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Wicker T, Yahiaoui N, Guyot R, Schlagenhauf E, Liu ZD, Dubcovsky J, Keller B. Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat. THE PLANT CELL 2003; 15:1186-97. [PMID: 12724543 PMCID: PMC153725 DOI: 10.1105/tpc.011023] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2003] [Accepted: 02/20/2003] [Indexed: 05/18/2023]
Abstract
To study genome evolution in wheat, we have sequenced and compared two large physical contigs of 285 and 142 kb covering orthologous low molecular weight (LMW) glutenin loci on chromosome 1AS of a diploid wheat species (Triticum monococcum subsp monococcum) and a tetraploid wheat species (Triticum turgidum subsp durum). Sequence conservation between the two species was restricted to small regions containing the orthologous LMW glutenin genes, whereas >90% of the compared sequences were not conserved. Dramatic sequence rearrangements occurred in the regions rich in repetitive elements. Dating of long terminal repeat retrotransposon insertions revealed different insertion events occurring during the last 5.5 million years in both species. These insertions are partially responsible for the lack of homology between the intergenic regions. In addition, the gene space was conserved only partially, because different predicted genes were identified on both contigs. Duplications and deletions of large fragments that might be attributable to illegitimate recombination also have contributed to the differentiation of this region in both species. The striking differences in the intergenic landscape between the A and A(m) genomes that diverged 1 to 3 million years ago provide evidence for a dynamic and rapid genome evolution in wheat species.
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Affiliation(s)
- Thomas Wicker
- Institute of Plant Biology, University of Zürich, Switzerland
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302
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Hampson S, McLysaght A, Gaut B, Baldi P. LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome Res 2003; 13:999-1010. [PMID: 12695327 PMCID: PMC430881 DOI: 10.1101/gr.814403] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The identification of homologous regions between chromosomes forms the basis for studies of genome organization, comparative genomics, and evolutionary genomics. Identification of these regions can be based on either synteny or colinearity, but there are few methods to test statistically for significant evidence of homology. In the present study, we improve a preexisting method that used colinearity as the basis for statistical tests. Improvements include computational efficiency and a relaxation of the colinearity assumption. Two algorithms perform the method: FullPermutation, which searches exhaustively for runs of markers, and FastRuns, which trades faster run times for exhaustive searches. The algorithms described here are available in the LineUp package (http://www.igb.uci.edu/ approximately baldig/lineup). We explore the performance of both algorithms on simulated data and also on genetic map data from maize (Zea mays ssp. mays). The method has reasonable power to detect a homologous region; for example, in >90% of simulations, both algorithms detect a homologous region of 10 markers buried in a random background, even when the homologous regions have diverged by numerous inversion events. The methods were applied to four maize molecular maps. All maps indicate that the maize genome contains extensive regions of genomic duplication and multiplication. Nonetheless, maps differ substantially in the location of homologous regions, probably reflecting the incomplete nature of genetic map data. The variation among maps has important implications for evolutionary inference from genetic map data.
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Affiliation(s)
- Steve Hampson
- Institute for Genomics and Bioinformatics, Department of Information and Computer Science and Department of Ecology and Evolutionary Biology, and Department of Biological Chemistry, University of California at Irvine, Irvine, California 92697, USA
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303
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Abstract
New alleles are constantly accumulated during intentional crop selection. The molecular understanding of these alleles has stimulated new genomic approaches to mapping quantitative trait loci (QTL) and haplotype multiplicity of the genes concerned. A limited number of quantitative trait nucleotides responsible for QTL variation have been described, but an acceleration in their rate of discovery is expected with the adoption of linkage disequilibrium and candidate gene strategies for QTL fine mapping and cloning. Additional layers of regulatory variation have been studied that could also contribute to the molecular basis of quantitative genetics of crop traits. Despite this progress, the role of marker-assisted selection in plant breeding will ultimately depend on the genetic model underlying quantitative variation.
