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Boideau F, Huteau V, Maillet L, Brunet A, Coriton O, Deniot G, Trotoux G, Taburel-Lodé M, Eber F, Gilet M, Baron C, Boutte J, Richard G, Aury JM, Belser C, Labadie K, Morice J, Falentin C, Martin O, Falque M, Chèvre AM, Rousseau-Gueutin M. Alternating between even and odd ploidy levels switches on and off the recombination control, even near the centromeres. THE PLANT CELL 2024:koae208. [PMID: 39121028 DOI: 10.1093/plcell/koae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/12/2024] [Indexed: 08/11/2024]
Abstract
Meiotic recombination is a key biological process in plant evolution and breeding, as it generates genetic diversity in each generation through the formation of crossovers (COs). However, due to their importance in genome stability, COs are highly regulated in frequency and distribution. We previously demonstrated that this strict regulation of COs can be modified, both in terms of CO frequency and distribution, in allotriploid Brassica hybrids (2n = 3x = 29; AAC) resulting from a cross between Brassica napus (2n = 4x = 38; AACC) and Brassica rapa (2n = 2x = 20; AA). Using the recently updated B. napus genome now including pericentromeres, we demonstrated that COs occur in these cold regions in allotriploids, as close as 375 kb from the centromere. Reverse transcription quantitative PCR (RT-qPCR) of various meiotic genes indicated that Class I COs are likely involved in the increased recombination frequency observed in allotriploids. We also demonstrated that this modified recombination landscape can be maintained via successive generations of allotriploidy (odd ploidy level). This deregulated meiotic behavior reverts to strict regulation in allotetraploid (even ploidy level) progeny in the second generation. Overall, we provide an easy way to manipulate tight recombination control in a polyploid crop.
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Affiliation(s)
- Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Anael Brunet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | | | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Marie Gilet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Cécile Baron
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Julien Boutte
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, 91057 Evry, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Olivier Martin
- Institute of Plant Sciences Paris-Saclay, Université de Paris-Saclay, Paris-Cité and Evry, CNRS, INRAE, 91192 Gif-sur-Yvette, France
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Matthieu Falque
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
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Johnston SE. Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future. Mol Biol Evol 2024; 41:msae112. [PMID: 38959451 PMCID: PMC11221659 DOI: 10.1093/molbev/msae112] [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: 04/17/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 07/05/2024] Open
Abstract
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms of recombination are remarkably conserved across eukaryotes, yet meiotic genes and proteins show substantial variation in their sequence and function, even between closely related species. Furthermore, the rate and distribution of recombination shows a huge diversity within and between chromosomes, individuals, sexes, populations, and species. This variation has implications for many molecular and evolutionary processes, yet how and why this diversity has evolved is not well understood. A key step in understanding trait evolution is to determine its genetic basis-that is, the number, effect sizes, and distribution of loci underpinning variation. In this perspective, I discuss past and current knowledge on the genetic basis of variation in recombination rate and distribution, explore its evolutionary implications, and present open questions for future research.
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Affiliation(s)
- Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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3
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Gianinetti A, Ghizzoni R, Desiderio F, Morcia C, Terzi V, Baronchelli M. QTL Analysis of β-Glucan Content and Other Grain Traits in a Recombinant Population of Spring Barley. Int J Mol Sci 2024; 25:6296. [PMID: 38928003 PMCID: PMC11204098 DOI: 10.3390/ijms25126296] [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: 05/09/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Barley with high grain β-glucan content is valuable for functional foods. The identification of loci for high β-glucan content is, thus, of great importance for barley breeding. Segregation mapping for the content in β-glucan and other barley grain components (starch, protein, lipid, ash, phosphorous, calcium, sodium) was performed using the progeny of the cross between Glacier AC38, a mutant with high amylose, and CDC Fibar, a high β-glucan waxy cultivar. The offspring of this cross showed transgressive segregation for β-glucan content. Linkage analysis based on single-nucleotide polymorphism (SNP) molecular markers was used for the genotyping of the parents and recombinant inbred lines (RILs). Two Quantitative Trait Loci (QTL) for β-glucan content and several QTL for other grain components were found. The former ones, located on chromosomes 1H and 7H, explained 27.9% and 27.4% of the phenotypic variance, respectively. Glacier AC38 provided the allele for high β-glucan content at the QTL on chromosome 1H, whereas CDC Fibar contributed the allele at the QTL on chromosome 7H. Their recombination resulted in a novel haplotype with higher β-glucan content, up to 18.4%. Candidate genes are proposed for these two QTL: HvCslF9, involved in β-glucan biosynthesis, for the QTL on chromosome 1H; Horvu_PLANET_7H01G069300, a gene encoding an ATP-Binding Cassette (ABC) transporter, for the QTL on chromosome 7H.
