounds and can simultaneously silence different gene copies. The successful knock-down of these genes in A. thaliana suggests that VIGS can be exploited to manipulate any process during or shortly after meiosis. Hence, the transient induction of changes in inheritance patterns can be used as a powerful tool for applied research and biotechnological applications.
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Affiliation(s)
- Vanesa Calvo‐Baltanás
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Joke De Jaeger‐Braet
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Wei Yuan Cher
- A*STAR, Institute of Molecular and Cell Biology (IMCB)61 Biopolis DriveProteos138673Singapore
| | - Nils Schönbeck
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- UKEMartinistrasse 5220251HamburgGermany
| | - Eunyoung Chae
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Arp Schnittger
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Erik Wijnker
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
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18
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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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19
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Li J, Llorente B, Liti G, Yue JX. RecombineX: A generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis. PLoS Genet 2022; 18:e1010047. [PMID: 35533184 PMCID: PMC9119626 DOI: 10.1371/journal.pgen.1010047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/19/2022] [Accepted: 04/14/2022] [Indexed: 01/09/2023] Open
Abstract
Meiotic recombination is an essential biological process that ensures faithful chromosome segregation and promotes parental allele shuffling. Tetrad analysis is a powerful approach to quantify the genetic makeups and recombination landscapes of meiotic products. Here we present RecombineX (https://github.com/yjx1217/RecombineX), a generalized computational framework that automates the full workflow of marker identification, gamete genotyping, and tetrad-based recombination profiling based on any organism or genetic background with batch processing capability. Aside from conventional reference-based analysis, RecombineX can also perform analysis based on parental genome assemblies, which facilitates analyzing meiotic recombination landscapes in their native genomic contexts. Additional features such as copy number variation profiling and missing genotype inference further enhance downstream analysis. RecombineX also includes a dedicate module for simulating the genomes and reads of recombinant tetrads, which enables fine-tuned simulation-based hypothesis testing. This simulation module revealed the power and accuracy of RecombineX even when analyzing tetrads with very low sequencing depths (e.g., 1-2X). Tetrad sequencing data from the budding yeast Saccharomyces cerevisiae and green alga Chlamydomonas reinhardtii were further used to demonstrate the accuracy and robustness of RecombineX for organisms with both small and large genomes, manifesting RecombineX as an all-around one stop solution for future tetrad analysis. Interestingly, our re-analysis of the budding yeast tetrad sequencing data with RecombineX and Oxford Nanopore sequencing revealed two unusual structural rearrangement events that were not noticed before, which exemplify the occasional genome instability triggered by meiosis.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Bertrand Llorente
- Aix-Marseille Université, CNRS, INSERM, CRCM, Institut Paoli-Calmettes, Marseille, France
| | - Gianni Liti
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
- * E-mail: (GL); (JXY)
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
- * E-mail: (GL); (JXY)
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20
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Xie M, Yang L, Jiang C, Wu S, Luo C, Yang X, He L, Chen S, Deng T, Ye M, Yan J, Yang N. gcaPDA: a haplotype-resolved diploid assembler. BMC Bioinformatics 2022; 23:68. [PMID: 35164674 PMCID: PMC8842951 DOI: 10.1186/s12859-022-04591-4] [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: 12/21/2021] [Accepted: 01/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background Generating chromosome-scale haplotype resolved assembly is important for functional studies. However, current de novo assemblers are either haploid assemblers that discard allelic information, or diploid assemblers that can only tackle genomes of low complexity. Results Here, Using robust programs, we build a diploid genome assembly pipeline called gcaPDA (gamete cells assisted Phased Diploid Assembler), which exploits haploid gamete cells to assist in resolving haplotypes. We demonstrate the effectiveness of gcaPDA based on simulated HiFi reads of maize genome which is highly heterozygous and repetitive, and real data from rice. Conclusions With applicability of coping with complex genomes and fewer restrictions on application than most of diploid assemblers, gcaPDA is likely to find broad applications in studies of eukaryotic genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04591-4.
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Affiliation(s)
- Min Xie
- Guangdong Engineering Research Center of Plant and Animal Genomics, BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Linfeng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Guangdong Engineering Research Center of Plant and Animal Genomics, BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Chenglin Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Yang
- Guangdong Engineering Research Center of Plant and Animal Genomics, BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lijuan He
- Guangdong Engineering Research Center of Plant and Animal Genomics, BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Shixuan Chen
- Guangdong Engineering Research Center of Plant and Animal Genomics, BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Tianquan Deng
- Guangdong Engineering Research Center of Plant and Animal Genomics, BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Mingzhi Ye
- Guangdong Engineering Research Center of Plant and Animal Genomics, BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Hongshan Laboratory, Wuhan, 430070, China.
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21
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Chromosome-Wide Characterization of Intragenic Crossover in Shiitake Mushroom, Lentinula edodes. J Fungi (Basel) 2021; 7:jof7121076. [PMID: 34947058 PMCID: PMC8704546 DOI: 10.3390/jof7121076] [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: 11/04/2021] [Revised: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022] Open
Abstract
Meiotic crossover plays a critical role in generating genetic variations and is a central component of breeding. However, our understanding of crossover in mushroom-forming fungi is limited. Here, in Lentinula edodes, we characterized the chromosome-wide intragenic crossovers, by utilizing the single-nucleotide polymorphisms (SNPs) datasets of an F1 haploid progeny. A total of 884 intragenic crossovers were identified in 110 single-spore isolates, the majority of which were closer to transcript start sites. About 71.5% of the intragenic crossovers were clustered into 65 crossover hotspots. A 10 bp motif (GCTCTCGAAA) was significantly enriched in the hotspot regions. Crossover frequencies around mating-type A (MAT-A) loci were enhanced and formed a hotspot in L. edodes. Genome-wide quantitative trait loci (QTLs) mapping identified sixteen crossover-QTLs, contributing 8.5–29.1% of variations. Most of the detected crossover-QTLs were co-located with crossover hotspots. Both cis- and trans-QTLs contributed to the nonuniformity of crossover along chromosomes. On chr2, we identified a QTL hotspot that regulated local, global crossover variation and crossover hotspot in L. edodes. These findings and observations provide a comprehensive view of the crossover landscape in L. edodes, and advance our understandings of conservation and diversity of meiotic recombination in mushroom-forming fungi.
