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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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2
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Wang Y, Dong Z, Ma Y, Zheng Y, Huang S, Yang X. Comprehensive dissection of meiotic DNA double-strand breaks and crossovers in cucumber. PLANT PHYSIOLOGY 2023; 193:1913-1932. [PMID: 37530486 PMCID: PMC10602612 DOI: 10.1093/plphys/kiad432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/21/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Meiotic recombination drives genetic diversity and crop genome optimization. In plant breeding, parents with favorable traits are crossed to create elite varieties. Different hybridizations produce diverse types of segment reshuffling between homologous chromosomes. However, little is known about the factors that cause hybrid-specific changes in crossovers (COs). Here, we constructed 2 F2 populations from crosses between a semiwild and 2 domesticated cucumber (Cucumis sativus) accessions and examined CO events. COs mainly occurred around genes and differed unevenly along chromosomes between the 2 hybrids. Fine-scale CO distributions were suppressed in regions of heterozygous structural variations (SVs) and were accelerated by high sequence polymorphism. C. sativus RADiation sensitive 51A (CsRAD51A) binding, histone H3 lysine 4 trimethylation (H3K4me3) modification, chromatin accessibility, and hypomethylation were positively associated with global CO landscapes and in local DNA double-strand break (DSB) hotspots and genes. The frequency and suppression of COs could be roughly predicted based on multiomic information. Differences in CO events between hybrids could be partially traced to distinct genetic and epigenetic features and were significantly associated with specific DSB hotspots and heterozygous SVs. Our findings identify the genomic and epigenetic features that contribute to CO formation and hybrid-specific divergence in cucumber and provide theoretical support for selecting parental combinations and manipulating recombination events at target genomic regions during plant breeding.
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Affiliation(s)
- Yanling Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhaonian Dong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yalin Ma
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yi Zheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xueyong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Zhang T, Zhao SH, Wang Y, He Y. FIGL1 coordinates with dosage-sensitive BRCA2 in modulating meiotic recombination in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2107-2121. [PMID: 37293848 DOI: 10.1111/jipb.13541] [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: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Meiotic crossover (CO) formation between homologous chromosomes ensures their subsequent proper segregation and generates genetic diversity among offspring. In maize, however, the mechanisms that modulate CO formation remain poorly characterized. Here, we found that both maize BREAST CANCER SUSCEPTIBILITY PROTEIN 2 (BRCA2) and AAA-ATPase FIDGETIN-LIKE-1 (FIGL1) act as positive factors of CO formation by controlling the assembly or/and stability of two conserved DNA recombinases RAD51 and DMC1 filaments. Our results revealed that ZmBRCA2 is not only involved in the repair of DNA double-stranded breaks (DSBs), but also regulates CO formation in a dosage-dependent manner. In addition, ZmFIGL1 interacts with RAD51 and DMC1, and Zmfigl1 mutants had a significantly reduced number of RAD51/DMC1 foci and COs. Further, simultaneous loss of ZmFIGL1 and ZmBRCA2 abolished RAD51/DMC1 foci and exacerbated meiotic defects compared with the single mutant Zmbrca2 or Zmfigl1. Together, our data demonstrate that ZmBRCA2 and ZmFIGL1 act coordinately to regulate the dynamics of RAD51/DMC1-dependent DSB repair to promote CO formation in maize. This conclusion is surprisingly different from the antagonistic roles of BRCA2 and FIGL1 in Arabidopsis, implying that, although key factors that control CO formation are evolutionarily conserved, specific characteristics have been adopted in diverse plant species.
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Affiliation(s)
- Ting Zhang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Shuang-Hui Zhao
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yan Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Rafiei N, Ronceret A. Crossover interference mechanism: New lessons from plants. Front Cell Dev Biol 2023; 11:1156766. [PMID: 37274744 PMCID: PMC10236007 DOI: 10.3389/fcell.2023.1156766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Plants are the source of our understanding of several fundamental biological principles. It is well known that Gregor Mendel discovered the laws of Genetics in peas and that maize was used for the discovery of transposons by Barbara McClintock. Plant models are still useful for the understanding of general key biological concepts. In this article, we will focus on discussing the recent plant studies that have shed new light on the mysterious mechanisms of meiotic crossover (CO) interference, heterochiasmy, obligatory CO, and CO homeostasis. Obligatory CO is necessary for the equilibrated segregation of homologous chromosomes during meiosis. The tight control of the different male and female CO rates (heterochiasmy) enables both the maximization and minimization of genome shuffling. An integrative model can now predict these observed aspects of CO patterning in plants. The mechanism proposed considers the Synaptonemal Complex as a canalizing structure that allows the diffusion of a class I CO limiting factor linearly on synapsed bivalents. The coarsening of this limiting factor along the SC explains the interfering spacing between COs. The model explains the observed coordinated processes between synapsis, CO interference, CO insurance, and CO homeostasis. It also easily explains heterochiasmy just considering the different male and female SC lengths. This mechanism is expected to be conserved in other species.
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Koury SA. Predicting recombination suppression outside chromosomal inversions in Drosophila melanogaster using crossover interference theory. Heredity (Edinb) 2023; 130:196-208. [PMID: 36721031 PMCID: PMC10076299 DOI: 10.1038/s41437-023-00593-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 02/02/2023] Open
Abstract
Recombination suppression in chromosomal inversion heterozygotes is a well-known but poorly understood phenomenon. Surprisingly, recombination suppression extends far outside of inverted regions where there are no intrinsic barriers to normal chromosome pairing, synapsis, double-strand break formation, or recovery of crossover products. The interference hypothesis of recombination suppression proposes heterozygous inversion breakpoints possess chiasma-like properties such that recombination suppression extends from these breakpoints in a process analogous to crossover interference. This hypothesis is qualitatively consistent with chromosome-wide patterns of recombination suppression extending to both inverted and uninverted regions of the chromosome. The present study generated quantitative predictions for this hypothesis using a probabilistic model of crossover interference with gamma-distributed inter-event distances. These predictions were then tested with experimental genetic data (>40,000 meioses) on crossing-over in intervals that are external and adjacent to four common inversions of Drosophila melanogaster. The crossover interference model accurately predicted the partially suppressed recombination rates in euchromatic intervals outside inverted regions. Furthermore, assuming interference does not extend across centromeres dramatically improved model fit and partially accounted for excess recombination observed in pericentromeric intervals. Finally, inversions with breakpoints closest to the centromere had the greatest excess of recombination in pericentromeric intervals, an observation that is consistent with negative crossover interference previously documented near Drosophila melanogaster centromeres. In conclusion, the experimental data support the interference hypothesis of recombination suppression, validate a mathematical framework for integrating distance-dependent effects of structural heterozygosity on crossover distribution, and highlight the need for improved modeling of crossover interference in pericentromeric regions.
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Affiliation(s)
- Spencer A Koury
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY, 11794, USA.
