1
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Singh J, van der Knaap E. Unintended Consequences of Plant Domestication. PLANT & CELL PHYSIOLOGY 2022; 63:1573-1583. [PMID: 35715986 DOI: 10.1093/pcp/pcac083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/12/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Human selection on wild populations mostly favored a common set of plant traits during domestication. This process of direct selection also altered other independent traits that were not directly perceived or desired during crop domestication and improvement. A deeper knowledge of the inadvertent and undesirable phenotypic effects and their underlying genetic causes can help design strategies to mitigate their effects and improve genetic gain in crop plants. We review different factors explaining the negative consequences of plant domestication at the phenotypic and genomic levels. We further describe the genetic causes of undesirable effects that originate from the selection of favorable alleles during plant domestication. In addition, we propose strategies that could be useful in attenuating such effects for crop improvement. With novel -omics and genome-editing tools, it is relatively approachable to understand and manipulate the genetic and biochemical mechanisms responsible for the undesirable phenotypes in domesticated plants.
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Affiliation(s)
- Jugpreet Singh
- Center for Applied Genetic Technologies, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
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2
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Fuentes RR, de Ridder D, van Dijk ADJ, Peters SA. Domestication shapes recombination patterns in tomato. Mol Biol Evol 2021; 39:6379725. [PMID: 34597400 PMCID: PMC8763028 DOI: 10.1093/molbev/msab287] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Meiotic recombination is a biological process of key importance in breeding, to generate genetic diversity and develop novel or agronomically relevant haplotypes. In crop tomato, recombination is curtailed as manifested by linkage disequilibrium decay over a longer distance and reduced diversity compared with wild relatives. Here, we compared domesticated and wild populations of tomato and found an overall conserved recombination landscape, with local changes in effective recombination rate in specific genomic regions. We also studied the dynamics of recombination hotspots resulting from domestication and found that loss of such hotspots is associated with selective sweeps, most notably in the pericentromeric heterochromatin. We detected footprints of genetic changes and structural variants, among them associated with transposable elements, linked with hotspot divergence during domestication, likely causing fine-scale alterations to recombination patterns and resulting in linkage drag.
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Affiliation(s)
- Roven Rommel Fuentes
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Sander A Peters
- Applied Bioinformatics, Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
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3
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Shen C, Wang N, Huang C, Wang M, Zhang X, Lin Z. Population genomics reveals a fine-scale recombination landscape for genetic improvement of cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:494-505. [PMID: 31002209 DOI: 10.1111/tpj.14339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/17/2019] [Accepted: 04/01/2019] [Indexed: 05/28/2023]
Abstract
Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population-scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population-scaled recombination rate between Gossypium hirsutum and G. arboreum and sub-genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome-wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high-recombination regions than were those of yield and early maturity traits. These results provide insights into the population-scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species.
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Affiliation(s)
- Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Nian Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Cong Huang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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4
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Velmurugan J, Milbourne D, Connolly V, Heslop-Harrison JS, Anhalt UCM, Lynch MB, Barth S. An Immortalized Genetic Mapping Population for Perennial Ryegrass: A Resource for Phenotyping and Complex Trait Mapping. FRONTIERS IN PLANT SCIENCE 2018; 9:717. [PMID: 29904390 PMCID: PMC5991167 DOI: 10.3389/fpls.2018.00717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
To address the lack of a truly portable, universal reference mapping population for perennial ryegrass, we have been developing a recombinant inbred line (RIL) mapping population of perennial ryegrass derived via single seed descent from a well-characterized F2 mapping population based on genetically distinct inbred parents in which the natural self-incompatibility (SI) system of perennial ryegrass has been overcome. We examined whether it is possible to create a genotyping by sequencing (GBS) based genetic linkage map in a small population of the F6 generation of this population. We used 41 F6 genotypes for GBS with PstI/MspI-based libraries. We successfully developed a genetic linkage map comprising 6074 SNP markers, placing a further 22080 presence and absence variation (PAV) markers on the map. We examined the resulting genetic map for general and RIL specific features. Overall segregation distortion levels were similar to those experienced in the F2 generation, but segregation distortion was reduced on linkage group 6 and increased on linkage group 7. Residual heterozygosity in the F6 generation was observed at a level of 5.4%. There was a high proportion of chromosomes (30%) exhibiting the intact haplotype of the original inbred parents of the F1 genotype from which the population is derived, pointing to a tendency for chromosomes to assort without recombining. This could affect the applicability of these lines and might make them more suitable for situations where repressed recombination is an advantage. Inter- and intra-chromosomal linkage disequilibrium (LD) analysis suggested that the map order was robust. We conclude that this RIL population, and subsequent F7 and F8 generations will be useful for genetic analysis and phenotyping of agronomic and biological important traits in perennial ryegrass.
