In Silico identification of candidate genes for grain Fe and Zn in sorghum using reported cereals gene homologs
Sorghum is among the top 10 crops that feed the world. It is a good source of energy, protein, carbohydrate, vitamins and minerals including the trace elements.
Abstract
Sorghum is among the top 10 crops that feed the world. It is a good source of energy, protein, carbohydrate, vitamins and minerals including the trace elements. It is one of the cheapest and sustainable options to combat the micronutrient malnutrition, particularly Fe and Zn in predominantly sorghum eating populations. Identification of genes governing grain Fe and Zn concentration in sorghum is of interest. Earlier studies on other cereals showed role of number of genes for grain Fe Zn homeostasis and uptake, transport and loading but so far no reports available on genomic regions/ QTLs and candidate genes governing sorghum grain Fe and Zn concentration. A homology (In-silico) search of91 candidate genes involved in governing grain Fe and Zn concentration in cereals (rice, wheat, maize and barley) is performed on sorghum genome. Blast is performed against the sorghum genome database and downloaded Fe and Zn gene sequences as query. Total 77 hits are found on sorghum genomic regions, which are involved in Fe and Zn homeostasis. Highest number of genes found on chromosome 1(24 blast hits) and least on chromosome 8. Genes associated with grain Fe and Zn concentration from maize and wheat showed 100 % homology on sorghum genome. On sorghum genome, highest number of hits are identified on chr 1 and 6,from all the 4 crops. Out of 24 hits on chromosome 1, 10 hits (from genes of wheat, barley, rice, maize) pertaining to Nicotianamine synthase (N AS) gene are in same general genomic region around 61Mbp on sorghum chromosome 1. Blast hits on sorghum chromosomes from genes of wheat, barley, rice, maize pertaining to Nicotianamine synthase (NAS), Zip (Zn transporter protein) and YSL (yellow stripe like) gene are shown higher %homology. These could be putatively associated with Fe and Zn grain concentration in sorghum. Candidate genes (Homologs) identified in this study can be used for the development of 'functional markers for improving grain Fe and Zn concentration in sorghum.
Citation
Anuradha, K.; Prakash, B.; Ramu, P.; Shah, T.; Ashok Kumar, A.; Deshpande, S.P. In Silico identification of candidate genes for grain Fe and Zn in sorghum using reported cereals gene homologs. (2013) Compendium of papers abstracts: Global consultation on millets promotion for health nutritional security,18-20 December, 2013 (Editors: S Rakshit, IK Das, G Shyamprasad, JS Mishra, CV Ratnavathi, RR Chapke,Vilas A Tonapi, B Dayakar Rao and N Patil).
Links
In Silico identification of candidate genes for grain Fe and Zn in sorghum using reported cereals gene homologs (PDF, 3.1MB)