- 2613 Ashwood Ave, Nashville, TN, 37212, USA.
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Abstract
KEY MESSAGE Chromatin state, and dynamic loading of pro-crossover protein HEI10 at recombination intermediates shape meiotic chromosome patterning in plants. Meiosis is the basis of sexual reproduction, and its basic progression is conserved across eukaryote kingdoms. A key feature of meiosis is the formation of crossovers which result in the reciprocal exchange of segments of maternal and paternal chromosomes. This exchange generates chromosomes with new combinations of alleles, increasing the efficiency of both natural and artificial selection. Crossovers also form a physical link between homologous chromosomes at metaphase I which is critical for accurate chromosome segregation and fertility. The patterning of crossovers along the length of chromosomes is a highly regulated process, and our current understanding of its regulation forms the focus of this review. At the global scale, crossover patterning in plants is largely governed by the classically observed phenomena of crossover interference, crossover homeostasis and the obligatory crossover which regulate the total number of crossovers and their relative spacing. The molecular actors behind these phenomena have long remained obscure, but recent studies in plants implicate HEI10 and ZYP1 as key players in their coordination. In addition to these broad forces, a wealth of recent studies has highlighted how genomic and epigenomic features shape crossover formation at both chromosomal and local scales, revealing that crossovers are primarily located in open chromatin associated with gene promoters and terminators with low nucleosome occupancy.
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Affiliation(s)
- Andrew Lloyd
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, Ceredigion, UK.
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Dissecting the Meiotic Recombination Patterns in a Brassica napus Double Haploid Population Using 60K SNP Array. Int J Mol Sci 2023; 24:ijms24054469. [PMID: 36901901 PMCID: PMC10003086 DOI: 10.3390/ijms24054469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Meiotic recombination not only maintains the stability of the chromosome structure but also creates genetic variations for adapting to changeable environments. A better understanding of the mechanism of crossover (CO) patterns at the population level is useful for crop improvement. However, there are limited cost-effective and universal methods to detect the recombination frequency at the population level in Brassica napus. Here, the Brassica 60K Illumina Infinium SNP array (Brassica 60K array) was used to systematically study the recombination landscape in a double haploid (DH) population of B. napus. It was found that COs were unevenly distributed across the whole genome, and a higher frequency of COs existed at the distal ends of each chromosome. A considerable number of genes (more than 30%) in the CO hot regions were associated with plant defense and regulation. In most tissues, the average gene expression level in the hot regions (CO frequency of greater than 2 cM/Mb) was significantly higher than that in the regions with a CO frequency of less than 1 cM/Mb. In addition, a bin map was constructed with 1995 recombination bins. For seed oil content, Bin 1131 to 1134, Bin 1308 to 1311, Bin 1864 to 1869, and Bin 2184 to 2230 were identified on chromosomes A08, A09, C03, and C06, respectively, which could explain 8.5%, 17.3%, 8.6%, and 3.9% of the phenotypic variation. These results could not only deepen our understanding of meiotic recombination in B. napus at the population level, and provide useful information for rapeseed breeding in the future, but also provided a reference for studying CO frequency in other species.
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Hyde L, Osman K, Winfield M, Sanchez‐Moran E, Higgins JD, Henderson IR, Sparks C, Franklin FCH, Edwards KJ. Identification, characterization, and rescue of CRISPR/Cas9 generated wheat SPO11-1 mutants. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:405-418. [PMID: 36373224 PMCID: PMC9884015 DOI: 10.1111/pbi.13961] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 05/29/2023]
Abstract
Increasing crop yields through plant breeding is time consuming and laborious, with the generation of novel combinations of alleles being limited by chromosomal linkage blocks and linkage-drag. Meiotic recombination is essential to create novel genetic variation via the reshuffling of parental alleles. The exchange of genetic information between homologous chromosomes occurs at crossover (CO) sites but CO frequency is often low and unevenly distributed. This bias creates the problem of linkage-drag in recombination 'cold' regions, where undesirable variation remains linked to useful traits. In plants, programmed meiosis-specific DNA double-strand breaks, catalysed by the SPO11 complex, initiate the recombination pathway, although only ~5% result in the formation of COs. To study the role of SPO11-1 in wheat meiosis, and as a prelude to manipulation, we used CRISPR/Cas9 to generate edits in all three SPO11-1 homoeologues of hexaploid wheat. Characterization of progeny lines shows plants deficient in all six SPO11-1 copies fail to undergo chromosome synapsis, lack COs and are sterile. In contrast, lines carrying a single copy of any one of the three wild-type homoeologues are phenotypically indistinguishable from unedited plants both in terms of vegetative growth and fertility. However, cytogenetic analysis of the edited plants suggests that homoeologues differ in their ability to generate COs and in the dynamics of synapsis. In addition, we show that the transformation of wheat mutants carrying six edited copies of SPO11-1 with the TaSPO11-1B gene, restores synapsis, CO formation, and fertility and hence opens a route to modifying recombination in this agronomically important crop.
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Affiliation(s)
- Lucy Hyde
- School of Biological Sciences, Life SciencesUniversity of BristolBristolUK
| | - Kim Osman
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Mark Winfield
- School of Biological Sciences, Life SciencesUniversity of BristolBristolUK
| | | | - James D. Higgins
- Department of Genetics and Genome BiologyUniversity of LeicesterLeicesterUK
| | | | | | | | - Keith J. Edwards
- School of Biological Sciences, Life SciencesUniversity of BristolBristolUK
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Zhang X, Zhang S, Liu Z, Zhao W, Zhang X, Song J, Jia H, Yang W, Ma Y, Wang Y, Xie K, Budahn H, Wang H. Characterization and acceleration of genome shuffling and ploidy reduction in synthetic allopolyploids by genome sequencing and editing. Nucleic Acids Res 2022; 51:198-217. [PMID: 36583364 PMCID: PMC9841408 DOI: 10.1093/nar/gkac1209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022] Open
Abstract
Polyploidy and the subsequent ploidy reduction and genome shuffling are the major driving forces of genome evolution. Here, we revealed short-term allopolyploid genome evolution by sequencing a synthetic intergeneric hybrid (Raphanobrassica, RRCC). In this allotetraploid, the genome deletion was quick, while rearrangement was slow. The core and high-frequency genes tended to be retained while the specific and low-frequency genes tended to be deleted in the hybrid. The large-fragment deletions were enriched in the heterochromatin region and probably derived from chromosome breaks. The intergeneric translocations were primarily of short fragments dependent on homoeology, indicating a gene conversion origin. To accelerate genome shuffling, we developed an efficient genome editing platform for Raphanobrassica. By editing Fanconi Anemia Complementation Group M (FANCM) genes, homoeologous recombination, chromosome deletion and secondary meiosis with additional ploidy reduction were accelerated. FANCM was shown to be a checkpoint of meiosis and controller of ploidy stability. By simultaneously editing FLIP genes, gene conversion was precisely introduced, and mosaic genes were produced around the target site. This intergeneric hybrid and genome editing platform not only provides models that facilitate experimental evolution research by speeding up genome shuffling and conversion but also accelerates plant breeding by enhancing intergeneric genetic exchange and creating new genes.