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4
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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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5
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Wong ELY, Filatov DA. The role of recombination landscape in species hybridisation and speciation. FRONTIERS IN PLANT SCIENCE 2023; 14:1223148. [PMID: 37484464 PMCID: PMC10361763 DOI: 10.3389/fpls.2023.1223148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023]
Abstract
It is now well recognised that closely related species can hybridize and exchange genetic material, which may promote or oppose adaptation and speciation. In some cases, interspecific hybridisation is very common, making it surprising that species identity is preserved despite active gene exchange. The genomes of most eukaryotic species are highly heterogeneous with regard to gene density, abundance of repetitive DNA, chromatin compactisation etc, which can make certain genomic regions more prone or more resistant to introgression of genetic material from other species. Heterogeneity in local recombination rate underpins many of the observed patterns across the genome (e.g. actively recombining regions are typically gene rich and depleted for repetitive DNA) and it can strongly affect the permeability of genomic regions to interspecific introgression. The larger the region lacking recombination, the higher the chance for the presence of species incompatibility gene(s) in that region, making the entire non- or rarely recombining block impermeable to interspecific introgression. Large plant genomes tend to have highly heterogeneous recombination landscape, with recombination frequently occurring at the ends of the chromosomes and central regions lacking recombination. In this paper we review the relationship between recombination and introgression in plants and argue that large rarely recombining regions likely play a major role in preserving species identity in actively hybridising plant species.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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6
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Ziolkowski PA. Why do plants need the ZMM crossover pathway? A snapshot of meiotic recombination from the perspective of interhomolog polymorphism. PLANT REPRODUCTION 2023; 36:43-54. [PMID: 35819509 PMCID: PMC9958190 DOI: 10.1007/s00497-022-00446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/20/2022] [Indexed: 06/06/2023]
Abstract
At the heart of meiosis is crossover recombination, i.e., reciprocal exchange of chromosome fragments between parental genomes. Surprisingly, in most eukaryotes, including plants, several recombination pathways that can result in crossover event operate in parallel during meiosis. These pathways emerged independently in the course of evolution and perform separate functions, which directly translate into their roles in meiosis. The formation of one crossover per chromosome pair is required for proper chromosome segregation. This "obligate" crossover is ensured by the major crossover pathway in plants, and in many other eukaryotes, known as the ZMM pathway. The secondary pathways play important roles also in somatic cells and function mainly as repair mechanisms for DNA double-strand breaks (DSBs) not used for crossover formation. One of the consequences of the functional differences between ZMM and other DSB repair pathways is their distinct sensitivities to polymorphisms between homologous chromosomes. From a population genetics perspective, these differences may affect the maintenance of genetic variability. This might be of special importance when considering that a significant portion of plants uses inbreeding as a predominant reproductive strategy, which results in loss of interhomolog polymorphism. While we are still far from fully understanding the relationship between meiotic recombination pathways and genetic variation in populations, recent studies of crossovers in plants offer a new perspective.
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Affiliation(s)
- Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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7
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Cai C, Pelé A, Bucher J, Finkers R, Bonnema G. Fine mapping of meiotic crossovers in Brassica oleracea reveals patterns and variations depending on direction and combination of crosses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1192-1210. [PMID: 36626115 DOI: 10.1111/tpj.16104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Meiotic recombination is crucial for assuring proper segregation of parental chromosomes and generation of novel allelic combinations. As this process is tightly regulated, identifying factors influencing rate, and distribution of meiotic crossovers (COs) is of major importance, notably for plant breeding programs. However, high-resolution recombination maps are sparse in most crops including the Brassica genus and knowledge about intraspecific variation and sex differences is lacking. Here, we report fine-scale resolution recombination landscapes for 10 female and 10 male crosses in Brassica oleracea, by analyzing progenies of five large four-way-cross populations from two reciprocally crossed F1s per population. Parents are highly diverse inbred lines representing major crops, including broccoli, cauliflower, cabbage, kohlrabi, and kale. We produced approximately 4.56T Illumina data from 1248 progenies and identified 15 353 CO across the 10 reciprocal crosses, 51.13% of which being mapped to <10 kb. We revealed fairly similar Mb-scale recombination landscapes among all cross combinations and between the sexes, and provided evidence that these landscapes are largely independent of sequence divergence. We evidenced strong influence of gene density and large structural variations on CO formation in B. oleracea. Moreover, we found extensive variations in CO number depending on the direction and combination of the initial parents crossed with, for the first time, a striking interdependency between these factors. These data improve our current knowledge on meiotic recombination and are important for Brassica breeders.
