1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Anchoring a genetic map of an interspecific backcross two family to the genome builds of Elaeis. J Genet 2021. [DOI: 10.1007/s12041-020-01240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
3
|
Schwarzkopf EJ, Motamayor JC, Cornejo OE. Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations. BMC Genomics 2020; 21:332. [PMID: 32349675 PMCID: PMC7191684 DOI: 10.1186/s12864-020-6746-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/21/2020] [Indexed: 12/16/2022] Open
Abstract
Background Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic variation in a population, we can construct fine-scale recombination maps. Such maps have been used to study a variety of model organisms and proven to be informative of how selection and demographics shape species-wide variation. Here we present a fine-scale recombination map for ten populations of Theobroma cacao – a non-model, long-lived, woody crop. We use this map to elucidate the dynamics of recombination rates in distinct populations of the same species, one of which is domesticated. Results Mean recombination rates in range between 2.5 and 8.6 cM/Mb for most populations of T. cacao with the exception of the domesticated Criollo (525 cM/Mb) and Guianna, a more recently established population (46.5 cM/Mb). We found little overlap in the location of hotspots of recombination across populations. We also found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. We find mutations in FIGL-1, a protein shown to downregulate cross-over frequency in Arabidopsis, statistically associated to higher recombination rates in domesticated Criollo. Conclusions We generated fine-scale recombination maps for ten populations of Theobroma cacao and used them to understand what processes are associated with population-level variation in this species. Our results provide support to the hypothesis of increased recombination rates in domesticated plants (Criollo population). We propose a testable mechanistic hypothesis for the change in recombination rate in domesticated populations in the form of mutations to a previously identified recombination-suppressing protein. Finally, we establish a number of possible correlates of recombination hotspots that help explain general patterns of recombination in this species.
Collapse
Affiliation(s)
| | | | - Omar E Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
| |
Collapse
|
4
|
Yang Z, Li X, Liao H, Hu L, Peng C, Wang S, Huang X, Bao Z. A Molecular Cytogenetic Map of Scallop (Patinopecten yessoensis). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:731-742. [PMID: 31473865 DOI: 10.1007/s10126-019-09918-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
To consolidate the genetic, physical, and cytogenetic maps of scallop (Patinopecten yessoensis), we constructed a molecular cytogenetic map by localizing 84 fosmid clones that contain different SNP markers from 19 linkage groups (LGs) using fluorescence in situ hybridization (FISH). Among these 84 SNP-anchored clones, 56 clones produced specific and stable signals on one pair of chromosomes. Dual-color FISH assigned 19 LGs to their corresponding chromosomes with 38 SNP-anchored clones as probes. Among these 19 LGs, 17 LGs were assigned to their corresponding one pair of chromosomes, while two clones containing SNPs from LG10 and LG19 were located on two different pairs of chromosomes separately. The orientation of 7 LGs was corrected according to the chromosome location of SNPs within the same LG. In addition, a probe panel of SNP-anchored clones was developed to identify each chromosome of P. yessoensis. The molecular cytogenetic map will facilitate molecular breeding in scallop and enable comparative studies on chromosome evolution of bivalve mollusk.
Collapse
Affiliation(s)
- Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Post Office Box 11103, 9700 CC, Groningen, Netherlands
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, China
| | - Liping Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Yantai Fisheries Research Institute, Yantai, China
| | - Cheng Peng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shenhai Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
5
|
Naranjo T. Contribution of Structural Chromosome Mutants to the Study of Meiosis in Plants. Cytogenet Genome Res 2015; 147:55-69. [PMID: 26658116 DOI: 10.1159/000442219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2015] [Indexed: 11/19/2022] Open
Abstract
Dissection of the molecular mechanisms underlying the transition through the complex events of the meiotic process requires the use of gene mutants or RNAi-mediated gene silencing. A considerable number of meiotic mutants have been isolated in plant species such as Arabidopsis thaliana, maize or rice. However, structural chromosome mutants are also important for the identification of the role developed by different chromosome domains in the meiotic process. This review summarizes the contribution of studies carried out in plants using structural chromosome variations. Meiotic events concerning the search of the homologous partner, the control of number and distribution of chiasmata, the mechanism of pairing correction, and chromosome segregation are considered.
Collapse
Affiliation(s)
- Tomás Naranjo
- Departamento de Genética, Facultad de Biología, Universidad Complutense, Madrid, Spain
| |
Collapse
|
6
|
Naranjo T. Forcing the shift of the crossover site to proximal regions in wheat chromosomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1855-63. [PMID: 26066968 DOI: 10.1007/s00122-015-2552-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/30/2015] [Indexed: 05/23/2023]
Abstract
Terminal deletions obligate the first crossover to be formed in more proximal positions. This increases the recombination rate in intercalary intervals but not in the proximity of the centromere. Crossovers are not uniformly distributed along chromosomes in wheat. They take place preferentially in distal positions. The effect of the chromosomal architecture on crossover positioning has been analyzed from the chiasmate bonds at metaphase I formed by the truncated arms of 51 terminal deletion lines of eight wheat chromosomes. Chromosome 4A and the B genome chromosomes, in their standard or truncated conformation, and their arms, were identified by C-banding. Chromosomes studied show a similar chiasma distribution. Reduction of the size of the truncated arms is accompanied by a gradual decrease of the chiasma frequency in chromosome arms 1BL, 3BS, 3BL, 4BL, 5BS, 5BL, 6BL, 7BS, 7BL and 4AL. In chromosome arm 1BS, most chiasmata are concentrated in the distal half of the satellite and, in 4AS, in the distal 24 %. The arms 2BS, 2BL and 6BS do not show a simple decreasing gradient of the recombination rate, the chiasma frequency increases in subdistal intervals compared to more distal regions. Although terminal deletions usually induce an increase of chiasma frequency in intercalary regions, the level of intact chromosome arms is maintained in only a few deletion lines. Truncated arms containing only the 20 % proximal of the intact arm do not form chiasmata. The relationships of chiasma positioning with chromatin structure and genome organization is discussed.
Collapse
Affiliation(s)
- Tomás Naranjo
- Departamento de Genética, Facultad de Biología, Universidad Complutense, 28040, Madrid, Spain,
| |
Collapse
|
7
|
Del Priore L, Pigozzi MI. Sex-specific recombination maps for individual macrochromosomes in the Japanese quail (Coturnix japonica). Chromosome Res 2015; 23:199-210. [PMID: 25596820 DOI: 10.1007/s10577-014-9448-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 11/29/2022]
Abstract
Meiotic recombination in the Japanese quail was directly studied by immunolocalization of mutL homolog 1 (MLH1), a mismatch repair protein of mature recombination nodules. In total, 15,862 crossovers were scored along the autosomal synaptonemal complexes in 308 meiotic nuclei from males and females. Crossover frequencies calculated from MLH1 foci show wide similitude between males and females with slightly higher number of foci in females. From this analysis, we predict that the sex-averaged map length of the Japanese quail is 2580 cM, with a genome-wide recombination rate of 1.9 cM/Mb. MLH1 focus mapping along the six largest bivalents showed few intersex differences in the distribution of crossovers along with variant patterns in metacentric and acrocentric macrobivalents. These results provide valuable information to complement linkage map analysis in the species while providing insight into our understanding of the mechanisms of crossover distribution along chromosome arms.