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22
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Geng X, Xia Y, Chen H, Du K, Yang J, Kang X. High-Frequency Homologous Recombination Occurred Preferentially in Populus. Front Genet 2021; 12:703077. [PMID: 34490036 PMCID: PMC8417060 DOI: 10.3389/fgene.2021.703077] [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: 04/30/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination (HR), the most significant event in meiosis, has important implications for genetic diversity and evolution in organisms. Heteroduplex DNA (hDNA), the product of HR, can be captured by artificially induced chromosome doubling during the development of the embryo sac to inhibit postmeiotic segregation, subsequently, and hDNAs are directly detected using codominant simple sequence repeat (SSR) markers. In the present study, two hybrid triploid populations derived from doubling the chromosomes of the embryo sac induced by high temperature in Populus tomentosa served as starting materials. Eighty-seven, 62, and 79 SSR markers on chromosomes 01, 04, and 19, respectively, that were heterozygous in the maternal parent and different from the paternal parent were screened to detect and characterize the hDNA in P. tomentosa. The results showed that the hDNA frequency patterns on chromosomes changed slightly when the number of SSR primers increased. The highest hDNA frequency occurred at the adjacent terminal on chromosomes, which was slightly higher than those at the terminals in the two genotypic individuals, and the hDNA frequency gradually decreased as the locus-centromere distance decreased. With the increase in the number of SSR markers employed for detection, the number of recombination events (REs) detected significantly increased. In regions with high methylation or long terminal repeat (LTR) retrotransposon enrichment, the frequency of hDNA was low, and high frequencies were observed in regions with low sequence complexity and high gene density. High-frequency recombination occurring at high gene density regions strongly affected the association between molecular markers and quantitative trait loci (QTLs), which was an important factor contributing to the difficulty encountered by MAS in achieving the expected breeding results.
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Affiliation(s)
- Xining Geng
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-Economic Woody Plant, Pingdingshan University, Pingdingshan, China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Yufei Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Hao Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Kang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Jun Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
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23
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Abstract
Meiotic recombination is a fundamental process that generates genetic diversity and ensures the accurate segregation of homologous chromosomes. While a great deal is known about genetic factors that regulate recombination, relatively little is known about epigenetic factors, such as DNA methylation. In maize, we examined the effects on meiotic recombination of a mutation in a component of the RNA-directed DNA methylation pathway, Mop1 (Mediator of paramutation1), as well as a mutation in a component of the trans-acting small interference RNA biogenesis pathway, Lbl1 (Leafbladeless1). MOP1 is of particular interest with respect to recombination because it is responsible for methylation of transposable elements that are immediately adjacent to transcriptionally active genes. In the mop1 mutant, we found that meiotic recombination is uniformly decreased in pericentromeric regions but is generally increased in gene rich chromosomal arms. This observation was further confirmed by cytogenetic analysis showing that although overall crossover numbers are unchanged, they occur more frequently in chromosomal arms in mop1 mutants. Using whole genome bisulfite sequencing, our data show that crossover redistribution is driven by loss of CHH (where H = A, T, or C) methylation within regions near genes. In contrast to what we observed in mop1 mutants, no significant changes were observed in the frequency of meiotic recombination in lbl1 mutants. Our data demonstrate that CHH methylation has a significant impact on the overall recombination landscape in maize despite its low frequency relative to CG and CHG methylation.
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24
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Kuo P, Da Ines O, Lambing C. Rewiring Meiosis for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:708948. [PMID: 34349775 PMCID: PMC8328115 DOI: 10.3389/fpls.2021.708948] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 05/10/2023]
Abstract
Meiosis is a specialized cell division that contributes to halve the genome content and reshuffle allelic combinations between generations in sexually reproducing eukaryotes. During meiosis, a large number of programmed DNA double-strand breaks (DSBs) are formed throughout the genome. Repair of meiotic DSBs facilitates the pairing of homologs and forms crossovers which are the reciprocal exchange of genetic information between chromosomes. Meiotic recombination also influences centromere organization and is essential for proper chromosome segregation. Accordingly, meiotic recombination drives genome evolution and is a powerful tool for breeders to create new varieties important to food security. Modifying meiotic recombination has the potential to accelerate plant breeding but it can also have detrimental effects on plant performance by breaking beneficial genetic linkages. Therefore, it is essential to gain a better understanding of these processes in order to develop novel strategies to facilitate plant breeding. Recent progress in targeted recombination technologies, chromosome engineering, and an increasing knowledge in the control of meiotic chromosome segregation has significantly increased our ability to manipulate meiosis. In this review, we summarize the latest findings and technologies on meiosis in plants. We also highlight recent attempts and future directions to manipulate crossover events and control the meiotic division process in a breeding perspective.
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Affiliation(s)
- Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Olivier Da Ines
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293 CNRS, U1103 INSERM, Clermont-Ferrand, France
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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Hasan AR, Ness RW. Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii. Genome Biol Evol 2021; 12:370-380. [PMID: 32181819 PMCID: PMC7186780 DOI: 10.1093/gbe/evaa057] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.
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Affiliation(s)
- Ahmed R Hasan
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Ontario, Canada
| | - Rob W Ness
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Ontario, Canada
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26
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Pei L, Li G, Lindsey K, Zhang X, Wang M. Plant 3D genomics: the exploration and application of chromatin organization. THE NEW PHYTOLOGIST 2021; 230:1772-1786. [PMID: 33560539 PMCID: PMC8252774 DOI: 10.1111/nph.17262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/01/2021] [Indexed: 05/29/2023]
Abstract
Eukaryotic genomes are highly folded for packing into higher-order chromatin structures in the nucleus. With the emergence of state-of-the-art chromosome conformation capture methods and microscopic imaging techniques, the spatial organization of chromatin and its functional implications have been interrogated. Our knowledge of 3D chromatin organization in plants has improved dramatically in the past few years, building on the early advances in animal systems. Here, we review recent advances in 3D genome mapping approaches, our understanding of the sophisticated organization of spatial structures, and the application of 3D genomic principles in plants. We also discuss directions for future developments in 3D genomics in plants.