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Affiliation(s)
- Chengcheng Cai
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Alexandre Pelé
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Gennovation B.V., Agro Business Park 10, 6708 PW, Wageningen, The Netherlands
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
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8
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Cheng H, Zhang Z, Wen J, Lenstra JA, Heller R, Cai Y, Guo Y, Li M, Li R, Li W, He S, Wang J, Shao J, Song Y, Zhang L, Billah M, Wang X, Liu M, Jiang Y. Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep. PLoS Genet 2023; 19:e1010615. [PMID: 36821549 PMCID: PMC9949681 DOI: 10.1371/journal.pgen.1010615] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/13/2023] [Indexed: 02/24/2023] Open
Abstract
The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. Here, we analyze whole-genome sequencing individuals of 1,098 domestic sheep from 154 breeds, and 69 wild sheep from seven Ovis species. On average, we detected 6.8%, 1.0% and 0.2% introgressed sequence in domestic sheep originating from Iranian mouflon, urial and argali, respectively, with rare introgressions from other wild species. Interestingly, several introgressed haplotypes contributed to the morphological differentiations across sheep breeds, such as a RXFP2 haplotype from Iranian mouflon conferring the spiral horn trait, a MSRB3 haplotype from argali strongly associated with ear morphology, and a VPS13B haplotype probably originating from urial and mouflon possibly associated with facial traits. Our results reveal that introgression events from wild Ovis species contributed to the high rate of morphological differentiation in sheep breeds, but also to individual variation within breeds. We propose that long divergent haplotypes are a ubiquitous source of phenotypic variation that allows adaptation to a variable environment, and that these remain intact in the receiving population probably due to reduced recombination.
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Affiliation(s)
- Hong Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhuangbiao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiayue Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yingwei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenrong Li
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Sangang He
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Jintao Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Junjie Shao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuxuan Song
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Masum Billah
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Mingjun Liu
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
- * E-mail: (ML); (YJ)
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- * E-mail: (ML); (YJ)
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9
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Lisker A, Maurer A, Schmutzer T, Kazman E, Cöster H, Holzapfel J, Ebmeyer E, Alqudah AM, Sannemann W, Pillen K. A Haplotype-Based GWAS Identified Trait-Improving QTL Alleles Controlling Agronomic Traits under Contrasting Nitrogen Fertilization Treatments in the MAGIC Wheat Population WM-800. PLANTS (BASEL, SWITZERLAND) 2022; 11:3508. [PMID: 36559621 PMCID: PMC9784842 DOI: 10.3390/plants11243508] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/27/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The multi-parent-advanced-generation-intercross (MAGIC) population WM-800 was developed by intercrossing eight modern winter wheat cultivars to enhance the genetic diversity present in breeding populations. We cultivated WM-800 during two seasons in seven environments under two contrasting nitrogen fertilization treatments. WM-800 lines exhibited highly significant differences between treatments, as well as high heritabilities among the seven agronomic traits studied. The highest-yielding WM-line achieved an average yield increase of 4.40 dt/ha (5.2%) compared to the best founder cultivar Tobak. The subsequent genome-wide-association-study (GWAS), which was based on haplotypes, located QTL for seven agronomic traits including grain yield. In total, 40, 51, and 46 QTL were detected under low, high, and across nitrogen treatments, respectively. For example, the effect of QYLD_3A could be associated with the haplotype allele of cultivar Julius increasing yield by an average of 4.47 dt/ha (5.2%). A novel QTL on chromosome 2B exhibited pleiotropic effects, acting simultaneously on three-grain yield components (ears-per-square-meter, grains-per-ear, and thousand-grain-weight) and plant-height. These effects may be explained by a member of the nitrate-transporter-1 (NRT1)/peptide-family, TaNPF5.34, located 1.05 Mb apart. The WM-800 lines and favorable QTL haplotypes, associated with yield improvements, are currently implemented in wheat breeding programs to develop advanced nitrogen-use efficient wheat cultivars.