Collapse
Affiliation(s)
- Lucía Del Priore
- INBIOMED (CONICET-UBA), Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 10, C1121ABG, Buenos Aires, Argentina
| | | |
Collapse
|
8
|
Mondin M, Santos-Serejo JA, Bertäo MR, Laborda P, Pizzaia D, Aguiar-Perecin MLR. Karyotype variability in tropical maize sister inbred lines and hybrids compared with KYS standard line. FRONTIERS IN PLANT SCIENCE 2014; 5:544. [PMID: 25352856 PMCID: PMC4195276 DOI: 10.3389/fpls.2014.00544] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/24/2014] [Indexed: 05/27/2023]
Abstract
Maize karyotype variability has been extensively investigated. The identification of maize somatic and pachytene chromosomes has improved with the development of fluorescence in situ hybridization (FISH) using tandemly repeated DNA sequences as probes. We identified the somatic chromosomes of sister inbred lines that were derived from a tropical flint maize population (Jac Duro [JD]), and hybrids between them, using FISH probes for the 180-bp knob repeat, centromeric satellite (CentC), centromeric satellite 4 (Cent4), subtelomeric clone 4-12-1, 5S ribosomal DNA and nucleolus organizing region DNA sequences. The observations were integrated with data based on C-banded mitotic metaphases and conventional analysis of pachytene chromosomes. Heterochromatic knobs visible at pachynema were coincident with C-bands and 180-bp FISH signals on somatic chromosomes, and most of them were large. Variation in the presence of some knobs was observed among lines. Small 180-bp knob signals were invariant on the short arms of chromosomes 1, 6, and 9. The subtelomeric 4-12-1 signal was also invariant and useful for identifying some chromosomes. The centromere location of chromosomes 2 and 4 differed from previous reports on standard maize lines. Somatic chromosomes of a JD line and the commonly used KYS line were compared by FISH in a hybrid of these lines. The pairing behavior of chromosomes 2 and 4 at pachytene stage in this hybrid was investigated using FISH with chromosome-specific probes. The homologues were fully synapsed, including the 5S rDNA and CentC sites on chromosome 2, and Cent4 and subtelomeric 4-12-1 sites on chromosome 4. This suggests that homologous chromosomes could pair through differential degrees of chromatin packaging in homologous arms differing in size. The results contribute to current knowledge of maize global diversity and also raise questions concerning the meiotic pairing of homologous chromosomes possibly differing in their amounts of repetitive DNA.
Collapse
Affiliation(s)
- Mateus Mondin
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
| | - Janay A. Santos-Serejo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
- Embrapa Cassava and Fruits, Brazilian Agricultural Research CorporationCruz das Almas, Brazil
| | - Mônica R. Bertäo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
- Department of Biological Sciences, Faculty of Sciences and Letters, São Paulo State UniversityAssis, Brazil
| | - Prianda Laborda
- Center for Molecular Biology and Genetic Engineering, State University of CampinasCampinas, Brazil
| | - Daniel Pizzaia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of SãoPaulo, Piracicaba, Brazil
- Herminio Ometto University Center, Herminio Ometto FoundationAraras, Brazil
| | | |
Collapse
|
9
|
Li H, Wang C, Fu S, Guo X, Yang B, Chen C, Zhang H, Wang Y, Liu X, Han F, Ji W. Development and discrimination of 12 double ditelosomics in tetraploid wheat cultivar DR147. Genome 2014; 57:89-95. [DOI: 10.1139/gen-2013-0153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As an important group in Triticum, tetraploid wheat plays a significant role in the research of wheat evolution. Several complete aneuploid sets of common wheat have provided valuable tools for genetic and breeding studies, while similar aneuploids of tetraploid wheat are still not well developed. Here, 12 double ditelosomics developed in Triticum turgidum L. var. durum cultivar DR147 (excluding dDT2B and dDT3A) were reported. Hybrids between DR147 and the original double-ditelosomic dDT2B of Langdon lost vigor and died prematurely after the three-leaf stage; therefore, the dDT2B line was not obtained. The cytogenetic behaviors and phenotypic characteristics of each line were detailedly described. To distinguish the entire chromosome complement of tetraploid wheat, the DR147 karyotype was established by fluorescence in situ hybridization (FISH), using the Aegilops tauschii clone pAsl and the barley clone pHvG38 as probes. FISH using a cereal-specific centromere repeat (6C6) probe suggested that all the lines possessed four telosomes, except for 4AS of double-ditelosomic dDT4A, which carried a small segment of the long arm. On the basis of the idiogram of DR147, these lines were successfully discriminated by FISH using the probes pAsl and pHvG38 and were then accurately designated.
Collapse
Affiliation(s)
- Hao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shulan Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baoju Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| |
Collapse
|
10
|
Identifying crossover-rich regions and their effect on meiotic homologous interactions by partitioning chromosome arms of wheat and rye. Chromosome Res 2013; 21:433-45. [PMID: 23843032 DOI: 10.1007/s10577-013-9372-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/21/2013] [Accepted: 06/26/2013] [Indexed: 10/26/2022]
Abstract
Chiasmata are usually formed in the distal half of cereal chromosomes. Previous studies showed that the crossover-rich region displays a more active role in homologous recognition at early meiosis than crossover-poor regions in the long arm of rye chromosome 1R, but not in the long arm of chromosome 5R. In order to determine what happens in other chromosomes of rye and wheat, we have partitioned, by wheat-rye translocations of variable-size, the distal fourth part of chromosome arms 1BS and 2BL of wheat and 1RS and 2RL of rye. Synapsis and chiasma formation in chromosome pairs with homologous (wheat-wheat or rye-rye) and homoeologous (wheat-rye) stretches, positioned distally and proximally, respectively, or vice versa, have been studied by rye chromatin labelling using fluorescence in situ hybridisation. Chromosome arm partitioning showed that the distal 12 % of 1BS form one crossover in 50 % of the cells, while the distal 6.7 % of 2RL and the distal 10.5 % of 2BL account for 94 % and 81 % of chiasmata formed in these arms. Distal homoeologous segments reduce the frequency of chiasmata and the possibility of interaction between the intercalary/proximal homologous segments. Such a reduction is related to the size of the homoeologous (translocated) segment. The effect on synapsis and chiasma formation was much lower in chromosome constructions with distal homology and proximal homoeology. All of these data support that among wheat and rye chromosomes, recombining regions are more often involved in homologous recognition and pairing than crossover-poor regions.
