1
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Wang C, Chen Z, Copenhaver GP, Wang Y. Heterochromatin in plant meiosis. Nucleus 2024; 15:2328719. [PMID: 38488152 PMCID: PMC10950279 DOI: 10.1080/19491034.2024.2328719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/05/2024] [Indexed: 03/19/2024] Open
Abstract
Heterochromatin is an organizational property of eukaryotic chromosomes, characterized by extensive DNA and histone modifications, that is associated with the silencing of transposable elements and repetitive sequences. Maintaining heterochromatin is crucial for ensuring genomic integrity and stability during the cell cycle. During meiosis, heterochromatin is important for homologous chromosome synapsis, recombination, and segregation, but our understanding of meiotic heterochromatin formation and condensation is limited. In this review, we focus on the dynamics and features of heterochromatin and how it condenses during meiosis in plants. We also discuss how meiotic heterochromatin influences the interaction and recombination of homologous chromosomes during prophase I.
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Affiliation(s)
- Cong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zhiyu Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - 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, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Yingxiang Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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2
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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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3
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Busoms S, Pérez-Martín L, Terés J, Huang XY, Yant L, Tolrà R, Salt DE, Poschenrieder C. Combined genomics to discover genes associated with tolerance to soil carbonate. PLANT, CELL & ENVIRONMENT 2023; 46:3986-3998. [PMID: 37565316 DOI: 10.1111/pce.14691] [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: 01/05/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Carbonate-rich soils limit plant performance and crop production. Previously, local adaptation to carbonated soils was detected in wild Arabidopsis thaliana accessions, allowing the selection of two demes with contrasting phenotypes: A1 (carbonate tolerant, c+) and T6 (carbonate sensitive, c-). Here, A1(c+) and T6(c - ) seedlings were grown hydroponically under control (pH 5.9) and bicarbonate conditions (10 mM NaHCO3 , pH 8.3) to obtain ionomic profiles and conduct transcriptomic analysis. In parallel, A1(c+) and T6(c - ) parental lines and their progeny were cultivated on carbonated soil to evaluate fitness and segregation patterns. To understand the genetic architecture beyond the contrasted phenotypes, a bulk segregant analysis sequencing (BSA-Seq) was performed. Transcriptomics revealed 208 root and 2503 leaf differentially expressed genes in A1(c+) versus T6(c - ) comparison under bicarbonate stress, mainly involved in iron, nitrogen and carbon metabolism, hormones and glycosylates biosynthesis. Based on A1(c+) and T6(c - ) genome contrasts and BSA-Seq analysis, 69 genes were associated with carbonate tolerance. Comparative analysis of genomics and transcriptomics discovered a final set of 18 genes involved in bicarbonate stress responses that may have relevant roles in soil carbonate tolerance.
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Affiliation(s)
- Silvia Busoms
- Department of Animal Biology, Plant Biology, and Ecology, Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Pérez-Martín
- Department of Animal Biology, Plant Biology, and Ecology, Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joana Terés
- Department of Animal Biology, Plant Biology, and Ecology, Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Levi Yant
- Future Food Beacon of Excellence & School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Roser Tolrà
- Department of Animal Biology, Plant Biology, and Ecology, Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton, UK
| | - Charlotte Poschenrieder
- Department of Animal Biology, Plant Biology, and Ecology, Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
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4
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Tavares H, Readshaw A, Kania U, de Jong M, Pasam RK, McCulloch H, Ward S, Shenhav L, Forsyth E, Leyser O. Artificial selection reveals complex genetic architecture of shoot branching and its response to nitrate supply in Arabidopsis. PLoS Genet 2023; 19:e1010863. [PMID: 37616321 PMCID: PMC10482290 DOI: 10.1371/journal.pgen.1010863] [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: 06/18/2022] [Revised: 09/06/2023] [Accepted: 07/08/2023] [Indexed: 08/26/2023] Open
Abstract
Quantitative traits may be controlled by many loci, many alleles at each locus, and subject to genotype-by-environment interactions, making them difficult to map. One example of such a complex trait is shoot branching in the model plant Arabidopsis, and its plasticity in response to nitrate. Here, we use artificial selection under contrasting nitrate supplies to dissect the genetic architecture of this complex trait, where loci identified by association mapping failed to explain heritability estimates. We found a consistent response to selection for high branching, with correlated responses in other traits such as plasticity and flowering time. Genome-wide scans for selection and simulations suggest that at least tens of loci control this trait, with a distinct genetic architecture between low and high nitrate treatments. While signals of selection could be detected in the populations selected for high branching on low nitrate, there was very little overlap in the regions selected in three independent populations. Thus the regulatory network controlling shoot branching can be tuned in different ways to give similar phenotypes.
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Affiliation(s)
- Hugo Tavares
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Anne Readshaw
- Department of Biology, University of York, York, United Kingdom
| | - Urszula Kania
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Maaike de Jong
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Raj K. Pasam
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Hayley McCulloch
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Sally Ward
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Liron Shenhav
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth Forsyth
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ottoline Leyser
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of York, York, United Kingdom
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5
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Schoen DJ, Baldwin SJ. Self-incompatibility and the genetic architecture of inbreeding depression. THE NEW PHYTOLOGIST 2023; 237:1040-1049. [PMID: 36263709 DOI: 10.1111/nph.18550] [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: 08/07/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Inbreeding depression plays a fundamental role in evolution. To help detect and characterize the loci that underlie inbreeding depression, we used bud pollination and salt treatments to circumvent self-incompatibility (SI) in plants from populations of Leavenworthia alabamica and produced families of progeny that were then genotyped at genetically mapped single-nucleotide polymorphism (SNP) loci. Using Bayesian inference, the segregation patterns for each SNP were used to explore support for different dominance and selection coefficients at linked viability loci in different genomic regions. There was support for several partially recessive viability loci in one of the populations, and one such locus mapped to the genomic region of the novel SI locus in L. alabamica. These results are consistent with earlier findings that showed purging of inbreeding depression for germination rate in L. alabamica. They are also consistent with expectations from evolutionary genetic theory that recessive, deleterious alleles linked to loci under balancing selection can be sheltered from selection.
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Affiliation(s)
- Daniel J Schoen
- Department of Biology, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Sarah J Baldwin
- Department of Biology, McGill University, Montreal, QC, H3A 1B1, Canada
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6
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Liu K, Chen E, Gu Z, Dai B, Wang A, Zhu Z, Feng Q, Zhou C, Zhu J, Shangguan Y, Wang Y, Li Z, Hou Q, Lv D, Wang C, Huang T, Wang Z, Huang X, Han B. A retrotransposon insertion in MUTL-HOMOLOG 1 affects wild rice seed set and cultivated rice crossover rate. PLANT PHYSIOLOGY 2022; 190:1747-1762. [PMID: 35976143 PMCID: PMC9614510 DOI: 10.1093/plphys/kiac378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/12/2022] [Indexed: 06/06/2023]
Abstract
Wild rice (Oryza rufipogon) has a lower panicle seed setting rate (PSSR) and gamete fertility than domesticated rice (Oryza sativa), but the genetic mechanisms of this phenomenon remain unknown. Here, we cloned a null allele of OsMLH1, an ortholog of MutL-homolog 1 to yeast and mammals, from wild rice O. rufipogon W1943 and revealed a 5.4-kb retrotransposon insertion in OsMLH1 is responsible for the low PSSR in wild rice. In contrast to the wild-type, a near isogenic line NIL-mlh1 exhibits defective crossover (CO) formation during meiosis, resulting in reduced pollen viability, partial embryo lethality, and low PSSR. Except for the mutant of mismatch repair gene postmeiotic segregation 1 (Ospms1), all other MutL mutants from O. sativa indica subspecies displayed male and female semi-sterility similar to NIL-mlh1, but less severe than those from O. sativa japonica subspecies. MLH1 and MLH3 did not contribute in an additive fashion to fertility. Two types of MutL heterodimers, MLH1-PMS1 and MLH1-MLH3, were identified in rice, but only the latter functions in promoting meiotic CO formation. Compared to japonica varieties, indica cultivars had greater numbers of CO events per meiosis. Our results suggest that low fertility in wild rice may be caused by different gene defects, and indica and japonica subspecies have substantially different CO rates responsible for the discrepancy between the fertility of mlh1 and mlh3 mutants.
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Affiliation(s)
- Kun Liu
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Erwang Chen
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Zhoulin Gu
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Bingxin Dai
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Ahong Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Zhou Zhu
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qi Feng
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Congcong Zhou
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Jingjie Zhu
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Yingying Shangguan
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Yongchun Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Zhen Li
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qingqing Hou
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Danfeng Lv
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Changsheng Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Tao Huang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Zixuan Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
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7
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Poethig RS, Cullina WL, Doody E, Floyd T, Fouracre JP, Hu T, Xu M, Zhao J. Short-interval traffic lines: versatile tools for genetic analysis in Arabidopsis thaliana. G3 (BETHESDA, MD.) 2022; 12:6677228. [PMID: 36018241 PMCID: PMC9526051 DOI: 10.1093/g3journal/jkac202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/17/2022] [Indexed: 12/30/2022]
Abstract
Traffic lines are transgenic stocks of Arabidopsis thaliana that contain a pair of linked seed-specific eGFP and DsRed markers. These stocks were originally developed for the purpose of studying recombination, but can also be used to follow the inheritance of unmarked chromosomes placed in trans to the marked chromosome. They are particularly useful for this latter purpose if the distance between markers is short, making double recombination within this interval relatively rare. We generated 163 traffic lines that cover the Arabidopsis genome in overlapping intervals of approximately 1.2 Mb (6.9 cM). These stocks make it possible to predict the genotype of a plant based on its seed fluorescence (or lack thereof) and facilitate many experiments in genetic analysis that are difficult, tedious, or expensive to perform using current techniques. Here, we show how these lines enable a phenotypic analysis of alleles with weak or variable phenotypes, genetic mapping of novel mutations, introducing transgenes into a lethal or sterile genetic background, and separating closely linked mutations.