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Affiliation(s)
- Janaki Velmurugan
- Crops Environment and Land Use Programme, Oak Park Research Centre, Teagasc – The Irish Agriculture and Food Development Authority, Carlow, Ireland
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Dan Milbourne
- Crops Environment and Land Use Programme, Oak Park Research Centre, Teagasc – The Irish Agriculture and Food Development Authority, Carlow, Ireland
| | - Vincent Connolly
- Crops Environment and Land Use Programme, Oak Park Research Centre, Teagasc – The Irish Agriculture and Food Development Authority, Carlow, Ireland
| | - J. S. Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ulrike C. M. Anhalt
- Crops Environment and Land Use Programme, Oak Park Research Centre, Teagasc – The Irish Agriculture and Food Development Authority, Carlow, Ireland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - M. B. Lynch
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Susanne Barth
- Crops Environment and Land Use Programme, Oak Park Research Centre, Teagasc – The Irish Agriculture and Food Development Authority, Carlow, Ireland
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5
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Haenel Q, Laurentino TG, Roesti M, Berner D. Meta-analysis of chromosome-scale crossover rate variation in eukaryotes and its significance to evolutionary genomics. Mol Ecol 2018; 27:2477-2497. [PMID: 29676042 DOI: 10.1111/mec.14699] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 01/02/2023]
Abstract
Understanding the distribution of crossovers along chromosomes is crucial to evolutionary genomics because the crossover rate determines how strongly a genome region is influenced by natural selection on linked sites. Nevertheless, generalities in the chromosome-scale distribution of crossovers have not been investigated formally. We fill this gap by synthesizing joint information on genetic and physical maps across 62 animal, plant and fungal species. Our quantitative analysis reveals a strong and taxonomically widespread reduction of the crossover rate in the centre of chromosomes relative to their peripheries. We demonstrate that this pattern is poorly explained by the position of the centromere, but find that the magnitude of the relative reduction in the crossover rate in chromosome centres increases with chromosome length. That is, long chromosomes often display a dramatically low crossover rate in their centre, whereas short chromosomes exhibit a relatively homogeneous crossover rate. This observation is compatible with a model in which crossover is initiated from the chromosome tips, an idea with preliminary support from mechanistic investigations of meiotic recombination. Consequently, we show that organisms achieve a higher genome-wide crossover rate by evolving smaller chromosomes. Summarizing theory and providing empirical examples, we finally highlight that taxonomically widespread and systematic heterogeneity in crossover rate along chromosomes generates predictable broad-scale trends in genetic diversity and population differentiation by modifying the impact of natural selection among regions within a genome. We conclude by emphasizing that chromosome-scale heterogeneity in crossover rate should urgently be incorporated into analytical tools in evolutionary genomics, and in the interpretation of resulting patterns.
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Affiliation(s)
- Quiterie Haenel
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | - Marius Roesti
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
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6
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Harper J, Phillips D, Thomas A, Gasior D, Evans C, Powell W, King J, King I, Jenkins G, Armstead I. B chromosomes are associated with redistribution of genetic recombination towards lower recombination chromosomal regions in perennial ryegrass. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1861-1871. [PMID: 29635481 PMCID: PMC6019035 DOI: 10.1093/jxb/ery052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/10/2018] [Indexed: 05/26/2023]
Abstract
Supernumerary 'B' chromosomes are non-essential components of the genome present in a range of plant and animal species-including many grasses. Within diploid and polyploid ryegrass and fescue species, including the forage grass perennial ryegrass (Lolium perenne L.), the presence of B chromosomes has been reported as influencing both chromosome pairing and chiasma frequencies. In this study, the effects of the presence/absence of B chromosomes on genetic recombination has been investigated through generating DArT (Diversity Arrays Technology) marker genetic maps for six perennial ryegrass diploid populations, the pollen parents of which contained either two B or zero B chromosomes. Through genetic and cytological analyses of these progeny and their parents, we have identified that, while overall cytological estimates of chiasma frequencies were significantly lower in pollen mother cells with two B chromosomes as compared with zero B chromosomes, the recombination frequencies within some marker intervals were actually increased, particularly for marker intervals in lower recombination regions of chromosomes, namely pericentromeric regions. Thus, in perennial ryegrass, the presence of two B chromosomes redistributed patterns of meiotic recombination in pollen mother cells in ways which could increase the range of allelic variation available to plant breeders.
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Affiliation(s)
- John Harper
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Dylan Phillips
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ann Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Dagmara Gasior
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Caron Evans
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - Julie King
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Ian King
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Glyn Jenkins
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ian Armstead
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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7
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Xie Z, Wang L, Wang L, Wang Z, Lu Z, Tian D, Yang S, Hurst LD. Mutation rate analysis via parent-progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids. Proc Biol Sci 2017; 283:rspb.2016.1016. [PMID: 27798292 PMCID: PMC5095371 DOI: 10.1098/rspb.2016.1016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/01/2016] [Indexed: 12/30/2022] Open
Abstract
Mutation rates vary between species, between strains within species and between regions within a genome. What are the determinants of these forms of variation? Here, via parent–offspring sequencing of the peach we ask whether (i) woody perennials tend to have lower per unit time mutation rates compared to annuals, and (ii) hybrid strains have high mutation rates. Between a leaf from a low heterozygosity individual, derived from an intraspecific cross, to a leaf of its selfed progeny, the mutation rate is 7.77 × 10−9 point mutations per bp per generation, similar to Arabidopsis thaliana (7.0–7.4 × 10−9 point mutations per bp per generation). This suggests a low per unit time mutation rate as the generation time is much longer in peach. This is supported by our estimate of 9.48 × 10−9 point mutations per bp per generation from a 200-year-old low heterozygosity peach to its progeny. From a more highly heterozygous individual derived from an interspecific cross to its selfed progeny, the mutation rate is 1.38 × 10−8 mutations per site per generation, consistent with raised rates in hybrids. Our data thus suggest that (i) peach has an approximately order of magnitude lower mutation rate per unit time than Arabidopsis, consistent with reports of low evolutionary rates in woody perennials, and (ii) hybridization may, indeed, be associated with increased mutation rates as considered over a century ago.
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Affiliation(s)
- Zhengqing Xie
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Lirong Wang
- Chinese Academy of Agriculture Sciences, Zhengzhou Fruit Research Institute, Zhengzhou 450009, People's Republic of China
| | - Zhiqiang Wang
- Chinese Academy of Agriculture Sciences, Zhengzhou Fruit Research Institute, Zhengzhou 450009, People's Republic of China
| | - Zhenhua Lu
- Chinese Academy of Agriculture Sciences, Zhengzhou Fruit Research Institute, Zhengzhou 450009, People's Republic of China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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8
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Wang L, Zhang Y, Qin C, Tian D, Yang S, Hurst LD. Mutation rate analysis via parent-progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation. Proc Biol Sci 2017; 283:rspb.2016.1785. [PMID: 27798307 PMCID: PMC5095386 DOI: 10.1098/rspb.2016.1785] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/29/2016] [Indexed: 12/30/2022] Open
Abstract
Mutation rates and recombination rates vary between species and between regions within a genome. What are the determinants of these forms of variation? Prior evidence has suggested that the recombination might be mutagenic with an excess of new mutations in the vicinity of recombination break points. As it is conjectured that domesticated taxa have higher recombination rates than wild ones, we expect domesticated taxa to have raised mutation rates. Here, we use parent–offspring sequencing in domesticated and wild peach to ask (i) whether recombination is mutagenic, and (ii) whether domesticated peach has a higher recombination rate than wild peach. We find no evidence that domesticated peach has an increased recombination rate, nor an increased mutation rate near recombination events. If recombination is mutagenic in this taxa, the effect is too weak to be detected by our analysis. While an absence of recombination-associated mutation might explain an absence of a recombination–heterozygozity correlation in peach, we caution against such an interpretation.