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Affiliation(s)
- Antonia Lisker
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Thomas Schmutzer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Ebrahim Kazman
- Syngenta Seeds GmbH, Kroppenstedter Str. 4, 39387 Oschersleben, Germany
| | | | - Josef Holzapfel
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg an der Isar, Germany
| | - Erhard Ebmeyer
- KWS Lochow GMBH, Ferdinand-Lochow-Str. 5, 29303 Bergen, Germany
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha P.O. Box 2713, Qatar
| | - Wiebke Sannemann
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
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10
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Pourkheirandish M, Komatsuda T. Grain Disarticulation in Wild Wheat and Barley. PLANT & CELL PHYSIOLOGY 2022; 63:1584-1591. [PMID: 35765920 PMCID: PMC9680857 DOI: 10.1093/pcp/pcac091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/17/2022] [Accepted: 08/04/2022] [Indexed: 05/26/2023]
Abstract
Our industrial-scale crop monocultures, which are necessary to provide grain for large-scale food and feed production, are highly vulnerable to biotic and abiotic stresses. Crop wild relatives have adapted to harsh environmental conditions over millennia; thus, they are an important source of genetic variation and crop diversification. Despite several examples where significant yield increases have been achieved through the introgression of genomic regions from wild relatives, more detailed understanding of the differences between wild and cultivated species for favorable and unfavorable traits is still required to harness these valuable resources. Recently, as an alternative to the introgression of beneficial alleles from the wild into domesticated species, a radical suggestion is to domesticate wild relatives to generate new crops. A first and critical step for the domestication of cereal wild relatives would be to prevent grain disarticulation from the inflorescence at maturity. Discovering the molecular mechanisms and understanding the network of interactions behind grain retention/disarticulation would enable the implementation of approaches to select for this character in targeted species. Brittle rachis 1 and Brittle rachis 2 are major genes responsible for grain disarticulation in the wild progenitors of wheat and barley that were the target of mutations during domestication. These two genes are only found in the Triticeae tribe and are hypothesized to have evolved by a duplication followed by neo-functionalization. Current knowledge gaps include the molecular mechanisms controlling grain retention in cereals and the genomic consequences of strong selection for this essential character.
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Affiliation(s)
| | - Takao Komatsuda
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
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11
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Genome-Wide Association Study of Salt Tolerance-Related Traits during Germination and Seedling Development in an Intermedium-Spike Barley Collection. Int J Mol Sci 2022; 23:ijms231911060. [PMID: 36232362 PMCID: PMC9569600 DOI: 10.3390/ijms231911060] [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: 07/13/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Increased salinity is one of the major consequences of climatic change affecting global crop production. The early stages in the barley (Hordeum vulgare L.) life cycle are considered the most critical phases due to their contributions to final crop yield. Particularly, the germination and seedling development are sensitive to numerous environmental stresses, especially soil salinity. In this study, we aimed to identify SNP markers linked with germination and seedling development at 150 mM NaCl as a salinity treatment. We performed a genome-wide association study (GWAS) using a panel of 208 intermedium-spike barley (H. vulgare convar. intermedium (Körn.) Mansf.) accessions and their genotype data (i.e., 10,323 SNPs) using the genome reference sequence of “Morex”. The phenotypic results showed that the 150 mM NaCl salinity treatment significantly reduced all recorded germination and seedling-related traits compared to the control treatment. Furthermore, six accessions (HOR 11747, HOR 11718, HOR 11640, HOR 11256, HOR 11275 and HOR 11291) were identified as the most salinity tolerant from the intermedium-spike barley collection. GWAS analysis indicated that a total of 38 highly significantly associated SNP markers under control and/or salinity traits were identified. Of these, two SNP markers on chromosome (chr) 1H, two on chr 3H, and one on chr 4H were significantly linked to seedling fresh and dry weight under salinity stress treatment. In addition, two SNP markers on chr 7H were also significantly associated with seedling fresh and dry weight but under control condition. Under salinity stress, one SNP marker on chr 1H, 5H and 7H were detected for more than one phenotypic trait. We found that in most of the accessions exhibiting the highest salinity tolerance, most of the salinity-related QTLs were presented. These results form the basis for detailed studies, leading to improved salt tolerance breeding programs in barley.