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Affiliation(s)
- Liuling Pei
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Guoliang Li
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanHubei430070China
| | - Keith Lindsey
- Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
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27
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Li R, Qu H, Chen J, Wang S, Chater JM, Zhang L, Wei J, Zhang YM, Xu C, Zhong WD, Zhu J, Lu J, Feng Y, Chen W, Ma R, Ferrante SP, Roose ML, Jia Z. Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes. Mol Biol Evol 2021; 37:3684-3698. [PMID: 32668004 PMCID: PMC7743722 DOI: 10.1093/molbev/msaa176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.
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Affiliation(s)
- Ruidong Li
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
| | - Han Qu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Jinfeng Chen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Shibo Wang
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - John M Chater
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Le Zhang
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
| | - Julong Wei
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI
| | - Yuan-Ming Zhang
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chenwu Xu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wei-De Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jianguo Zhu
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
| | - Jianming Lu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yuanfa Feng
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Weiming Chen
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
| | - Renyuan Ma
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Department of Mathematics, Bowdoin College, Brunswick, ME
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
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Cuacos M, Lambing C, Pachon-Penalba M, Osman K, Armstrong SJ, Henderson IR, Sanchez-Moran E, Franklin FCH, Heckmann S. Meiotic chromosome axis remodelling is critical for meiotic recombination in Brassica rapa. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3012-3027. [PMID: 33502451 PMCID: PMC8023211 DOI: 10.1093/jxb/erab035] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/21/2021] [Indexed: 05/23/2023]
Abstract
Meiosis generates genetic variation through homologous recombination (HR) that is harnessed during breeding. HR occurs in the context of meiotic chromosome axes and the synaptonemal complex. To study the role of axis remodelling in crossover (CO) formation in a crop species, we characterized mutants of the axis-associated protein ASY1 and the axis-remodelling protein PCH2 in Brassica rapa. asy1 plants form meiotic chromosome axes that fail to synapse. CO formation is almost abolished, and residual chiasmata are proportionally enriched in terminal chromosome regions, particularly in the nucleolar organizing region (NOR)-carrying chromosome arm. pch2 plants show impaired ASY1 loading and remodelling, consequently achieving only partial synapsis, which leads to reduced CO formation and loss of the obligatory CO. PCH2-independent chiasmata are proportionally enriched towards distal chromosome regions. Similarly, in Arabidopsis pch2, COs are increased towards telomeric regions at the expense of (peri-) centromeric COs compared with the wild type. Taken together, in B. rapa, axis formation and remodelling are critical for meiotic fidelity including synapsis and CO formation, and in asy1 and pch2 CO distributions are altered. While asy1 plants are sterile, pch2 plants are semi-sterile and thus PCH2 could be an interesting target for breeding programmes.
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Affiliation(s)
- Maria Cuacos
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, D-06466 Seeland, Germany
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Kim Osman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Susan J Armstrong
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | | | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, D-06466 Seeland, Germany
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29
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Sarens M, Copenhaver GP, De Storme N. The Role of Chromatid Interference in Determining Meiotic Crossover Patterns. FRONTIERS IN PLANT SCIENCE 2021; 12:656691. [PMID: 33767725 PMCID: PMC7985435 DOI: 10.3389/fpls.2021.656691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/15/2021] [Indexed: 06/06/2023]
Abstract
Plants, like all sexually reproducing organisms, create genetic variability by reshuffling parental alleles during meiosis. Patterns of genetic variation in the resulting gametes are determined by the independent assortment of chromosomes in meiosis I and by the number and positioning of crossover (CO) events during meiotic recombination. On the chromosome level, spatial distribution of CO events is biased by multiple regulatory mechanisms, such as CO assurance, interference and homeostasis. However, little is known about how multiple COs are distributed among the four chromatids of a bivalent. Chromatid interference (CI) has been proposed as a regulatory mechanism that biases distribution of multiple COs toward specific chromatid partners, however, its existence has not been well-studied and its putative mechanistic basis remains undescribed. Here, we introduce a novel method to quantitatively express CI, and take advantage of available tetrad-based genotyping data from Arabidopsis and maize male meiosis to quantify CI effects on a genome-wide and chromosomal scale. Overall, our analyses reveal random involvement of sister chromatids in double CO events across paired chromosomes, indicating an absence of CI. However, on a genome-wide level, CI was found to vary with physical distance between COs, albeit with different effects in Arabidopsis and maize. While effects of CI are minor in Arabidopsis and maize, the novel methodology introduced here enables quantitative interpretation of CI both on a local and genome-wide scale, and thus provides a key tool to study CI with relevance for both plant genetics and crop breeding.
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Affiliation(s)
- Marie Sarens
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nico De Storme
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Leuven, Belgium
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30
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Ferreira MTM, Glombik M, Perničková K, Duchoslav M, Scholten O, Karafiátová M, Techio VH, Doležel J, Lukaszewski AJ, Kopecký D. Direct evidence for crossover and chromatid interference in meiosis of two plant hybrids (Lolium multiflorum×Festuca pratensis and Allium cepa×A. roylei). JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:254-267. [PMID: 33029645 PMCID: PMC7853598 DOI: 10.1093/jxb/eraa455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/05/2020] [Indexed: 05/02/2023]
Abstract
Crossing over, in addition to its strictly genetic role, also performs a critical mechanical function, by bonding homologues in meiosis. Hence, it is responsible for an orderly reduction of the chromosome number. As such, it is strictly controlled in frequency and distribution. The well-known crossover control is positive crossover interference which reduces the probability of a crossover in the vicinity of an already formed crossover. A poorly studied aspect of the control is chromatid interference. Such analyses are possible in very few organisms as they require observation of all four products of a single meiosis. Here, we provide direct evidence of chromatid interference. Using in situ probing in two interspecific plant hybrids (Lolium multiflorum×Festuca pratensis and Allium cepa×A. roylei) during anaphase I, we demonstrate that the involvement of four chromatids in double crossovers is significantly more frequent than expected (64% versus 25%). We also provide a physical measure of the crossover interference distance, covering ~30-40% of the relative chromosome arm length, and show that the centromere acts as a barrier for crossover interference. The two arms of a chromosome appear to act as independent units in the process of crossing over. Chromatid interference has to be seriously addressed in genetic mapping approaches and further studies.