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Affiliation(s)
- R Scott Poethig
- Corresponding author: Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA.
| | - William L Cullina
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Erin Doody
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Taré Floyd
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | | | - Tieqiang Hu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Mingli Xu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA,Department of Biological Sciences, University of South Carolina, Charlottesville, SC 29208, USA
| | - Jianfei Zhao
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
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8
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Martínez-Fortún J, Phillips DW, Jones HD. Natural and artificial sources of genetic variation used in crop breeding: A baseline comparator for genome editing. Front Genome Ed 2022; 4:937853. [PMID: 36072906 PMCID: PMC9441798 DOI: 10.3389/fgeed.2022.937853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Traditional breeding has successfully selected beneficial traits for food, feed, and fibre crops over the last several thousand years. The last century has seen significant technological advancements particularly in marker assisted selection and the generation of induced genetic variation, including over the last few decades, through mutation breeding, genetic modification, and genome editing. While regulatory frameworks for traditional varietal development and for genetic modification with transgenes are broadly established, those for genome editing are lacking or are still evolving in many regions. In particular, the lack of “foreign” recombinant DNA in genome edited plants and that the resulting SNPs or INDELs are indistinguishable from those seen in traditional breeding has challenged development of new legislation. Where products of genome editing and other novel breeding technologies possess no transgenes and could have been generated via traditional methods, we argue that it is logical and proportionate to apply equivalent legislative oversight that already exists for traditional breeding and novel foods. This review analyses the types and the scale of spontaneous and induced genetic variation that can be selected during traditional plant breeding activities. It provides a base line from which to judge whether genetic changes brought about by techniques of genome editing or other reverse genetic methods are indeed comparable to those routinely found using traditional methods of plant breeding.
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9
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Schreiber M, Chen YY, Ramsay L, Waugh R. Measuring the frequency and distribution of meiotic crossovers in homozygous barley inbred lines. FRONTIERS IN PLANT SCIENCE 2022; 13:965217. [PMID: 36035701 PMCID: PMC9403744 DOI: 10.3389/fpls.2022.965217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
We report a novel approach for establishing the number and position of CO events in individual homozygous inbred plants by combining low level EMS mutagenesis, speed breeding, whole genome shotgun sequencing and sliding window analysis of the induced molecular variant data. We demonstrate the approach by exploring CO frequency and distribution in self-fertilised progeny of the inbred barley cultivar Bowman and compare these observations to similar data obtained from a Bowman nearly isogenic line (BW230 Hvmlh3) containing a mutation in the DNA mismatch repair gene HvMLH3. We have previously shown that Hvmlh3 decreases both plant fertility and recombination by ~50%. We compare our results to those from previously published traditional genetic analysis of F3 families derived from multiple F2 lines containing WT or mutant alleles of HvMLH3, revealing a high level of correspondence between analyses. We discuss possible applications of the approach in streamlining the assessment of recombination in plant meiosis research.
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Affiliation(s)
- Miriam Schreiber
- Informational and Computational Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Yun-Yu Chen
- Cell and Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Luke Ramsay
- Cell and Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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10
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Yelina NE, Holland D, Gonzalez-Jorge S, Hirsz D, Yang Z, Henderson IR. Coexpression of MEIOTIC-TOPOISOMERASE VIB-dCas9 with guide RNAs specific to a recombination hotspot is insufficient to increase crossover frequency in Arabidopsis. G3 (BETHESDA, MD.) 2022; 12:jkac105. [PMID: 35485960 PMCID: PMC9258527 DOI: 10.1093/g3journal/jkac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 11/14/2022]
Abstract
During meiosis, homologous chromosomes pair and recombine, which can result in reciprocal crossovers that increase genetic diversity. Crossovers are unevenly distributed along eukaryote chromosomes and show repression in heterochromatin and the centromeres. Within the chromosome arms, crossovers are often concentrated in hotspots, which are typically in the kilobase range. The uneven distribution of crossovers along chromosomes, together with their low number per meiosis, creates a limitation during crop breeding, where recombination can be beneficial. Therefore, targeting crossovers to specific genome locations has the potential to accelerate crop improvement. In plants, meiotic crossovers are initiated by DNA double-strand breaks that are catalyzed by SPO11 complexes, which consist of 2 catalytic (SPO11-1 and SPO11-2) and 2 noncatalytic subunits (MTOPVIB). We used the model plant Arabidopsis thaliana to coexpress an MTOPVIB-dCas9 fusion protein with guide RNAs specific to the 3a crossover hotspot. We observed that this was insufficient to significantly change meiotic crossover frequency or pattern within 3a. We discuss the implications of our findings for targeting meiotic recombination within plant genomes.
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Affiliation(s)
- Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
- Department of Plant Sciences, Crop Science Centre, University of Cambridge, Cambridge CB3 0LE, UK
| | - Daniel Holland
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Dominique Hirsz
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Ziyi Yang
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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11
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Simon M, Durand S, Ricou A, Vrielynck N, Mayjonade B, Gouzy J, Boyer R, Roux F, Camilleri C, Budar F. APOK3, a pollen killer antidote in Arabidopsis thaliana. Genetics 2022; 221:6603116. [PMID: 35666201 DOI: 10.1093/genetics/iyac089] [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: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 11/14/2022] Open
Abstract
The principles of heredity state that the two alleles carried by a heterozygote are equally transmitted to the progeny. However, genomic regions that escape this rule have been reported in many organisms. It is notably the case of genetic loci referred to as gamete killers, where one allele enhances its transmission by causing the death of the gametes that do not carry it. Gamete killers are of great interest, particularly to understand mechanisms of evolution and speciation. Although being common in plants, only a few, all in rice, have so far been deciphered to the causal genes. Here, we studied a pollen killer found in hybrids between two accessions of Arabidopsis thaliana. Exploring natural variation, we observed this pollen killer in many crosses within the species. Genetic analyses revealed that three genetically linked elements are necessary for pollen killer activity. Using mutants, we showed that this pollen killer works according to a poison-antidote model, where the poison kills pollen grains not producing the antidote. We identified the gene encoding the antidote, a chimeric protein addressed to mitochondria. De novo genomic sequencing in twelve natural variants with different behaviors regarding the pollen killer revealed a hyper variable locus, with important structural variations particularly in killer genotypes, where the antidote gene recently underwent duplications. Our results strongly suggest that the gene has newly evolved within A. thaliana. Finally, we identified in the protein sequence polymorphisms related to its antidote activity.
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Affiliation(s)
- Matthieu Simon
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Stéphanie Durand
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Anthony Ricou
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Nathalie Vrielynck
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | | | - Jérôme Gouzy
- LIPME,Université de Toulouse,INRAE,CNRS, 31326 Castanet-Tolosan, France
| | - Roxane Boyer
- INRAE, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France(doi : 10.15454/1.5572370921303193E12)
| | - Fabrice Roux
- LIPME,Université de Toulouse,INRAE,CNRS, 31326 Castanet-Tolosan, France
| | - Christine Camilleri
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Françoise Budar
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
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12
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Kim H, Choi K. Fast and Precise: How to Measure Meiotic Crossovers in Arabidopsis. Mol Cells 2022; 45:273-283. [PMID: 35444069 PMCID: PMC9095510 DOI: 10.14348/molcells.2022.2054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/21/2022] [Accepted: 03/04/2022] [Indexed: 11/27/2022] Open
Abstract
During meiosis, homologous chromosomes (homologs) pair and undergo genetic recombination via assembly and disassembly of the synaptonemal complex. Meiotic recombination is initiated by excess formation of DNA double-strand breaks (DSBs), among which a subset are repaired by reciprocal genetic exchange, called crossovers (COs). COs generate genetic variations across generations, profoundly affecting genetic diversity and breeding. At least one CO between homologs is essential for the first meiotic chromosome segregation, but generally only one and fewer than three inter-homolog COs occur in plants. CO frequency and distribution are biased along chromosomes, suppressed in centromeres, and controlled by pro-CO, anti-CO, and epigenetic factors. Accurate and high-throughput detection of COs is important for our understanding of CO formation and chromosome behavior. Here, we review advanced approaches that enable precise measurement of the location, frequency, and genomic landscapes of COs in plants, with a focus on Arabidopsis thaliana.
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Affiliation(s)
- Heejin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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13
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Tergemina E, Elfarargi AF, Flis P, Fulgione A, Göktay M, Neto C, Scholle M, Flood PJ, Xerri SA, Zicola J, Döring N, Dinis H, Krämer U, Salt DE, Hancock AM. A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment. SCIENCE ADVANCES 2022; 8:eabm9385. [PMID: 35584228 PMCID: PMC9116884 DOI: 10.1126/sciadv.abm9385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Most well-characterized cases of adaptation involve single genetic loci. Theory suggests that multilocus adaptive walks should be common, but these are challenging to identify in natural populations. Here, we combine trait mapping with population genetic modeling to show that a two-step process rewired nutrient homeostasis in a population of Arabidopsis as it colonized the base of an active stratovolcano characterized by extremely low soil manganese (Mn). First, a variant that disrupted the primary iron (Fe) uptake transporter gene (IRT1) swept quickly to fixation in a hard selective sweep, increasing Mn but limiting Fe in the leaves. Second, multiple independent tandem duplications occurred at NRAMP1 and together rose to near fixation in the island population, compensating the loss of IRT1 by improving Fe homeostasis. This study provides a clear case of a multilocus adaptive walk and reveals how genetic variants reshaped a phenotype and spread over space and time.