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Affiliation(s)
- Xiaohui Zhang
- To whom correspondence should be addressed. Tel: +86 10 82105947; Fax: +86 10 62174123;
| | | | | | - Wei Zhao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoxue Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiangping Song
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huixia Jia
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenlong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Ma
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan); College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Holger Budahn
- Institute for Breeding Research on Horticultural Crops, Julius-Kuehn-Institute, Federal Research Centre for Cultivated Plants, D-06484 Quedlinburg, Germany
| | - Haiping Wang
- Correspondence may also be addressed to Haiping Wang. Tel: +86 10 82105942; Fax: +86 10 62174123;
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Abeyratne CR, Macaya-Sanz D, Zhou R, Barry KW, Daum C, Haiby K, Lipzen A, Stanton B, Yoshinaga Y, Zane M, Tuskan GA, DiFazio SP. High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa. G3 (BETHESDA, MD.) 2022; 13:6762080. [PMID: 36250890 PMCID: PMC9836356 DOI: 10.1093/g3journal/jkac269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/28/2022] [Indexed: 12/14/2022]
Abstract
Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.
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Affiliation(s)
| | - David Macaya-Sanz
- Department of Forest Ecology & Genetics, CIFOR-INIA, CSIC, Madrid 28040, Spain
| | - Ran Zhou
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Anna Lipzen
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Yuko Yoshinaga
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Matthew Zane
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Gerald A Tuskan
- Biosciences Division, Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Stephen P DiFazio
- Corresponding author: Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
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11
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Garcia N, Yin L, Dukowic-Schulze S, Milsted C, Kianian PMA, Kianian S, Pawlowski WP, Chen C. Comparison of meiotic transcriptomes of three maize inbreds with different origins reveals differences in cell cycle and recombination. BMC Genomics 2022; 23:702. [PMID: 36224518 PMCID: PMC9554999 DOI: 10.1186/s12864-022-08922-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
Background Cellular events during meiosis can differ between inbred lines in maize. Substantial differences in the average numbers of chiasmata and double-strand breaks (DSBs) per meiotic cell have been documented among diverse inbred lines of maize: CML228, a tropical maize inbred line, B73 and Mo17, temperate maize lines. To determine if gene expression might explain these observed differences, an RNA-Seq experiment was performed on CML228 male meiocytes which was compared to B73 and Mo17 male meiocytes, where plants were grown in the same controlled environment. Results We found that a few DSB-repair/meiotic genes which promote class I crossovers (COs) and the Zyp1 gene which limits newly formed class I COs were up-regulated, whereas Mus81 homolog 2 which promotes class II COs was down-regulated in CML228. Although we did not find enriched gene ontology (GO) categories directly related to meiosis, we found that GO categories in membrane, localization, proteolysis, energy processes were up-regulated in CML228, while chromatin remodeling, epigenetic regulation, and cell cycle related processes including meiosis related cell cycle processes were down-regulated in CML228. The degree of similarity in expression patterns between the three maize lines reflect their genetic relatedness: B73 and Mo17 had similar meiotic expressions and CML228 had a more distinct expression profile. Conclusions We found that meiotic related genes were mostly conserved among the three maize inbreds except for a few DSB-repair/meiotic genes. The findings that the molecular players in limiting class I CO formation (once CO assurance is achieved) were up-regulated and those involved in promoting class II CO formation were down-regulated in CML228 agree with the lower chiasmata number observed in CML228 previously. In addition, epigenetics such as chromatin remodeling and histone modification might play a role. Transport and energy-related processes was up-regulated and Cyclin13 was down-regulated in CML228. The direction of gene expression of these processes agree with that previously found in meiotic tissues compared with vegetative tissues. In summary, we used different natural maize inbred lines from different climatic conditions and have shown their differences in expression landscape in male meiocytes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08922-w.
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Affiliation(s)
- Nelson Garcia
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, USA.,Present Address: Sound Agriculture, 5858 Horton St, Emeryville, CA, USA
| | - Lu Yin
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Stefanie Dukowic-Schulze
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, USA.,Microvascular Biology and Pathobiology, University of Heidelberg, Mannheim, Germany
| | - Claire Milsted
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Penny M A Kianian
- PepsiCo Inc., 210 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN, USA
| | - Shahryar Kianian
- Department of Agriculture - Agricultural Research Service, Cereal Disease Lab, U.S., Saint Paul, MN, USA
| | | | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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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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Abstract
Flowering plants alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. Pollen actively transcribes its haploid genome, providing phenotypic diversity even among pollen grains from a single plant. In this study, we used allele-specific RNA sequencing of single pollen precursors to follow the shift to haploid expression in maize pollen. We observed widespread biallelic expression for 11 days after meiosis, indicating that transcripts synthesized by the diploid sporophyte persist long into the haploid phase. Subsequently, there was a rapid and global conversion to monoallelic expression at pollen mitosis I, driven by active new transcription from the haploid genome. Genes showed evidence of increased purifying selection if they were expressed after (but not before) pollen mitosis I. This work establishes the timing during which haploid selection may act in pollen.
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Affiliation(s)
- Brad Nelms
- Department of Plant Biology, University of Georgia, Athens, GA 30606, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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14
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Demonstration of targeted crossovers in hybrid maize using CRISPR technology. Commun Biol 2022; 5:53. [PMID: 35027641 PMCID: PMC8758740 DOI: 10.1038/s42003-022-03004-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/23/2021] [Indexed: 12/17/2022] Open
Abstract
Naturally occurring chromosomal crossovers (CO) during meiosis are a key driver of genetic diversity. The ability to target CO at specific allelic loci in hybrid plants would provide an advantage to the plant breeding process by facilitating trait introgression, and potentially increasing the rate of genetic gain. We present the first demonstration of targeted CO in hybrid maize utilizing the CRISPR Cas12a system. Our experiments showed that stable and heritable targeted CO can be produced in F1 somatic cells using Cas12a at a significantly higher rate than the natural CO in the same interval. Molecular characterization of the recombinant plants demonstrated that the targeted CO were driven by the non-homologous end joining (NHEJ) or HDR repair pathways, presumably during the mitotic cell cycle. These results are a step towards the use of RNA-guided nuclease technology to simplify the creation of targeted genome combinations in progeny and accelerate breeding. Kouranov et al. demonstrate Cas12a-mediated targeted chromosomal crossover (CO) in transgenic hybrid maize plants and produce heritable crossover in F1 plants when Cas12a transgene is segregated away. The authors also report that the frequency of LbCas12a-mediated CO is higher than control natural CO in the same intervals in the progeny of 4 different events.