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Affiliation(s)
- Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yanchun Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Chao Qin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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9
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Affiliation(s)
- John M Dearn
- Department of Population Biology, Research School of Biological Sciences, Australian National University, Canberra
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10
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Si W, Yuan Y, Huang J, Zhang X, Zhang Y, Zhang Y, Tian D, Wang C, Yang Y, Yang S. Widely distributed hot and cold spots in meiotic recombination as shown by the sequencing of rice F2 plants. THE NEW PHYTOLOGIST 2015; 206:1491-502. [PMID: 25664766 DOI: 10.1111/nph.13319] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/29/2014] [Indexed: 05/02/2023]
Abstract
Numerous studies have argued that environmental variations may contribute to evolution through the generation of novel heritable variations via meiotic recombination, which plays a crucial role in crop domestication and improvement. Rice is one of the most important staple crops, but no direct estimate of recombination events has yet been made at a fine scale. Here, we address this limitation by sequencing 41 rice individuals with high sequencing coverage and c. 900 000 accurate markers. An average of 33.9 crossover (c. 4.53 cM Mb(-1) ) and 2.47 non-crossover events were detected per F2 plant, which is similar to the values in Arabidopsis. Although not all samples in the stress treatment group showed an increased number of crossover events, environmental stress increased the recombination rate in c. 28.5% of samples. Interestingly, the crossovers showed a highly uneven distribution among and along chromosomes, with c. 13.9% of the entire genome devoid of crossovers, including 11 of the 12 centromere regions, and c. 0.72% of the genome containing large numbers of crossovers (> 50 cM Mb(-1) ). The gene ontology (GO) categories showed that genes clustered within the recombination hot spot regions primarily tended to be involved in responses to environmental stimuli, suggesting that recombination plays an important role for adaptive evolution in rapidly changing environments.
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Affiliation(s)
- Weina Si
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Yang Yuan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Yanchun Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China
| | - Yonghua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
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11
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Liu H, Zhang X, Huang J, Chen JQ, Tian D, Hurst LD, Yang S. Causes and consequences of crossing-over evidenced via a high-resolution recombinational landscape of the honey bee. Genome Biol 2015; 16:15. [PMID: 25651211 PMCID: PMC4305242 DOI: 10.1186/s13059-014-0566-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/08/2014] [Indexed: 11/20/2022] Open
Abstract
Background Social hymenoptera, the honey bee (Apis mellifera) in particular, have ultra-high crossover rates and a large degree of intra-genomic variation in crossover rates. Aligned with haploid genomics of males, this makes them a potential model for examining the causes and consequences of crossing over. To address why social insects have such high crossing-over rates and the consequences of this, we constructed a high-resolution recombination atlas by sequencing 55 individuals from three colonies with an average marker density of 314 bp/marker. Results We find crossing over to be especially high in proximity to genes upregulated in worker brains, but see no evidence for a coupling with immune-related functioning. We detect only a low rate of non-crossover gene conversion, contrary to current evidence. This is in striking contrast to the ultrahigh crossing-over rate, almost double that previously estimated from lower resolution data. We robustly recover the predicted intragenomic correlations between crossing over and both population level diversity and GC content, which could be best explained as indirect and direct consequences of crossing over, respectively. Conclusions Our data are consistent with the view that diversification of worker behavior, but not immune function, is a driver of the high crossing-over rate in bees. While we see both high diversity and high GC content associated with high crossing-over rates, our estimate of the low non-crossover rate demonstrates that high non-crossover rates are not a necessary consequence of high recombination rates. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0566-0) contains supplementary material, which is available to authorized users.
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12
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Muñoz-Fuentes V, Marcet-Ortega M, Alkorta-Aranburu G, Linde Forsberg C, Morrell JM, Manzano-Piedras E, Söderberg A, Daniel K, Villalba A, Toth A, Di Rienzo A, Roig I, Vilà C. Strong artificial selection in domestic mammals did not result in an increased recombination rate. Mol Biol Evol 2014; 32:510-23. [PMID: 25414125 DOI: 10.1093/molbev/msu322] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recombination rates vary in intensity and location at the species, individual, sex and chromosome levels. Despite the fundamental biological importance of this process, the selective forces that operate to shape recombination rate and patterns are unclear. Domestication offers a unique opportunity to study the interplay between recombination and selection. In domesticates, intense selection for particular traits is imposed on small populations over many generations, resulting in organisms that differ, sometimes dramatically, in morphology and physiology from their wild ancestor. Although earlier studies suggested increased recombination rate in domesticates, a formal comparison of recombination rates between domestic mammals and their wild congeners was missing. In order to determine broad-scale recombination rate, we used immunolabeling detection of MLH1 foci as crossover markers in spermatocytes in three pairs of closely related wild and domestic species (dog and wolf, goat and ibex, and sheep and mouflon). In the three pairs, and contrary to previous suggestions, our data show that contemporary recombination rate is higher in the wild species. Subsequently, we inferred recombination breakpoints in sequence data for 16 genomic regions in dogs and wolves, each containing a locus associated with a dog phenotype potentially under selection during domestication. No difference in the number and distribution of recombination breakpoints was found between dogs and wolves. We conclude that our data indicate that strong directional selection did not result in changes in recombination in domestic mammals, and that both upper and lower bounds for crossover rates may be tightly regulated.