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12
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Lian Q, Solier V, Walkemeier B, Durand S, Huettel B, Schneeberger K, Mercier R. The megabase-scale crossover landscape is largely independent of sequence divergence. Nat Commun 2022; 13:3828. [PMID: 35780220 PMCID: PMC9250513 DOI: 10.1038/s41467-022-31509-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/20/2022] [Indexed: 02/01/2023] Open
Abstract
Meiotic recombination frequency varies along chromosomes and strongly correlates with sequence divergence. However, the causal relationship between recombination landscapes and polymorphisms is unclear. Here, we characterize the genome-wide recombination landscape in the quasi-absence of polymorphisms, using Arabidopsis thaliana homozygous inbred lines in which a few hundred genetic markers were introduced through mutagenesis. We find that megabase-scale recombination landscapes in inbred lines are strikingly similar to the recombination landscapes in hybrids, with the notable exception of heterozygous large rearrangements where recombination is prevented locally. In addition, the megabase-scale recombination landscape can be largely explained by chromatin features. Our results show that polymorphisms are not a major determinant of the shape of the megabase-scale recombination landscape but rather favour alternative models in which recombination and chromatin shape sequence divergence across the genome. The frequency of recombination varies along chromosomes and highly correlates with sequence divergence. Here, the authors show that polymorphisms are not a major determinant of the megabase-scale recombination landscape in Arabidopsis, which is rather determined by chromatin accessibility and DNA methylation.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Victor Solier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Birgit Walkemeier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Stéphanie Durand
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Bruno Huettel
- Max Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany. .,Faculty of Biology, LMU Munich, 82152, Planegg-Martinsried, Germany.
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
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13
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Schneider M, Casale F, Stich B. Accurate recombination estimation from pooled genotyping and sequencing: a case study on barley. BMC Genomics 2022; 23:468. [PMID: 35752769 PMCID: PMC9233355 DOI: 10.1186/s12864-022-08701-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/15/2022] [Indexed: 11/15/2022] Open
Abstract
Sexual reproduction involves meiotic recombination and the creation of crossing over between homologous chromosomes, which leads to new allele combinations. We present a new approach that uses the allele frequency differences and the physical distance of neighboring polymorphisms to estimate the recombination rate from pool genotyping or sequencing. This allows a considerable cost reduction compared to conventional mapping based on genotyping or sequencing data of single individuals. We evaluated the approach based on computer simulations at various genotyping depths and population sizes as well as applied it to experimental data of 45 barley populations, comprising 4182 RIL. High correlations between the recombination rates from this new pool genetic mapping approach and conventional mapping in simulated and experimental barley populations were observed. The proposed method therefore provides a reliable genetic map position and recombination rate estimation in defined genomic windows.
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Affiliation(s)
- Michael Schneider
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Federico Casale
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225, Düsseldorf, Germany. .,Max Planck Institute for Plant Breeding Research, 50829, Köln, Germany. .,Cluster of Excellence on Plant Sciences, From Complex Traits Towards Synthetic Modules, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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14
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Schreiber M, Gao Y, Koch N, Fuchs J, Heckmann S, Himmelbach A, Börner A, Özkan H, Maurer A, Stein N, Mascher M, Dreissig S. Recombination landscape divergence between populations is marked by larger low-recombining regions in domesticated rye. Mol Biol Evol 2022; 39:msac131. [PMID: 35687854 PMCID: PMC9218680 DOI: 10.1093/molbev/msac131] [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: 02/01/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The genomic landscape of recombination plays an essential role in evolution. Patterns of recombination are highly variable along chromosomes, between sexes, individuals, populations, and species. In many eukaryotes, recombination rates are elevated in sub-telomeric regions and drastically reduced near centromeres, resulting in large low-recombining (LR) regions. The processes of recombination are influenced by genetic factors, such as different alleles of genes involved in meiosis and chromatin structure, as well as external environmental stimuli like temperature and overall stress. In this work, we focused on the genomic landscapes of recombination in a collection of 916 rye (Secale cereale) individuals. By analysing population structure among individuals of different domestication status and geographic origin, we detected high levels of admixture, reflecting the reproductive biology of a self-incompatible, wind-pollinating grass species. We then analysed patterns of recombination in overlapping subpopulations, which revealed substantial variation in the physical size of LR regions, with a tendency for larger LR regions in domesticated subpopulations. Genome-wide association scans (GWAS) for LR region size revealed a major quantitative-trait-locus (QTL) at which, among 18 annotated genes, an ortholog of histone H4 acetyltransferase ESA1 was located. Rye individuals belonging to domesticated subpopulations showed increased synaptonemal complex length, but no difference in crossover frequency, indicating that only the recombination landscape is different. Furthermore, the genomic region harbouring rye ScESA1 showed moderate patterns of selection in domesticated subpopulations, suggesting that larger LR regions were indirectly selected for during domestication to achieve more homogeneous populations for agricultural use.