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15
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Wang Y, van Rengs WMJ, Zaidan MWAM, Underwood CJ. Meiosis in crops: from genes to genomes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6091-6109. [PMID: 34009331 PMCID: PMC8483783 DOI: 10.1093/jxb/erab217] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/14/2021] [Indexed: 05/06/2023]
Abstract
Meiosis is a key feature of sexual reproduction. During meiosis homologous chromosomes replicate, recombine, and randomly segregate, followed by the segregation of sister chromatids to produce haploid cells. The unique genotypes of recombinant gametes are an essential substrate for the selection of superior genotypes in natural populations and in plant breeding. In this review we summarize current knowledge on meiosis in diverse monocot and dicot crop species and provide a comprehensive resource of cloned meiotic mutants in six crop species (rice, maize, wheat, barley, tomato, and Brassica species). Generally, the functional roles of meiotic proteins are conserved between plant species, but we highlight notable differences in mutant phenotypes. The physical lengths of plant chromosomes vary greatly; for instance, wheat chromosomes are roughly one order of magnitude longer than those of rice. We explore how chromosomal distribution for crossover recombination can vary between species. We conclude that research on meiosis in crops will continue to complement that in Arabidopsis, and alongside possible applications in plant breeding will facilitate a better understanding of how the different stages of meiosis are controlled in plant species.
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Affiliation(s)
- Yazhong Wang
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
| | - Willem M J van Rengs
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
| | - Mohd Waznul Adly Mohd Zaidan
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
| | - Charles J Underwood
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany
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16
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Gutiérrez Pinzón Y, González Kise JK, Rueda P, Ronceret A. The Formation of Bivalents and the Control of Plant Meiotic Recombination. FRONTIERS IN PLANT SCIENCE 2021; 12:717423. [PMID: 34557215 PMCID: PMC8453087 DOI: 10.3389/fpls.2021.717423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/13/2021] [Indexed: 06/06/2023]
Abstract
During the first meiotic division, the segregation of homologous chromosomes depends on the physical association of the recombined homologous DNA molecules. The physical tension due to the sites of crossing-overs (COs) is essential for the meiotic spindle to segregate the connected homologous chromosomes to the opposite poles of the cell. This equilibrated partition of homologous chromosomes allows the first meiotic reductional division. Thus, the segregation of homologous chromosomes is dependent on their recombination. In this review, we will detail the recent advances in the knowledge of the mechanisms of recombination and bivalent formation in plants. In plants, the absence of meiotic checkpoints allows observation of subsequent meiotic events in absence of meiotic recombination or defective meiotic chromosomal axis formation such as univalent formation instead of bivalents. Recent discoveries, mainly made in Arabidopsis, rice, and maize, have highlighted the link between the machinery of double-strand break (DSB) formation and elements of the chromosomal axis. We will also discuss the implications of what we know about the mechanisms regulating the number and spacing of COs (obligate CO, CO homeostasis, and interference) in model and crop plants.
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17
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Abstract
Meiotic recombination is a fundamental process that generates genetic diversity and ensures the accurate segregation of homologous chromosomes. While a great deal is known about genetic factors that regulate recombination, relatively little is known about epigenetic factors, such as DNA methylation. In maize, we examined the effects on meiotic recombination of a mutation in a component of the RNA-directed DNA methylation pathway, Mop1 (Mediator of paramutation1), as well as a mutation in a component of the trans-acting small interference RNA biogenesis pathway, Lbl1 (Leafbladeless1). MOP1 is of particular interest with respect to recombination because it is responsible for methylation of transposable elements that are immediately adjacent to transcriptionally active genes. In the mop1 mutant, we found that meiotic recombination is uniformly decreased in pericentromeric regions but is generally increased in gene rich chromosomal arms. This observation was further confirmed by cytogenetic analysis showing that although overall crossover numbers are unchanged, they occur more frequently in chromosomal arms in mop1 mutants. Using whole genome bisulfite sequencing, our data show that crossover redistribution is driven by loss of CHH (where H = A, T, or C) methylation within regions near genes. In contrast to what we observed in mop1 mutants, no significant changes were observed in the frequency of meiotic recombination in lbl1 mutants. Our data demonstrate that CHH methylation has a significant impact on the overall recombination landscape in maize despite its low frequency relative to CG and CHG methylation.
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18
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Kuo P, Da Ines O, Lambing C. Rewiring Meiosis for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:708948. [PMID: 34349775 PMCID: PMC8328115 DOI: 10.3389/fpls.2021.708948] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 05/10/2023]
Abstract
Meiosis is a specialized cell division that contributes to halve the genome content and reshuffle allelic combinations between generations in sexually reproducing eukaryotes. During meiosis, a large number of programmed DNA double-strand breaks (DSBs) are formed throughout the genome. Repair of meiotic DSBs facilitates the pairing of homologs and forms crossovers which are the reciprocal exchange of genetic information between chromosomes. Meiotic recombination also influences centromere organization and is essential for proper chromosome segregation. Accordingly, meiotic recombination drives genome evolution and is a powerful tool for breeders to create new varieties important to food security. Modifying meiotic recombination has the potential to accelerate plant breeding but it can also have detrimental effects on plant performance by breaking beneficial genetic linkages. Therefore, it is essential to gain a better understanding of these processes in order to develop novel strategies to facilitate plant breeding. Recent progress in targeted recombination technologies, chromosome engineering, and an increasing knowledge in the control of meiotic chromosome segregation has significantly increased our ability to manipulate meiosis. In this review, we summarize the latest findings and technologies on meiosis in plants. We also highlight recent attempts and future directions to manipulate crossover events and control the meiotic division process in a breeding perspective.
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Affiliation(s)
- Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Olivier Da Ines
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293 CNRS, U1103 INSERM, Clermont-Ferrand, France
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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19
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Pecinka A, Chevalier C, Colas I, Kalantidis K, Varotto S, Krugman T, Michailidis C, Vallés MP, Muñoz A, Pradillo M. Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5205-5222. [PMID: 31626285 DOI: 10.1093/jxb/erz457] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Genetic information in the cell nucleus controls organismal development and responses to the environment, and finally ensures its own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organization of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to genome size, ploidy, and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organization and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits.