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Affiliation(s)
- Violeta Muñoz-Fuentes
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana EBD-CSIC, Sevilla, Spain Department of Population and Conservation Biology, Uppsala University, Uppsala, Sweden
| | - Marina Marcet-Ortega
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain Cytology and Histology Unit, Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | | | - Jane M Morrell
- Division of Reproduction, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Arne Söderberg
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Katrin Daniel
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Adrian Villalba
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain Cytology and Histology Unit, Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Attila Toth
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Anna Di Rienzo
- Department of Human Genetics, Cummings Life Science Center, University of Chicago
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain Cytology and Histology Unit, Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana EBD-CSIC, Sevilla, Spain
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13
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Noormohammadi Z, Shamee MH, Sheidai M. Chromosome pairing analysis of some parental and F2 cotton progenies. THE NUCLEUS 2013. [DOI: 10.1007/s13237-013-0078-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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14
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Smukowski CS, Noor MAF. Recombination rate variation in closely related species. Heredity (Edinb) 2011; 107:496-508. [PMID: 21673743 PMCID: PMC3242630 DOI: 10.1038/hdy.2011.44] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 03/21/2011] [Accepted: 04/27/2011] [Indexed: 11/09/2022] Open
Abstract
Despite their importance to successful meiosis and various evolutionary processes, meiotic recombination rates sometimes vary within species or between closely related species. For example, humans and chimpanzees share virtually no recombination hotspot locations in the surveyed portion of the genomes. However, conservation of recombination rates between closely related species has also been documented, raising an apparent contradiction. Here, we evaluate how and why conflicting patterns of recombination rate conservation and divergence may be observed, with particular emphasis on features that affect recombination, and the scale and method with which recombination is surveyed. Additionally, we review recent studies identifying features influencing fine-scale and broad-scale recombination patterns and informing how quickly recombination rates evolve, how changes in recombination impact selection and evolution in natural populations, and more broadly, which forces influence genome evolution.
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Affiliation(s)
- C S Smukowski
- Department of Biology, Duke University, Durham, NC 27708, USA.
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15
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Mur LAJ, Allainguillaume J, Catalán P, Hasterok R, Jenkins G, Lesniewska K, Thomas I, Vogel J. Exploiting the Brachypodium Tool Box in cereal and grass research. THE NEW PHYTOLOGIST 2011; 191:334-347. [PMID: 21623796 DOI: 10.1111/j.1469-8137.2011.03748.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
It is now a decade since Brachypodium distachyon (Brachypodium) was suggested as a model species for temperate grasses and cereals. Since then transformation protocols, large expressed sequence tag (EST) databases, tools for forward and reverse genetic screens, highly refined cytogenetic probes, germplasm collections and, recently, a complete genome sequence have been generated. In this review, we will describe the current status of the Brachypodium Tool Box and how it is beginning to be applied to study a range of biological traits. Further, as genomic analysis of larger cereals and forage grasses genomes are becoming easier, we will re-evaluate Brachypodium as a model species. We suggest that there remains an urgent need to employ reverse genetic and functional genomic approaches to identify the functionality of key genetic elements, which could be employed subsequently in plant breeding programmes; and a requirement for a Pooideae reference genome to aid assembling large pooid genomes. Brachypodium is an ideal system for functional genomic studies, because of its easy growth requirements, small physical stature, and rapid life cycle, coupled with the resources offered by the Brachypodium Tool Box.
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Affiliation(s)
- Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth, Wales SY23 3DA, UK
| | - Joel Allainguillaume
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth, Wales SY23 3DA, UK
| | - Pilar Catalán
- Department of Agriculture, University of Zaragoza, High Polytechnic School of Huesca, Ctra. Cuarte km 1, ES-22071 Huesca, Spain
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, PL-40-032 Katowice, Poland
| | - Glyn Jenkins
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth, Wales SY23 3DA, UK
| | - Karolina Lesniewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, PL-40-032 Katowice, Poland
| | - Ianto Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth, Wales SY23 3DA, UK
| | - John Vogel
- USDA ARS Western Regional Research Center, Albany, CA 94710 USA
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16
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Basheva EA, Torgasheva AA, Sakaeva GR, Bidau C, Borodin PM. A- and B-chromosome pairing and recombination in male meiosis of the silver fox (Vulpes vulpes L., 1758, Carnivora, Canidae). Chromosome Res 2010; 18:689-96. [PMID: 20697834 DOI: 10.1007/s10577-010-9149-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/22/2010] [Accepted: 07/26/2010] [Indexed: 11/26/2022]
Abstract
We examined A- and B-chromosome pairing and recombination in 12 males from the farm-bred population of the silver fox (2n = 34 + 0-10 Bs) by means of electron and immunofluorescent microscopy. To detect recombination at A and B chromosomes, we used immunolocalisation of MLH1, a mismatch repair protein of mature recombination nodules, at synaptonemal complexes. The mean total number of MLH1 foci at A-autosomes was 29.6 foci per cell. The XY bivalent had one MLH1 focus at the pairing region. Total recombination length of the male fox genome map was estimated as 1,530 centimorgans. We detected single MLH1 foci at 61% of linear synaptic configurations involving B chromosomes. The distribution of the foci along B- and A-bivalents was the same. This may be considered as a first molecular evidence that meiotic recombination does occur in mammalian B chromosomes. There was no correlation between the number of synaptic configurations involving B chromosomes per cell and the recombination rate of the A-genome.
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Affiliation(s)
- Ekaterina A Basheva
- Institute of Cytology and Genetics, Siberian Department, Russian Academy of Sciences, Novosibirsk, 630090, Russia
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17
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Abstract
Thirteen populations of three Aegilops (Poaceae) species were analysed for meiotic characters including chiasma frequency and distribution, as well as chromosomal association and segregation. Populations of A. triuncialis and A. cylindrica possessed n= 14 chromosome number (tetraploid) while populations of A. umbellulata possessed n = 7 (diploid). Tetraploid species showed diplontic behavior and formed bivalents only. Cluster analysis of meiotic data showed distinctness of the species, although variations were observed in the chiasma frequency and distribution among different populations of each species. Cytomixis and chromosome elimination led to ancuploid and unreduced pollen mother cell formation in the species studied.