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Affiliation(s)
- Mona Schreiber
- Department of Biology, University of Marburg, 35037 Marburg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Yixuan Gao
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Natalie Koch
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Hakan Özkan
- Faculty of Agriculture, Department of Field Crops, University of Cukurova, 01330 Adana, Turkey
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Steven Dreissig
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
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15
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Genome-wide analyses of introgression between two sympatric Asian oak species. Nat Ecol Evol 2022; 6:924-935. [PMID: 35513577 DOI: 10.1038/s41559-022-01754-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/29/2022] [Indexed: 12/13/2022]
Abstract
Introgression can be an important source of new alleles for adaption under rapidly changing environments, perhaps even more important than standing variation. Though introgression has been extensively studied in many plants and animals, key questions on the underlying mechanisms of introgression still remain unanswered. In particular, we are yet to determine the genomic distribution of introgressed regions along the genome; whether the extent and patterns of introgression are influenced by ecological factors; and when and how introgression contributes to adaptation. Here, we generated high-quality genomic resources for two sympatric widespread Asian oak species, Quercus acutissima and Q. variabilis, sampled in multiple forests to study introgression between them. We show that introgressed regions are broadly distributed across the genome. Introgression was affected by genetic divergence between pairs of populations and by the similarity of the environments in which they live-populations occupying similar ecological sites tended to share the same introgressed regions. Introgressed genomic footprints of adaptation were preferentially located in regions with suppressed recombination rate. Introgression probably confers adaptation in these oak populations by introducing allelic variation in cis-regulatory elements, in particular through transposable element insertions, thereby altering the regulation of genes related to stress. Our results provide new avenues of research for uncovering mechanisms of adaptation due to hybridization in sympatric species.
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16
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Casale F, Van Inghelandt D, Weisweiler M, Li J, Stich B. Genomic prediction of the recombination rate variation in barley - A route to highly recombinogenic genotypes. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:676-690. [PMID: 34783155 PMCID: PMC8989500 DOI: 10.1111/pbi.13746] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/06/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Meiotic recombination is not only fundamental to the adaptation of sexually reproducing eukaryotes in nature but increased recombination rates facilitate the combination of favourable alleles into a single haplotype in breeding programmes. The main objectives of this study were to (i) assess the extent and distribution of the recombination rate variation in cultivated barley (Hordeum vulgare L.), (ii) quantify the importance of the general and specific recombination effects, and (iii) evaluate a genomic selection approach's ability to predict the recombination rate variation. Genetic maps were created for the 45 segregating populations that were derived from crosses among 23 spring barley inbreds with origins across the world. The genome-wide recombination rate among populations ranged from 0.31 to 0.73 cM/Mbp. The crossing design used in this study allowed to separate the general recombination effects (GRE) of individual parental inbreds from the specific recombination effects (SRE) caused by the combinations of parental inbreds. The variance of the genome-wide GRE was found to be about eight times the variance of the SRE. This finding indicated that parental inbreds differ in the efficiency of their recombination machinery. The ability to predict the chromosome or genome-wide recombination rate of an inbred ranged from 0.80 to 0.85. These results suggest that a reliable screening of large genetic materials for their potential to cause a high extent of genetic recombination in their progeny is possible, allowing to systematically manipulate the recombination rate using natural variation.