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Affiliation(s)
- Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Agricultural and Biotechnological Research, Olomouc, Czech Republic
| | | | - Isabelle Colas
- James Hutton Institute, Cell and Molecular Science, Pr Waugh's Lab, Invergowrie, Dundee, UK
| | - Kriton Kalantidis
- Department of Biology, University of Crete, and Institute of Molecular Biology Biotechnology, FoRTH, Heraklion, Greece
| | - Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment (DAFNAE) University of Padova, Agripolis viale dell'Università, Legnaro (PD), Italy
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Christos Michailidis
- Institute of Experimental Botany, Czech Acad Sci, Praha 6 - Lysolaje, Czech Republic
| | - María-Pilar Vallés
- Department of Genetics and Plant Breeding, Estación Experimental Aula Dei (EEAD), Spanish National Research Council (CSIC), Zaragoza, Spain
| | - Aitor Muñoz
- Department of Plant Molecular Genetics, National Center of Biotechnology/Superior Council of Scientific Research, Autónoma University of Madrid, Madrid, Spain
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
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20
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Gage JL, Monier B, Giri A, Buckler ES. Ten Years of the Maize Nested Association Mapping Population: Impact, Limitations, and Future Directions. THE PLANT CELL 2020; 32:2083-2093. [PMID: 32398275 PMCID: PMC7346555 DOI: 10.1105/tpc.19.00951] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/02/2020] [Accepted: 05/11/2020] [Indexed: 05/21/2023]
Abstract
It has been just over a decade since the release of the maize (Zea mays) Nested Association Mapping (NAM) population. The NAM population has been and continues to be an invaluable resource for the maize genetics community and has yielded insights into the genetic architecture of complex traits. The parental lines have become some of the most well-characterized maize germplasm, and their de novo assemblies were recently made publicly available. As we enter an exciting new stage in maize genomics, this retrospective will summarize the design and intentions behind the NAM population; its application, the discoveries it has enabled, and its influence in other systems; and use the past decade of hindsight to consider whether and how it will remain useful in a new age of genomics.
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Affiliation(s)
- Joseph L Gage
- U.S. Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
| | - Brandon Monier
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
| | - Anju Giri
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
| | - Edward S Buckler
- U.S. Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
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21
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Ku JC, Ronceret A, Golubovskaya I, Lee DH, Wang C, Timofejeva L, Kao YH, Gomez Angoa AK, Kremling K, Williams-Carrier R, Meeley R, Barkan A, Cande WZ, Wang CJR. Dynamic localization of SPO11-1 and conformational changes of meiotic axial elements during recombination initiation of maize meiosis. PLoS Genet 2020; 16:e1007881. [PMID: 32310948 PMCID: PMC7192515 DOI: 10.1371/journal.pgen.1007881] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 04/30/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
Meiotic double-strand breaks (DSBs) are generated by the evolutionarily conserved SPO11 complex in the context of chromatin loops that are organized along axial elements (AEs) of chromosomes. However, how DSBs are formed with respect to chromosome axes and the SPO11 complex remains unclear in plants. Here, we confirm that DSB and bivalent formation are defective in maize spo11-1 mutants. Super-resolution microscopy demonstrates dynamic localization of SPO11-1 during recombination initiation, with variable numbers of SPO11-1 foci being distributed in nuclei but similar numbers of SPO11-1 foci being found on AEs. Notably, cytological analysis of spo11-1 meiocytes revealed an aberrant AE structure. At leptotene, AEs of wild-type and spo11-1 meiocytes were similarly curly and discontinuous. However, during early zygotene, wild-type AEs become uniform and exhibit shortened axes, whereas the elongated and curly AEs persisted in spo11-1 mutants, suggesting that loss of SPO11-1 compromised AE structural maturation. Our results reveal an interesting relationship between SPO11-1 loading onto AEs and the conformational remodeling of AEs during recombination initiation. Meiosis is essential during sexual reproduction to produce haploid gametes. Recombination is the most crucial step during meiotic prophase I. It enables pairing of homologous chromosomes prior to their reductional division and generates new combinations of genetic alleles for transmission to the next generation. Meiotic recombination is initiated by generating DNA double-strand breaks (DSBs) via SPO11, a topoisomerase-related enzyme. The activity, timing and location of this DSB machinery must be controlled precisely, but how this is achieved remains obscure. Here, we show dynamic localization of SPO11-1 on chromatin during meiotic initiation in maize, yet a similar number of SPO11-1 is able to load onto axial elements (AEs), which accompanies a structural change of the AEs of wild-type meiotic chromosomes. Interestingly, loss of SPO11-1 not only affects DSB formation but also impairs structural alterations of AEs, resulting in abnormally long and curly AEs during early meiosis. Our study provides new insights into SPO11-1 localization during recombination initiation and suggests an intimate relationship between DSB formation and AE structural changes.
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Affiliation(s)
- Jia-Chi Ku
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Arnaud Ronceret
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
- Instituto de Biotecnología / UNAM Cuernavaca, Morelos Mexico
| | - Inna Golubovskaya
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
- N.I. Vavilov Institute of Plant Industry, St. Petersburg, Russia
| | - Ding Hua Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chiting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ljudmilla Timofejeva
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Yu-Hsin Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | | | - Karl Kremling
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | | | - Robert Meeley
- Corteva Agriscience, Johnston, Iowa, United States of America
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR, United States of America
| | - W. Zacheus Cande
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Chung-Ju Rachel Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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22
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Sidhu G, Pawlowski W. Chiasma Counting in Maize Male Meiocytes. Bio Protoc 2020. [DOI: 10.21769/bioprotoc.3604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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23
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Abstract
Through recombination, genes are freed to evolve more independently of one another, unleashing genetic variance hidden in the linkage disequilibrium that accumulates through selection combined with drift. Yet crossover numbers are evolutionarily constrained, with at least one and not many more than one crossover per bivalent in most taxa. Crossover interference, whereby a crossover reduces the probability of a neighboring crossover, contributes to this homogeneity. The mechanisms by which interference is achieved and crossovers are regulated are a major current subject of inquiry, facilitated by novel methods to visualize crossovers and to pinpoint recombination events. Here, we review patterns of crossover interference and the models built to describe this process. We then discuss the selective forces that have likely shaped interference and the regulation of crossover numbers.
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Affiliation(s)
- Sarah P Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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24
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Termolino P, Falque M, Aiese Cigliano R, Cremona G, Paparo R, Ederveen A, Martin OC, Consiglio FM, Conicella C. Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1163-1175. [PMID: 31436858 PMCID: PMC6973161 DOI: 10.1111/tpj.14505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/31/2019] [Accepted: 08/07/2019] [Indexed: 05/02/2023]
Abstract
During meiosis, recombination ensures allelic exchanges through crossovers (COs) between the homologous chromosomes. Advances in our understanding of the rules of COs have come from studies of mutations including structural chromosomal rearrangements that, when heterozygous, are known to impair COs in various organisms. In this work, we investigate the effect of a large heterozygous pericentric inversion on male and female recombination in Arabidopsis. The inversion was discovered in the Atmcc1 mutant background and was characterized through genetic and next-generation sequencing analysis. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the mutant and the wild type, both crossed with Landsberg erecta, were analyzed genome-wide by 143 single-nucleotide polymorphisms. The negative impact of inversion became evident in terms of CO loss in the rearranged chromosome in both male and female meiosis. No single-CO event was detected within the inversion, consistent with a post-meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F1 plants confirmed that COs were reduced in male meiosis in the chromosome with inversion. Crossover suppression on the rearranged chromosome is associated with a significant increase of COs in the other chromosomes, thereby maintaining unchanged the number of COs per cell. The CO pattern observed in our study is consistent with the interchromosomal (IC) effect as first described in Drosophila. In contrast to male meiosis, in female meiosis no IC effect is visible. This may be related to the greater strength of interference that constrains the CO number in excess of the minimum value imposed by CO assurance in Arabidopsis female meiosis.