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Affiliation(s)
- Emmanuel Tergemina
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ahmed F. Elfarargi
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Paulina Flis
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough, LE12 5RD Nottingham, UK
| | - Andrea Fulgione
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Mehmet Göktay
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Célia Neto
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Marleen Scholle
- Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Pádraic J. Flood
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Sophie-Asako Xerri
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Johan Zicola
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Nina Döring
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Herculano Dinis
- Parque Natural do Fogo, Direção Nacional do Ambiente, 115 Chã d’Areia, Praia, Santiago, Cabo Verde, Africa
- Associação Projecto Vitó, 8234, Xaguate, Cidade de São Filipe, Fogo, Cabo Verde, Africa
| | - Ute Krämer
- Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - David E. Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough, LE12 5RD Nottingham, UK
| | - Angela M. Hancock
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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14
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Casale F, Van Inghelandt D, Weisweiler M, Li J, Stich B. Genomic prediction of the recombination rate variation in barley - A route to highly recombinogenic genotypes. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:676-690. [PMID: 34783155 PMCID: PMC8989500 DOI: 10.1111/pbi.13746] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/06/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Meiotic recombination is not only fundamental to the adaptation of sexually reproducing eukaryotes in nature but increased recombination rates facilitate the combination of favourable alleles into a single haplotype in breeding programmes. The main objectives of this study were to (i) assess the extent and distribution of the recombination rate variation in cultivated barley (Hordeum vulgare L.), (ii) quantify the importance of the general and specific recombination effects, and (iii) evaluate a genomic selection approach's ability to predict the recombination rate variation. Genetic maps were created for the 45 segregating populations that were derived from crosses among 23 spring barley inbreds with origins across the world. The genome-wide recombination rate among populations ranged from 0.31 to 0.73 cM/Mbp. The crossing design used in this study allowed to separate the general recombination effects (GRE) of individual parental inbreds from the specific recombination effects (SRE) caused by the combinations of parental inbreds. The variance of the genome-wide GRE was found to be about eight times the variance of the SRE. This finding indicated that parental inbreds differ in the efficiency of their recombination machinery. The ability to predict the chromosome or genome-wide recombination rate of an inbred ranged from 0.80 to 0.85. These results suggest that a reliable screening of large genetic materials for their potential to cause a high extent of genetic recombination in their progeny is possible, allowing to systematically manipulate the recombination rate using natural variation.
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Affiliation(s)
- Federico Casale
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
| | - Delphine Van Inghelandt
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
| | - Marius Weisweiler
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
| | - Jinquan Li
- Max Planck Institute for Plant Breeding ResearchKölnGermany
- Strube D&S GmbHSöllingenGermany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
- Max Planck Institute for Plant Breeding ResearchKölnGermany
- Cluster of Excellence on Plant SciencesFrom Complex Traits Towards Synthetic ModulesDüsseldorfGermany
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15
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Dukić M, Bomblies K. Male and female recombination landscapes of diploid Arabidopsis arenosa. Genetics 2022; 220:6499271. [PMID: 35100396 PMCID: PMC8893250 DOI: 10.1093/genetics/iyab236] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022] Open
Abstract
Abstract
The number and placement of meiotic crossover events during meiosis have important implications for the fidelity of chromosome segregation as well as patterns of inheritance. Despite the functional importance of recombination, recombination landscapes vary widely among and within species, and this can have a strong impact on evolutionary processes. A good knowledge of recombination landscapes is important for model systems in evolutionary and ecological genetics, since it can improve interpretation of genomic patterns of differentiation and genome evolution, and provides an important starting point for understanding the causes and consequences of recombination rate variation. Arabidopsis arenosa is a powerful evolutionary genetic model for studying the molecular basis of adaptation and recombination rate evolution. Here, we generate genetic maps for 2 diploid A. arenosa individuals from distinct genetic lineages where we have prior knowledge that meiotic genes show evidence of selection. We complement the genetic maps with cytological approaches to map and quantify recombination rates, and test the idea that these populations might have distinct patterns of recombination. We explore how recombination differs at the level of populations, individuals, sexes and genomic regions. We show that the positioning of crossovers along a chromosome correlates with their number, presumably a consequence of crossover interference, and discuss how this effect can cause differences in recombination landscape among sexes or species. We identify several instances of female segregation distortion. We found that averaged genome-wide recombination rate is lower and sex differences subtler in A. arenosa than in Arabidopsis thaliana.
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Affiliation(s)
- Marinela Dukić
- Department of Biology, Plant Evolutionary Genetics, Institute of Plant Molecular Biology, ETH Zürich, Zürich 8092, Switzerland
| | - Kirsten Bomblies
- Department of Biology, Plant Evolutionary Genetics, Institute of Plant Molecular Biology, ETH Zürich, Zürich 8092, Switzerland
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16
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Aggarwal DD, Rybnikov S, Sapielkin S, Rashkovetsky E, Frenkel Z, Singh M, Michalak P, Korol AB. Seasonal changes in recombination characteristics in a natural population of Drosophila melanogaster. Heredity (Edinb) 2021; 127:278-287. [PMID: 34163036 PMCID: PMC8405755 DOI: 10.1038/s41437-021-00449-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Environmental seasonality is a potent evolutionary force, capable of maintaining polymorphism, promoting phenotypic plasticity and causing bet-hedging. In Drosophila, environmental seasonality has been reported to affect life-history traits, tolerance to abiotic stressors and immunity. Oscillations in frequencies of alleles underlying fitness-related traits were also documented alongside SNPs across the genome. Here, we test for seasonal changes in two recombination characteristics, crossover rate and crossover interference, in a natural D. melanogaster population from India using morphological markers of the three major chromosomes. We show that winter flies, collected after the dry season, have significantly higher desiccation tolerance than their autumn counterparts. This difference proved to hold also for hybrids with three independent marker stocks, suggesting its genetic rather than plastic nature. Significant between-season changes are documented for crossover rate (in 9 of 13 studied intervals) and crossover interference (in four of eight studied pairs of intervals); both single and double crossovers were usually more frequent in the winter cohort. The winter flies also display weaker plasticity of both recombination characteristics to desiccation. We ascribe the observed differences to indirect selection on recombination caused by directional selection on desiccation tolerance. Our findings suggest that changes in recombination characteristics can arise even after a short period of seasonal adaptation (~8-10 generations).
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Affiliation(s)
- Dau Dayal Aggarwal
- Department of Zoology, Banaras Hindu University, Varanasi, India.
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India.
| | - Sviatoslav Rybnikov
- Institute of Evolution, University of Haifa, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.
| | - Shaul Sapielkin
- Institute of Evolution, University of Haifa, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | | | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Manvender Singh
- Department of Biotechnology, UIET, MD University, Rohtak, India
| | - Pawel Michalak
- Institute of Evolution, University of Haifa, Haifa, Israel
- Edward Via College of Osteopathic Medicine, Monroe, LA, USA
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.
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Danguy des Déserts A, Bouchet S, Sourdille P, Servin B. Evolution of Recombination Landscapes in Diverging Populations of Bread Wheat. Genome Biol Evol 2021; 13:evab152. [PMID: 34185074 PMCID: PMC8350361 DOI: 10.1093/gbe/evab152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Abstract
Reciprocal exchanges of DNA (crossovers) that occur during meiosis are mandatory to ensure the production of fertile gametes in sexually reproducing species. They also contribute to shuffle parental alleles into new combinations thereby fueling genetic variation and evolution. However, due to biological constraints, the recombination landscape is highly heterogeneous along the genome which limits the range of allelic combinations and the adaptability of populations. An approach to better understand the constraints on the recombination process is to study how it evolved in the past. In this work, we tackled this question by constructing recombination profiles in four diverging bread wheat (Triticum aestivum L.) populations established from 371 landraces genotyped at 200,062 SNPs. We used linkage disequilibrium (LD) patterns to estimate in each population the past distribution of recombination along the genome and characterize its fine-scale heterogeneity. At the megabase scale, recombination rates derived from LD patterns were consistent with family-based estimates obtained from a population of 406 recombinant inbred lines. Among the four populations, recombination landscapes were positively correlated between each other and shared a statistically significant proportion of highly recombinant intervals. However, this comparison also highlighted that the similarity in recombination landscapes between populations was significantly decreasing with their genetic differentiation in most regions of the genome. This observation was found to be robust to SNPs ascertainment and demography and suggests a relatively rapid evolution of factors determining the fine-scale localization of recombination in bread wheat.
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Affiliation(s)
- Alice Danguy des Déserts
- INRAE-Université Clermont-Auvergne, UMR1095, Génétique Diversité Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Sophie Bouchet
- INRAE-Université Clermont-Auvergne, UMR1095, Génétique Diversité Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Pierre Sourdille
- INRAE-Université Clermont-Auvergne, UMR1095, Génétique Diversité Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Bertrand Servin
- INRAE, Université de Toulouse, GenPhySE, Castanet-Tolosan, France
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18
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Tourrette E, Falque M, Martin OC. Enhancing backcross programs through increased recombination. Genet Sel Evol 2021; 53:25. [PMID: 33750291 PMCID: PMC7941899 DOI: 10.1186/s12711-021-00619-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/24/2021] [Indexed: 11/28/2022] Open
Abstract
Background Introgression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two recombination parameters. Results In this paper, we assess, by simulations in the context of Brassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that, when the QTL is in a region that initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental. Conclusions Depending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00619-0.