Collapse
|
11
|
Figueroa DM, Bass HW. Development of pachytene FISH maps for six maize chromosomes and their integration with other maize maps for insights into genome structure variation. Chromosome Res 2012; 20:363-80. [PMID: 22588802 PMCID: PMC3391363 DOI: 10.1007/s10577-012-9281-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/27/2012] [Accepted: 03/28/2012] [Indexed: 12/18/2022]
Abstract
Integrated cytogenetic pachytene fluorescence in situ hybridization (FISH) maps were developed for chromosomes 1, 3, 4, 5, 6, and 8 of maize using restriction fragment length polymorphism marker-selected Sorghum propinquum bacterial artificial chromosomes (BACs) for 19 core bin markers and 4 additional genetic framework loci. Using transgenomic BAC FISH mapping on maize chromosome addition lines of oats, we found that the relative locus position along the pachytene chromosome did not change as a function of total arm length, indicative of uniform axial contraction along the fibers during mid-prophase for tested loci on chromosomes 4 and 5. Additionally, we cytogenetically FISH mapped six loci from chromosome 9 onto their duplicated syntenic regions on chromosomes 1 and 6, which have varying amounts of sequence divergence, using sorghum BACs homologous to the chromosome 9 loci. We found that successful FISH mapping was possible even when the chromosome 9 selective marker had no counterpart in the syntenic block. In total, these 29 FISH-mapped loci were used to create the most extensive pachytene FISH maps to date for these six maize chromosomes. The FISH-mapped loci were then merged into one composite karyotype for direct comparative analysis with the recombination nodule-predicted cytogenetic, genetic linkage, and genomic physical maps using the relative marker positions of the loci on all the maps. Marker colinearity was observed between all pair-wise map comparisons, although marker distribution patterns varied widely in some cases. As expected, we found that the recombination nodule-based predictions most closely resembled the cytogenetic map positions overall. Cytogenetic and linkage map comparisons agreed with previous studies showing a decrease in marker spacing in the peri-centromeric heterochromatin region on the genetic linkage maps. In fact, there was a general trend with most loci mapping closer towards the telomere on the linkage maps than on the cytogenetic maps, regardless of chromosome number or maize inbred line source, with just some of the telomeric loci exempted. Finally and somewhat surprisingly, we observed considerable variation between the relative arm positions of loci when comparing our cytogenetic FISH map to the B73 genomic physical maps, even where comparisons were to a B73-derived cytogenetic map. This variation is more evident between different chromosome arms, but less so within a given arm, ruling out any type of inbred-line dependent global features of linear deoxyribonucleic acid compared with the meiotic fiber organization. This study provides a means for analyzing the maize genome structure by producing new connections for integrating the cytogenetic, linkage, and physical maps of maize.
Collapse
Affiliation(s)
- Debbie M Figueroa
- Department of Biological Science, Florida State University, Tallahassee, 32306-4295, USA.
| | | |
Collapse
|
12
|
Paape T, Zhou P, Branca A, Briskine R, Young N, Tiffin P. Fine-scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome. Genome Biol Evol 2012; 4:726-37. [PMID: 22554552 PMCID: PMC3381680 DOI: 10.1093/gbe/evs046] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Recombination rates vary across the genome and in many species show significant relationships with several genomic features, including distance to the centromere, gene density, and GC content. Studies of fine-scale recombination rates have also revealed that in several species, there are recombination hotspots, that is, short regions with recombination rates 10–100 greater than those in surrounding regions. In this study, we analyzed whole-genome resequence data from 26 accessions of the model legume Medicago truncatula to gain insight into the genomic features that are related to high- and low-recombination rates and recombination hotspots at 1 kb scales. We found that high-recombination regions (1-kb windows among those in the highest 5% of the distribution) on all three chromosomes were significantly closer to the centromere, had higher gene density, and lower GC content than low-recombination windows. High-recombination windows are also significantly overrepresented among some gene functional categories—most strongly NB–ARC and LRR genes, both of which are important in plant defense against pathogens. Similar to high-recombination windows, recombination hotspots (1-kb windows with significantly higher recombination than the surrounding region) are significantly nearer to the centromere than nonhotspot windows. By contrast, we detected no difference in gene density or GC content between hotspot and nonhotspot windows. Using linear model wavelet analysis to examine the relationship between recombination and genomic features across multiple spatial scales, we find a significant negative correlation with distance to the centromere across scales up to 512 kb, whereas gene density and GC content show significantly positive and negative correlations, respectively, only up to 64 kb. Correlations between recombination and genomic features, particularly gene density and polymorphism, suggest that they are scale dependent and need to be assessed at scales relevant to the evolution of those features.
Collapse
Affiliation(s)
- Timothy Paape
- Department of Plant Biology, University of Minnesota, MN, USA.
| | | | | | | | | | | |
Collapse
|
13
|
Valenzuela NT, Perera E, Naranjo T. Dynamics of rye chromosome 1R regions with high or low crossover frequency in homology search and synapsis development. PLoS One 2012; 7:e36385. [PMID: 22558456 PMCID: PMC3340359 DOI: 10.1371/journal.pone.0036385] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 04/01/2012] [Indexed: 02/02/2023] Open
Abstract
In many organisms, homologous pairing and synapsis depend on the meiotic recombination machinery that repairs double-strand DNA breaks (DSBs) produced at the onset of meiosis. The culmination of recombination via crossover gives rise to chiasmata, which locate distally in many plant species such as rye, Secale cereale. Although, synapsis initiates close to the chromosome ends, a direct effect of regions with high crossover frequency on partner identification and synapsis initiation has not been demonstrated. Here, we analyze the dynamics of distal and proximal regions of a rye chromosome introgressed into wheat to define their role on meiotic homology search and synapsis. We have used lines with a pair of two-armed chromosome 1R of rye, or a pair of telocentrics of its long arm (1RL), which were homozygous for the standard 1RL structure, homozygous for an inversion of 1RL that changes chiasma location from distal to proximal, or heterozygous for the inversion. Physical mapping of recombination produced in the ditelocentric heterozygote (1RL/1RLinv) showed that 70% of crossovers in the arm were confined to a terminal segment representing 10% of the 1RL length. The dynamics of the arms 1RL and 1RLinv during zygotene demonstrates that crossover-rich regions are more active in recognizing the homologous partner and developing synapsis than crossover-poor regions. When the crossover-rich regions are positioned in the vicinity of chromosome ends, their association is facilitated by telomere clustering; when they are positioned centrally in one of the two-armed chromosomes and distally in the homolog, their association is probably derived from chromosome elongation. On the other hand, chromosome movements that disassemble the bouquet may facilitate chromosome pairing correction by dissolution of improper chromosome associations. Taken together, these data support that repair of DSBs via crossover is essential in both the search of the homologous partner and consolidation of homologous synapsis.