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Affiliation(s)
- Pasquale Termolino
- Institute of Biosciences and Bioresources (IBBR)National Research Council of Italy (CNR)80055PorticiItaly
| | - Matthieu Falque
- Génétique Quantitative et Evolution‐Le MoulonInstitut National de la Recherche AgronomiqueUniversité Paris‐SudCNRSAgroParisTechUniversité Paris‐Saclay91190Gif‐sur‐YvetteFrance
| | | | - Gaetana Cremona
- Institute of Biosciences and Bioresources (IBBR)National Research Council of Italy (CNR)80055PorticiItaly
| | - Rosa Paparo
- Institute of Biosciences and Bioresources (IBBR)National Research Council of Italy (CNR)80055PorticiItaly
| | - Antoine Ederveen
- Department of Molecular Plant PhysiologyInstitute for Water and Wetland Research (IWWR)Radboud University Nijmegen9102 6500Nijmegenthe Netherlands
| | - Olivier C. Martin
- Génétique Quantitative et Evolution‐Le MoulonInstitut National de la Recherche AgronomiqueUniversité Paris‐SudCNRSAgroParisTechUniversité Paris‐Saclay91190Gif‐sur‐YvetteFrance
| | - Federica M. Consiglio
- Institute of Biosciences and Bioresources (IBBR)National Research Council of Italy (CNR)80055PorticiItaly
| | - Clara Conicella
- Institute of Biosciences and Bioresources (IBBR)National Research Council of Italy (CNR)80055PorticiItaly
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25
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Fayos I, Mieulet D, Petit J, Meunier AC, Périn C, Nicolas A, Guiderdoni E. Engineering meiotic recombination pathways in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2062-2077. [PMID: 31199561 PMCID: PMC6790369 DOI: 10.1111/pbi.13189] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 06/01/2019] [Accepted: 06/05/2019] [Indexed: 05/02/2023]
Abstract
In the last 15 years, outstanding progress has been made in understanding the function of meiotic genes in the model dicot and monocot plants Arabidopsis and rice (Oryza sativa L.), respectively. This knowledge allowed to modulate meiotic recombination in Arabidopsis and, more recently, in rice. For instance, the overall frequency of crossovers (COs) has been stimulated 2.3- and 3.2-fold through the inactivation of the rice FANCM and RECQ4 DNA helicases, respectively, two genes involved in the repair of DNA double-strand breaks (DSBs) as noncrossovers (NCOs) of the Class II crossover pathway. Differently, the programmed induction of DSBs and COs at desired sites is currently explored by guiding the SPO11-1 topoisomerase-like transesterase, initiating meiotic recombination in all eukaryotes, to specific target regions of the rice genome. Furthermore, the inactivation of 3 meiosis-specific genes, namely PAIR1, OsREC8 and OsOSD1, in the Mitosis instead of Meiosis (MiMe) mutant turned rice meiosis into mitosis, thereby abolishing recombination and achieving the first component of apomixis, apomeiosis. The successful translation of Arabidopsis results into a crop further allowed the implementation of two breakthrough strategies that triggered parthenogenesis from the MiMe unreduced clonal egg cell and completed the second component of diplosporous apomixis. Here, we review the most recent advances in and future prospects of the manipulation of meiotic recombination in rice and potentially other major crops, all essential for global food security.
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Affiliation(s)
- Ian Fayos
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Delphine Mieulet
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Julie Petit
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Anne Cécile Meunier
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Christophe Périn
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Alain Nicolas
- Institut Curie, CNRS UMR 3244University PSLParisFrance
- MeiogenixParisFrance
| | - Emmanuel Guiderdoni
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
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26
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Luo C, Li X, Zhang Q, Yan J. Single gametophyte sequencing reveals that crossover events differ between sexes in maize. Nat Commun 2019; 10:785. [PMID: 30770831 PMCID: PMC6377631 DOI: 10.1038/s41467-019-08786-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/24/2019] [Indexed: 11/24/2022] Open
Abstract
Meiotic crossover (CO) plays a key role in producing gametophytes and generating genetic variation. The patterns of CO production differ inter- and intra-species, as well as between sexes. However, sex-specific patterns of CO production have not been accurately profiled independently of genetic backgrounds in maize. Here, we develop a method to isolate single female gametophyte for genomes sequencing in maize. We show that more COs are observed in male (19.3 per microspore) than in female (12.4 per embryo sac). Based on Beam-Film model, the more designated class I and II COs are identified in male than in female. In addition, CO maturation inefficiency (CMI) is detected in some genetic backgrounds, suggesting that maize may be an ideal model for dissecting CMI. This research provides insights toward understanding the molecular mechanism of CO production between sexes and may help to improve maize breeding efficiency through paternal selection.
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Affiliation(s)
- Cheng Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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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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28
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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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29
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Xue M, Wang J, Jiang L, Wang M, Wolfe S, Pawlowski WP, Wang Y, He Y. The Number of Meiotic Double-Strand Breaks Influences Crossover Distribution in Arabidopsis. THE PLANT CELL 2018; 30:2628-2638. [PMID: 30282794 PMCID: PMC6241269 DOI: 10.1105/tpc.18.00531] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/17/2018] [Accepted: 09/30/2018] [Indexed: 05/06/2023]
Abstract
Meiotic recombination generates genetic diversity and ensures proper chromosome segregation. Recombination is initiated by the programmed formation of double-strand breaks (DSBs) in chromosomal DNA by DNA Topoisomerase VI-A Subunit (SPO11), a topoisomerase-like enzyme. Repair of some DSBs leads to the formation of crossovers (COs). In most organisms, including plants, the number of DSBs greatly exceeds the number of COs and which DSBs become CO sites is tightly controlled. The CO landscape is affected by DNA sequence and epigenome features of chromosomes as well as by global mechanisms controlling recombination dynamics. The latter are poorly understood and their effects on CO distribution are not well elucidated. To study how recombination dynamics affects CO distribution, we engineered Arabidopsis thaliana plants to carry hypomorphic alleles of SPO11-1 Two independent transgenic lines showed ∼30% and 40% reductions in DSB numbers, which were commensurate with the dosage of the SPO11-1 transcript. The reduction in DSB number resulted in proportional, although smaller, reductions of the number of COs. Most interestingly, CO distribution along the chromosomes was dramatically altered, with substantially fewer COs forming in pericentromeric chromosome regions. These results indicate that SPO11 activity, and the resulting DSB numbers are major factors shaping the CO landscape.