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Affiliation(s)
- Michele Morgante
- Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Universita' di Udine, Via delle Scienze 208, 33100, Udine, Italy.
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304
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Han B, Xue Y. Genome-wide intraspecific DNA-sequence variations in rice. CURRENT OPINION IN PLANT BIOLOGY 2003; 6:134-138. [PMID: 12667869 DOI: 10.1016/s1369-5266(03)00004-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genome-wide comparative analysis of the DNA sequences of two major cultivated rice subspecies, Oryza sativa L. ssp indica and Oryza sativa L. ssp japonica, have revealed their extensive microcolinearity in gene order and content. However, deviations from colinearity are frequent owing to insertions or deletions. Intraspecific sequence polymorphisms commonly occur in both coding and non-coding regions. These variations often affect gene structures and may contribute to intraspecific phenotypic adaptations.
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Affiliation(s)
- Bin Han
- National Centre for Gene Research, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China.
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305
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Young ND, Mudge J, Ellis THN. Legume genomes: more than peas in a pod. CURRENT OPINION IN PLANT BIOLOGY 2003; 6:199-204. [PMID: 12667879 DOI: 10.1016/s1369-5266(03)00006-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A growing array of sequence-based tools is helping to reveal the organization, evolution and syntenic relationships of legume genomes. The results indicate that legumes form a coherent taxonomic group with frequent and widespread macro- and microsynteny. This is good news for two model legume systems, Medicago truncatula and Lotus japonicus. Indeed, both models have recently been used to clone and characterize genes for nodulation-related receptors that were originally described in legumes with more complex genomes. Studies of legume genomes have also provided insight into genome size, gene clustering, genome duplications and repetitive elements. To understand legume genomes better, it will be necessary to develop tools for studying under-represented taxa beyond the relatively small group of economically important species that have been examined so far.
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Affiliation(s)
- Nevin Dale Young
- Department of Plant Pathology, 495 Borlaug Hall, University of Minnesota, St. Paul, Minnesota 55108, USA.
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306
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Lal SK, Giroux MJ, Brendel V, Vallejos CE, Hannah LC. The maize genome contains a helitron insertion. THE PLANT CELL 2003; 15:381-91. [PMID: 12566579 PMCID: PMC141208 DOI: 10.1105/tpc.008375] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2002] [Accepted: 11/11/2002] [Indexed: 05/18/2023]
Abstract
The maize mutation sh2-7527 was isolated in a conventional maize breeding program in the 1970s. Although the mutant contains foreign sequences within the gene, the mutation is not attributable to an interchromosomal exchange or to a chromosomal inversion. Hence, the mutation was caused by an insertion. Sequences at the two Sh2 borders have not been scrambled or mutated, suggesting that the insertion is not caused by a catastrophic reshuffling of the maize genome. The insertion is large, at least 12 kb, and is highly repetitive in maize. As judged by hybridization, sorghum contains only one or a few copies of the element, whereas no hybridization was seen to the Arabidopsis genome. The insertion acts from a distance to alter the splicing of the sh2 pre-mRNA. Three distinct intron-bearing maize genes were found in the insertion. Of most significance, the insertion bears striking similarity to the recently described DNA helicase-bearing transposable elements termed HELITRONS: Like Helitrons, the inserted sequence of sh2-7527 is large, lacks terminal repeats, does not duplicate host sequences, and was inserted between a host dinucleotide AT. Like Helitrons, the maize element contains 5' TC and 3' CTRR termini as well as two short palindromic sequences near the 3' terminus that potentially can form a 20-bp hairpin. Although the maize element lacks sequence information for a DNA helicase, it does contain four exons with similarity to a plant DEAD box RNA helicase. A second Helitron insertion was found in the maize genomic database. These data strongly suggest an active Helitron in the present-day maize genome.