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Affiliation(s)
- Elise Tourrette
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Matthieu Falque
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France.
| | - Olivier C Martin
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France.,Université Paris-Saclay, INRAE, CNRS, Univ. Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.,Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
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19
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Hodgens C, Chang N, Schaller GE, Kieber JJ. Mutagenomics: A Rapid, High-Throughput Method to Identify Causative Mutations from a Genetic Screen. PLANT PHYSIOLOGY 2020; 184:1658-1673. [PMID: 32887734 PMCID: PMC7723078 DOI: 10.1104/pp.20.00609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/02/2020] [Indexed: 05/30/2023]
Abstract
Genetic screens are powerful tools to dissect complex biological processes, but a rate-limiting step is often the cloning of targeted genes. Here, we present a strategy, "mutagenomics," to identify causal mutations from a screen in a high throughput fashion in the absence of backcrossing. Mutagenomics is initiated by sequencing the genomes of the mutants identified, which are then subjected to a three-stage pipeline. The first stage identifies sequence changes in genes previously linked to the targeted pathway. The second stage uses heuristics derived from a simulation strategy to identify genes that are represented by multiple independent alleles more often than expected by chance. The third stage identifies candidate genes for the remaining lines by sequencing multiple lines of common descent. Our simulations indicate that sequencing as few as three to four sibling lines generally results in fewer than five candidate genes. We applied mutagenomics to a screen for Arabidopsis (Arabidopsis thaliana) mutants involved in the response to the phytohormone cytokinin. Mutagenomics identified likely causative genes for many of the mutant lines analyzed from this screen, including 13 alleles of the gene encoding the ARABIDOPSIS HIS KINASE4 cytokinin receptor. The screen also identified 1-AMINOCYCLOPROPANE-1-CARBOXYLATE (ACC) SYNTHASE7, an ACC synthase homolog involved in ethylene biosynthesis, and ELONGATED HYPOCOTYL5 (HY5), a master transcriptional regulator of photomorphogenesis. HY5 was found to mediate a subset of the transcriptional response to cytokinin. Mutagenomics has the potential to accelerate the pace and utility of genetic screens in Arabidopsis.
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Affiliation(s)
- Charles Hodgens
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Nicole Chang
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599
| | - G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
| | - Joseph J Kieber
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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20
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Schumer M, Powell DL, Corbett-Detig R. Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer. Mol Ecol Resour 2020; 20:1141-1151. [PMID: 32324964 PMCID: PMC7384932 DOI: 10.1111/1755-0998.13175] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/09/2020] [Accepted: 04/15/2020] [Indexed: 12/13/2022]
Abstract
It has become clear that hybridization between species is much more common than previously recognized. As a result, we now know that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Increasingly researchers are interested in disentangling which regions of the genome originated from each parental species using local ancestry inference methods. Due to the diverse effects of admixture, this interest is shared across disparate fields, from human genetics to research in ecology and evolutionary biology. However, local ancestry inference methods are sensitive to a range of biological and technical parameters which can impact accuracy. Here we present paired simulation and ancestry inference pipelines, mixnmatch and ancestryinfer, to help researchers plan and execute local ancestry inference studies. mixnmatch can simulate arbitrarily complex demographic histories in the parental and hybrid populations, selection on hybrids, and technical variables such as coverage and contamination. ancestryinfer takes as input sequencing reads from simulated or real individuals, and implements an efficient local ancestry inference pipeline. We perform a series of simulations with mixnmatch to pinpoint factors that influence accuracy in local ancestry inference and highlight useful features of the two pipelines. mixnmatch is a powerful tool for simulations of hybridization while ancestryinfer facilitates local ancestry inference on real or simulated data.
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Affiliation(s)
- Molly Schumer
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”
- Hanna H. Gray Fellow, Howard Hughes Medical Institute
| | - Daniel L. Powell
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”
- Department of Biology, Texas A&M University
| | - Russ Corbett-Detig
- Genomics Institute, University of California, Santa Cruz
- Department of Biomolecular Engineering, University of California, Santa Cruz
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21
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Adrion JR, Cole CB, Dukler N, Galloway JG, Gladstein AL, Gower G, Kyriazis CC, Ragsdale AP, Tsambos G, Baumdicker F, Carlson J, Cartwright RA, Durvasula A, Gronau I, Kim BY, McKenzie P, Messer PW, Noskova E, Ortega-Del Vecchyo D, Racimo F, Struck TJ, Gravel S, Gutenkunst RN, Lohmueller KE, Ralph PL, Schrider DR, Siepel A, Kelleher J, Kern AD. A community-maintained standard library of population genetic models. eLife 2020; 9:e54967. [PMID: 32573438 PMCID: PMC7438115 DOI: 10.7554/elife.54967] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/15/2020] [Indexed: 12/18/2022] Open
Abstract
The explosion in population genomic data demands ever more complex modes of analysis, and increasingly, these analyses depend on sophisticated simulations. Recent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to inconsistency and duplication of effort. This situation presents a major barrier to empirical researchers seeking to use simulations for power analyses of upcoming studies or sanity checks on existing genomic data. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here, we describe a new resource, stdpopsim, that attempts to rectify this situation. Stdpopsim is a community-driven open source project, which provides easy access to a growing catalog of published simulation models from a range of organisms and supports multiple simulation engine backends. This resource is available as a well-documented python library with a simple command-line interface. We share some examples demonstrating how stdpopsim can be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource.
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Affiliation(s)
- Jeffrey R Adrion
- Department of Biology and Institute of Ecology and Evolution, University of OregonEugeneUnited States
| | - Christopher B Cole
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | - Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Jared G Galloway
- Department of Biology and Institute of Ecology and Evolution, University of OregonEugeneUnited States
| | - Ariella L Gladstein
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
| | - Graham Gower
- Lundbeck GeoGenetics Centre, Globe Institute, University of CopenhagenCopenhagenDenmark
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
| | | | - Georgia Tsambos
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of MelbourneMelbourneAustralia
| | - Franz Baumdicker
- Department of Mathematical Stochastics, University of FreiburgFreiburgGermany
| | - Jedidiah Carlson
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Reed A Cartwright
- The Biodesign Institute and The School of Life Sciences, Arizona State UniversityTempeUnited States
| | - Arun Durvasula
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Ilan Gronau
- The Efi Arazi School of Computer Science, Herzliya Interdisciplinary CenterHerzliyaIsrael
| | - Bernard Y Kim
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Patrick McKenzie
- Department of Ecology, Evolution, and Environmental Biology, Columbia UniversityNew YorkUnited States
| | - Philipp W Messer
- Department of Computational BiologyCornell UniversityIthacaUnited States
| | - Ekaterina Noskova
- Computer Technologies Laboratory, ITMO UniversitySaint PetersburgRussian Federation
| | - Diego Ortega-Del Vecchyo
- International Laboratory for Human Genome Research, National Autonomous University of MexicoJuriquillaMexico
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, Globe Institute, University of CopenhagenCopenhagenDenmark
| | - Travis J Struck
- Departmentof Molecular and Cellular Biology, University of ArizonaTucsonUnited States
| | - Simon Gravel
- Department of Human Genetics, McGill UniversityMontrealCanada
| | - Ryan N Gutenkunst
- Departmentof Molecular and Cellular Biology, University of ArizonaTucsonUnited States
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Peter L Ralph
- Department of Biology and Institute of Ecology and Evolution, University of OregonEugeneUnited States
- Department of Mathematics, University of OregonEugeneUnited States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of OxfordOxfordUnited Kingdom
| | - Andrew D Kern
- Department of Biology and Institute of Ecology and Evolution, University of OregonEugeneUnited States
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22
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Wilson-Sánchez D, Lup SD, Sarmiento-Mañús R, Ponce MR, Micol JL. Next-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsis. Nucleic Acids Res 2020; 47:e140. [PMID: 31544937 PMCID: PMC6868388 DOI: 10.1093/nar/gkz806] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 09/07/2019] [Accepted: 09/10/2019] [Indexed: 12/25/2022] Open
Abstract
Forward genetic screens have successfully identified many genes and continue to be powerful tools for dissecting biological processes in Arabidopsis and other model species. Next-generation sequencing technologies have revolutionized the time-consuming process of identifying the mutations that cause a phenotype of interest. However, due to the cost of such mapping-by-sequencing experiments, special attention should be paid to experimental design and technical decisions so that the read data allows to map the desired mutation. Here, we simulated different mapping-by-sequencing scenarios. We first evaluated which short-read technology was best suited for analyzing gene-rich genomic regions in Arabidopsis and determined the minimum sequencing depth required to confidently call single nucleotide variants. We also designed ways to discriminate mutagenesis-induced mutations from background Single Nucleotide Polymorphisms in mutants isolated in Arabidopsis non-reference lines. In addition, we simulated bulked segregant mapping populations for identifying point mutations and monitored how the size of the mapping population and the sequencing depth affect mapping precision. Finally, we provide the computational basis of a protocol that we already used to map T-DNA insertions with paired-end Illumina-like reads, using very low sequencing depths and pooling several mutants together; this approach can also be used with single-end reads as well as to map any other insertional mutagen. All these simulations proved useful for designing experiments that allowed us to map several mutations in Arabidopsis.
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Affiliation(s)
- David Wilson-Sánchez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Samuel Daniel Lup
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Raquel Sarmiento-Mañús
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
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Samuk K, Manzano-Winkler B, Ritz KR, Noor MAF. Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura. Curr Biol 2020; 30:1517-1528.e6. [PMID: 32275873 DOI: 10.1016/j.cub.2020.03.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/16/2019] [Accepted: 03/20/2020] [Indexed: 12/30/2022]
Abstract
While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of Drosophila pseudoobscura from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8,000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a QST-FST analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short- and long-read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400 kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations, (2) at the 200-400 kb scale, recombination rate appears to vary largely genome-wide, rather than in specific intervals, and (3) interpopulation differences in recombination rate may be the result of local adaptation.
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Affiliation(s)
- Kieran Samuk
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | | | - Kathryn R Ritz
- Department of Biology, Duke University, Durham, NC 27708, USA
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Sellinger TPP, Abu Awad D, Moest M, Tellier A. Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data. PLoS Genet 2020; 16:e1008698. [PMID: 32251472 PMCID: PMC7173940 DOI: 10.1371/journal.pgen.1008698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 04/21/2020] [Accepted: 02/24/2020] [Indexed: 02/04/2023] Open
Abstract
Several methods based on the Sequential Markovian coalescence (SMC) have been developed that make use of genome sequence data to uncover population demographic history, which is of interest in its own right and is a key requirement to generate a null model for selection tests. While these methods can be applied to all possible kind of species, the underlying assumptions are sexual reproduction in each generation and non-overlapping generations. However, in many plants, invertebrates, fungi and other taxa, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization or long term dormant structures (seed or egg-banking). We develop a novel SMC-based method to infer 1) the rates/parameters of dormancy and of self-fertilization, and 2) the populations' past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. Finally, we apply our method to a Swedish and a German population of Arabidopsis thaliana demonstrating a selfing rate of ca. 0.87 and the absence of any detectable seed-bank. In contrast, we show that the water flea Daphnia pulex exhibits a long lived egg-bank of three to 18 generations. In conclusion, we here present a novel method to infer accurate demographies and life-history traits for species with selfing and/or seed/egg-banks. Finally, we provide recommendations for the use of SMC-based methods for non-model organisms, highlighting the importance of the per site and the effective ratios of recombination over mutation.