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18
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Saggoo MIS, Gupta RC, Kaur R. Seasonal variation in chiasma frequency among three morphotypes of Eclipta alba. ACTA ACUST UNITED AC 2010. [DOI: 10.3199/iscb.5.33] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Marii L, Chiriac G. The role of viral infection in inducing variability in virus-free progeny in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2009; 51:476-488. [PMID: 19508359 DOI: 10.1111/j.1744-7909.2009.00817.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The effect of virus-host interactions on subsequent generations is poorly understood. The evaluation of the effects of viral infection on inheritance of quantitative traits in the progeny of infected plants and elucidation of a possible relationship between chiasma frequency in the infected plants and variability of traits in the progeny were investigated. The current study involved genotypes of four intraspecific hybrids of tomato (Solanum lycopersicum L.), their parental forms and two additional cultivars. Used as infection were the tobacco mosaic virus (TMV) and potato virus X (PVX). The consequences of the effect of viral infection were evaluated based on chromosome pairing in diakinesis and/or by examining quantitative and qualitative traits in the progeny of the infected tomato plants. Tomato plants infected with TMV + PVX were found to differ in chiasma frequency per pollen mother cell or per bivalent. Deviations have been observed for genotypes of both F(1) hybrids and cultivars. At the same time, differences in mean values of the traits under study have only been found for progeny populations (F(2)-F(4)) derived from virus-infected F(1) hybrids, but not in the case of progeny of the infected cultivars. The rate of recombinants combining traits of both parents increased significantly (2.22-8.24 times) in progeny populations of hybrids infected with TMV + PVX. The above suggests that the observed effects could be the result of modification of recombination frequencies that can be manifested in heterozygous hybrids and make small contributions to variability in cases of 'homozygous' tomato genotypes (i.e. cultivars).
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Affiliation(s)
- Liliana Marii
- Institute of Genetics and Plant Physiology, Academy of Sciences of Moldova, Chisinau, MD 2002, Republic Moldova.
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20
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Sheidai M, Jafari S, Taleban P, Keshavarzi M. Cytomixis and Unreduced Pollen Grain Formation in Alopecurus L. and Catbrosa Beauv. (Poaceae). CYTOLOGIA 2009. [DOI: 10.1508/cytologia.74.31] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Masoud Sheidai
- Shahid Beheshti University, GC, Faculty of Biological Sciences
| | - Sodabeh Jafari
- Shahid Beheshti University, GC, Faculty of Biological Sciences
| | - Parisa Taleban
- Shahid Beheshti University, GC, Faculty of Biological Sciences
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21
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Sheidai M, Moghaddam K. Cytogenetic Studies in Some Species of <i>Melica</i> L. and <i>Milium</i> L. in Iran. CYTOLOGIA 2009. [DOI: 10.1508/cytologia.74.185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Masoud Sheidai
- Faculty of Biological Sciences, Shahid Beheshti University
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22
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Groeters FR, Shaw DD. Evidence for association of chromosomal form and development time from complex clines and geographic races in the grasshopperCaledia captiva(Orthoptera: Acridadae). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.1996.tb01465.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Ponting RC, Drayton MC, Cogan NOI, Dobrowolski MP, Spangenberg GC, Smith KF, Forster JW. SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass (Lolium perenne L.). Mol Genet Genomics 2007; 278:585-97. [PMID: 17647019 DOI: 10.1007/s00438-007-0275-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2007] [Revised: 06/20/2007] [Accepted: 06/29/2007] [Indexed: 11/24/2022]
Abstract
Development of accurate high-throughput molecular marker systems such as SNPs permits evaluation and selection of favourable gene variants to accelerate elite varietal production. SNP discovery in perennial ryegrass has been based on PCR amplification and sequencing of multiple amplicons designed to scan all components of the transcriptional unit. Full-length genes (with complete intron-exon structure and promoter information) corresponding to well-defined biochemical functions such as lignin biosynthesis and oligosaccharide metabolism are ideal for complete SNP haplotype determination. Multiple SNPs at regular intervals across the transcriptional unit were detected within and between the heterozygous parents and validated in the progeny of the F (1)(NA(6) x AU(6)) genetic mapping family. Haplotype structures in the parental genotypes were defined and haplotypic abundance, structure and variation were assessed in diverse germplasm sources. Decay of LD to r (2) values of c. 0.2 typically occurs over 500-3,000 bp, comparable with gene length and with little apparent variation between diverse, ecotypic and varietal population sub-groups. Similar patterns were revealed as limited blocks of intragenic LD. The results are compatible with the reproductive biology of perennial ryegrass and the effects of large ancestral population size. This analysis provides crucial information to validate strategies for correlation of haplotypic diversity and phenotypic variation through association mapping.
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Affiliation(s)
- Rebecca C Ponting
- Primary Industries Research Victoria, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, VIC, 3083, Australia
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24
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Abstract
Despite dramatic differences in genome size--and thus space for recombination to occur--previous workers found no correlation between recombination rate and genome size in flowering plants. Here I re-investigate these claims using phylogenetic comparative methods to test a large data set of recombination data in angiosperms. I show that genome size is significantly correlated with recombination rate across a wide sampling of species and that change in genome size explains a meaningful proportion ( approximately 20%) of variation in recombination rate. I show that the strength of this correlation is comparable with that of several characters previously linked to evolutionary change in recombination rate, but argue that consideration of processes of genome size change likely make the observed correlation a conservative estimate. And finally, although I find that recombination rate increases less than proportionally to change in genome size, several mechanistic and theoretical arguments suggest that this result is not unexpected.
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Affiliation(s)
- J Ross-Ibarra
- Department of Genetics, University of Georgia, Athens, GA, USA.
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25
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Abstract
AbstractThe evidence of increased crossing over rate in tomato hybrids infected with TAV (Tomato aspermy virus), PVX (Potato virus X), TMV (Tobacco mosaic virus), TMV+PVX indicates the recombinogenic effect of viral infection. Cytological studies of the early diakinesis in healthy and virus-infected tomato revealed significant changes in chiasma number and position. The most significant changes were established for bivalents with two interstitial chiasmata and with one terminal and one interstitial. The data obtained indicate redistribution of the chiasmata position and induction of additional exchanges. The virus-induced recombination is segment-specific and depends on the host plant genotype, virus infection and the interaction between them.
