title: Comparative genomics and association mapping approaches for blast resistant genes in finger millet using SSRs.
abstract: The major limiting factor for production and productivity of finger millet crop is blast disease caused by Magnaporthe grisea. Since, the genome sequence information available in finger millet crop is scarce, comparative genomics plays a very important role in identification of genes/QTLs linked to the blast resistance genes using SSR markers. In the present study, a total of 58 genic SSRs were developed for use in genetic analysis of a global collection of 190 finger millet genotypes. The 58 SSRs yielded ninety five scorable alleles and the polymorphism information content varied from 0.186 to 0.677 at an average of 0.385. The gene diversity was in the range of 0.208 to 0.726 with an average of 0.487. Association mapping for blast resistance was done using 104 SSR markers which identified four QTLs for finger blast and one QTL for neck blast resistance. The genomic marker RM262 and genic marker FMBLEST32 were linked to finger blast disease at a P value of 0.007 and explained phenotypic variance (R²) of 10% and 8% respectively. The genomic marker UGEP81 was associated to finger blast at a P value of 0.009 and explained 7.5% of R². The QTLs for neck blast was associated with the genomic SSR marker UGEP18 at a P value of 0.01, which explained 11% of R². Three QTLs for blast resistance were found common by using both GLM and MLM approaches. The resistant alleles were found to be present mostly in the exotic genotypes. Among the genotypes of NW Himalayan region of India, VHC3997, VHC3996 and VHC3930 were found highly resistant, which may be effectively used as parents for developing blast resistant cultivars in the NW Himalayan region of India. The markers linked to the QTLs for blast resistance in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of blast resistant alleles into locally adapted cultivars.
authors.affiliation: Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India; Biotechnology laboratory, Vivekananda Parvateeya Krishi Anusanthan Sansthan (VPKAS), Almora, Uttarakhand, India.
authors.forename: B Kalyana
authors.initials: BK
authors.lastname: Babu
authors.affiliation: Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India.
authors.forename: Pandey
authors.initials: P
authors.lastname: Dinesh
authors.affiliation: Biotechnology laboratory, Vivekananda Parvateeya Krishi Anusanthan Sansthan (VPKAS), Almora, Uttarakhand, India.
authors.forename: Pawan K
authors.initials: PK
authors.lastname: Agrawal
authors.affiliation: Biotechnology laboratory, Vivekananda Parvateeya Krishi Anusanthan Sansthan (VPKAS), Almora, Uttarakhand, India.
authors.forename: S
authors.initials: S
authors.lastname: Sood
authors.affiliation: Biotechnology laboratory, Vivekananda Parvateeya Krishi Anusanthan Sansthan (VPKAS), Almora, Uttarakhand, India.
authors.forename: C
authors.initials: C
authors.lastname: Chandrashekara
authors.affiliation: Biotechnology laboratory, Vivekananda Parvateeya Krishi Anusanthan Sansthan (VPKAS), Almora, Uttarakhand, India.
authors.forename: Jagadish C
authors.initials: JC
authors.lastname: Bhatt
authors.affiliation: Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India.
authors.forename: Anil
authors.initials: A
authors.lastname: Kumar
mesh_terms: D000483:Alleles; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics*; D031748:Eleusine / Q000235:genetics* / Q000276:immunology / Q000382:microbiology*; D005787:Gene Frequency / Q000235:genetics; D017343:Genes, Plant; D005819:Genetic Markers; D023281:Genomics / Q000379:methods*; D005838:Genotype; D016014:Linear Models; D020082:Magnaporthe / Q000502:physiology*; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D011110:Polymorphism, Genetic; D017434:Protein Structure, Tertiary
chemical_list: D005819:Genetic Markers; D010940:Plant Proteins