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Affiliation(s)
- Marco Tulio Mendes Ferreira
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Department of Biology, Federal University of Lavras, Lavras-MG, Brazil
| | - Marek Glombik
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska, Brno, Czech Republic
| | - Kateřina Perničková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska, Brno, Czech Republic
| | - Martin Duchoslav
- Department of Botany, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Olga Scholten
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Adam J Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Correspondence:
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31
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Gong W, Song X, Xie C, Zhou Y, Zhu Z, Xu C, Peng Y. Landscape of meiotic crossovers in Hericium erinaceus. Microbiol Res 2021; 245:126692. [PMID: 33453565 DOI: 10.1016/j.micres.2020.126692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/10/2020] [Accepted: 12/30/2020] [Indexed: 10/22/2022]
Abstract
Meiotic crossover shows marked interspecific and intraspecific variation, and knowledge about the molecular mechanism of crossover variation remains limited. Herein, we described the genome-wide scanning of crossover in one mushroom-forming fungus Hericium erinaceus. Utilizing the whole-genome single-nucleotide polymorphism (SNP) data-sets of a 127 F1 haploid progeny, we localized a total of 1316 crossover events and found that they were more likely to occur in the genic than intergenic regions. More than 30 % of the crossovers were concentrated in 59 crossover hotspots that were preferentially located close to chromosome ends. We then examined the genomic features around crossover hotspots. Results showed that the crossover hotspots were associated with increased gene density and guanine-cytosine (GC) content. An 8-bp GC-rich motif (GCGTCAGC) was found to be significantly enriched in these hotspots. The presence of mating-type loci affected the crossover at local scale rather than the overall crossover number. In order to dissect the genetic mechanisms shaping crossover variation, we then conducted quantitative trait locus (QTL) mapping for the total crossovers (TCO) and the crossover events that solely occurred within hotspots (HCO). Genome-wide QTL scanning identified four TCO-QTLs and two HCO-QTLs, which all located within or next to the crossover-hotspots. Crossover variations were shaped by multiple small-effect loci, with individual QTL contributing 6.9 %-11.7 % of variation. A few recombination pathway genes, including Spo11, Msh5, and Smc5 were found to be co-localized with the mapped crossover QTLs. Taken together, findings of this study offer insights into the crossover distribution and genetic factors conferring crossover variation in H. erinaceus, and advance our understandings for meiotic recombination in mushroom-forming fungi.
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Affiliation(s)
- Wenbing Gong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Xiaoya Song
- Lishui Academy of Agricultural and Forestry Sciences, Lishui 323000, PR China
| | - Chunliang Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Yingjun Zhou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Zuohua Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Chao Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Yuande Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China.
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32
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Zhang W, Luo C, Scossa F, Zhang Q, Usadel B, Fernie AR, Mei H, Wen W. A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:197-208. [PMID: 33118252 DOI: 10.1111/tpj.15051] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 05/27/2023]
Abstract
For diploid organisms that are highly heterozygous, a phased haploid genome can greatly aid in functional genomic, population genetic and breeding studies. Based on the genome sequencing of 135 single sperm cells of the elite tea cultivar 'Fudingdabai', we herein phased the genome of Camellia sinensis, one of the most popular beverage crops worldwide. High-resolution genetic and recombination maps of Fudingdabai were constructed, which revealed that crossover (CO) positions were frequently located in the 5' and 3' ends of annotated genes, while CO distributions across the genome were random. The low CO frequency in tea can be explained by strong CO interference, and CO simulation revealed the proportion of interference insensitive CO ranged from 5.2% to 11.7%. We furthermore developed a method to infer the relatedness between tea accessions and detected complex kinship and genetic signatures of 106 tea accessions. Among them, 59 accessions were closely related with Fudingdabai and 31 of them were first-degree relatives. We additionally identified genes displaying allele specific expression patterns between the two haplotypes of Fudingdabai and genes displaying significantly differential expression levels between Fudingdabai and other haplotypes. These results lay the foundation for further investigation of genetic and epigenetic factors underpinning the regulation of gene expression and provide insights into the evolution of tea plants as well as a valuable genetic resource for future breeding efforts.
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Affiliation(s)
- Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
- Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics, Via Ardeatina 546, Rome, 00178, Italy
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Björn Usadel
- Institute for Biological Data Science, Heinrich Heine University, Düsseldorf, Germany
- Institute of Bio- and Geosciences, IBG-4: Bioinformatics, CEPLAS, Forschungszentrum Jülich, Leo-Brandt-Straße, Jülich, 52425, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Hanwei Mei
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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Calvo‐Baltanás V, Wijnen CL, Yang C, Lukhovitskaya N, de Snoo CB, Hohenwarter L, Keurentjes JJB, de Jong H, Schnittger A, Wijnker E. Meiotic crossover reduction by virus-induced gene silencing enables the efficient generation of chromosome substitution lines and reverse breeding in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1437-1452. [PMID: 32955759 PMCID: PMC7756339 DOI: 10.1111/tpj.14990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 05/16/2023]
Abstract
Plant breeding applications exploiting meiotic mutant phenotypes (like the increase or decrease of crossover (CO) recombination) have been proposed over the last years. As recessive meiotic mutations in breeding lines may affect fertility or have other pleiotropic effects, transient silencing techniques may be preferred. Reverse breeding is a breeding technique that would benefit from the transient downregulation of CO formation. The technique is essentially the opposite of plant hybridization: a method to extract parental lines from a hybrid. The method can also be used to efficiently generate chromosome substitution lines (CSLs). For successful reverse breeding, the two homologous chromosome sets of a heterozygous plant must be divided over two haploid complements, which can be achieved by the suppression of meiotic CO recombination and the subsequent production of doubled haploid plants. Here we show the feasibility of transiently reducing CO formation using virus-induced gene silencing (VIGS) by targeting the meiotic gene MSH5 in a wild-type heterozygote of Arabidopsis thaliana. The application of VIGS (rather than using lengthy stable transformation) generates transgene-free offspring with the desired genetic composition: we obtained parental lines from a wild-type heterozygous F1 in two generations. In addition, we obtained 20 (of the 32 possible) CSLs in one experiment. Our results demonstrate that meiosis can be modulated at will in A. thaliana to generate CSLs and parental lines rapidly for hybrid breeding. Furthermore, we illustrate how the modification of meiosis using VIGS can open routes to develop efficient plant breeding strategies.