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Affiliation(s)
- Ming Xue
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Jun Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Luguang Jiang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Minghui Wang
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
- Bioinformatics Facility, Cornell University, Ithaca, New York 14853
| | - Sarah Wolfe
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | | | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
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30
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Kianian PMA, Wang M, Simons K, Ghavami F, He Y, Dukowic-Schulze S, Sundararajan A, Sun Q, Pillardy J, Mudge J, Chen C, Kianian SF, Pawlowski WP. High-resolution crossover mapping reveals similarities and differences of male and female recombination in maize. Nat Commun 2018; 9:2370. [PMID: 29915302 PMCID: PMC6006299 DOI: 10.1038/s41467-018-04562-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 05/04/2018] [Indexed: 12/19/2022] Open
Abstract
Meiotic crossovers (COs) are not uniformly distributed across the genome. Factors affecting this phenomenon are not well understood. Although many species exhibit large differences in CO numbers between sexes, sex-specific aspects of CO landscape are particularly poorly elucidated. Here, we conduct high-resolution CO mapping in maize. Our results show that CO numbers as well as their overall distribution are similar in male and female meioses. There are, nevertheless, dissimilarities at local scale. Male and female COs differ in their locations relative to transcription start sites in gene promoters and chromatin marks, including nucleosome occupancy and tri-methylation of lysine 4 of histone H3 (H3K4me3). Our data suggest that sex-specific factors not only affect male–female CO number disparities but also cause fine differences in CO positions. Differences between male and female CO landscapes indicate that recombination has distinct implications for population structure and gene evolution in male and in female meioses. Sex-specific meiotic crossover (CO) landscapes have been identified in multiple species. Here, the authors show that male and female meioses in maize have similar CO landscapes, and differences between COs in the two sexes only exists in their location relative to transcription start sites and some chromatin marks.
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Affiliation(s)
- Penny M A Kianian
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Minghui Wang
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.,Bioinformatics Facility, Cornell University, Ithaca, NY, 14853, USA
| | - Kristin Simons
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA.,Eurofins BioDiagnostics, River Falls, WI, 54022, USA
| | - Yan He
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.,National Maize Improvement Center, China Agricultural University, Beijing, China
| | | | | | - Qi Sun
- Bioinformatics Facility, Cornell University, Ithaca, NY, 14853, USA
| | | | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Wojciech P Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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31
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Leem J, Kim JS, Oh JS. WIP1 phosphatase suppresses the DNA damage response during G2/prophase arrest in mouse oocytes†. Biol Reprod 2018; 99:798-805. [DOI: 10.1093/biolre/ioy108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/30/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jiyeon Leem
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
| | - Jae-Sung Kim
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul, South Korea
| | - Jeong Su Oh
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
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32
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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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33
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Raffoux X, Bourge M, Dumas F, Martin OC, Falque M. High-throughput measurement of recombination rates and genetic interference in Saccharomyces cerevisiae. Yeast 2018; 35:431-442. [PMID: 29577404 DOI: 10.1002/yea.3315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 01/23/2023] Open
Abstract
Allelic recombination owing to meiotic crossovers is a major driver of genome evolution, as well as a key player for the selection of high-performing genotypes in economically important species. Therefore, we developed a high-throughput and low-cost method to measure recombination rates and crossover patterning (including interference) in large populations of the budding yeast Saccharomyces cerevisiae. Recombination and interference were analysed by flow cytometry, which allows time-consuming steps such as tetrad microdissection or spore growth to be avoided. Moreover, our method can also be used to compare recombination in wild-type vs. mutant individuals or in different environmental conditions, even if the changes in recombination rates are small. Furthermore, meiotic mutants often present recombination and/or pairing defects affecting spore viability but our method does not involve growth steps and thus avoids filtering out non-viable spores.
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Affiliation(s)
- Xavier Raffoux
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mickael Bourge
- Cytometry/Electronic Microscopy/Light Microcopy Facility, Imagerie-Gif, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Fabrice Dumas
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Olivier C Martin
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Matthieu Falque
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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34
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Lawrence EJ, Griffin CH, Henderson IR. Modification of meiotic recombination by natural variation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5471-5483. [PMID: 28992351 DOI: 10.1093/jxb/erx306] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Meiosis is a specialized cell division that produces haploid gametes required for sexual reproduction. During the first meiotic division, homologous chromosomes pair and undergo reciprocal crossing over, which recombines linked sequence variation. Meiotic recombination frequency varies extensively both within and between species. In this review, we will examine the molecular basis of meiotic recombination rate variation, with an emphasis on plant genomes. We first consider cis modification caused by polymorphisms at the site of recombination, or elsewhere on the same chromosome. We review cis effects caused by mismatches within recombining joint molecules, the effect of structural hemizygosity, and the role of specific DNA sequence motifs. In contrast, trans modification of recombination is exerted by polymorphic loci encoding diffusible molecules, which are able to modulate recombination on the same and/or other chromosomes. We consider trans modifiers that act to change total recombination levels, hotspot locations, or interactions between homologous and homeologous chromosomes in polyploid species. Finally, we consider the significance of genetic variation that modifies meiotic recombination for adaptation and evolution of plant species.
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Affiliation(s)
- Emma J Lawrence
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Catherine H Griffin
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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35
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Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize. Proc Natl Acad Sci U S A 2017; 114:12231-12236. [PMID: 29087335 DOI: 10.1073/pnas.1713225114] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers (COs) and noncrossovers (NCOs). Recombination events are not distributed evenly along chromosomes but cluster at recombination hotspots. How specific sites become hotspots is poorly understood. Studies in yeast and mammals linked initiation of meiotic recombination to active chromatin features present upstream from genes, such as absence of nucleosomes and presence of trimethylation of lysine 4 in histone H3 (H3K4me3). Core recombination components are conserved among eukaryotes, but it is unclear whether this conservation results in universal characteristics of recombination landscapes shared by a wide range of species. To address this question, we mapped meiotic DSBs in maize, a higher eukaryote with a large genome that is rich in repetitive DNA. We found DSBs in maize to be frequent in all chromosome regions, including sites lacking COs, such as centromeres and pericentromeric regions. Furthermore, most DSBs are formed in repetitive DNA, predominantly Gypsy retrotransposons, and only one-quarter of DSB hotspots are near genes. Genic and nongenic hotspots differ in several characteristics, and only genic DSBs contribute to crossover formation. Maize hotspots overlap regions of low nucleosome occupancy but show only limited association with H3K4me3 sites. Overall, maize DSB hotspots exhibit distribution patterns and characteristics not reported previously in other species. Understanding recombination patterns in maize will shed light on mechanisms affecting dynamics of the plant genome.