Collapse
Affiliation(s)
- Nohelia T. Valenzuela
- Departamento de Genética, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Esther Perera
- Departamento de Biología Vegetal, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Tomás Naranjo
- Departamento de Genética, Facultad de Biología, Universidad Complutense, Madrid, Spain
- * E-mail:
| |
Collapse
|
14
|
Ren Y, Zhao H, Kou Q, Jiang J, Guo S, Zhang H, Hou W, Zou X, Sun H, Gong G, Levi A, Xu Y. A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome. PLoS One 2012; 7:e29453. [PMID: 22247776 PMCID: PMC3256148 DOI: 10.1371/journal.pone.0029453] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 11/22/2011] [Indexed: 11/19/2022] Open
Abstract
As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F(8) population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits.
Collapse
Affiliation(s)
- Yi Ren
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
| | - Hong Zhao
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
| | - Qinghe Kou
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
- College of Life Science, Capital Normal University, Beijing, China
| | - Jiao Jiang
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
- College of Life Science, Capital Normal University, Beijing, China
| | - Shaogui Guo
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
| | - Haiying Zhang
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
| | - Wenju Hou
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
| | - Xiaohua Zou
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
| | - Honghe Sun
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
| | - Guoyi Gong
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
| | - Amnon Levi
- U.S. Vegetable Laboratory, United States Department of Agriculture-Agricultural Research Service, Charleston, South Carolina, United States of America
| | - Yong Xu
- National Engineering Research Center for Vegetables, BAAFS, Beijing, China
- * E-mail:
| |
Collapse
|
15
|
Jacquemin J, Chaparro C, Laudié M, Berger A, Gavory F, Goicoechea JL, Wing RA, Cooke R. Long-range and targeted ectopic recombination between the two homeologous chromosomes 11 and 12 in Oryza species. Mol Biol Evol 2011; 28:3139-50. [PMID: 21616911 DOI: 10.1093/molbev/msr144] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Whole genome duplication (WGD) and subsequent evolution of gene pairs have been shown to have shaped the present day genomes of most, if not all, plants and to have played an essential role in the evolution of many eukaryotic genomes. Analysis of the rice (Oryza sativa ssp. japonica) genome sequence suggested an ancestral WGD ∼50-70 Ma common to all cereals and a segmental duplication between chromosomes 11 and 12 as recently as 5 Ma. More recent studies based on coding sequences have demonstrated that gene conversion is responsible for the high sequence conservation which suggested such a recent duplication. We previously showed that gene conversion has been a recurrent process throughout the Oryza genus and in closely related species and that orthologous duplicated regions are also highly conserved in other cereal genomes. We have extended these studies to compare megabase regions of genomic (coding and noncoding) sequences between two cultivated (O. sativa, Oryza glaberrima) and one wild (Oryza brachyantha) rice species using a novel approach of topological incongruency. The high levels of intraspecies conservation of both gene and nongene sequences, particularly in O. brachyantha, indicate long-range conversion events less than 4 Ma in all three species. These observations demonstrate megabase-scale conversion initiated within a highly rearranged region located at ∼2.1 Mb from the chromosome termini and emphasize the importance of gene conversion in cereal genome evolution.
Collapse
Affiliation(s)
- J Jacquemin
- Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Institut de Recherche pour le Développement/Université de Perpignan Via Domitia, Université de Perpignan, Perpignan-Cedex, France.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Wang J, Lydiate DJ, Parkin IAP, Falentin C, Delourme R, Carion PWC, King GJ. Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa. BMC Genomics 2011; 12:101. [PMID: 21306613 PMCID: PMC3042011 DOI: 10.1186/1471-2164-12-101] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 02/09/2011] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available. RESULTS We report the first genome-wide integration of Brassica maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid Brassica napus (2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the B. napus integrated map we identified 103 conserved collinearity blocks relative to Arabidopsis, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of Brassica rapa. CONCLUSIONS Our results provide a comprehensive genetic integration of the B. napus genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.
Collapse
Affiliation(s)
- Jun Wang
- Department of Plant Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | | | | | | | | | | | | |
Collapse
|
17
|
The selection and use of sorghum (Sorghum propinquum) bacterial artificial chromosomes as cytogenetic FISH probes for maize (Zea mays L.). J Biomed Biotechnol 2011; 2011:386862. [PMID: 21234422 PMCID: PMC3014715 DOI: 10.1155/2011/386862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 11/02/2010] [Indexed: 02/03/2023] Open
Abstract
The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.
Collapse
|
18
|
Peto M, Grant DM, Shoemaker RC, Cannon SB. Applying small-scale DNA signatures as an aid in assembling soybean chromosome sequences. Adv Bioinformatics 2010; 2010:976792. [PMID: 20827309 PMCID: PMC2933861 DOI: 10.1155/2010/976792] [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: 11/19/2009] [Accepted: 06/28/2010] [Indexed: 11/18/2022] Open
Abstract
Previous work has established a genomic signature based on relative counts of the 16 possible dinucleotides. Until now, it has been generally accepted that the dinucleotide signature is characteristic of a genome and is relatively homogeneous across a genome. However, we found some local regions of the soybean genome with a signature differing widely from that of the rest of the genome. Those regions were mostly centromeric and pericentromeric, and enriched for repetitive sequences. We found that DNA binding energy also presented large-scale patterns across soybean chromosomes. These two patterns were helpful during assembly and quality control of soybean whole genome shotgun scaffold sequences into chromosome pseudomolecules.
Collapse
Affiliation(s)
- Myron Peto
- USDA-ARS-CICGR Unit and Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - David M. Grant
- USDA-ARS-CICGR Unit and Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Randy C. Shoemaker
- USDA-ARS-CICGR Unit and Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Steven B. Cannon
- USDA-ARS-CICGR Unit and Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
19
|
Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S, Forrest DK, Wise R, Ware D, Wing RA, Waterman MS, Livny M, Schwartz DC. A single molecule scaffold for the maize genome. PLoS Genet 2009; 5:e1000711. [PMID: 19936062 PMCID: PMC2774507 DOI: 10.1371/journal.pgen.1000711] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 10/05/2009] [Indexed: 11/18/2022] Open
Abstract
About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars. The maize genome contains abundant repeats interspersed by low-copy, gene-coding sequences that make it a challenge to sequence; consequently, current BAC sequence assemblies average 11 contigs per clone. The iMap deals with such complexity by the judicious integration of IBM genetic and B73 physical maps, but the B73 genome structure could differ from the IBM population because of genetic recombination and subsequent rearrangements. Accordingly, we report a genome-wide, high-resolution optical map of maize B73 genome that was constructed from the direct analysis of genomic DNA molecules without using genetic markers. The integration of optical and iMap resources with comparisons to FPC maps enabled a uniquely comprehensive and scalable assessment of a given BAC's sequence assembly, its placement within a FPC contig, and the location of this FPC contig within a chromosome-wide pseudomolecule. As such, the overall utility of the maize optical map for the validation of sequence assemblies has been significant and demonstrates the inherent advantages of single molecule platforms. Construction of the maize optical map represents the first physical map of a eukaryotic genome larger than 400 Mb that was created de novo from individual genomic DNA molecules.