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Affiliation(s)
- Vanesa Calvo‐Baltanás
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Present address:
Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Cris L. Wijnen
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Chao Yang
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Department of Developmental BiologyInstitut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Nina Lukhovitskaya
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Centre National de la Recherche ScientifiqueInstitut de Biologie Moléculaire des PlantesUniversité de Strasbourg12, rue du général ZimmerStrasbourg67084France
- Present address:
Division of VirologyDepartment of PathologyUniversity of CambridgeTennis Court RdCambridgeCB2 1QPUK
| | - C. Bastiaan de Snoo
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Rijk Zwaan R&D FijnaartEerste Kruisweg 9Fijnaart4793 RSthe Netherlands
| | - Linus Hohenwarter
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Department of Developmental BiologyInstitut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Joost J. B. Keurentjes
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Hans de Jong
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Arp Schnittger
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
- Department of Developmental BiologyInstitut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Erik Wijnker
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
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Luo C, Fernie AR, Yan J. Single-Cell Genomics and Epigenomics: Technologies and Applications in Plants. TRENDS IN PLANT SCIENCE 2020; 25:1030-1040. [PMID: 32532595 DOI: 10.1016/j.tplants.2020.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
The development of genomics and epigenomics has allowed rapid advances in our understanding of plant biology. However, conventional bulk analysis dilutes cell-specific information by providing only average information, thereby limiting the resolution of genomic and functional genomic studies. Recent advances in single-cell sequencing technology concerning genomics and epigenomics open new avenues to dissect cell heterogeneity in multiple biological processes. Recent applications of these approaches to plants have provided exciting insights into diverse biological questions. We highlight the methodologies underlying the current techniques of single-cell genomics and epigenomics before covering their recent applications, potential significance, and future perspectives in plant biology.
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Affiliation(s)
- Cheng Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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35
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Blackwell AR, Dluzewska J, Szymanska-Lejman M, Desjardins S, Tock AJ, Kbiri N, Lambing C, Lawrence EJ, Bieluszewski T, Rowan B, Higgins JD, Ziolkowski PA, Henderson IR. MSH2 shapes the meiotic crossover landscape in relation to interhomolog polymorphism in Arabidopsis. EMBO J 2020; 39:e104858. [PMID: 32935357 PMCID: PMC7604573 DOI: 10.15252/embj.2020104858] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 11/09/2022] Open
Abstract
During meiosis, DNA double-strand breaks undergo interhomolog repair to yield crossovers between homologous chromosomes. To investigate how interhomolog sequence polymorphism affects crossovers, we sequenced multiple recombinant populations of the model plant Arabidopsis thaliana. Crossovers were elevated in the diverse pericentromeric regions, showing a local preference for polymorphic regions. We provide evidence that crossover association with elevated diversity is mediated via the Class I crossover formation pathway, although very high levels of diversity suppress crossovers. Interhomolog polymorphism causes mismatches in recombining molecules, which can be detected by MutS homolog (MSH) mismatch repair protein heterodimers. Therefore, we mapped crossovers in a msh2 mutant, defective in mismatch recognition, using multiple hybrid backgrounds. Although total crossover numbers were unchanged in msh2 mutants, recombination was remodelled from the diverse pericentromeres towards the less-polymorphic sub-telomeric regions. Juxtaposition of megabase heterozygous and homozygous regions causes crossover remodelling towards the heterozygous regions in wild type Arabidopsis, but not in msh2 mutants. Immunostaining showed that MSH2 protein accumulates on meiotic chromosomes during prophase I, consistent with MSH2 regulating meiotic recombination. Our results reveal a pro-crossover role for MSH2 in regions of higher sequence diversity in A. thaliana.
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Affiliation(s)
| | - Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Stuart Desjardins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Nadia Kbiri
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | | | - Emma J Lawrence
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Tomasz Bieluszewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Beth Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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Homoeologous exchanges occur through intragenic recombination generating novel transcripts and proteins in wheat and other polyploids. Proc Natl Acad Sci U S A 2020; 117:14561-14571. [PMID: 32518116 DOI: 10.1073/pnas.2003505117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses. In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica, rice, Arabidopsis suecica, banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them. HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.
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37
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Qi X, Wu H, Jiang H, Zhu J, Huang C, Zhang X, Liu C, Cheng B. Conversion of a normal maize hybrid into a waxy version using in vivo CRISPR/Cas9 targeted mutation activity. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2020.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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38
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Norrell AE, Jones KL, Saillant EA. Development and characterization of genomic resources for a non-model marine teleost, the red snapper (Lutjanus campechanus, Lutjanidae): Construction of a high-density linkage map, anchoring of genome contigs and comparative genomic analysis. PLoS One 2020; 15:e0232402. [PMID: 32348345 PMCID: PMC7190162 DOI: 10.1371/journal.pone.0232402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/15/2020] [Indexed: 11/19/2022] Open
Abstract
The red snapper Lutjanus campechanus is an exploited reef fish of major economic importance in the Gulf of Mexico region. Studies of genome wide genetic variation are needed to understand the structure of wild populations and develop breeding programs for aquaculture but interpretation of these genome scans is limited by the absence of reference genome. In this work, the first draft of a reference genome was developed and characterized for the red snapper. P-454 and Illumina sequencing were conducted to produce paired-end reads that were assembled into reference contigs and scaffolds. The current assembly spans over 770 Mb, representing an estimated 69% of the red snapper genome in 67,254 scaffolds (N50 = 16,803 bp). The genome contigs were applied to map double digest Restriction-Site Associated DNA Tags and characterize Single Nucleotide Polymorphisms (SNPs) in five outbred full-sib families. The identified SNPs and 97 microsatellite loci were used to generate a high-density linkage map that includes 7,420 markers distributed across 24 linkage groups and spans 1,346.64 cM with an average inter–marker distance of 0.18 cM. Sex-specific maps revealed a 1.10:1 female to male map length ratio. A total of 4,422 genome contigs (10.5% of the assembly) were anchored to the map and used in a comparative genomic analysis of the red snapper and two model teleosts. Red snapper showed a high degree of chromosome level syntenic conservation with both medaka and spotted green puffer and a near one to one correspondence between the 24 red snapper linkage groups and corresponding medaka chromosomes was observed. This work established the first draft of a reference genome for a lutjanid fish. The obtained genomic resources will serve as a framework for the interpretation of genome scans during studies of wild populations and captive breeding programs.
