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Moolhuijzen P, Cakir M, Hunter A, Schibeci D, Macgregor A, Smith C, Francki M, Jones M, Appels R, Bellgard M. Erratum: LegumeDB bioinformatics resource: comparative genomic analysis and novel cross genera marker identification in lupin and pasture legume species. Genome 2006. [DOI: 10.1139/g06-124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- P. Moolhuijzen
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Western Australia
- Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
- Cooperative Research Centre, Valued-added Wheat, Murdoch University, Perth 6150, Western Australia
- State Agricultural Biotechnology Centre, Murdoch University, Perth 6150, Western Australia
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia; Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
| | - M. Cakir
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Western Australia
- Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
- Cooperative Research Centre, Valued-added Wheat, Murdoch University, Perth 6150, Western Australia
- State Agricultural Biotechnology Centre, Murdoch University, Perth 6150, Western Australia
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia; Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
| | - A. Hunter
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Western Australia
- Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
- Cooperative Research Centre, Valued-added Wheat, Murdoch University, Perth 6150, Western Australia
- State Agricultural Biotechnology Centre, Murdoch University, Perth 6150, Western Australia
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia; Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
| | - D. Schibeci
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Western Australia
- Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
- Cooperative Research Centre, Valued-added Wheat, Murdoch University, Perth 6150, Western Australia
- State Agricultural Biotechnology Centre, Murdoch University, Perth 6150, Western Australia
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia; Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
| | - A. Macgregor
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Western Australia
- Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
- Cooperative Research Centre, Valued-added Wheat, Murdoch University, Perth 6150, Western Australia
- State Agricultural Biotechnology Centre, Murdoch University, Perth 6150, Western Australia
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia; Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
| | - C. Smith
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Western Australia
- Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
- Cooperative Research Centre, Valued-added Wheat, Murdoch University, Perth 6150, Western Australia
- State Agricultural Biotechnology Centre, Murdoch University, Perth 6150, Western Australia
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia; Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
| | - M. Francki
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Western Australia
- Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
- Cooperative Research Centre, Valued-added Wheat, Murdoch University, Perth 6150, Western Australia
- State Agricultural Biotechnology Centre, Murdoch University, Perth 6150, Western Australia
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia; Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
| | - M.G.K. Jones
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Western Australia
- Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
- Cooperative Research Centre, Valued-added Wheat, Murdoch University, Perth 6150, Western Australia
- State Agricultural Biotechnology Centre, Murdoch University, Perth 6150, Western Australia
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia; Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
| | - R. Appels
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Western Australia
- Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
- Cooperative Research Centre, Valued-added Wheat, Murdoch University, Perth 6150, Western Australia
- State Agricultural Biotechnology Centre, Murdoch University, Perth 6150, Western Australia
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia; Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
| | - M. Bellgard
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Western Australia
- Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
- Cooperative Research Centre, Valued-added Wheat, Murdoch University, Perth 6150, Western Australia
- State Agricultural Biotechnology Centre, Murdoch University, Perth 6150, Western Australia
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia; Molecular Plant Breeding Cooperative Research Centre. Murdoch University, Perth 6150, Western Australia
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Moolhuijzen P, Cakir M, Hunter A, Schibeci D, Macgregor A, Smith C, Francki M, Jones MGK, Appels R, Bellgard M. LegumeDB1 bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species. Genome 2006; 49:689-99. [PMID: 16936848 DOI: 10.1139/g06-009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The identification of markers in legume pasture crops, which can be associated with traits such as protein and lipid production, disease resistance, and reduced pod shattering, is generally accepted as an important strategy for improving the agronomic performance of these crops. It has been demonstrated that many quantitative trait loci (QTLs) identified in one species can be found in other plant species. Detailed legume comparative genomic analyses can characterize the genome organization between model legume species (e.g., Medicago truncatula, Lotus japonicus) and economically important crops such as soybean (Glycine max), pea (Pisum sativum), chickpea (Cicer arietinum), and lupin (Lupinus angustifolius), thereby identifying candidate gene markers that can be used to track QTLs in lupin and pasture legume breeding. LegumeDB is a Web-based bioinformatics resource for legume researchers. LegumeDB analysis of Medicago truncatula expressed sequence tags (ESTs) has identified novel simple sequence repeat (SSR) markers (16 tested), some of which have been putatively linked to symbiosome membrane proteins in root nodules and cell-wall proteins important in plant-pathogen defence mechanisms. These novel markers by preliminary PCR assays have been detected in Medicago truncatula and detected in at least one other legume species, Lotus japonicus, Glycine max, Cicer arietinum, and (or) Lupinus angustifolius (15/16 tested). Ongoing research has validated some of these markers to map them in a range of legume species that can then be used to compile composite genetic and physical maps. In this paper, we outline the features and capabilities of LegumeDB as an interactive application that provides legume genetic and physical comparative maps, and the efficient feature identification and annotation of the vast tracks of model legume sequences for convenient data integration and visualization. LegumeDB has been used to identify potential novel cross-genera polymorphic legume markers that map to agronomic traits, supporting the accelerated identification of molecular genetic factors underpinning important agronomic attributes in lupin.