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Affiliation(s)
| | - Diala Abu Awad
- Department of Population Genetics, Technische Universitaet Muenchen, Freising, Germany
| | - Markus Moest
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Aurélien Tellier
- Department of Population Genetics, Technische Universitaet Muenchen, Freising, Germany
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25
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Jiao WB, Schneeberger K. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nat Commun 2020; 11:989. [PMID: 32080174 PMCID: PMC7033125 DOI: 10.1038/s41467-020-14779-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
Despite hundreds of sequenced Arabidopsis genomes, very little is known about the degree of genomic collinearity within single species, due to the low number of chromosome-level assemblies. Here, we report chromosome-level reference-quality assemblies of seven Arabidopsis thaliana accessions selected across its global range. Each genome reveals between 13–17 Mb rearranged, and 5–6 Mb non-reference sequences introducing copy-number changes in ~5000 genes, including ~1900 non-reference genes. Quantifying the collinearity between the genomes reveals ~350 euchromatic regions, where accession-specific tandem duplications destroy the collinearity between the genomes. These hotspots of rearrangements are characterized by reduced meiotic recombination in hybrids and genes implicated in biotic stress response. This suggests that hotspots of rearrangements undergo altered evolutionary dynamics, as compared to the rest of the genome, which are mostly based on the accumulation of new mutations and not on the recombination of existing variation, and thereby enable a quick response to the biotic stress. Despite tremendous genomic resources in the Arabidopsis community, only a few whole genome de novo assemblies are available. Here, the authors report chromosome-level reference-quality assemblies of seven A. thaliana accessions and reveal hotspots of rearrangements with altered evolutionary dynamics.
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Affiliation(s)
- Wen-Biao Jiao
- Max Planck Institute for Plant Breeding Research, Department of Chromosome Biology, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Department of Chromosome Biology, Carl-von-Linné-Weg 10, 50829, Cologne, Germany. .,Faculty of Biology, LMU Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany.
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26
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Dreissig S, Mascher M, Heckmann S. Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley. Mol Biol Evol 2020; 36:2029-2039. [PMID: 31209472 PMCID: PMC6736446 DOI: 10.1093/molbev/msz141] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Meiotic recombination generates genetic diversity upon which selection can act. Recombination rates are highly variable between species, populations, individuals, sexes, chromosomes, and chromosomal regions. The underlying mechanisms are controlled at the genetic and epigenetic level and show plasticity toward the environment. Environmental plasticity may be divided into short- and long-term responses. We estimated recombination rates in natural populations of wild barley and domesticated landraces using a population genetics approach. We analyzed recombination landscapes in wild barley and domesticated landraces at high resolution. In wild barley, high recombination rates are found in more interstitial chromosome regions in contrast to distal chromosome regions in domesticated barley. Among subpopulations of wild barley, natural variation in effective recombination rate is correlated with temperature, isothermality, and solar radiation in a nonlinear manner. A positive linear correlation was found between effective recombination rate and annual precipitation. We discuss our findings with respect to how the environment might shape effective recombination rates in natural populations. Higher recombination rates in wild barley populations subjected to specific environmental conditions could be a means to maintain fitness in a strictly inbreeding species.
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Affiliation(s)
- Steven Dreissig
- Meiosis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Seeland, Germany
| | - Martin Mascher
- Domestication Genomics Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Stefan Heckmann
- Meiosis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Seeland, Germany
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Rowan BA, Heavens D, Feuerborn TR, Tock AJ, Henderson IR, Weigel D. An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features. Genetics 2019; 213:771-787. [PMID: 31527048 PMCID: PMC6827372 DOI: 10.1534/genetics.119.302406] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/28/2019] [Indexed: 11/18/2022] Open
Abstract
Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of >17,000 COs between the Col-0 and Ler-0 accessions of Arabidopsis thaliana COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large- and small-scale SVs, representing an influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.
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Affiliation(s)
- Beth A Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | | | - Tatiana R Feuerborn
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, CB2 3EA, United Kingdom
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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28
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Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination. Nat Commun 2019; 10:4310. [PMID: 31541084 PMCID: PMC6754367 DOI: 10.1038/s41467-019-12209-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 08/19/2019] [Indexed: 12/12/2022] Open
Abstract
Meiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the next generation. Large populations and the demand for genome-wide, fine-scale resolution challenge existing methods for CO identification. Taking advantage of linked-read sequencing, we develop a highly efficient method for genome-wide identification of COs at kilobase resolution in pooled recombinants. We first test this method using a pool of Arabidopsis F2 recombinants, and recapitulate results obtained from the same plants using individual whole-genome sequencing. By applying this method to a pool of pollen DNA from an F1 plant, we establish a highly accurate CO landscape without generating or sequencing a single recombinant plant. The simplicity of this approach enables the simultaneous generation and analysis of multiple CO landscapes, accelerating the pace at which mechanisms for the regulation of recombination can be elucidated through efficient comparisons of genotypic and environmental effects on recombination. Meiotic crossovers (COs) generate genetic variation and ensure proper chromosome segregation. Here, the authors develop a method for identifying COs at kilobase resolution in pooled recombinants using linked-read sequencing data, and apply it to investigate genome-wide CO landscapes of Arabidopsis thaliana.
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29
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Sun H, Rowan BA, Flood PJ, Brandt R, Fuss J, Hancock AM, Michelmore RW, Huettel B, Schneeberger K. Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination. Nat Commun 2019. [PMID: 31541084 DOI: 10.1101/484022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Meiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the next generation. Large populations and the demand for genome-wide, fine-scale resolution challenge existing methods for CO identification. Taking advantage of linked-read sequencing, we develop a highly efficient method for genome-wide identification of COs at kilobase resolution in pooled recombinants. We first test this method using a pool of Arabidopsis F2 recombinants, and recapitulate results obtained from the same plants using individual whole-genome sequencing. By applying this method to a pool of pollen DNA from an F1 plant, we establish a highly accurate CO landscape without generating or sequencing a single recombinant plant. The simplicity of this approach enables the simultaneous generation and analysis of multiple CO landscapes, accelerating the pace at which mechanisms for the regulation of recombination can be elucidated through efficient comparisons of genotypic and environmental effects on recombination.
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Affiliation(s)
- Hequan Sun
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Beth A Rowan
- The Genome Center and Department of Plant Sciences, University of California, Davis, 451 East Health Sciences Drive, Davis, CA, 95616, USA.
| | - Pádraic J Flood
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Ronny Brandt
- Max Planck-Genome-Center Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Janina Fuss
- Max Planck-Genome-Center Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Angela M Hancock
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Richard W Michelmore
- The Genome Center and Department of Plant Sciences, University of California, Davis, 451 East Health Sciences Drive, Davis, CA, 95616, USA
| | - Bruno Huettel
- Max Planck-Genome-Center Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
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30
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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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31
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Luo H, Pandey MK, Khan AW, Guo J, Wu B, Cai Y, Huang L, Zhou X, Chen Y, Chen W, Liu N, Lei Y, Liao B, Varshney RK, Jiang H. Discovery of genomic regions and candidate genes controlling shelling percentage using QTL-seq approach in cultivated peanut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1248-1260. [PMID: 30549165 PMCID: PMC6576108 DOI: 10.1111/pbi.13050] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 05/12/2023]
Abstract
Cultivated peanut (Arachis hypogaea L.) is an important grain legume providing high-quality cooking oil, rich proteins and other nutrients. Shelling percentage (SP) is the 2nd most important agronomic trait after pod yield and this trait significantly affects the economic value of peanut in the market. Deployment of diagnostic markers through genomics-assisted breeding (GAB) can accelerate the process of developing improved varieties with enhanced SP. In this context, we deployed the QTL-seq approach to identify genomic regions and candidate genes controlling SP in a recombinant inbred line population (Yuanza 9102 × Xuzhou 68-4). Four libraries (two parents and two extreme bulks) were constructed and sequenced, generating 456.89-790.32 million reads and achieving 91.85%-93.18% genome coverage and 14.04-21.37 mean read depth. Comprehensive analysis of two sets of data (Yuanza 9102/two bulks and Xuzhou 68-4/two bulks) using the QTL-seq pipeline resulted in discovery of two overlapped genomic regions (2.75 Mb on A09 and 1.1 Mb on B02). Nine candidate genes affected by 10 SNPs with non-synonymous effects or in UTRs were identified in these regions for SP. Cost-effective KASP (Kompetitive Allele-Specific PCR) markers were developed for one SNP from A09 and three SNPs from B02 chromosome. Genotyping of the mapping population with these newly developed KASP markers confirmed the major control and stable expressions of these genomic regions across five environments. The identified candidate genomic regions and genes for SP further provide opportunity for gene cloning and deployment of diagnostic markers in molecular breeding for achieving high SP in improved varieties.