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26
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Kosmala A, Zwierzykowska E, Zwierzykowski Z. Chromosome pairing in triploid intergeneric hybrids ofFestuca pratensis withLolium multiflorum, revealed by GISH. J Appl Genet 2006; 47:215-20. [PMID: 16877799 DOI: 10.1007/bf03194626] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Genomic in situ hybridisation (GISH) was used to reveal chromosome pairing in two partly fertile, triploid (2n = 3x = 21) hybrids obtained by crossing the diploid (2n = 2x = 14) Festuca pratensis Huds. (designated FpFp), used as a female parent, with the autotetraploid (2n = 4x = 28) Lolium multiflorum Lam. (designated LmLmLmLm), used as a male parent. The pattern of chromosome pairing calculated on the basis of the mean values of chromosome configurations identified in all 100 PMCs analysed, was: 0.71I Lm + 2.24I Fp + 2.18II Lm/Lm + 0.54II Lm/Fp + 4.18III Lm/Lm/Fp. A relatively high number of Lm/Lm bivalents and Fp univalents, and a low number of Lm/Fp bivalents and Lm univalents indicated that the pairing was preferential between L. multiflorum chromosomes. Other observations regarding chromosome pairing within the Lm/Lm/Fp trivalents also confirmed this preferential pairing in the analysed triploids, as the Fp chromosome was not randomly located in the chain- and frying-pan-shaped trivalents. The similarities and differences in chromosome pairing at metaphase I and the level of preferential pairing between Lolium chromosomes in the different triploid Lolium-Festuca hybrids are discussed.
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Affiliation(s)
- Arkadiusz Kosmala
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland.
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27
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Sheidai M, Mehdigholi K, Ghahreman A, Attar F. Cytogenetic study of the genus Cousinia (Asteraceae, section Serratuloideae) in Iran. Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000100022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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28
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Affiliation(s)
- Masoud Sheidai
- Biology Department, Shahid Beheshti University, Tehran, Iran.
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29
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Sheidai M, Attaei S. Meiotic Studies of Some Stipa (Poaceae) Species and Populations in Iran. CYTOLOGIA 2005. [DOI: 10.1508/cytologia.70.23] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Ross-Ibarra J. The evolution of recombination under domestication: a test of two hypotheses. Am Nat 2004; 163:105-12. [PMID: 14767840 DOI: 10.1086/380606] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2002] [Accepted: 05/13/2003] [Indexed: 11/03/2022]
Abstract
The successful domestication of wild plants has been one of the most important human accomplishments of the last 10,000 yr. Though our empirical knowledge of the genetic mechanisms of plant domestication is still relatively limited, there exists a large body of theory that offers a host of hypotheses on the genetics of domestication. Two of these that have not been addressed concern the role of recombination in the process of domestication. The first predicts an increase in recombination rate through domestication, while the second argues that recombination rate should serve as a preadaptation to domestication. This study makes use of data on chiasma frequencies available from almost a century of plant cytogenetical literature to test these two hypotheses. The results support the hypothesis that domestication selects for an increase in recombination, and in rejecting the preadaptation hypothesis, they suggest directions for future research into the possibility of preadaptation to domestication.
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Affiliation(s)
- Jeffrey Ross-Ibarra
- Department of Genetics, Life Sciences Building, University of Georgia, Athens, Georgia, 30602, USA.
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31
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Anderson LK, Hooker KD, Stack SM. The distribution of early recombination nodules on zygotene bivalents from plants. Genetics 2001; 159:1259-69. [PMID: 11729167 PMCID: PMC1461850 DOI: 10.1093/genetics/159.3.1259] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Early recombination nodules (ENs) are protein complexes approximately 100 nm in diameter that are associated with forming synaptonemal complexes (SCs) during leptotene and zygotene of meiosis. Although their functions are not yet clear, ENs may have roles in synapsis and recombination. Here we report on the frequency and distribution of ENs in zygotene SC spreads from six plant species that include one lower vascular plant, two dicots, and three monocots. For each species, the number of ENs per unit length is higher for SC segments than for (asynapsed) axial elements (AEs). In addition, EN number is strongly correlated with SC segment length. There are statistically significant differences in EN frequencies on SCs between species, but these differences are not related to genome size, number of chromosomes, or phylogenetic class. There is no difference in the frequency of ENs per unit length of SC from early to late zygotene. The distribution of distances between adjacent ENs on SC segments is random for all six species, but ENs are found at synaptic forks more often than expected for a random distribution of ENs on SCs. From these observations, we conclude that in plants: (1) some ENs bind to AEs prior to synapsis, (2) most ENs bind to forming SCs at synaptic forks, and (3) ENs do not bind to already formed SCs.
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Affiliation(s)
- L K Anderson
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA.
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32
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Armstead IP, Bollard A, King IP, Forster JW, Hayward MD, Evans GM, Thomas HM. Chromosome pairing in Lolium perenne x L. temulentum diploid hybrids: genetic and cytogenetic evaluation. Heredity (Edinb) 1999; 83 ( Pt 3):298-303. [PMID: 10504427 DOI: 10.1038/sj.hdy.6885730] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A Lolium perenne genotype (E5/2/5/10), which had been selected for low chiasma frequency over a number of generations and which was suspected of containing one or two heterozygous dominant genes with a significant effect on chiasma frequency, was crossed with L. temulentum (Ba3081) to create a hybrid population of 47 diploid plants. The mean chiasma or paired arm (PA) frequency of homoeologous chromosomes at meiosis in the population was 9.1/cell (1.3 PA/chromosome pair) with a distribution skewed towards high PA frequency. More than 90% of the hybrid chromosomes paired at meiosis in spite of the disparity in chromosome length and DNA quantity between the two species. Overall, the distribution of PAs between chromosomes for a given number of PAs/cell favoured the production of rod bivalents over ring bivalents and univalents, indicating that there is a mechanism present that maximizes the total number of bivalent associations formed. Molecular marker analysis using AFLPs and isoenzymes did not identify any clear major gene effect on PA frequency in the hybrid population. It was concluded that the control of PA frequency in E5/2/5/10 was not a simple genetic mechanism.