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Affiliation(s)
- P Moolhuijzen
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Western Australia
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Bariana HS, Parry N, Barclay IR, Loughman R, McLean RJ, Shankar M, Wilson RE, Willey NJ, Francki M. Identification and characterization of stripe rust resistance gene Yr34 in common wheat. Theor Appl Genet 2006; 112:1143-8. [PMID: 16435125 DOI: 10.1007/s00122-006-0216-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Accepted: 01/07/2006] [Indexed: 05/06/2023]
Abstract
An uncharacterized source of seedling resistance to Puccinia striiformis f.sp. tritici was identified in an advanced wheat breeding line WAWHT2046. Genetic analysis based on a WAWHT2046/Carnamah-derived double haploid (DH) population demonstrated monogenic inheritance of seedling stripe rust resistance in WAWHT2046. The gene controlling stripe rust resistance in line WAWHT2046 was tentatively designated YrWA. The chromosome 5AL located awn inhibitor gene B1, possessed by WAWHT2046, also showed monogenic inheritance when the DH population was scored for the presence and absence of awns. Joint segregation analysis at the B1 and YrWA loci indicated genetic linkage between the two loci. A recombination value of 12.2 cM was computed using Mapmanager. This association located YrWA in the chromosome arm 5AL. Molecular mapping using microsatellite markers placed YrWA distal to B1. All molecular markers mapped proximal to the awn inhibitor locus B1. As no other stripe rust resistance gene is reported to be located in the chromosome arm 5AL, YrWA was permanently designated as Yr34. Yr34 produced an intermediate (23C) seedling infection type and expressed very low stripe rust response (10R-MR) on adult plants in the field, similar to the resistance gene Yr17. In addition to Yr34, this mapping population segregated for three genetically independent adult plant stripe rust resistance genes. The detection of DH lines with completely susceptible response, higher than that shown by the Yr34-lacking parent Carnamah, suggested that both parents contributed adult plant resistance. The use of WAWHT2046 as a parent in breeding programs would also contribute APR in addition to Yr34.
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Affiliation(s)
- H S Bariana
- Faculty of Agriculture, Food and Natural Resources, University of Sydney Plant Breeding Institute-Cobbitty, PMB11, Camden, NSW 2570, Australia.
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Abstract
For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that insert between genes. These retroelements are less abundant in smaller genome plants, including rice and sorghum. Although 5- to 200-kb blocks of methylated, presumably heterochromatic, retrotransposons flank most maize genes, rice and sorghum genes are often adjacent. Similar genes are commonly found in the same relative chromosomal locations and orientations in each of these three species, although there are numerous exceptions to this collinearity (i.e., rearrangements) that can be detected at the levels of both the recombinational map and cloned DNA. Evolutionarily conserved sequences are largely confined to genes and their regulatory elements. Our results indicate that a knowledge of grass genome structure will be a useful tool for gene discovery and isolation, but the general rules and biological significance of grass genome organization remain to be determined. Moreover, the nature and frequency of exceptions to the general patterns of grass genome structure and collinearity are still largely unknown and will require extensive further investigation.
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Affiliation(s)
- J L Bennetzen
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA
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