title: Identification of putative candidate genes for red rot resistance in sugarcane (Saccharum species hybrid) using LD-based association mapping.
abstract: Red rot is a serious disease of sugarcane caused by the fungus Colletotrichum falcatum that has a colossal damage potential. The fungus, prevalent mainly in the Indian sub-continent, keeps on producing new pathogenic strains leading to breakdown of resistance in newly released varieties and hence the deployment of linked markers for marker-assisted selection for resistance to this disease can fine tune the breeding programme. This study based on a panel of 119 sugarcane genotypes fingerprinted for 944 SSR alleles was undertaken with an aim to identify marker-trait associations (MTAs) for resistance to red rot. Mixed linear model containing population structure and kinship as co-factor detected four MTAs that were able to explain 10-16 % of the trait variation, individually. Among the four MTAs, EST sequences diagnostic of three could be BLAST searched to the sorghum genome with significant sequence homology. Several genes encoding important plant defence related proteins, viz., cytochrome P450, Glycerol-3-phosphate transporter-1, MAP Kinase-4, Serine/threonine-protein kinase, Ring finger domain protein and others were localized to the vicinity of these MTAs. These positional candidate genes are worth of further investigation and possibly these could contribute directly to red rot resistance, and may find a potential application in marker-assisted sugarcane breeding.
authors.affiliation: ICAR-Indian Institute of Sugarcane Research, Raebareli Road, P.O. Dilkusha, Lucknow, UP, 226002, India. ikrps@yahoo.com.|Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA. ikrps@yahoo.com.
authors.forename: Ram K
authors.initials: RK
authors.lastname: Singh
authors.affiliation: ICAR-Indian Institute of Sugarcane Research, Raebareli Road, P.O. Dilkusha, Lucknow, UP, 226002, India.
authors.forename: Nandita
authors.initials: N
authors.lastname: Banerjee
authors.affiliation: ICAR-Indian Institute of Sugarcane Research, Raebareli Road, P.O. Dilkusha, Lucknow, UP, 226002, India.
authors.forename: M S
authors.initials: MS
authors.lastname: Khan
authors.affiliation: ICAR-Indian Institute of Sugarcane Research, Raebareli Road, P.O. Dilkusha, Lucknow, UP, 226002, India.
authors.forename: Sonia
authors.initials: S
authors.lastname: Yadav
authors.affiliation: ICAR-Indian Institute of Sugarcane Research, Raebareli Road, P.O. Dilkusha, Lucknow, UP, 226002, India.
authors.forename: Sanjeev
authors.initials: S
authors.lastname: Kumar
authors.affiliation: ICAR-Indian Institute of Sugarcane Research, Raebareli Road, P.O. Dilkusha, Lucknow, UP, 226002, India.
authors.forename: S K
authors.initials: SK
authors.lastname: Duttamajumder
authors.affiliation: ICAR-Indian Institute of Sugarcane Research, Raebareli Road, P.O. Dilkusha, Lucknow, UP, 226002, India.
authors.forename: Ram Ji
authors.initials: RJ
authors.lastname: Lal
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA.
authors.forename: Jinesh D
authors.initials: JD
authors.lastname: Patel
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA.
authors.forename: H
authors.initials: H
authors.lastname: Guo
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA.
authors.forename: Dong
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D060467:Disease Resistance; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D018895:Microsatellite Repeats; D010935:Plant Diseases / Q000382:microbiology; D010940:Plant Proteins / Q000235:genetics*; D031786:Saccharum / Q000235:genetics* / Q000382:microbiology; D045868:Sorghum / Q000235:genetics
chemical_list: D010940:Plant Proteins
keywords: Association mapping; Candidate gene; Comparative genomics; Red rot; SSR markers; Sugarcane