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36
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Lambing C, Franklin FCH, Wang CJR. Understanding and Manipulating Meiotic Recombination in Plants. PLANT PHYSIOLOGY 2017; 173:1530-1542. [PMID: 28108697 PMCID: PMC5338670 DOI: 10.1104/pp.16.01530] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/18/2017] [Indexed: 05/18/2023]
Abstract
Meiosis is a specialized cell division, essential in most reproducing organisms to halve the number of chromosomes, thereby enabling the restoration of ploidy levels during fertilization. A key step of meiosis is homologous recombination, which promotes homologous pairing and generates crossovers (COs) to connect homologous chromosomes until their separation at anaphase I. These CO sites, seen cytologically as chiasmata, represent a reciprocal exchange of genetic information between two homologous nonsister chromatids. This gene reshuffling during meiosis has a significant influence on evolution and also plays an essential role in plant breeding, because a successful breeding program depends on the ability to bring the desired combinations of alleles on chromosomes. However, the number and distribution of COs during meiosis is highly constrained. There is at least one CO per chromosome pair to ensure accurate segregation of homologs, but in most organisms, the CO number rarely exceeds three regardless of chromosome size. Moreover, their positions are not random on chromosomes but exhibit regional preference. Thus, genes in recombination-poor regions tend to be inherited together, hindering the generation of novel allelic combinations that could be exploited by breeding programs. Recently, much progress has been made in understanding meiotic recombination. In particular, many genes involved in the process in Arabidopsis (Arabidopsis thaliana) have been identified and analyzed. With the coming challenges of food security and climate change, and our enhanced knowledge of how COs are formed, the interest and needs in manipulating CO formation are greater than ever before. In this review, we focus on advances in understanding meiotic recombination and then summarize the attempts to manipulate CO formation. Last, we pay special attention to the meiotic recombination in polyploidy, which is a common genomic feature for many crop plants.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (C.L.)
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (F.C.H.F.); and
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan (C.-J.R.W.)
| | - F Chris H Franklin
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (C.L.)
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (F.C.H.F.); and
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan (C.-J.R.W.)
| | - Chung-Ju Rachel Wang
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (C.L.);
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (F.C.H.F.); and
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan (C.-J.R.W.)
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37
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Sidhu GK, Warzecha T, Pawlowski WP. Evolution of meiotic recombination genes in maize and teosinte. BMC Genomics 2017; 18:106. [PMID: 28122517 PMCID: PMC5267385 DOI: 10.1186/s12864-017-3486-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 01/11/2017] [Indexed: 11/25/2022] Open
Abstract
Background Meiotic recombination is a major source of genetic variation in eukaryotes. The role of recombination in evolution is recognized but little is known about how evolutionary forces affect the recombination pathway itself. Although the recombination pathway is fundamentally conserved across different species, genetic variation in recombination components and outcomes has been observed. Theoretical predictions and empirical studies suggest that changes in the recombination pathway are likely to provide adaptive abilities to populations experiencing directional or strong selection pressures, such as those occurring during species domestication. We hypothesized that adaptive changes in recombination may be associated with adaptive evolution patterns of genes involved in meiotic recombination. Results To examine how maize evolution and domestication affected meiotic recombination genes, we studied patterns of sequence polymorphism and divergence in eleven genes controlling key steps in the meiotic recombination pathway in a diverse set of maize inbred lines and several accessions of teosinte, the wild ancestor of maize. We discovered that, even though the recombination genes generally exhibited high sequence conservation expected in a pathway controlling a key cellular process, they showed substantial levels and diverse patterns of sequence polymorphism. Among others, we found differences in sequence polymorphism patterns between tropical and temperate maize germplasms. Several recombination genes displayed patterns of polymorphism indicative of adaptive evolution. Conclusions Despite their ancient origin and overall sequence conservation, meiotic recombination genes can exhibit extensive and complex patterns of molecular evolution. Changes in these genes could affect the functioning of the recombination pathway, and may have contributed to the successful domestication of maize and its expansion to new cultivation areas. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3486-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gaganpreet K Sidhu
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.,Current address: Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA
| | - Tomasz Warzecha
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.,Permanent address: Department of Plant Breeding and Seed Science, Agricultural University, Krakow, Poland
| | - Wojciech P Pawlowski
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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38
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Dreissig S, Fuchs J, Himmelbach A, Mascher M, Houben A. Sequencing of Single Pollen Nuclei Reveals Meiotic Recombination Events at Megabase Resolution and Circumvents Segregation Distortion Caused by Postmeiotic Processes. FRONTIERS IN PLANT SCIENCE 2017; 8:1620. [PMID: 29018459 PMCID: PMC5623100 DOI: 10.3389/fpls.2017.01620] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/04/2017] [Indexed: 05/21/2023]
Abstract
Meiotic recombination is a fundamental mechanism to generate novel allelic combinations which can be harnessed by breeders to achieve crop improvement. The recombination landscape of many crop species, including the major crop barley, is characterized by a dearth of recombination in 65% of the genome. In addition, segregation distortion caused by selection on genetically linked loci is a frequent and undesirable phenomenon in double haploid populations which hampers genetic mapping and breeding. Here, we present an approach to directly investigate recombination at the DNA sequence level by combining flow-sorting of haploid pollen nuclei of barley with single-cell genome sequencing. We confirm the skewed distribution of recombination events toward distal chromosomal regions at megabase resolution and show that segregation distortion is almost absent if directly measured in pollen. Furthermore, we show a bimodal distribution of inter-crossover distances, which supports the existence of two classes of crossovers which are sensitive or less sensitive to physical interference. We conclude that single pollen nuclei sequencing is an approach capable of revealing recombination patterns in the absence of segregation distortion.
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Affiliation(s)
- Steven Dreissig
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jörg Fuchs
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Axel Himmelbach
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Martin Mascher
- Domestication Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- *Correspondence: Martin Mascher
| | - Andreas Houben
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Andreas Houben
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39
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Abstract
Meiosis, the mechanism of creating haploid gametes, is a complex cellular process observed across sexually reproducing organisms. Fundamental to meiosis is the process of homologous recombination, whereby DNA double-strand breaks are introduced into the genome and are subsequently repaired to generate either noncrossovers or crossovers. Although homologous recombination is essential for chromosome pairing during prophase I, the resulting crossovers are critical for maintaining homolog interactions and enabling accurate segregation at the first meiotic division. Thus, the placement, timing, and frequency of crossover formation must be exquisitely controlled. In this review, we discuss the proteins involved in crossover formation, the process of their formation and designation, and the rules governing crossovers, all within the context of the important landmarks of prophase I. We draw together crossover designation data across organisms, analyze their evolutionary divergence, and propose a universal model for crossover regulation.
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Affiliation(s)
- Stephen Gray
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, New York 14853; ,
| | - Paula E Cohen
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, New York 14853; ,
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