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United States Department of Agriculture

Agricultural Research Service


item Miftahudin
item Rodriguez-milla, Miguel
item Ross, Kathleen
item Scoles, Graham
item Gustafson, J

Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 2/15/2005
Publication Date: 12/1/2005
Citation: Miftahudin, Rodriguez-Milla, M.A., Ross, K., Scoles, G.J., Gustafson, J.P. 2005. Targeting an aluminum tolerance gene region in rye using rice/rye micro-colinearity [abstract]. In: Proceedings In the Wake of the Double Helix: From the Green revolution to the Gene Revolution, Bologna, Italy. p.207-215.

Interpretive Summary: Aluminum, the most abundant metal on earth, is highly toxic to plant growth. There are about 2.5 billion hectares of acid soils high in aluminum around the world. A study was designed to exploit the rye/rice/barley syntenic relationship (correspondence between genomes of different crops) to characterize, map, and potentially clone the location of the gene(s) controlling aluminum tolerance in rye. The rye gene was located to a small region of a single piece of a rice chromosome 10 kilobases in size using a molecular marker from barley. However, at that point the rye/rice syntenic relationship broke down, due to the massive differences in genome size between rice and rye, and we were unable to continue to use rice as a tool to map-base clone a gene in rye. The rice sequence did prove to be an extremely valuable tool in supplying markers for high-resolution mapping in rye, and in studying the rye/rice microsyntenic relationship.

Technical Abstract: Characterization and manipulation of aluminum (Al) tolerance is important in order to improve cereal crop production on acid soils, which compose approximately 40% of all arable land. By exploiting the rice/rye syntenic relationship, the potential for map-based cloning of genes controlling Al tolerance in rye, the most Al-tolerant cereal, was explored. An attempt to clone an Al-tolerance gene (Alt3) from rye was initiated using DNA markers from a number of cereals. Two rice-derived PCR-based markers flanking the Alt3 gene, B1 and B4, were isolated and used to screen a rye F2 population segregating for Alt3. Fifteen recombinant plants were identified. Four additional RFLP markers were developed from rice, spanning 10 kb, and mapped to the Alt3 region. Two of the rice markers flanked the rye Alt3 locus at a distance of 0.05 cM, while two others co-segregated with it. The rice/rye micro-colinearity worked extremely well in delineating and mapping the Alt3 gene region in rye. But at the microsyntenic level, the rye/rice relationship broke down. Sequence differences between rice and rye and the complexity of the existing rye sequence have prevented the cloning of a full-length candidate gene in rye. Further attempts to clone a full-length rye Alt3 candidate gene will necessitate the creation of a large-insert, rye library.

Last Modified: 06/25/2017
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