Proceedings of the XLVII Italian Society of Agricultural Genetics - SIGA Annual Congress

Verona, Italy - 24/27 September, 2003

ISBN 88-900622-4-X

Poster Abstract - 4.13

GENETIC DISSECTION OF SHOOT DEVELOPMENT IN BARLEY (HORDEUM VULGARE L.): AN EST-BASED CANDIDATE GENE STRATEGY

L. NICOLOSO*, C. POZZI**, F. SALAMINI*^,***, L. ROSSINI*

*) University of Milan, Dipartimento di Produzione Vegetale, V. Celoria 2, 20133 Milan, Italy

**) Fondazione Parco Tecnologico Padano, V. Haussmann 11, 26900 Lodi, Italy

***) Max Planck Institute for Plant Breeding Reasearch, Carl-von-Linné Weg 10, 50829 Koeln, Germany

Hordeum vulgare, developmental mutants, candidate gene approach, linkage maps, SNP

A variety of barley mutants affecting shoot and floral architecture have been collected at the Max Planck Institute in Koeln. At present 35 developmental mutants have been positioned on the established high density molecular linkage map of barley (1, 2). Isolation of the corresponding genes will provide insight into the molecular mechanisms underlying development of the Triticeae. In barley, positional cloning is hampered by the low degree of polymorphism and the large size of the genome (4.873 Mbp). However, map-based cloning can be accelerated by the identification of candidate genes (CGs), as demonstrated by the association of the barley Hooded phenotype with a mutation in the homeobox gene Bkn3 (3).

In order to identify barley CGs for the mutants under study in our group, we initially compiled a list of 157 regulatory genes known for their key-role in shoot development of Arabidopsis, maize, rice etc. These sequences were used as queries in similarity searches on the barley EST database (http://www.ncbi.nlm.nih.gov/), uncovering a total number of 423 homologous ESTs, putatively assigned to different transcription factor families.

In the next step of this strategy, candidate ESTs are mapped and putative cosegregation with developmental mutants is analysed. SNPs are the ideal tool for EST mapping and can be identified in silico (isSNPs) by comparison of ESTs corresponding to the same gene but derived from different genotypes. This approach lead to the identification of 144 barley isSNPs in our candidate ESTs. Prior to mapping, these isSNPs are experimentally validated on the parents of available mapping populations. If polymorphism for a given gene is not detected on these lines, the screening proceeds on the 67 wild barley lines already utilised for mapping in our group (1).

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