title: Genome Wide Single Locus Single Trait, Multi-Locus and Multi-Trait Association Mapping for Some Important Agronomic Traits in Common Wheat (T. aestivum L.).
abstract: Genome wide association study (GWAS) was conducted for 14 agronomic traits in wheat following widely used single locus single trait (SLST) approach, and two recent approaches viz. multi locus mixed model (MLMM), and multi-trait mixed model (MTMM). Association panel consisted of 230 diverse Indian bread wheat cultivars (released during 1910-2006 for commercial cultivation in different agro-climatic regions in India). Three years phenotypic data for 14 traits and genotyping data for 250 SSR markers (distributed across all the 21 wheat chromosomes) was utilized for GWAS. Using SLST, as many as 213 MTAs (p ≤ 0.05, 129 SSRs) were identified for 14 traits, however, only 10 MTAs (~9%; 10 out of 123 MTAs) qualified FDR criteria; these MTAs did not show any linkage drag. Interestingly, these genomic regions were coincident with the genomic regions that were already known to harbor QTLs for same or related agronomic traits. Using MLMM and MTMM, many more QTLs and markers were identified; 22 MTAs (19 QTLs, 21 markers) using MLMM, and 58 MTAs (29 QTLs, 40 markers) using MTMM were identified. In addition, 63 epistatic QTLs were also identified for 13 of the 14 traits, flag leaf length (FLL) being the only exception. Clearly, the power of association mapping improved due to MLMM and MTMM analyses. The epistatic interactions detected during the present study also provided better insight into genetic architecture of the 14 traits that were examined during the present study. Following eight wheat genotypes carried desirable alleles of QTLs for one or more traits, WH542, NI345, NI170, Sharbati Sonora, A90, HW1085, HYB11, and DWR39 (Pragati). These genotypes and the markers associated with important QTLs for major traits can be used in wheat improvement programs either using marker-assisted recurrent selection (MARS) or pseudo-backcrossing method.
authors.affiliation: Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Vandana
authors.initials: V
authors.lastname: Jaiswal
authors.affiliation: Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Vijay
authors.initials: V
authors.lastname: Gahlaut
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, India.
authors.forename: Prabina Kumar
authors.initials: PK
authors.lastname: Meher
authors.affiliation: Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Reyazul Rouf
authors.initials: RR
authors.lastname: Mir
authors.affiliation: Dept of Genetics & Plant Breeding, G.B. Pant University of Agriculture & Technology, Pantnagar, India.
authors.forename: Jai Prakash
authors.initials: JP
authors.lastname: Jaiswal
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, India.
authors.forename: Atmakuri Ramakrishna
authors.initials: AR
authors.lastname: Rao
authors.affiliation: Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Harindra Singh
authors.initials: HS
authors.lastname: Balyan
authors.affiliation: Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Pushpendra Kumar
authors.initials: PK
authors.lastname: Gupta
mesh_terms: D000383:Agriculture; D000483:Alleles; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D004777:Environment; D004843:Epistasis, Genetic; D008040:Genetic Linkage; D056426:Genetic Loci; D005819:Genetic Markers; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D018895:Microsatellite Repeats / Q000235:genetics; D008957:Models, Genetic; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics; D019655:Quantitative Trait, Heritable; D014908:Triticum / Q000235:genetics*
chemical_list: D005819:Genetic Markers