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Affiliation(s)
- I P Armstead
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, U.K.
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33
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Zwierzykowski Z, Lukaszewski AJ, Naganowska B, Lesniewska A. The pattern of homoeologous recombination in triploid hybrids of Lolium multiflorum with Festuca pratensis. Genome 1999. [DOI: 10.1139/g98-169] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Homoeologous chromosomes of Lolium-Festuca hybrids are capable of frequent meiotic pairing and recombination. The frequency and distribution of recombination was studied by genomic in situ hybridization in backcross progenies of reciprocal triploid hybrids of Lolium multiflorum with Festuca pratensis. Significant differences in the male transmission of the parental and translocated chromosomes were observed depending on the cytoplasm of the F1 hybrids and the ploidy level of the female test cross partner. The frequency of intergeneric translocations in the progeny indicated that, on average, there must have been at least 4.5 homoeologous arms paired in the F1 hybrids; the actual frequency might have been higher because of pre- or post-zygotic selection against the F. pratensis chromatin, which probably eliminated certain gametes with Festuca-Lolium translocations. Both parental species are known for localized distal chiasmata, but the intergeneric translocation breakpoints were distributed along the entire lengths of the chromosome arms. The change in the distribution of homoeologous recombination might have been related to different pairing initiation of homologues and homoeologues. It probably resulted from allocation of additional chiasmata to chromosome arms and produced a net increase in recombination.Key words: homoeologous exchanges, Lolium-Festuca, translocations, recombination.
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34
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Wallace AJ, Callow RS. Meiotic variation in an intergenomic autopolyploid series. I. Chiasma frequency. Genome 1995; 38:122-32. [PMID: 18470158 DOI: 10.1139/g95-015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Variation in chiasma frequency has been studied in PMCs of diploids and C0 autotetraploids of seven Lathyrus species exhibiting a range of genome size (10.8-19.9 pg DNA/2C). Variation in chiasma frequency showed no relation to changes in genome size, either between species or between disomic sets within nuclei. Mean chiasma frequency of the tetraploids showed a 75% increase over that in the diploids. Half of this increase represents an additive effect of chromosome doubling. Total variance in chiasma frequency of autotetraploids increases by 80% over that in diploids, in line with the square of the multiplicative effect of chromosome doubling. At the diploid level, interspecific differences account for the major component of variance (63.1%). Phenotypic variation in chiasma frequency was apparent in all seven species but represented the smallest component of variance (2.8%). Chromosome doubling results in an eightfold increase in the absolute size of the phenotypic component of variance in chiasma frequency and a threefold increase in that of the cellular component. It has no effect on the absolute size of the interspecific component.
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35
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The effect of supernumerary segments on recombination in Euchorthippus pulvinatus (grasshopper): a comparative study between sexes and populations. Heredity (Edinb) 1993. [DOI: 10.1038/hdy.1993.21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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36
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Wallace AJ, Callow RS. Synaptic responses to concerted genomic evolution in Lathyrus. I. Intergenomic effects. Heredity (Edinb) 1993. [DOI: 10.1038/hdy.1993.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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37
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Synaptic responses to concerted genomic evolution in Lathyrus. II. Intragenomic effects. Heredity (Edinb) 1993. [DOI: 10.1038/hdy.1993.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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38
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Abstract
A multipoint test of heterogeneity on published data from 57 families with the fragile X syndrome has been undertaken. The hypothesis being tested was that there are two loci coding for fragile X expression, mutations at either of which can produce the phenotype. No predivision of the families was undertaken, as the test used an admixture parameter. Maximum likelihoods of the hypothesis have been calculated and compared with those produced on assuming a single locus for fragile X. The data do not suggest that there are two such loci within the interval between probes 52a and St14. In particular, the large kindred published by Camerino et al. (1983) does not supply convincing evidence of heterogeneity under this test. It is argued that the observed heterogeneity between factor IX and fragile X must have another explanation. There is some evidence for a second locus for fragile X outside the interval noted above; this locus being most probably proximal to these probes. The majority of the data suggesting this result comes from a family published by Davies et al. (1985).
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Affiliation(s)
- J F Clayton
- MRC Clinical and Population Cytogenetics Unit, Western General Hospital, Edinburg, UK
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39
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Abstract
A broad survey of asexuality in the animal kingdom is sufficient to reject all theories of sex and recombination except two: the Red Queen and the Tangled Bank. The Red Queen theory states that an organism's biotic environment tends to be 'contrary', consistently evolving to the detriment of the organism; sex and recombination result in progeny genetically distinct from their parents and grandparents and thus less susceptible to the antagonistic advances made during the previous generations, particularly by their parasites. The alternative theory, the Tangled Bank, states that sex and recombination function to diversify the progeny from each other, thus reducing competition between them. An extensive survey of mammalian recombination shows that the total number of chiasmata in excess of one per bivalent is strongly correlated with generation time but uncorrelated with fecundity. We conclude that crossing-over may function to combat antagonists with short generation times but does not function to reduce sib competition. Chromosome number is selectively neutral with respect to these factors.
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40
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The relationship between chiasma frequency and bivalent length: Effects of genotype and supernumerary chromosomes. Heredity (Edinb) 1986. [DOI: 10.1038/hdy.1986.51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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41
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42
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Thomson RL, Westerman M, Murray ND. B chromosomes in Rattus fuscipes I. Mitotic and meiotic chromosomes and the effects of B chromosomes on chiasma frequency. Heredity (Edinb) 1984. [DOI: 10.1038/hdy.1984.43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Chiasma frequency and variability of morphological characters in populations of two grasshopper species. Heredity (Edinb) 1983. [DOI: 10.1038/hdy.1983.61] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Karp A, Jones RN. Cytogenetics of Lolium perenne : Part 2. Chiasma distribution in inbred lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1983; 64:137-145. [PMID: 24264873 DOI: 10.1007/bf00272721] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/25/1982] [Indexed: 06/02/2023]
Abstract
An analysis of the patterns of chiasma distribution within bivalents, in a number of inbred lines of Lolium perenne, reveals a striking potential for variation in this character, as well as a polygenic genetic basis for its control. In parent plants the chiasmata have a regular pattern of localisation which restricts their formation to the ends of the chromosome arms: this strict localisation is progressively lost with inbreeding and novel patterns of distribution are found where chiasmata occur in more interstitial and proximal regions. The variation is continuous and originates from genotypic differences between the different parent plants, rather than from segregation among families deriving from individual parents.