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Affiliation(s)
- Adrienne E. Norrell
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, United States of America
| | - Kenneth L. Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Eric A. Saillant
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, United States of America
- * E-mail:
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39
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Dawe RK. Charting the path to fully synthetic plant chromosomes. Exp Cell Res 2020; 390:111951. [PMID: 32151492 DOI: 10.1016/j.yexcr.2020.111951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
The concepts of synthetic biology have the potential to transform plant genetics, both in how we analyze genetic pathways and how we transfer that knowledge into useful applications. While synthetic biology can be applied at the level of the single gene or small groups of genes, this commentary focuses on the ultimate challenge of designing fully synthetic plant chromosomes. Engineering at this scale will allow us to manipulate whole genome architecture and to modify multiple pathways and traits simultaneously. Advances in genome synthesis make it likely that the initial phases of plant chromosome construction will occur in bacteria and yeast. Here I discuss the next steps, including specific ways of overcoming technical barriers associated with plant transformation, functional centromere design, and ensuring accurate meiotic transmission.
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Affiliation(s)
- R Kelly Dawe
- Department of Genetics and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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40
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Liu HJ, Wang X, Xiao Y, Luo J, Qiao F, Yang W, Zhang R, Meng Y, Sun J, Yan S, Peng Y, Niu L, Jian L, Song W, Yan J, Li C, Zhao Y, Liu Y, Warburton ML, Zhao J, Yan J. CUBIC: an atlas of genetic architecture promises directed maize improvement. Genome Biol 2020; 21:20. [PMID: 31980033 PMCID: PMC6979394 DOI: 10.1186/s13059-020-1930-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/08/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we present the Complete-diallel design plus Unbalanced Breeding-like Inter-Cross (CUBIC) population, consisting of 1404 individuals created by extensively inter-crossing 24 widely used Chinese maize founders. RESULTS Hundreds of QTL for 23 agronomic traits are uncovered with 14 million high-quality SNPs and a high-resolution identity-by-descent map, which account for an average of 75% of the heritability for each trait. We find epistasis contributes to phenotypic variance widely. Integrative cross-population analysis and cross-omics mapping allow effective and rapid discovery of underlying genes, validated here with a case study on leaf width. CONCLUSIONS Through the integration of experimental genetics and genomics, our study provides useful resources and gene mining strategies to explore complex quantitative traits.
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Affiliation(s)
- Hai-Jun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaqing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100097, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Qiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Sanming Academy of Agricultural Sciences, Sanming, 365509, Fujian, China
| | - Wenyu Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruyang Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100097, China
| | - Yijiang Meng
- College of Life Science, Hebei Agricultural University, Baoding, 071001, China
| | - Jiamin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou, 510640, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Luyao Niu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100097, China
| | - Jiali Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunhui Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100097, China
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100097, China
| | - Ya Liu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100097, China
| | - Marilyn L Warburton
- Corn Host Plant Resistance Research Unit, United States Department of Agriculture-Agricultural Research Service, Box 9555, Mississippi State, MS, 39762, USA
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100097, China.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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41
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Nkhoma SC, Trevino SG, Gorena KM, Nair S, Khoswe S, Jett C, Garcia R, Daniel B, Dia A, Terlouw DJ, Ward SA, Anderson TJC, Cheeseman IH. Co-transmission of Related Malaria Parasite Lineages Shapes Within-Host Parasite Diversity. Cell Host Microbe 2020; 27:93-103.e4. [PMID: 31901523 PMCID: PMC7159252 DOI: 10.1016/j.chom.2019.12.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 10/17/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022]
Abstract
In high-transmission regions, we expect parasite lineages within complex malaria infections to be unrelated due to parasite inoculations from different mosquitoes. This project was designed to test this prediction. We generated 485 single-cell genome sequences from fifteen P. falciparum malaria patients from Chikhwawa, Malawi-an area of intense transmission. Patients harbored up to seventeen unique parasite lineages. Surprisingly, parasite lineages within infections tend to be closely related, suggesting that superinfection by repeated mosquito bites is rarer than co-transmission of parasites from a single mosquito. Both closely and distantly related parasites comprise an infection, suggesting sequential transmission of complex infections between multiple hosts. We identified tetrads and reconstructed parental haplotypes, which revealed the inbred ancestry of infections and non-Mendelian inheritance. Our analysis suggests strong barriers to secondary infection and outbreeding amongst malaria parasites from a high transmission setting, providing unexpected insights into the biology and transmission of malaria.
