Submitted to: Theoretical and Applied Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 12/13/2004
Publication Date: 3/1/2005
Citation: Miftahudin, Chikmawati, T., Ross, K., Scoles, G.J., Gustafson, J.P. 2005. Targeting the aluminum tolerance gene alt3 region in rye using rice/rye microcolinearity. Theoretical and Applied Genetics. 110(5):906-913. 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. The present study was designed to exploite the rye/rice syntenic relationship in order 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 that is 10 kilobases in size. However, at that point the rye/rice syntenic relationship broke down and we were unable to use rice as a tool to map-base clone a gene in rye. A rye large insert library is needed in order to clone the genes controlling aluminum tolerance. Rice 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. This information will benefit plant breeders and molecular geneticists as they explore relationships among cereal species and attempt to move desirable traits between species.
Technical Abstract: Characterization and manipulation of Al-tolerance genes is one of the solutions to overcome Al toxicity problems in crop cultivation on acid soils, which include approximately 40% of all arable land. By exploiting the rice/rye syntenic relationship, the potential for map-based cloning of genes controlling aluminum (Al) tolerance in rye, the most Al-tolerant cereal, was explored. An attempt at cloning an Al-tolerance gene (Alt3) from rye was initiated utilizing DNA markers flanking the rye Alt3 gene. Two rice-derived PCR-based markers flanking the Alt3 gene, B1 and B4, were used to screen 1123 plants of a rye F2 population segregating for Alt3. 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 the Alt3 region. Two rice markers flanked the 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. A rye fragment suspected to be part of the Alt3 candidate gene was identified, but at this level of rye/rice microsynteny, the rye/rice relationship broke down and because of sequence differences between rice and rye and the complexity of the existing rye sequence, we have been unable to clone 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.