Collapse
Affiliation(s)
- Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Fusheng Wei
- Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
| | - John Nguyen
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Mike Bechner
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Konstantinos Potamousis
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Steve Goldstein
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Louise Pape
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Michael R. Mehan
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Chris Churas
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Dan K. Forrest
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Roger Wise
- Corn Insects and Crop Genetics Research, United States Department of Agriculture–Agricultural Research Service and Department of Plant Pathology, Iowa State University, Ames, Iowa, United States of America
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Plant, Soil, and Nutrition Research, United States Department of Agriculture–Agricultural Research Service, Ithaca, New York, United States of America
| | - Rod A. Wing
- Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Michael S. Waterman
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Miron Livny
- Computer Sciences Department, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
| |
Collapse
|
20
|
Tang X, de Boer JM, van Eck HJ, Bachem C, Visser RGF, de Jong H. Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technology. Chromosome Res 2009; 17:899-915. [PMID: 19774472 PMCID: PMC2776164 DOI: 10.1007/s10577-009-9077-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 08/20/2009] [Indexed: 11/30/2022]
Abstract
A cytogenetic map has been developed for diploid potato (Solanum tuberosum), in which the arms of the 12 potato bivalents can be identified in pachytene complements using multicolor fluorescence in situ hybridization (FISH) with a set of 60 genetically anchored bacterial artificial chromosome (BAC) clones from the RHPOTKEY BAC library. This diagnostic set of selected BACs (five per chromosome) hybridizes to euchromatic regions and corresponds to well-defined loci in the ultradense genetic map, and with these probes a new detailed and reliable pachytene karyotype could be established. Chromosome size has been estimated both from microscopic length measurements and from 4′,6-diamidino-2-phenylindole fluorescence-based DNA content measurements. In both approaches, chromosome 1 is the largest (100–115 Mb) and chromosome 11 the smallest (49–53 Mb). Detailed measurements of mega-base-pair to micrometer ratios have been obtained for chromosome 5, with average values of 1.07 Mb/μm for euchromatin and 3.67 Mb/μm for heterochromatin. In addition, our FISH results helped to solve two discrepancies in the potato genetic map related to chromosomes 8 and 12. Finally, we discuss the significance of the potato cytogenetic map for extended FISH studies in potato and related Solanaceae, which will be especially beneficial for the potato genome-sequencing project.
Collapse
Affiliation(s)
- Xiaomin Tang
- Wageningen UR Plant Breeding, Wageningen University and Research Center, 6708 PB, Wageningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
21
|
Gupta V, Mathur S, Solanke AU, Sharma MK, Kumar R, Vyas S, Khurana P, Khurana JP, Tyagi AK, Sharma AK. Genome analysis and genetic enhancement of tomato. Crit Rev Biotechnol 2009; 29:152-81. [PMID: 19319709 DOI: 10.1080/07388550802688870] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Solanaceae is an important family of vegetable crops, ornamentals and medicinal plants. Tomato has served as a model member of this family largely because of its enriched cytogenetic, genetic, as well as physical, maps. Mapping has helped in cloning several genes of importance such as Pto, responsible for resistance against bacterial speck disease, Mi-1.2 for resistance against nematodes, and fw2.2 QTL for fruit weight. A high-throughput genome-sequencing program has been initiated by an international consortium of 10 countries. Since heterochromatin has been found to be concentrated near centromeres, the consortium is focusing on sequencing only the gene-rich euchromatic region. Genomes of the members of Solanaceae show a significant degree of synteny, suggesting that the tomato genome sequence would help in the cloning of genes for important traits from other Solanaceae members as well. ESTs from a large number of cDNA libraries have been sequenced, and microarray chips, in conjunction with wide array of ripening mutants, have contributed immensely to the understanding of the fruit-ripening phenomenon. Work on the analysis of the tomato proteome has also been initiated. Transgenic tomato plants with improved abiotic stress tolerance, disease resistance and insect resistance, have been developed. Attempts have also been made to develop tomato as a bioreactor for various pharmaceutical proteins. However, control of fruit quality and ripening remains an active and challenging area of research. Such efforts should pave the way to improve not only tomato, but also other solanaceous crops.
Collapse
Affiliation(s)
- Vikrant Gupta
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Khan N, Barba-Gonzalez R, Ramanna MS, Visser RGF, Van Tuyl JM. Construction of chromosomal recombination maps of three genomes of lilies (Lilium) based on GISH analysis. Genome 2009; 52:238-51. [PMID: 19234552 DOI: 10.1139/g08-122] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chromosomal recombination maps were constructed for three genomes of lily (Lilium) using GISH analyses. For this purpose, the backcross (BC) progenies of two diploid (2n = 2x = 24) interspecific hybrids of lily, viz. Longiflorum x Asiatic (LA) and Oriental x Asiatic (OA), were used. Mostly the BC progenies of LA hybrids consisted of both triploid (2n = 3x = 36) and diploid (2n = 2x = 24) with some aneuploid genotypes and those of OA hybrids consisted of triploid (2n = 3x = 36) and some aneuploid genotypes. In all cases, it was possible to identify the homoeologous recombinant chromosomes as well as accurately count the number of crossover points, which are called "recombination sites". Recombination sites were estimated in the BC progeny of 71 LA and 41 OA genotypes. In the case of BC progenies of LA hybrids, 248 recombination sites were cytologically localized on 12 different chromosomes of each genome (i.e., L and A). Similarly, 116 recombinant sites were localized on the 12 chromosomes each from the BC progenies of OA hybrids (O and A genomes). Cytological maps were constructed on the basis of the percentages of distances (micrometres) of the recombination sites from the centromeres. Since an Asiatic parent was involved in both hybrids, viz. LA and OA, two maps were constructed for the A genome that were indicated as Asiatic (L) and Asiatic (O). The other two maps were Longiflorum (A) and Oriental (A). Remarkably, the recombination sites were highly unevenly distributed among the different chromosomes of all four maps. Because the recombination sites can be unequivocally identified through GISH, they serve as reliable landmarks and pave the way for assigning molecular markers or desirable genes to chromosomes of Lilium and also monitor introgression of alien segments.