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Affiliation(s)
- Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Bei Wu
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Yan Cai
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
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Okazaki Y, Takahata S, Hirakawa H, Suzuki Y, Onodera Y. Molecular evidence for recent divergence of X- and Y-linked gene pairs in Spinacia oleracea L. PLoS One 2019; 14:e0214949. [PMID: 30964889 PMCID: PMC6456208 DOI: 10.1371/journal.pone.0214949] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/22/2019] [Indexed: 11/19/2022] Open
Abstract
Dioecy has evolved recently and independently from cosexual populations in many angiosperm lineages, providing opportunities to understand the evolutionary process underlying this transition. Spinach (Spinacia oleracea) is a dioecious plant with homomorphic sex chromosomes (XY). Although most of the spinach Y chromosome recombines with the X chromosome, a region around the male-determining locus on Y does not recombine with its X counterpart, suggesting that this region might be related to the evolution of dioecy in the species. To identify genes located in the non-recombining region (MSY, male-specific region of Y), RNA-seq analysis of male and female progeny plants (eight each) from a sib-cross of a dioecious line was performed. We discovered only 354 sex-chromosomal SNPs in 219 transcript sequences (genes). We randomly selected 39 sex-chromosomal genes to examine the reproducibility of the RNA-seq results and observed tight linkage to the male-determining locus in a spinach segregating population (140 individuals). Further analysis using a large-scale population (>1400) and over 100 spinach germplasm accessions and cultivars showed that SNPs in at least 12 genes are fully linked to the male-determining locus, suggesting that the genes reside in the spinach MSY. Synonymous substitution rates of the MSY genes and X homologues predict a recent divergence (0.40 ± 0.08 Mya). Furthermore, synonymous divergence between spinach and its wild relative (S. tetrandra), whose sex chromosomes (XY) originated from a common ancestral chromosome, predicted that the species diverged around 5.7 Mya. Assuming that dioecy in Spinacia evolved before speciation within the genus and has a monophyletic origin, our data suggest that recombination around the spinach sex-determining locus might have stopped significantly later than the evolution of dioecy in Spinacia.
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Affiliation(s)
- Yosuke Okazaki
- The Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Satoshi Takahata
- The Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hideki Hirakawa
- Facility for Genome Informatics, Kazusa DNA Research Institute, Kazusa–kamatari, Kisarazu, Chiba, Japan
| | - Yutaka Suzuki
- The Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Yasuyuki Onodera
- The Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
- * E-mail:
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33
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Genome-wide dissection of segregation distortion using multiple inter-subspecific crosses in rice. SCIENCE CHINA-LIFE SCIENCES 2019; 62:507-516. [DOI: 10.1007/s11427-018-9452-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/28/2018] [Indexed: 11/27/2022]
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34
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Seymour DK, Chae E, Arioz BI, Koenig D, Weigel D. Transmission ratio distortion is frequent in Arabidopsis thaliana controlled crosses. Heredity (Edinb) 2019; 122:294-304. [PMID: 29955170 PMCID: PMC6169738 DOI: 10.1038/s41437-018-0107-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/02/2018] [Accepted: 06/04/2018] [Indexed: 12/14/2022] Open
Abstract
The equal probability of transmission of alleles from either parent during sexual reproduction is a central tenet of genetics and evolutionary biology. Yet, there are many cases where this rule is violated. The preferential transmission of alleles or genotypes is termed transmission ratio distortion (TRD). Examples of TRD have been identified in many species, implying that they are universal, but the resolution of species-wide studies of TRD are limited. We have performed a species-wide screen for TRD in over 500 segregating F2 populations of Arabidopsis thaliana using pooled reduced-representation genome sequencing. TRD was evident in up to a quarter of surveyed populations. Most populations exhibited distortion at only one genomic region, with some regions being repeatedly affected in multiple populations. Our results begin to elucidate the species-level architecture of biased transmission of genetic material in A. thaliana, and serve as a springboard for future studies into the biological basis of TRD in this species.
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Affiliation(s)
- Danelle K Seymour
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Burak I Arioz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Daniel Koenig
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
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Jia X, Zhang Y, Zhang Q, Zhao Q, Traw MB, Wang L, Tian D, Wang C, Yang S. High-resolution insight into recombination events at the SD1 locus in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:683-692. [PMID: 30417595 DOI: 10.1111/tpj.14154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/28/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
Recombination during meiosis plays an important role in genome evolution by reshuffling existing genetic variations into fresh combinations with the possibility of recovery of lost ancestral genotypes. While crossover (CO) events have been well studied, gene conversion events (GCs), which represent non-reciprocal information transfer between chromosomes, are poorly documented and difficult to detect due to their relatively small converted tract size. Here, we document these GC events and their phenotypic effects at an important locus in rice containing the SD1 gene, where multiple defective alleles contributed to the semi-dwarf phenotype of rice in the 'Green Revolution' of the 1960s. Here, physical separation of two defects allows recombination to generate the wild-type SD1 gene, for which plant height can then be used as a reporter. By screening 18 000 F2 progeny from a cross between two semi-dwarf cultivars that carry these different defective alleles, we detected 24 GC events, indicating a conversion rate of ~3.3 × 10-4 per marker per generation in a single meiotic cycle in rice. Furthermore, our data show that indels and single-nucleotide polymorphisms (SNPs) do not differ significantly in GC rates, at least at the SD1 locus. Our results provide strong evidence that GC by itself can regain an ancestral phenotype that was lost through mutation. This GC detection approach is likely to be broadly applicable to natural or artificial alleles of other phenotype-related functional genes, which are abundant in other plant genomes.
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Affiliation(s)
- Xianqing Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Qijun Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Qingyong Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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Kawall K. New Possibilities on the Horizon: Genome Editing Makes the Whole Genome Accessible for Changes. FRONTIERS IN PLANT SCIENCE 2019; 10:525. [PMID: 31068963 PMCID: PMC6491833 DOI: 10.3389/fpls.2019.00525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/04/2019] [Indexed: 05/04/2023]
Abstract
The emergence of new genome editing techniques, such as the site-directed nucleases, clustered regulatory interspaced short palindromic repeats (CRISPRs)/Cas9, transcription activator-like effector nucleases (TALENs), or zinc finger nucleases (ZFNs), has greatly increased the feasibility of introducing any desired changes into the genome of a target organism. The ability to target a Cas nuclease to DNA sequences with a single-guide RNA (sgRNA) has provided a dynamic tool for genome editing and is naturally derived from an adaptive immune system in bacteria and archaea. CRISPR/Cas systems are being rapidly improved and refined, thereby opening up even more possibilities. Classical plant breeding is based on genetic variations that occur naturally and is used to select plants with improved traits. Induced mutagenesis is used to enhance mutational frequency and accelerate this process. Plants have evolved cellular processes, including certain repair mechanisms that ensure DNA integrity and the maintenance of distinct DNA loci. The focus of this review is on the characterization of new potentials in plant breeding through the use of CRISPR/Cas systems that eliminate natural limitations in order to induce thus far unachievable genomic changes.
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Vaid N, Laitinen RAE. Diverse paths to hybrid incompatibility in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:199-213. [PMID: 30098060 DOI: 10.1111/tpj.14061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 05/28/2023]
Abstract
One of the most essential questions of biology is to understand how different species have evolved. Hybrid incompatibility, a phenomenon in which hybrids show reduced fitness in comparison with their parents, can result in reproductive isolation and speciation. Therefore, studying hybrid incompatibility provides an entry point in understanding speciation. Hybrid incompatibilities are known throughout taxa, and the underlying mechanisms have mystified scientists since the theory of evolution by means of natural selection was introduced. In plants, it is only in recent years that the high-throughput genetic and molecular tools have become available for the Arabidopsis genus, thus helping to shed light on the different genes and molecular and evolutionary mechanisms that underlie hybrid incompatibilities. In this review, we highlight the current knowledge of diverse mechanisms that are known to contribute to hybrid incompatibility.
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Affiliation(s)
- Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
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Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes. PLoS Genet 2018; 14:e1007843. [PMID: 30543623 PMCID: PMC6307820 DOI: 10.1371/journal.pgen.1007843] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/27/2018] [Accepted: 11/20/2018] [Indexed: 12/11/2022] Open
Abstract
During meiosis, chromosomes undergo DNA double-strand breaks (DSBs), which can be repaired using a homologous chromosome to produce crossovers. Meiotic recombination frequency is variable along chromosomes and tends to concentrate in narrow hotspots. We mapped crossover hotspots located in the Arabidopsis thaliana RAC1 and RPP13 disease resistance genes, using varying haplotypic combinations. We observed a negative non-linear relationship between interhomolog divergence and crossover frequency within the hotspots, consistent with polymorphism locally suppressing crossover repair of DSBs. The fancm, recq4a recq4b, figl1 and msh2 mutants, or lines with increased HEI10 dosage, are known to show increased crossovers throughout the genome. Surprisingly, RAC1 crossovers were either unchanged or decreased in these genetic backgrounds, showing that chromosome location and local chromatin environment are important for regulation of crossover activity. We employed deep sequencing of crossovers to examine recombination topology within RAC1, in wild type, fancm, recq4a recq4b and fancm recq4a recq4b backgrounds. The RAC1 recombination landscape was broadly conserved in the anti-crossover mutants and showed a negative relationship with interhomolog divergence. However, crossovers at the RAC1 5'-end were relatively suppressed in recq4a recq4b backgrounds, further indicating that local context may influence recombination outcomes. Our results demonstrate the importance of interhomolog divergence in shaping recombination within plant disease resistance genes and crossover hotspots.
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Dluzewska J, Szymanska M, Ziolkowski PA. Where to Cross Over? Defining Crossover Sites in Plants. Front Genet 2018; 9:609. [PMID: 30619450 PMCID: PMC6299014 DOI: 10.3389/fgene.2018.00609] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022] Open
Abstract
It is believed that recombination in meiosis serves to reshuffle genetic material from both parents to increase genetic variation in the progeny. At the same time, the number of crossovers is usually kept at a very low level. As a consequence, many organisms need to make the best possible use from the one or two crossovers that occur per chromosome in meiosis. From this perspective, the decision of where to allocate rare crossover events becomes an important issue, especially in self-pollinating plant species, which experience limited variation due to inbreeding. However, the freedom in crossover allocation is significantly limited by other, genetic and non-genetic factors, including chromatin structure. Here we summarize recent progress in our understanding of those processes with a special emphasis on plant genomes. First, we focus on factors which influence the distribution of recombination initiation sites and discuss their effects at both, the single hotspot level and at the chromosome scale. We also briefly explain the aspects of hotspot evolution and their regulation. Next, we analyze how recombination initiation sites translate into the development of crossovers and their location. Moreover, we provide an overview of the sequence polymorphism impact on crossover formation and chromosomal distribution.