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Affiliation(s)
- Federico Casale
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
| | - Delphine Van Inghelandt
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
| | - Marius Weisweiler
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
| | - Jinquan Li
- Max Planck Institute for Plant Breeding ResearchKölnGermany
- Strube D&S GmbHSöllingenGermany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
- Max Planck Institute for Plant Breeding ResearchKölnGermany
- Cluster of Excellence on Plant SciencesFrom Complex Traits Towards Synthetic ModulesDüsseldorfGermany
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17
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Abstract
REC8 meiotic recombination protein (REC8) is a member of structural maintenance of chromosome (SMC) protein partners, which play an important role in meiosis, anti-tumor, and sperm formation. As the adapter proteins of RLR signaling and cGAS-DNA signaling, the activity and stability of MAVS (also known as VISA, Cardif and IPS-1) and STING (also known as MITA) are critical for innate immunity. Here, we report that REC8 interacts with MAVS and STING, and inhibits their ubiquitination and subsequent degradation, thereby promoting innate antiviral signaling. REC8 is upregulated through the JAK-STAT signaling pathway under viral infection. Knockdown of REC8 impair the innate immune responses against VSV (Vesicular Stomatitis Virus), NDV (Newcastle disease virus) and HSV (herpes simplex virus). Mechanistically, under the infection of viruses, the SUMOylated REC8 is transferred from the nucleus to the cytoplasm and then interacts with MAVS and STING to inhibit their K48-linked ubiquitination triggered by RNF5. Moreover, REC8 promotes the recruitment of TBK1 to MAVS and STING. Thus, REC8 functions as a positive modulator of innate immunity. Our work highlights a previously undocumented role of meiosis-associated protein REC8 in regulating innate immunity. IMPORTANCE The innate immune response is crucial for the host to resist the invasion of viruses and other pathogens. STING and MAVS play a critical role in the innate immune response to DNA and RNA viral infection, respectively. In this study, REC8 promotes the innate immune response by targeting STING and MAVS. Notably, REC8 interacts with MAVS and STING in the cytoplasm and inhibits K48-linked ubiquitination of MAVS and STING triggered by RNF5, stabilizing MAVS and STING protein to promote innate immunity and gradually inhibiting viral infection. Our study provides a new insight for the study of antiviral innate immune.
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18
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Chromosome-Wide Characterization of Intragenic Crossover in Shiitake Mushroom, Lentinula edodes. J Fungi (Basel) 2021; 7:jof7121076. [PMID: 34947058 PMCID: PMC8704546 DOI: 10.3390/jof7121076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022] Open
Abstract
Meiotic crossover plays a critical role in generating genetic variations and is a central component of breeding. However, our understanding of crossover in mushroom-forming fungi is limited. Here, in Lentinula edodes, we characterized the chromosome-wide intragenic crossovers, by utilizing the single-nucleotide polymorphisms (SNPs) datasets of an F1 haploid progeny. A total of 884 intragenic crossovers were identified in 110 single-spore isolates, the majority of which were closer to transcript start sites. About 71.5% of the intragenic crossovers were clustered into 65 crossover hotspots. A 10 bp motif (GCTCTCGAAA) was significantly enriched in the hotspot regions. Crossover frequencies around mating-type A (MAT-A) loci were enhanced and formed a hotspot in L. edodes. Genome-wide quantitative trait loci (QTLs) mapping identified sixteen crossover-QTLs, contributing 8.5–29.1% of variations. Most of the detected crossover-QTLs were co-located with crossover hotspots. Both cis- and trans-QTLs contributed to the nonuniformity of crossover along chromosomes. On chr2, we identified a QTL hotspot that regulated local, global crossover variation and crossover hotspot in L. edodes. These findings and observations provide a comprehensive view of the crossover landscape in L. edodes, and advance our understandings of conservation and diversity of meiotic recombination in mushroom-forming fungi.
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19
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Zhao X, Fu X, Yin C, Lu F. Wheat speciation and adaptation: perspectives from reticulate evolution. ABIOTECH 2021; 2:386-402. [PMID: 36311810 PMCID: PMC9590565 DOI: 10.1007/s42994-021-00047-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022]
Abstract
Reticulate evolution through the interchanging of genetic components across organisms can impact significantly on the fitness and adaptation of species. Bread wheat (Triticum aestivum subsp. aestivum) is one of the most important crops in the world. Allopolyploid speciation, frequent hybridization, extensive introgression, and occasional horizontal gene transfer (HGT) have been shaping a typical paradigm of reticulate evolution in bread wheat and its wild relatives, which is likely to have a substantial influence on phenotypic traits and environmental adaptability of bread wheat. In this review, we outlined the evolutionary history of bread wheat and its wild relatives with a highlight on the interspecific hybridization events, demonstrating the reticulate relationship between species/subspecies in the genera Triticum and Aegilops. Furthermore, we discussed the genetic mechanisms and evolutionary significance underlying the introgression of bread wheat and its wild relatives. An in-depth understanding of the evolutionary process of Triticum species should be beneficial to future genetic study and breeding of bread wheat.