Collapse
Affiliation(s)
- Nadeem Khan
- Laboratory of Plant Breeding, Wageningen University and Research, P.O. Box 386, Wageningen, 6708PB, The Netherlands
| | | | | | | | | |
Collapse
|
23
|
Relationship between physical and genetic distances along the zebra finch Z chromosome. Chromosome Res 2008; 16:839-49. [PMID: 18668333 DOI: 10.1007/s10577-008-1243-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/28/2008] [Accepted: 05/28/2008] [Indexed: 10/21/2022]
Abstract
Nine bacterial artificial chromosomes containing genes linked to the Z chromosome of the zebra finch (Taeniopygia guttata) were localized using FISH on synaptonemal complex spreads. Their positions were correlated with those previously reported on the mitotic Z chromosome, showing a linear relationship between positions along the mitotic chromosome and its synaptonemal complex. Distances in cM between the genes were calculated using a cytological map of the crossing-over based on the distribution of MLH1 foci along the ZZ synaptonemal complex (MLH1-cM map). It is shown that physical and genetic distances lack a linear relationship along most of the chromosome length, due to clustering of crossover events around the telomeres. This relationship departs strongly from that observed in the chicken Z chromosome and reflects the existence of different recombination rates and patterns among birds in spite of wide genomic conservation.
Collapse
|
24
|
Integration of cytogenetic and genetic linkage maps unveils the physical architecture of tomato chromosome 2. Genetics 2008; 179:1211-20. [PMID: 18622034 DOI: 10.1534/genetics.108.089532] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the integration of the linkage map of tomato chromosome 2 with a high-density bacterial artificial chromosome fluorescence in situ hybridization (BAC-FISH)-based cytogenetic map. The euchromatic block of chromosome 2 resides between 13 and 142 cM and has a physical length of 48.12 microm, with 1 microm equivalent to 540 kb. BAC-FISH resolved a pair of loci that were 3.7-3.9 Mb apart and were not resolved on the linkage map. Most of the regions had crossover densities close to the mean of approximately 200 kb/cM. Relatively hot and cold spots of recombination were unevenly distributed along the chromosome. The distribution of centimorgan/micrometer values was similar to the previously reported recombination nodule distribution along the pachytene chromosome. FISH-based physical maps will play an important role in advanced genomics research for tomato, including map-based cloning of agronomically important traits and whole-genome sequencing.
Collapse
|
25
|
Gill N, Hans CS, Jackson S. An overview of plant chromosome structure. Cytogenet Genome Res 2008; 120:194-201. [PMID: 18504347 DOI: 10.1159/000121067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2008] [Indexed: 11/19/2022] Open
Affiliation(s)
- N Gill
- Department of Agronomy, Purdue University, West Lafayette, IN 47906, USA
| | | | | |
Collapse
|
26
|
Danilova TV, Birchler JA. Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development. Chromosoma 2008; 117:345-56. [PMID: 18317793 DOI: 10.1007/s00412-008-0151-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2007] [Revised: 02/04/2008] [Accepted: 02/05/2008] [Indexed: 11/28/2022]
Abstract
To study the correlation of the sequence positions on the physical DNA finger print contig (FPC) map and cytogenetic maps of pachytene and somatic maize chromosomes, sequences located along the chromosome 9 FPC map approximately every 10 Mb were selected to place on maize chromosomes using fluorescent in situ hybridization (FISH). The probes were produced as pooled polymerase chain reaction products based on sequences of genetic markers or repeat-free portions of mapped bacterial artificial chromosome (BAC) clones. Fifteen probes were visualized on chromosome 9. The cytological positions of most sequences correspond on the pachytene, somatic, and FPC maps except some probes at the pericentromeric regions. Because of unequal condensation of mitotic metaphase chromosomes, being lower at pericentromeric regions and higher in the arms, probe positions are displaced to the distal ends of both arms. The axial resolution of FISH on somatic chromosome 9 varied from 3.3 to 8.2 Mb, which is 12-30 times lower than on pachytene chromosomes. The probe collection can be used as chromosomal landmarks or as a "banding paint" for the physical mapping of sequences including transgenes and BAC clones and for studying chromosomal rearrangements.
Collapse
Affiliation(s)
- Tatiana V Danilova
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
| | | |
Collapse
|
27
|
Okagaki RJ, Jacobs MS, Stec AO, Kynast RG, Buescher E, Rines HW, Vales MI, Riera-Lizarazu O, Schneerman M, Doyle G, Friedman KL, Staub RW, Weber DF, Kamps TL, Amarillo IFE, Chase CD, Bass HW, Phillips RL. Maize centromere mapping: a comparison of physical and genetic strategies. ACTA ACUST UNITED AC 2008; 99:85-93. [PMID: 18216028 DOI: 10.1093/jhered/esm111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Centromere positions on 7 maize chromosomes were compared on the basis of data from 4 to 6 mapping techniques per chromosome. Centromere positions were first located relative to molecular markers by means of radiation hybrid lines and centric fission lines recovered from oat-maize chromosome addition lines. These centromere positions were then compared with new data from centric fission lines recovered from maize plants, half-tetrad mapping, and fluorescence in situ hybridizations and to data from earlier studies. Surprisingly, the choice of mapping technique was not the critical determining factor. Instead, on 4 chromosomes, results from all techniques were consistent with a single centromere position. On chromosomes 1, 3, and 6, centromere positions were not consistent even in studies using the same technique. The conflicting centromere map positions on chromosomes 1, 3, and 6 could be explained by pericentric inversions or alternative centromere positions on these chromosomes.
Collapse
Affiliation(s)
- Ron J Okagaki
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108-6026, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Chang SB, Anderson LK, Sherman JD, Royer SM, Stack SM. Predicting and testing physical locations of genetically mapped loci on tomato pachytene chromosome 1. Genetics 2007; 176:2131-8. [PMID: 17565940 PMCID: PMC1950619 DOI: 10.1534/genetics.107.074138] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Predicting the chromosomal location of mapped markers has been difficult because linkage maps do not reveal differences in crossover frequencies along the physical structure of chromosomes. Here we combine a physical crossover map based on the distribution of recombination nodules (RNs) on Solanum lycopersicum (tomato) synaptonemal complex 1 with a molecular genetic linkage map from the interspecific hybrid S. lycopersicum x S. pennellii to predict the physical locations of 17 mapped loci on tomato pachytene chromosome 1. Except for one marker located in heterochromatin, the predicted locations agree well with the observed locations determined by fluorescence in situ hybridization. One advantage of this approach is that once the RN distribution has been determined, the chromosomal location of any mapped locus (current or future) can be predicted with a high level of confidence.