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Affiliation(s)
- Julia Dluzewska
- Department of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Maja Szymanska
- Department of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Piotr A Ziolkowski
- Department of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
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Liu S, Schnable JC, Ott A, Yeh CTE, Springer NM, Yu J, Muehlbauer G, Timmermans MCP, Scanlon MJ, Schnable PS. Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels. Mol Biol Evol 2018; 35:2762-2772. [PMID: 30184112 PMCID: PMC6231493 DOI: 10.1093/molbev/msy174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Meiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. Whereas multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5′ ends of some genes. Further, we identified cases of intragenic crossovers that generate transgressive transcript accumulation patterns, that is, recombinant alleles displayed higher or lower levels of expression than did nonrecombinant alleles in any of ∼100 RILs, implicating intragenic recombination in the generation of new variants upon which selection can act. Thousands of apparent gene conversion events were identified, allowing us to estimate the genome-wide rate of gene conversion at SNP sites (4.9 × 10−5). The density of syntenic genes (i.e., those conserved at the same genomic locations since the divergence of maize and sorghum) exhibits a substantial correlation with crossover frequency, whereas the density of nonsyntenic genes (i.e., those which have transposed or been lost subsequent to the divergence of maize and sorghum) shows little correlation, suggesting that crossovers occur at higher rates in syntenic genes than in nonsyntenic genes. Increased rates of crossovers in syntenic genes could be either a consequence of the evolutionary conservation of synteny or a biological process that helps to maintain synteny.
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Affiliation(s)
- Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS.,Department of Agronomy, Iowa State University, Ames, IA
| | - James C Schnable
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE
| | - Alina Ott
- Department of Agronomy, Iowa State University, Ames, IA.,Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI
| | | | - Nathan M Springer
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA
| | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN
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41
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Okagaki RJ, Dukowic-Schulze S, Eggleston WB, Muehlbauer GJ. A Critical Assessment of 60 Years of Maize Intragenic Recombination. FRONTIERS IN PLANT SCIENCE 2018; 9:1560. [PMID: 30420864 PMCID: PMC6215864 DOI: 10.3389/fpls.2018.01560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/04/2018] [Indexed: 06/09/2023]
Abstract
Until the mid-1950s, it was believed that genetic crossovers did not occur within genes. Crossovers occurred between genes, the "beads on a string" model. Then in 1956, Seymour Benzer published his classic paper describing crossing over within a gene, intragenic recombination. This result from a bacteriophage gene prompted Oliver Nelson to study intragenic recombination in the maize Waxy locus. His studies along with subsequent work by others working with maize and other organisms described the outcomes of intragenic recombination and provided some of the earliest evidence that genes, not intergenic regions, were recombination hotspots. High-throughput genotyping approaches have since replaced single gene intragenic studies for characterizing the outcomes of recombination. These large-scale studies confirm that genes, or more generally genic regions, are the most active recombinogenic regions, and suggested a pattern of crossovers similar to the budding yeast Saccharomyces cerevisiae. In S. cerevisiae recombination is initiated by double-strand breaks (DSBs) near transcription start sites (TSSs) of genes producing a polarity gradient where crossovers preferentially resolve at the 5' end of genes. Intragenic studies in maize yielded less evidence for either polarity or for DSBs near TSSs initiating recombination and in certain respects resembled Schizosaccharomyces pombe or mouse. These different perspectives highlight the need to draw upon the strengths of different approaches and caution against relying on a single model system or approach for understanding recombination.
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Affiliation(s)
- Ron J. Okagaki
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | | | - William B. Eggleston
- Department of Biology, Virginia Commonwealth University, St. Paul, MN, United States
| | - Gary J. Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States
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42
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Kim BY, Huber CD, Lohmueller KE. Deleterious variation shapes the genomic landscape of introgression. PLoS Genet 2018; 14:e1007741. [PMID: 30346959 PMCID: PMC6233928 DOI: 10.1371/journal.pgen.1007741] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/13/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022] Open
Abstract
While it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how gene flow affects and is affected by the dynamics of deleterious variation. Here we use population genetic simulations to examine how gene flow impacts deleterious variation under a variety of demographic scenarios, mating systems, dominance coefficients, and recombination rates. Our results show that admixture between populations can temporarily reduce the genetic load of smaller populations and cause increases in the frequency of introgressed ancestry, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. Together, these factors lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30–75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models of admixture include both demography and deleterious variation before invoking other mechanisms to explain unusual patterns of genetic variation. Individuals from distinct populations sometimes will produce fertile offspring and will exchange genetic material in a process called hybridization. Genomes of hybrid individuals often show non-random patterns of hybrid ancestry across the genome, where some regions have a high frequency of ancestry from the second population and other regions have less. Typically, this pattern has been attributed to adaptive introgression, where beneficial genetic variants are passed from one population to the other, or to genomic incompatibilities between these distinct species. However, other mechanisms could lead to these heterogeneous patterns of ancestry in hybrids. Here we use simulations to investigate whether deleterious mutations affect the patterns of introgressed ancestry across genomes. We show that when ancestry from a larger population is added to a smaller population, the ancestry from the larger population dramatically increases in frequency because it carries fewer deleterious mutations. This occurs even in the absence of beneficial mutations in either population. Additionally, we show that differences in sex chromosome evolution relative to autosomes, or differences in mating system, can affect patterns of introgression in similar ways. Our study argues that deleterious mutations should be included in population genetic models used to identify unusual regions of the genome that appear to be under selection in hybrids.
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Affiliation(s)
- Bernard Y. Kim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Christian D. Huber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- * E-mail:
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43
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Role of Cis, Trans, and Inbreeding Effects on Meiotic Recombination in Saccharomyces cerevisiae. Genetics 2018; 210:1213-1226. [PMID: 30291109 DOI: 10.1534/genetics.118.301644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/02/2018] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination is a major driver of genome evolution by creating new genetic combinations. To probe the factors driving variability of meiotic recombination, we used a high-throughput method to measure recombination rates in hybrids between SK1 and a total of 26 Saccharomyces cerevisiae strains from different geographic origins and habitats. Fourteen intervals were monitored for each strain, covering chromosomes VI and XI entirely, and part of chromosome I. We found an average number of crossovers per chromosome ranging between 1.0 and 9.5 across strains ("domesticated" or not), which is higher than the average between 0.5 and 1.5 found in most organisms. In the different intervals analyzed, recombination showed up to ninefold variation across strains but global recombination landscapes along chromosomes varied less. We also built an incomplete diallel experiment to measure recombination rates in one region of chromosome XI in 10 different crosses involving five parental strains. Our overall results indicate that recombination rate is increasingly positively correlated with sequence similarity between homologs (i) in DNA double-strand-break-rich regions within intervals, (ii) in entire intervals, and (iii) at the whole genome scale. Therefore, these correlations cannot be explained by cis effects only. We also estimated that cis and trans effects explained 38 and 17%, respectively, of the variance of recombination rate. In addition, by using a quantitative genetics analysis, we identified an inbreeding effect that reduces recombination rate in homozygous genotypes, while other interaction effects (specific combining ability) or additive effects (general combining ability) are found to be weak. Finally, we measured significant crossover interference in some strains, and interference intensity was positively correlated with crossover number.
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44
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de Haas LS, Koopmans R, Lelivelt CLC, Ursem R, Dirks R, Velikkakam James G. Low-coverage resequencing detects meiotic recombination pattern and features in tomato RILs. DNA Res 2018; 24:549-558. [PMID: 28605512 PMCID: PMC5726486 DOI: 10.1093/dnares/dsx024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 05/18/2017] [Indexed: 12/14/2022] Open
Abstract
Traditional plant breeding relies on meiotic recombination for mixing of parental alleles to create novel allele combinations. Detailed analysis of recombination patterns in model organisms shows that recombination is tightly regulated within the genome, but frequencies vary extensively along chromosomes. Despite being a model organism for fruit developmental studies, high-resolution recombination patterns are lacking in tomato. In this study, we developed a novel methodology to use low-coverage resequencing to identify genome-wide recombination patterns and applied this methodology on 60 tomato Recombinant Inbred Lines (RILs). Our methodology identifies polymorphic markers from the low-coverage resequencing population data and utilizes the same data to locate the recombination breakpoints in individuals by using a variable sliding window. We identified 1,445 recombination sites comprising 112 recombination prone regions enriched for AT-rich DNA motifs. Furthermore, the recombination prone regions in tomato preferably occurred in gene promoters over intergenic regions, an observation consistent with Arabidopsis thaliana, Zea mays and Mimulus guttatus. Overall, our cost effective method and findings enhance the understanding of meiotic recombination in tomato and suggest evolutionarily conserved recombination associated genomic features.