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Affiliation(s)
- A Karp
- Department of Agricultural Botany, University College of Wales, Aberystwyth, Wales
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The chromosomal component of reproductive isolation in the grasshopper Caledia captiva. Chromosoma 1982. [DOI: 10.1007/bf00330124] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Karp A, Jones RN. Cytogenetics of Lolium perenne : Part 1: Chiasma frequency variation in inbred lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1982; 62:177-183. [PMID: 24270568 DOI: 10.1007/bf00293355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/1982] [Indexed: 06/02/2023]
Abstract
A number of inbred lines of Lolium perenne have been developed as far as the fifth inbred generation and are being used for basic studies on the cytogenetics of the species. An analysis on variation in the pattern of chiasma frequency and distribution, including the parent plants and all generations down to the S5, reveals that the effect of inbreeding is to reduce chiasma frequency and to increase both the cell and bivalent variances. Evidence is presented for a genetic basis of polygenic control of chiasma formation and distribution, and a model is suggested for control over the three related components of variation which involves a two-stage level of regulation.
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Affiliation(s)
- A Karp
- Department of Agricultural Botany, University College of Wales, Aberystwyth, Wales
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Miklos GL, Gill AC. Nucleotide sequences of highly repeated DNAs; compilation and comments. Genet Res (Camb) 1982; 39:1-30. [PMID: 7040165 DOI: 10.1017/s0016672300020711] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
SummaryThe nucleotide sequence data from highly repeated DNAs of inverte-brates and mammals are summarized and briefly discussed. Very similar conclusions can be drawn from the two data bases. Sequence complexities can vary from 2 bp to at least 359 bp in invertebrates and from 3 bp to at least 2350 bp in mammals. The larger sequences may or may not exhibit a substructure. Significant sequence variation occurs for any given repeated array within a species, but the sources of this heterogeneity have not been systematically partitioned. The types of alterations in a basic repeating unit can involve base changes as well as deletions or additions which can vary from 1 bp to at least 98 bp in length. These changes indicate that sequenceper seis unlikely to be under significant biological constraints and may sensibly be examined by analogy to Kimura's neutral theory for allelic variation. It is not possible with the present evidence to discriminate between the roles ofneutralandselectivemechanisms in the evolution of highly repeated DNA.Tandemly repeated arrays are constantly subjected to cycles of amplification and deletion by mechanisms for which the available data stem largely from ribosomal genes. It is a matter of conjecture whether the solutions to the mechanistic puzzles involved in amplification or rapid redeployment of satellite sequences throughout a genome will necessarily give any insight into biological functions.The lack of significant somatic effects when the satellite DNA content of a genome is significantly perturbed indicates that the hunt for specific functions at thecellularlevel is unlikely to prove profitable.The presence or in some cases theamountof satellite DNA on a chromosome, however, can have significant effects in the germ line. There the data show that localized condensed chromatin, rich in satellite DNA, can have the effect of rendering adjacent euchromatic regionsrec−, or of altering levels of recombination on different chromosomes. No data stemming from natural populations however are yet available to tell us if these effects are of adaptive or evolutionary significance.
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Yamamoto M, Miklos GL. Genetic studies on heterochromatin in Drosophila melanogaster and their implications for the functions of satellite DNA. Chromosoma 1978; 66:71-98. [PMID: 416935 DOI: 10.1007/bf00285817] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In Drosophila melanogaster the centromeric heterochromatin of all chromosomes consists almost entirely of several different satellite DNA sequences. In view of this we have examined by genetic means the meiotic consequences of X chromosomes with partial deletions of their heterochromatin, and have found that the amount and position of recombination on each heterochromatically deleted X is substantially different from that of a normal X. It appears that the amount of heterochromatin is important in modifying the "centromere effect" on recombination.--In all the deleted Xs tested, chromosome segregation is not appreciably altered from that of a nondeleted control chromosome. Thus satellite DNA does not appear to be an important factor in determining the regular segregation of sex chromosomes in Drosophila. Additionally, since X chromosomes with massive satellite DNA deficiencies are able to participate in a chromocenter within salivary gland nuclei, a major role of satellite DNA in chromocenter formation in this tissue is also quite unlikely.--In order to examine the mechanisms by which the amount of satellite DNA is increased or decreased in vivo, we have measured cytologically the frequency of spontaneous sister chromatid exchanges in a ring Y chromosome which is entirely heterochromatic and consists almost exclusively of satellite DNA. In larval neuroblast cells the frequency of spontaneous SCE in this Y is approximately 0.3% per cell division. Since there is no meiotic recombination in D. melanogaster males and since meiotic recombination in the female does not occur in heterochromatin, our results provide a minimum estimate of the in vivo frequency of SCE in C-banded heterochromatin (which is predominantly simple sequence DNA), without the usual complications of substituted base analogs, incorporated radioactive label or substantial genetic content.--We emphasise that: (a) satellite DNA is not implicated in any major way in recognition processes such as meiotic homologue recognition or chromocenter formation in salivaries, (b) there is likely to be continuous variation in the amount of satellite DNA between individuals of a species; and (c) the amount of satellite DNA can have a crucial functional role in the meiotic recombination system.
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Seasonal variation of chiasma frequency in Phyllodactylus marmoratus (Gray) (Gekkonidae ? Reptilia). Chromosoma 1978. [DOI: 10.1007/bf00329913] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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