Collapse
Affiliation(s)
- Song-Bin Chang
- Departmrent of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | | | | | | | | |
Collapse
|
29
|
Lamb JC, Meyer JM, Corcoran B, Kato A, Han F, Birchler JA. Distinct chromosomal distributions of highly repetitive sequences in maize. Chromosome Res 2007; 15:33-49. [PMID: 17295125 DOI: 10.1007/s10577-006-1102-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The majority of genomic DNA in most plant species is made up of repetitive elements including satellites and retrotransposons. The maize genome is intermediate in size and abundance of repetitive elements between small genomes such as Arabidopsis and rice and larger genomes such as wheat. Although repetitive elements are present throughout the maize genome, individual families are non-randomly distributed along chromosomes. In this work we use fluorescence in-situ hybridization (FISH) to examine the distribution of abundant LTR retroelement families and satellites contained in heterochromatic blocks called knobs. Different retroelement families have distinct patterns of hybridization. Prem1 and Tekay, two very closely related elements, both hybridize along the length of all chromosomes but do so with greater intensity near the centromeres, although subtle differences are detectable between the hybridization patterns. Opie, Prem2/Ji, and Huck are enriched away from the centromeres and Grande is distributed uniformly along the chromosomes. Double labeling with proximally and distally enriched elements on pachytene chromosomes produces alternating blocks of element enrichment. The maize elements hybridized in the same general patterns to chromosomes of maize relatives including Zea diploperennis and Tripsacum dactyloides. Additionally, abundant Tripsacum LTR retroelements are enriched in similar chromosomal regions among the different species. The 180 bp knob satellite is present in large blocks at interstitial locations on chromosome arms. With long exposures, smaller sites of hybridization are detected at the ends of chromosomes, adjacent to the telomere tract. This distal position for knob satellites is conserved among Zea and Tripsacum species.
Collapse
Affiliation(s)
- Jonathan C Lamb
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
| | | | | | | | | | | |
Collapse
|
30
|
Lawrence CJ, Schaeffer ML, Seigfried TE, Campbell DA, Harper LC. MaizeGDB's new data types, resources and activities. Nucleic Acids Res 2007; 35:D895-900. [PMID: 17202174 PMCID: PMC1899092 DOI: 10.1093/nar/gkl1048] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MaizeGDB is the Maize Genetics and Genomics Database. Available at MaizeGDB are diverse data that support maize research including maps, gene product information, loci and their various alleles, phenotypes (both naturally occurring and as a result of directed mutagenesis), stocks, sequences, molecular markers, references and contact information for maize researchers worldwide. Also available through MaizeGDB are various community support service bulletin boards including the Editorial Board's list of high-impact papers, information about the Annual Maize Genetics Conference and the Jobs board where employment opportunities are posted. Reported here are data updates, improvements to interfaces and changes to standard operating procedures that have been made during the past 2 years. MaizeGDB is freely available and can be accessed online at http://www.maizegdb.org.
Collapse
Affiliation(s)
- Carolyn J Lawrence
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA 50011-3260, USA.
| | | | | | | | | |
Collapse
|
31
|
Able JA, Langridge P, Milligan AS. Capturing diversity in the cereals: many options but little promiscuity. TRENDS IN PLANT SCIENCE 2007; 12:71-9. [PMID: 17224300 DOI: 10.1016/j.tplants.2006.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Revised: 11/06/2006] [Accepted: 12/20/2006] [Indexed: 05/13/2023]
Abstract
It is generally recognized by geneticists and plant breeders alike that there is a need to further improve the ability to capture and manipulate genetic diversity. The effective harnessing of diversity in traditional breeding programmes is limited and, therefore, it is vital that meiotic recombination can be manipulated given that it plays a pivotal role in generating diversity. With the advent of a wider range of genomics technologies, our understanding of meiotic processes should increase rapidly. Although comparative genetics has been useful, particularly in the broader grass family, the development of physical maps, long-range sequencing and transcript profiles promises to unravel the complexities of genomes as large or larger than wheat. Highlighting the most significant findings to date, this review pools the knowledge on these tools and reproductive processes.
Collapse
Affiliation(s)
- Jason A Able
- Molecular Plant Breeding Cooperative Research Centre, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.
| | | | | |
Collapse
|
32
|
Abstract
Many studies have demonstrated that the distribution of meiotic crossover events along chromosomes is non-random in plants and other species with sexual reproduction. Large differences in recombination frequencies appear at several scales. On a large scale, regions of high and low rates of crossover have been found to alternate along the chromosomes in all plant species studied. High crossover rates have been reported to be correlated with several chromosome features (e.g. gene density and distance to the centromeres). However, most of these correlations cannot be extended to all plant species. Only a few plant species have been studied on a finer scale. Hotspots of meiotic recombination (i.e. DNA fragments of a few kilobases in length with a higher rate of recombination than the surrounding DNA) have been identified in maize and rice. Most of these hotspots are intragenic. In Arabidopsis thaliana, we have identified several DNA fragments (less than 5 kb in size) with genetic recombination rates at least 5 times higher than the whole-chromosome average [4.6 cM (centimorgan)/Mb], which are therefore probable hotspots for meiotic recombination. Most crossover breakpoints lie in intergenic or non-coding regions. Major efforts should be devoted to characterizing meiotic recombination at the molecular level, which should help to clarify the role of this process in genome evolution.
Collapse
Affiliation(s)
- C Mézard
- Station de Génétique et d'Amélioration des Plantes, Institut Jean-Pierre Bourgin, INRA, route de Saint-Cyr, 78026 Versailles cedex, France.
| |
Collapse
|
33
|
Shi J, Dawe RK. Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27. Genetics 2006; 173:1571-83. [PMID: 16624902 PMCID: PMC1526679 DOI: 10.1534/genetics.106.056853] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report a detailed analysis of maize chromosome structure with respect to seven histone H3 methylation states (dimethylation at lysine 4 and mono-, di-, and trimethylation at lysines 9 and 27). Three-dimensional light microscopy and the fine cytological resolution of maize pachytene chromosomes made it possible to compare the distribution of individual histone methylation events to each other and to DNA staining intensity. Major conclusions are that (1) H3K27me2 marks classical heterochromatin; (2) H3K4me2 is limited to areas between and around H3K27me2-marked chromomeres, clearly demarcating the euchromatic gene space; (3) H3K9me2 is restricted to the euchromatic gene space; (4) H3K27me3 occurs in a few (roughly seven) focused euchromatic domains; (5) centromeres and CENP-C are closely associated with H3K9me2 and H3K9me3; and (6) histone H4K20 di- and trimethylation are nearly or completely absent in maize. Each methylation state identifies different regions of the epigenome. We discuss the evolutionary lability of histone methylation profiles and draw a distinction between H3K9me2-mediated gene silencing and heterochromatin formation.