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Affiliation(s)
- Lars S de Haas
- Rijk Zwaan Breeding B.V., 4793 RS Fijnaart, The Netherlands
| | - Roy Koopmans
- Rijk Zwaan Breeding B.V., 4793 RS Fijnaart, The Netherlands
| | | | - Remco Ursem
- Rijk Zwaan Breeding B.V., 4793 RS Fijnaart, The Netherlands
| | - Rob Dirks
- Rijk Zwaan Breeding B.V., 4793 RS Fijnaart, The Netherlands
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45
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Pang W, Fu P, Li X, Zhan Z, Yu S, Piao Z. Identification and Mapping of the Clubroot Resistance Gene CRd in Chinese Cabbage ( Brassica rapa ssp. pekinensis). FRONTIERS IN PLANT SCIENCE 2018; 9:653. [PMID: 29868100 DOI: 10.3389/fpls.2015.0653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/27/2018] [Indexed: 05/26/2023]
Abstract
The rapid spread of clubroot disease, which is caused by Plasmodiophora brassicae, threatens Brassicaceae crop production worldwide. Breeding plants that have broad-spectrum disease resistance is one of the best ways to prevent clubroot. In the present study, eight Chinese cabbage germplasms were screened using published clubroot-resistant (CR) loci-/gene-linked markers. A CR gene Crr3 potential carrier "85-74" was detected which linked to marker BRSTS61; however, "85-74" shows different responses to local pathogens "LAB-19," "LNND-2," and "LAB-10" from "CR-73" which harbors Crr3. We used a next-generation sequencing-based bulked segregant analysis approach combined with genetic mapping to detect CR genes in an F2 segregant population generated from a cross between the Chinese cabbage inbred lines "85-74" (CR) and "BJN3-1" (clubroot susceptible). The "85-74" line showed resistance to a local pathogen "LAB-19" which was identified as race 4; a genetic analysis revealed that the resistance was conferred by a single dominant gene. The CR gene which we named CRd was mapped to a 60 kb (1 cM) region between markers yau389 and yau376 on chromosome A03. CRd is located upstream of Crr3 which was confirmed based on the physical positions of Crr3 linked markers. The identification of CRd linked markers can be applied to marker-assisted selection in the breeding of new CR cultivars of Chinese cabbage and other Brassica crops.
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Affiliation(s)
- Wenxing Pang
- Molecular Biology of Vegetable Laboratory, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Pengyu Fu
- Molecular Biology of Vegetable Laboratory, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiaonan Li
- Molecular Biology of Vegetable Laboratory, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zongxiang Zhan
- Molecular Biology of Vegetable Laboratory, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Sha Yu
- Molecular Biology of Vegetable Laboratory, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhongyun Piao
- Molecular Biology of Vegetable Laboratory, College of Horticulture, Shenyang Agricultural University, Shenyang, China
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46
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Pang W, Fu P, Li X, Zhan Z, Yu S, Piao Z. Identification and Mapping of the Clubroot Resistance Gene CRd in Chinese Cabbage ( Brassica rapa ssp. pekinensis). FRONTIERS IN PLANT SCIENCE 2018; 9:653. [PMID: 29868100 PMCID: PMC5968122 DOI: 10.3389/fpls.2018.00653] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/27/2018] [Indexed: 05/23/2023]
Abstract
The rapid spread of clubroot disease, which is caused by Plasmodiophora brassicae, threatens Brassicaceae crop production worldwide. Breeding plants that have broad-spectrum disease resistance is one of the best ways to prevent clubroot. In the present study, eight Chinese cabbage germplasms were screened using published clubroot-resistant (CR) loci-/gene-linked markers. A CR gene Crr3 potential carrier "85-74" was detected which linked to marker BRSTS61; however, "85-74" shows different responses to local pathogens "LAB-19," "LNND-2," and "LAB-10" from "CR-73" which harbors Crr3. We used a next-generation sequencing-based bulked segregant analysis approach combined with genetic mapping to detect CR genes in an F2 segregant population generated from a cross between the Chinese cabbage inbred lines "85-74" (CR) and "BJN3-1" (clubroot susceptible). The "85-74" line showed resistance to a local pathogen "LAB-19" which was identified as race 4; a genetic analysis revealed that the resistance was conferred by a single dominant gene. The CR gene which we named CRd was mapped to a 60 kb (1 cM) region between markers yau389 and yau376 on chromosome A03. CRd is located upstream of Crr3 which was confirmed based on the physical positions of Crr3 linked markers. The identification of CRd linked markers can be applied to marker-assisted selection in the breeding of new CR cultivars of Chinese cabbage and other Brassica crops.
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47
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Ding X, Pervere LM, Bascom C, Bibeau JP, Khurana S, Butt AM, Orr RG, Flaherty PJ, Bezanilla M, Vidali L. Conditional genetic screen in Physcomitrella patens reveals a novel microtubule depolymerizing-end-tracking protein. PLoS Genet 2018; 14:e1007221. [PMID: 29746462 PMCID: PMC5944918 DOI: 10.1371/journal.pgen.1007221] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/24/2018] [Indexed: 11/19/2022] Open
Abstract
Our ability to identify genes that participate in cell growth and division is limited because their loss often leads to lethality. A solution to this is to isolate conditional mutants where the phenotype is visible under restrictive conditions. Here, we capitalize on the haploid growth-phase of the moss Physcomitrella patens to identify conditional loss-of-growth (CLoG) mutants with impaired growth at high temperature. We used whole-genome sequencing of pooled segregants to pinpoint the lesion of one of these mutants (clog1) and validated the identified mutation by rescuing the conditional phenotype by homologous recombination. We found that CLoG1 is a novel and ancient gene conserved in plants. At the restrictive temperature, clog1 plants have smaller cells but can complete cell division, indicating an important role of CLoG1 in cell growth, but not an essential role in cell division. Fluorescent protein fusions of CLoG1 indicate it is localized to microtubules with a bias towards depolymerizing microtubule ends. Silencing CLoG1 decreases microtubule dynamics, suggesting that CLoG1 plays a critical role in regulating microtubule dynamics. By discovering a novel gene critical for plant growth, our work demonstrates that P. patens is an excellent genetic system to study genes with a fundamental role in plant cell growth.
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Affiliation(s)
- Xinxin Ding
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
| | - Leah M. Pervere
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
| | - Carl Bascom
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA
- Department of Biological Sciences, Dartmouth College, Hanover, NH
| | - Jeffrey P. Bibeau
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Sakshi Khurana
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Allison M. Butt
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Robert G. Orr
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Patrick J. Flaherty
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA
| | | | - Luis Vidali
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
- * E-mail:
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48
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Abstract
Meiosis halves diploid chromosome numbers to haploid levels that are essential for sexual reproduction in most eukaryotes. Meiotic recombination ensures the formation of bivalents between homologous chromosomes (homologs) and their subsequent proper segregation. It also results in genetic diversity among progeny that influences evolutionary responses to selection. Moreover, crop breeding depends upon the action of meiotic recombination to rearrange elite traits between parental chromosomes. An understanding of the molecular mechanisms that drive meiotic recombination is important for both fundamental research and practical applications. This review emphasizes advances made during the past 5 years, primarily in Arabidopsis and rice, by summarizing newly characterized genes and proteins and examining the regulatory mechanisms that modulate their action.
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Affiliation(s)
- Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China;
| | - Gregory P Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA;
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-3280, USA
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49
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A High-Resolution Map of Meiotic Recombination in Cryptococcus deneoformans Demonstrates Decreased Recombination in Unisexual Reproduction. Genetics 2018; 209:567-578. [PMID: 29625994 PMCID: PMC5972427 DOI: 10.1534/genetics.118.300996] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/05/2018] [Indexed: 11/18/2022] Open
Abstract
Multiple species within the basidiomycete genus Cryptococcus cause cryptococcal disease. These species are estimated to affect nearly a quarter of a million people leading to ∼180,000 mortalities, annually. Sexual reproduction, which can occur between haploid yeasts of the same or opposite mating type, is a potentially important contributor to pathogenesis as recombination can generate novel genotypes and transgressive phenotypes. However, our quantitative understanding of recombination in this clinically important yeast is limited. Here, we describe genome-wide estimates of recombination rates in Cryptococcus deneoformans and compare recombination between progeny from α-α unisexual and a-α bisexual crosses. We find that offspring from bisexual crosses have modestly higher average rates of recombination than those derived from unisexual crosses. Recombination hot and cold spots across the C. deneoformans genome are also identified and are associated with increased GC content. Finally, we observed regions genome-wide with allele frequencies deviating from the expected parental ratio. These findings and observations advance our quantitative understanding of the genetic events that occur during sexual reproduction in C. deneoformans, and the impact that different forms of sexual reproduction are likely to have on genetic diversity in this important fungal pathogen.
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50
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Underwood CJ, Choi K, Lambing C, Zhao X, Serra H, Borges F, Simorowski J, Ernst E, Jacob Y, Henderson IR, Martienssen RA. Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation. Genome Res 2018; 28:519-531. [PMID: 29530927 PMCID: PMC5880242 DOI: 10.1101/gr.227116.117] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/15/2018] [Indexed: 02/02/2023]
Abstract
Eukaryotic centromeres contain the kinetochore, which connects chromosomes to the spindle allowing segregation. During meiosis, centromeres are suppressed for inter-homolog crossover, as recombination in these regions can cause chromosome missegregation and aneuploidy. Plant centromeres are surrounded by transposon-dense pericentromeric heterochromatin that is epigenetically silenced by histone 3 lysine 9 dimethylation (H3K9me2), and DNA methylation in CG and non-CG sequence contexts. However, the role of these chromatin modifications in control of meiotic recombination in the pericentromeres is not fully understood. Here, we show that disruption of Arabidopsis thaliana H3K9me2 and non-CG DNA methylation pathways, for example, via mutation of the H3K9 methyltransferase genes KYP/SUVH4 SUVH5 SUVH6, or the CHG DNA methyltransferase gene CMT3, increases meiotic recombination in proximity to the centromeres. Using immunocytological detection of MLH1 foci and genotyping by sequencing of recombinant plants, we observe that H3K9me2 and non-CG DNA methylation pathway mutants show increased pericentromeric crossovers. Increased pericentromeric recombination in H3K9me2/non-CG mutants occurs in hybrid and inbred backgrounds and likely involves contributions from both the interfering and noninterfering crossover repair pathways. We also show that meiotic DNA double-strand breaks (DSBs) increase in H3K9me2/non-CG mutants within the pericentromeres, via purification and sequencing of SPO11-1-oligonucleotides. Therefore, H3K9me2 and non-CG DNA methylation exert a repressive effect on both meiotic DSB and crossover formation in plant pericentromeric heterochromatin. Our results may account for selection of enhancer trap Dissociation (Ds) transposons into the CMT3 gene by recombination with proximal transposon launch-pads.
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Affiliation(s)
- Charles J. Underwood
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;,Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Filipe Borges
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joe Simorowski
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Evan Ernst
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yannick Jacob
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ian R. Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Robert A. Martienssen
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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