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Affiliation(s)
- Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Liverpool School of Tropical Medicine, Liverpool, UK; Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK; Texas Biomedical Research Institute, San Antonio, TX, USA.
| | | | - Karla M Gorena
- University of Texas Health Science Center San Antonio, San Antonio, TX, USA
| | - Shalini Nair
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Stanley Khoswe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Catherine Jett
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Roy Garcia
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Benjamin Daniel
- University of Texas Health Science Center San Antonio, San Antonio, TX, USA
| | - Aliou Dia
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Dianne J Terlouw
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Liverpool School of Tropical Medicine, Liverpool, UK
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42
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Lambing C, Choi K, Blackwell AR, Henderson IR. Chromatin Immunoprecipitation of Meiotically Expressed Proteins from Arabidopsis thaliana Flowers. Methods Mol Biol 2020; 2061:219-236. [PMID: 31583663 DOI: 10.1007/978-1-4939-9818-0_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
During meiosis recombination occurs between homologous chromosomes which can result in reciprocal exchanges of genetic information, called crossovers. Crossover rate is heterogeneous within the genome, with local regions having a significantly higher recombination rate relative to the genome average. These regions are termed hotspots and typically occur with widths of kilobases. Therefore, there is a need to profile recombination factors at a similar resolution during meiosis via techniques such as chromatin immunoprecipitation (ChIP). Here we describe a ChIP protocol, combined with high throughput sequencing (ChIP-seq) optimised for analysis of meiotically expressed proteins in Arabidopsis thaliana flowers. We provide methods to (1) isolate nuclei and prepare the chromatin for shearing, (2) immunoprecipitate DNA molecules cross-linked to a protein of interest, (3) to size-select and purify immunoprecipitated DNA molecules, and (4) to prepare DNA sequencing libraries suitable for high-throughput sequencing. Together, these methods allow the detection of binding sites for meiotic proteins in the Arabidopsis genome at high resolution, which will provide insights into relationships between meiotic chromosome organization, chromatin and recombination.
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Affiliation(s)
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.,Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | | | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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43
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Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R. Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. THE NEW PHYTOLOGIST 2020; 225:511-529. [PMID: 31418861 DOI: 10.1111/nph.16122] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/06/2019] [Indexed: 05/21/2023]
Abstract
Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning important traits is of great importance. MADS-box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC-type MADS-box genes. Homoeolog retention is significantly above the average genome-wide retention rate for wheat genes, indicating that many MIKC-type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily-specific expression pattern, indicating broad conservation of function of MIKC-type genes during wheat evolution. We also found extensive expansion of some MIKC-type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC-type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC-type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Alice Kennedy
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sirui Pan
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Lars S Jermiin
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
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44
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Wang H, Gao Y, Mao F, Xiong L, Mou T. Directional upgrading of brown planthopper resistance in an elite rice cultivar by precise introgression of two resistance genes using genomics-based breeding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110211. [PMID: 31521227 DOI: 10.1016/j.plantsci.2019.110211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 05/23/2023]
Abstract
Brown planthopper (BPH) is a devastating pest that threatens the food security of rice-producing countries. At present, most cultivars planted in farmers' paddies lack effective BPH resistance, which constitutes a potential threat to rice yield. Moreover, developing BPH-resistant rice varieties using traditional breeding approaches is time-consuming, labor-intensive, and unpredictable. In this study, we successfully enhanced BPH resistance of the elite rice cultivar Wushansimiao by introgressing the resistance genes BPH14 and BPH15 through positive selection, negative selection, and whole genome background selection. Through backcrossing, the introgression fragments were reduced to 428.3 kb for BPH14 and 413.1 kb for BPH15. Except for these two fragments, the residual genetic background of the selected near-isogenic lines (NILs) was nearly identical to that of the recurrent parent, with a genetic background recovery rate of 99.78%. As a result, the selected NILs exhibited much stronger BPH resistance at the seedling and adult stages compared to the recurrent parent. Moreover, field tests showed that grain yield, major agronomic traits, and grain quality of the five selected NILs were statistically indistinguishable from those of the recurrent parent. Our results provide an effective approach for directionally upgrading the target traits and will inform and facilitate rice breeding.
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Affiliation(s)
- Hongbo Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Gao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Fangming Mao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Tongmin Mou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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45
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Shi D, Wu J, Tang H, Yin H, Wang H, Wang R, Wang R, Qian M, Wu J, Qi K, Xie Z, Wang Z, Zhao X, Zhang S. Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants. Genome Res 2019; 29:1889-1899. [PMID: 31649061 PMCID: PMC6836740 DOI: 10.1101/gr.251033.119] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/01/2019] [Indexed: 11/30/2022]
Abstract
Genome assemblies from diploid organisms create mosaic sequences alternating between parental alleles, which can create erroneous gene models and other problems. In animals, a popular strategy to generate haploid genome-resolved assemblies has been the sampling of (haploid) gametes, and the advent of single-cell sequencing has further advanced such methods. However, several challenges for the isolation and amplification of DNA from plant gametes have limited such approaches in plants. Here, we combined a new approach for pollen protoplast isolation with a single-cell DNA amplification technique and then used a “barcoding” bioinformatics strategy to incorporate haploid-specific sequence data from 12 pollen cells, ultimately enabling the efficient and accurate phasing of the pear genome into its A and B haploid genomes. Beyond revealing that 8.12% of the genes in the pear reference genome feature mosaic assemblies and enabling a previously impossible analysis of allelic affects in pear gene expression, our new haploid genome assemblies provide high-resolution information about recombination during meiosis in pollen. Considering that outcrossing pear is an angiosperm species featuring very high heterozygosity, our method for rapidly phasing genome assemblies is potentially applicable to several yet-unsequenced outcrossing angiosperm species in nature.
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Affiliation(s)
- Dongqing Shi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Hao Yin
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongtao Wang
- School of Life Science, Henan University, Kaifeng 475004, China
| | - Ran Wang
- College of Agriculture, Qingdao Agricultural University, Qingdao 266109, China
| | - Runze Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Qian
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Juyou Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaijie Qi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihua Xie
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | | | | | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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46
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Quantification of Recombination Rate and Segregation Distortion by Genotyping and Sequencing of Single Pollen Nuclei. Methods Mol Biol 2019. [PMID: 31583667 DOI: 10.1007/978-1-4939-9818-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Meiosis is a specialized cell division during which homologous chromosomes can exchange genetic material through recombination. This mechanism generates novel allelic combinations, which can be exploited by plant breeders to achieve crop improvement. Pollen grains are the haploid products of meiosis required in fertilization. Here, we describe two approaches to measure meiotic recombination in single haploid pollen nuclei. Pollen nuclei are first separated by fluorescence-activated cell-sorting. Afterwards, the DNA of single pollen nuclei can be amplified by multiple-displacement-amplification using Phi29 DNA polymerase and meiotic recombination events can be measured using KASP markers. Alternatively, the PicoPLEX DNA-seq kit can be used to amplify the DNA of single pollen nuclei followed by library preparation for whole-genome sequencing and subsequent bioinformatic analysis.