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Affiliation(s)
- Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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20
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Maurer A, Pillen K. Footprints of Selection Derived From Temporal Heterozygosity Patterns in a Barley Nested Association Mapping Population. FRONTIERS IN PLANT SCIENCE 2021; 12:764537. [PMID: 34721490 PMCID: PMC8551860 DOI: 10.3389/fpls.2021.764537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Nowadays, genetic diversity more than ever represents a key driver of adaptation to climate challenges like drought, heat, and salinity. Therefore, there is a need to replenish the limited elite gene pools with favorable exotic alleles from the wild progenitors of our crops. Nested association mapping (NAM) populations represent one step toward exotic allele evaluation and enrichment of the elite gene pool. We investigated an adaptive selection strategy in the wild barley NAM population HEB-25 based on temporal genomic data by studying the fate of 214,979 SNP loci initially heterozygous in individual BC1S3 lines after five cycles of selfing and field propagation. We identified several loci exposed to adaptive selection in HEB-25. In total, 48.7% (104,725 SNPs) of initially heterozygous SNP calls in HEB-25 were fixed in BC1S3:8 generation, either toward the wild allele (19.9%) or the cultivated allele (28.8%). Most fixed SNP loci turned out to represent gene loci involved in domestication and flowering time as well as plant height, for example, btr1/btr2, thresh-1, Ppd-H1, and sdw1. Interestingly, also unknown loci were found where the exotic allele was fixed, hinting at potentially useful exotic alleles for plant breeding.
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21
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Natural variation identifies SNI1, the SMC5/6 component, as a modifier of meiotic crossover in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2021970118. [PMID: 34385313 PMCID: PMC8379953 DOI: 10.1073/pnas.2021970118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination plays a fundamental role in shaping genetic diversity in eukaryotes. Extensive variation in crossover rate exists between populations and species. The identity of modifier loci and their roles in genome evolution remain incompletely understood. We explored natural variation in Arabidopsis crossover and identified SNI1 as the causal gene underlying a major modifier locus. To date, SNI1 had no known role in crossover. SNI1 is a component of the SMC5/6 complex that is closely related to cohesin and condensin. Arabidopsis sni1 and other SMC5/6 mutants show similar effects on the interference-independent crossover pathway. Hence, our findings demonstrate that the SMC5/6 complex, which is known for its role in DNA damage repair, is also important for control of meiotic crossover. The frequency and distribution of meiotic crossovers are tightly controlled; however, variation in this process can be observed both within and between species. Using crosses of two natural Arabidopsis thaliana accessions, Col and Ler, we mapped a crossover modifier locus to semidominant polymorphisms in SUPPRESSOR OF NPR1-1 INDUCIBLE 1 (SNI1), which encodes a component of the SMC5/6 complex. The sni1 mutant exhibits a modified pattern of recombination across the genome with crossovers elevated in chromosome distal regions but reduced in pericentromeres. Mutations in SNI1 result in reduced crossover interference and can partially restore the fertility of a Class I crossover pathway mutant, which suggests that the protein affects noninterfering crossover repair. Therefore, we tested genetic interactions between SNI1 and both RECQ4 and FANCM DNA helicases, which showed that additional Class II crossovers observed in the sni1 mutant are FANCM independent. Furthermore, genetic analysis of other SMC5/6 mutants confirms the observations of crossover redistribution made for SNI1. The study reveals the importance of the SMC5/6 complex in ensuring the proper progress of meiotic recombination in plants.
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22
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Abstract
Sex, as well as meiotic recombination between homologous chromosomes, is nearly ubiquitous among eukaryotes. In those species that use it, recombination is important for chromosome segregation during gamete production, and thus for fertility. Strikingly, although in most species only one crossover event per chromosome is required to ensure proper segregation, recombination rates vary considerably above this minimum and show variation within and among species. However, whether this variation in recombination is adaptive or neutral and what might shape it remain unclear. Empirical studies and theory support the idea that recombination is generally beneficial but can also have costs. Here, we review variation in genome-wide recombination rates, explore what might cause this, and discuss what is known about its mechanistic basis. We end by discussing the environmental sensitivity of meiosis and recombination rates, how these features may relate to adaptation, and their implications for a broader understanding of recombination rate evolution. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
| | - Kirsten Bomblies
- Plant Evolutionary Genetics, Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, 8092 Zürich, Switzerland;
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