Deliverables
The project delivered the first cloning of glutamine synthetase (GS) genes in wheat (Triticum aestivum L.).
Based on sequence analysis, phylogenetic studies and mapping data, ten GS sequences were classified into four sub-families: GS2 (a, b and c), GS1 (a, b and c), GSr (1 and 2) and GSe (1 and 2) with each of these sub-families being composed of homeoalleles. Phylogenetic analysis showed that the wheat GS sub-families together with the GS genes from other monocotyledonous species form four distinct clades, including that for the chloroplastic GS. Phylogenetic analysis showed that the wheat GS sub-families together with the GS genes from other monocotyledonous species form four distinct clades, including that for the chloroplastic GS.
These sequences were submitted to GenBank during the lifetime of the project to make the sequences publicly available. This is an essential aspect of genomic and genetic research to forward research in wheat and by comparative genomics to other cereals and species.
Stephanie M. Bernard, Anders Laurell Blom Moller, Giuseppe Dionisio, Thomas P. Jahn, Marcela Baudo, Marta S. Lopes, Therese Terce-Laforgue, Christine H. Foyer, Martin Parry, Brian G. Forde, Jose Luis Araus, Bertrand Hirel, Jan K. Schjoerring, Dimah Z. Habash. Gene expression and function of glutamine synthetase isozymes in wheat (Triticum aestivum L.). Plant Molecular Biology DOI: 10.1007/s11103-008-9303-y
The advent of molecular markers has revolutionised the genetic analysis of complex traits, and reports on the location of quantitative trait loci (QTLs) for yield for many cereal crops are commonplace for barley, rice and maize.
However, QTL analysis of quantitative traits in bread wheat has in part been hampered by its large genome size. Thus, many markers are required to cover the whole genome adequately. In addition, because of the relatively recent origin of the species, hexaploid wheat also suffers from relatively low levels of polymorphism.
In consequence, detailed genetic maps of the whole genome are much more difficult to achieve than for most other crop species. A few genetic maps covering all of the hexaploid wheat genome have been reported, the most detailed of which is the International Triticeae Mapping Initiative (ITMI) wheat map. To increase the levels of polymorphism, several of these maps have been made by crossing relatively distantly related parental lines. The number of whole genome maps developed from crosses between wheat cultivars or breeding lines is more limited.
We have used in this project a newly developed bread wheat mapping population generated from the cross between hexaploid wheat (Triticum aestivum L.) genotypes Chinese Spring (CS) and SQ1 (a high abscisic acid breeding line). Although one of the parents used for this mapping population (Chinese Spring) is unsuitable agronomically, it is well characterised genetically, and many aneuploid stocks are available to help assign chromosomal locations to molecular markers. We added a further 38 informative markers, mainly SSRs, to a final map containing 449 loci.
This was used for QTL detection and discovery. This map is now available to the public for studies on wheat and for comparative genomics.
Habash DZ, Bernard S, Schondelmaier J, Weyen J and Quarrie SA (2007) A genetic study of nitrogen use in hexaploid wheat in relation to N utilisation, development and yield. Theor Appl Genet. 114(3)403-419.
Quarrie, SA; Steed, A; Calestani, C; Semikhodskii, A; Lebreton, C; Chinoy, C; Steele, N; Pljevljakusic, D; Waterman, E; Weyen, J; Schondelmaier, J; Habash, DZ; Farmer, P; Saker, L; Clarkson, DT; Abugalieva, A; Yessimbekova, M; Turuspekov, Y; Abugalieva, S; Tuberosa, R; Sanguineti, MC; Hollington, PA; Aragues, R; Royo, A; Dodig, D. 2005. A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring X SQ1 and its use to compare QTLs for grain yield across a range of environments. Theor Appl Genet. 110 (5): 865-880
The addition of markers is very important for industrial activities: "The successful mapping of 100 SSRs to the map of wheat is very important for partner 3. By this deliverable partner 3 is able to react very fast and exact on publications in marker assisted selection procedures in wheat. In so far a first exploitation could be started immediately by choosing SSR markers for wheat breeding programmes and marker assisted selection". This defines the ability of the consortium to react fast to the latest technologies and to apply them to provide solutions to important economic and environmental problems in farming wheat.
The successful addition of SSR markers to the CSxSQ1 DHL mapping population is critical for QTL discovery. The genetic map has been published and is available to the public to utilise for molecular breeding in wheat and for comparative genomic studies. QTLs discovered using this map are also published and are publically available for research.
Quarrie, SA; Steed, A; Calestani, C; Semikhodskii, A; Lebreton, C; Chinoy, C; Steele, N; Pljevljakusic, D; Waterman, E; Weyen, J; Schondelmaier, J; Habash, DZ; Farmer, P; Saker, L; Clarkson, DT; Abugalieva, A; Yessimbekova, M; Turuspekov, Y; Abugalieva, S; Tuberosa, R; Sanguineti, MC; Hollington, PA; Aragues, R; Royo, A; Dodig, D. 2005. A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring X SQ1 and its use to compare QTLs for grain yield across a range of environments. Theor Appl Genet. 110 (5): 865-880.arch and molecular breeding in wheat.
The genetic studies on the bread wheat mapping population were very successful both for the immediate project and for the EU and global efforts of identifying loci regulating aspects of N use in this major crop.
This project delivered the first identification and study of loci defining nitrogen use in bread wheat. The results demonstrate the importance of the enzyme glutamine synthetase in controlling aspects of grain and stem nitrogen content. This was further supported by the results on the field trials of two French wheat cultivars. This result can now be further explored in association mapping studies to enable us to look for allelic variation for GS in current elite cultivars and exploit this in breeding for new lines and MAS. Some of the major loci for GS activity were localised away from the mapped genes.
This result is very interesting and supports the data on gene expression, obtained in this project, which shows that this enzyme is highly regulated in wheat. These are the first loci established for regulators of GS activity and exploring those in future studies is critical. Whilst we have focused on processes in leaves that control grain N and production, we have also established peduncle N as a good marker both for leaf N metabolism and for the status of grain N. The major locus on chromosome 6B, or potentially cul2, established in our study and supported by data from field trials, should receive further work since it harbours genes influencing assimilate partitioning.
These regulatory loci should be further explored in studies to identify the nature of these GS regulators in wheat; another target for MAS. Furthermore, these loci should be examined in the future in other major crops such as rice and maize, through the use of comparative mapping, to enable us to widen the impact of this work and enable us to uncover generic or species specific regulatory factors that govern N use.
The loci, identified in this project on chromosome gps 6 and 7 are currently major targets for near isogeneic line (NILs) production by Steve Quarrie. They are currently being produced in another project and will be made available to researchers in a new FP7 proposal on mineral use in crops. The genetical anlaysis identified genomic regions regulating aspects of N metabolism, stem and grain N assimilation, C and N remobilisation that should help plant breeders in MAS and in the search for allelic variation within traits that improve N use in wheat.
In particular, the loci, identified in this project on chromosome gps 6 and 7 are currently major targets for near isogeneic line (NILs) production. These regions are involved in the control of tiller production and grain yield. Hence, they are of direct importance to breeders searching for molecular markers closely related to key traits in wheat. Once these regions are verified using NILs, fine mapping can narrow down the locus and establish precise molecular markers for MAS.
Habash DZ, Bernard S, Schondelmaier J, Weyen J and Quarrie SA (2007) A genetic study of nitrogen use in hexaploid wheat in relation to N utilisation, development and yield. Theor Appl Genet. 114(3)403-419.
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