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Wang C, Wang C, Zou J, Yang Y, Li Z, Zhu S. Epigenetics in the plant-virus interaction. PLANT CELL REPORTS 2019; 38:1031-1038. [PMID: 31065780 DOI: 10.1007/s00299-019-02414-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 04/25/2019] [Indexed: 05/23/2023]
Abstract
Plants have developed diverse molecular mechanisms to resist viruses. RNA silencing plays a dominant role in antiviral defense. Recent studies have correlated plant antiviral silencing to epigenetic modification in genomic DNA and protein by remodeling the expression levels of coding genes. The plant host methylation level is reprogrammed in response to viral challenge. Genomes of some viruses have been implicated in the epigenetic modification via small RNA-mediated transcriptional gene silencing and post-transcriptional gene silencing. These mechanisms can be primed prior to a virus attack through methylation changes for antiviral defense. This review highlights the findings concerning the methylation changes in plant-virus interactions and demonstrates a possible direction to improve the understanding of plant host methylation regulation in response to viral infection.
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Affiliation(s)
- Chenguang Wang
- College of Plant Protection, China Agricultural University, Beijing, 100083, China
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Chaonan Wang
- College of Plant Protection, China Agricultural University, Beijing, 100083, China
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Jingze Zou
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Yunshu Yang
- Beijing Academy of Food Sciences, Beijing, 100162, China
| | - Zhihong Li
- College of Plant Protection, China Agricultural University, Beijing, 100083, China
| | - Shuifang Zhu
- College of Plant Protection, China Agricultural University, Beijing, 100083, China.
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
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Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination. Chromosoma 2019; 128:279-296. [PMID: 31332531 DOI: 10.1007/s00412-019-00718-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 02/01/2023]
Abstract
During meiosis, DNA double-strand breaks are initiated by the topoisomerase-like enzyme SPO11 and are repaired by inter-sister chromatid and inter-homologue DNA repair pathways. Genome-wide maps of initiating DNA double-strand breaks and inter-homologue repair events are now available for a number of mammalian, fungal and plant species. In mammals, PRDM9 specifies the location of meiotic recombination initiation via recognition of specific DNA sequence motifs by its C2H2 zinc finger array. In fungi and plants, meiotic recombination appears to be initiated less discriminately in accessible chromatin, including at gene promoters. Generally, meiotic crossover is suppressed in highly repetitive genomic regions that are made up of transposable elements (TEs), to prevent deleterious non-allelic homologous recombination events. However, recent and older studies have revealed intriguing relationships between meiotic recombination initiation and repair, and transposable elements. For instance, gene conversion events have been detected in maize centromeric retroelements, mouse MULE-MuDR DNA transposons undergo substantial meiotic recombination initiation, Arabidopsis Helitron TEs are among the hottest of recombination initiation hotspots, and human TE sequences can modify the crossover rate at adjacent PRDM9 motifs in cis. Here, we summarize the relationship between meiotic recombination and TEs, discuss recent insights from highly divergent eukaryotes and highlight outstanding questions in the field.
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Quantifying the Power and Precision of QTL Analysis in Autopolyploids Under Bivalent and Multivalent Genetic Models. G3-GENES GENOMES GENETICS 2019; 9:2107-2122. [PMID: 31036677 PMCID: PMC6643892 DOI: 10.1534/g3.119.400269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
New genotyping technologies, offering the possibility of high genetic resolution at low cost, have helped fuel a surge in interest in the genetic analysis of polyploid species. Nevertheless, autopolyploid species present extra challenges not encountered in diploids and allopolyploids, such as polysomic inheritance or double reduction. Here we investigate the power and precision of quantitative trait locus (QTL) analysis in outcrossing autopolyploids, comparing the results of a model that assumes random bivalent chromosomal pairing during meiosis to one that also allows for multivalents and double reduction. Through a series of simulation studies we found that marginal gains in QTL detection power are achieved using the double reduction model when multivalent pairing occurs. However, when exploring the effect of variable genotypic information across parental homologs, we found that both QTL detection power and precision require high and uniform genotypic information contents. This effect far outweighed considerations regarding bivalent or multivalent pairing (and double reduction) during meiosis. We propose that autopolyploid QTL studies be accompanied by both marker coverage information and per-homolog genotypic information coefficients (GIC). Application of these methods to an autotetraploid potato (Solanum tuberosum L.) mapping population confirmed our ability to locate and dissect QTL in highly heterozygous outcrossing autotetraploid populations.
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Luo C, Li X, Zhang Q, Yan J. Single gametophyte sequencing reveals that crossover events differ between sexes in maize. Nat Commun 2019; 10:785. [PMID: 30770831 PMCID: PMC6377631 DOI: 10.1038/s41467-019-08786-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/24/2019] [Indexed: 11/24/2022] Open
Abstract
Meiotic crossover (CO) plays a key role in producing gametophytes and generating genetic variation. The patterns of CO production differ inter- and intra-species, as well as between sexes. However, sex-specific patterns of CO production have not been accurately profiled independently of genetic backgrounds in maize. Here, we develop a method to isolate single female gametophyte for genomes sequencing in maize. We show that more COs are observed in male (19.3 per microspore) than in female (12.4 per embryo sac). Based on Beam-Film model, the more designated class I and II COs are identified in male than in female. In addition, CO maturation inefficiency (CMI) is detected in some genetic backgrounds, suggesting that maize may be an ideal model for dissecting CMI. This research provides insights toward understanding the molecular mechanism of CO production between sexes and may help to improve maize breeding efficiency through paternal selection.
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Affiliation(s)
- Cheng Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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