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Affiliation(s)
- Shailesh K Lal
- Program in Plant Molecular and Cellular Biology and Horticultural Sciences, University of Florida, Gainesville, Florida 32611-0690, USA
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307
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Flint-Garcia SA, Thornsberry JM, Buckler ES. Structure of linkage disequilibrium in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2003; 54:357-74. [PMID: 14502995 DOI: 10.1146/annurev.arplant.54.031902.134907] [Citation(s) in RCA: 814] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Future advances in plant genomics will make it possible to scan a genome for polymorphisms associated with qualitative and quantitative traits. Before this potential can be realized, we must understand the nature of linkage disequilibrium (LD) within a genome. LD, the nonrandom association of alleles at different loci, plays an integral role in association mapping, and determines the resolution of an association study. Recently, association mapping has been exploited to dissect quantitative trait loci (QTL). With the exception of maize and Arabidopsis, little research has been conducted on LD in plants. The mating system of the species (selfing versus outcrossing), and phenomena such as population structure and recombination hot spots, can strongly influence patterns of LD. The basic patterns of LD in plants will be better understood as more species are analyzed.
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Affiliation(s)
- Sherry A Flint-Garcia
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA.
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308
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Affiliation(s)
- Vicki L Chandler
- Plant Sciences Department, University of Arizona, Tuscon 85721, USA.
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309
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Beachy R, Bennetzen JL, Chassy BM, Chrispeels M, Chory J, Ecker JR, Noel JP, Kay SA, Dean C, Lamb C, Jones J, Santerre CR, Schroeder JI, Umen J, Yanofsky M, Wessler S, Zhao Y, Parrott W. Divergent perspectives on GM food. Nat Biotechnol 2002; 20:1195-6; author reply 1197. [PMID: 12454665 DOI: 10.1038/nbt1202-1195] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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310
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Ching A, Caldwell KS, Jung M, Dolan M, Smith OS(H, Tingey S, Morgante M, Rafalski AJ. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 2002; 3:19. [PMID: 12366868 PMCID: PMC130040 DOI: 10.1186/1471-2156-3-19] [Citation(s) in RCA: 230] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2002] [Accepted: 10/07/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. RESULTS We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp), but rare in coding regions. A small number (2-8) of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. CONCLUSIONS No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry.
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Affiliation(s)
- Ada Ching
- DuPont Crop Genetics, Delaware Technology Park, Suite 200, P.O. Box 6104, Newark, Delaware 19714, USA
| | - Katherine S Caldwell
- DuPont Crop Genetics, Delaware Technology Park, Suite 200, P.O. Box 6104, Newark, Delaware 19714, USA
- Present address: Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Mark Jung
- DuPont Crop Genetics, Delaware Technology Park, Suite 200, P.O. Box 6104, Newark, Delaware 19714, USA
| | - Maurine Dolan
- DuPont Crop Genetics, Delaware Technology Park, Suite 200, P.O. Box 6104, Newark, Delaware 19714, USA
| | | | - Scott Tingey
- DuPont Crop Genetics, Delaware Technology Park, Suite 200, P.O. Box 6104, Newark, Delaware 19714, USA
| | - Michele Morgante
- DuPont Crop Genetics, Delaware Technology Park, Suite 200, P.O. Box 6104, Newark, Delaware 19714, USA
| | - Antoni J Rafalski
- DuPont Crop Genetics, Delaware Technology Park, Suite 200, P.O. Box 6104, Newark, Delaware 19714, USA
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311
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Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 2002. [PMID: 12366868 DOI: 10.1186/1471‐2156‐3‐19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. RESULTS We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp), but rare in coding regions. A small number (2-8) of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. CONCLUSIONS No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry.
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Affiliation(s)
- Ada Ching
- DuPont Crop Genetics, Delaware Technology Park, Suite 200, P,O, Box 6104, Newark, Delaware 19714, USA.
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312
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Affiliation(s)
- Jeffrey L Bennetzen
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.
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