Targeting the aluminum tolerance geneAlt3region in rye, using rice/rye micro-colinearity.

Characterization and manipulation of aluminum (Al) tolerance genes offers a solution to Al toxicity problems in crop cultivation on acid soil, which composes approximately 40% of all arable land. By exploiting the rice (Oryza sativaL.)/rye (Secale cerealeL.) 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 by using DNA markers flanking the ryeAlt3gene, from many cereals. Two rice-derived, PCR-based markers flanking theAlt3gene, B1 and B4, were used to screen 1,123 plants of a rye F₂ population segregating forAlt3. Fifteen recombinant plants were identified. Four additional RFLP markers developed from rice genes/putative genes, spanning 10 kb of a 160-kb rice BAC, were mapped to theAlt3region. Two rice markers flanked theAlt3locus at a distance of 0.05 cM, while two others co-segregated with it. The rice/rye micro-colinearity worked very well to delineate and map theAlt3gene region in rye. A rye fragment suspected to be part of theAlt3candidate gene was identified, but at this level, the rye/rice microsynteny relationship broke down. Because of sequence differences between rice and rye and the complexity of the rye sequence, we have been unable to clone a full-length candidate gene in rye. Further attempts to clone a full-length ryeAlt3candidate gene will necessitate the creation of a rye large-insert library. [ABSTRACT FROM AUTHOR]