Collapse
Affiliation(s)
- Jinghua Shi
- Department of Pathology, University of Georgia, Athens, Georgia 30602, USA
| | | |
Collapse
|
34
|
Lamb JC, Birchler JA. Retroelement genome painting: cytological visualization of retroelement expansions in the genera Zea and Tripsacum. Genetics 2006; 173:1007-21. [PMID: 16582446 PMCID: PMC1526525 DOI: 10.1534/genetics.105.053165] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Divergence of abundant genomic elements among the Zea and Tripsacum genera was examined cytologically and a tool kit established for subsequent studies. The LTR regions from the CRM, Huck, Grande, Prem1, Prem2/Ji, Opie, Cinful-1, and Tekay retroelement families were used as FISH probes on mitotic chromosome spreads from a "trispecies" hybrid containing chromosomes from each of three species: Zea mays (2n = 20), Z. diploperennis (2n = 20), and Tripsacum dactyloides (2n = 36). Except for Tekay, which painted both Zea and Tripsacum chromosomes with nearly equal intensity, the retroelement probes hybridized strongly to the Zea chromosomes, allowing them to be distinguished from those of Tripsacum. Huck and Grande hybridized more intensely to maize than to Z. diploperennis chromosomes. Tripsacum genomic clones containing retroelement sequences were isolated that specifically paint Tripsacum chromosomes. The retroelement paints proved effective for distinguishing different genomes in interspecific hybrids and visualizing alien chromatin from T. dactyloides introgressed into maize lines. Other FISH probes (180-bp knob, TR-1, 5S, NOR, Cent4, CentC, rp1, rp3, and alpha-ZeinA) could be simultaneously visualized with the retroelement probes, emphasizing the value of the retroelement probes for cytogenetic studies of Zea and Tripsacum.
Collapse
Affiliation(s)
- Jonathan C Lamb
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211-7400, USA
| | | |
Collapse
|
35
|
Lawrence CJ, Seigfried TE, Bass HW, Anderson LK. Predicting chromosomal locations of genetically mapped loci in maize using the Morgan2McClintock Translator. Genetics 2005; 172:2007-9. [PMID: 16387866 PMCID: PMC1456272 DOI: 10.1534/genetics.105.054155] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Morgan2McClintock Translator permits prediction of meiotic pachytene chromosome map positions from recombination-based linkage data using recombination nodule frequency distributions. Its outputs permit estimation of DNA content between mapped loci and help to create an integrated overview of the maize nuclear genome structure.
Collapse
Affiliation(s)
- Carolyn J Lawrence
- USDA-ARS, Corn Insect and Crop Genetics Research Unit, Iowa State University, Ames 50011, USA.
| | | | | | | |
Collapse
|
36
|
Anderson LK, Lai A, Stack SM, Rizzon C, Gaut BS. Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Res 2005; 16:115-22. [PMID: 16339046 PMCID: PMC1356135 DOI: 10.1101/gr.4249906] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Examining the relationships among DNA sequence, meiotic recombination, and chromosome structure at a genome-wide scale has been difficult because only a few markers connect genetic linkage maps with physical maps. Here, we have positioned 1195 genetically mapped expressed sequence tag (EST) markers onto the 10 pachytene chromosomes of maize by using a newly developed resource, the RN-cM map. The RN-cM map charts the distribution of crossing over in the form of recombination nodules (RNs) along synaptonemal complexes (SCs, pachytene chromosomes) and allows genetic cM distances to be converted into physical micrometer distances on chromosomes. When this conversion is made, most of the EST markers used in the study are located distally on the chromosomes in euchromatin. ESTs are significantly clustered on chromosomes, even when only euchromatic chromosomal segments are considered. Gene density and recombination rate (as measured by EST and RN frequencies, respectively) are strongly correlated. However, crossover frequencies for telomeric intervals are much higher than was expected from their EST frequencies. For pachytene chromosomes, EST density is about fourfold higher in euchromatin compared with heterochromatin, while DNA density is 1.4 times higher in heterochromatin than in euchromatin. Based on DNA density values and the fraction of pachytene chromosome length that is euchromatic, we estimate that approximately 1500 Mbp of the maize genome is in euchromatin. This overview of the organization of the maize genome will be useful in examining genome and chromosome evolution in plants.
Collapse
Affiliation(s)
- Lorinda K Anderson
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA.
| | | | | | | | | |
Collapse
|
37
|
Smith JJ, Kump DK, Walker JA, Parichy DM, Voss SR. A comprehensive expressed sequence tag linkage map for tiger salamander and Mexican axolotl: enabling gene mapping and comparative genomics in Ambystoma. Genetics 2005; 171:1161-71. [PMID: 16079226 PMCID: PMC1456819 DOI: 10.1534/genetics.105.046433] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Accepted: 07/26/2005] [Indexed: 11/18/2022] Open
Abstract
Expressed sequence tag (EST) markers were developed for Ambystoma tigrinum tigrinum (Eastern tiger salamander) and for A. mexicanum (Mexican axolotl) to generate the first comprehensive linkage map for these model amphibians. We identified 14 large linkage groups (125.5-836.7 cM) that presumably correspond to the 14 haploid chromosomes in the Ambystoma genome. The extent of genome coverage for these linkage groups is apparently high because the total map size (5251 cM) falls within the range of theoretical estimates and is consistent with independent empirical estimates. Unlike most vertebrate species, linkage map size in Ambystoma is not strongly correlated with chromosome arm number. Presumably, the large physical genome size ( approximately 30 Gbp) is a major determinant of map size in Ambystoma. To demonstrate the utility of this resource, we mapped the position of two historically significant A. mexicanum mutants, white and melanoid, and also met, a quantitative trait locus (QTL) that contributes to variation in metamorphic timing. This new collection of EST-based PCR markers will better enable the Ambystoma system by facilitating development of new molecular probes, and the linkage map will allow comparative studies of this important vertebrate group.
Collapse
Affiliation(s)
- J J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA.
| | | | | | | | | |
Collapse
|
38
|
Khrustaleva LI, de Melo PE, van Heusden AW, Kik C. The integration of recombination and physical maps in a large-genome monocot using haploid genome analysis in a trihybrid allium population. Genetics 2005; 169:1673-85. [PMID: 15654085 PMCID: PMC1449564 DOI: 10.1534/genetics.104.038687] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Integrated mapping in large-genome monocots has been carried out on a limited number of species. Furthermore, integrated maps are difficult to construct for these species due to, among other reasons, the specific plant populations needed. To fill these gaps, Alliums were chosen as target species and a new strategy for constructing suitable populations was developed. This strategy involves the use of trihybrid genotypes in which only one homeolog of a chromosome pair is recombinant due to interspecific recombination. We used genotypes from a trihybrid Allium cepa x (A. roylei x A. fistulosum) population. Recombinant chromosomes 5 and 8 from the interspecific parent were analyzed using genomic in situ hybridization visualization of recombination points and the physical positions of recombination were integrated into AFLP linkage maps of both chromosomes. The integrated maps showed that in Alliums recombination predominantly occurs in the proximal half of chromosome arms and that 57.9% of PstI/MseI markers are located in close proximity to the centromeric region, suggesting the presence of genes in this region. These findings are different from data obtained on cereals, where recombination rate and gene density tends to be higher in distal regions.
Collapse
Affiliation(s)
- L I Khrustaleva
- Plant Research International, Wageningen University and Research Center, The Netherlands
| | | | | | | |
Collapse
|