title: Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice.
abstract: Single nucleotide polymorphism (SNP) is the most abundant DNA sequence variation present in plant genomes. Here, we report the design and validation of a unique genic-SNP genotyping chip for genetic and evolutionary studies as well as molecular breeding applications in rice. The chip incorporates 50,051 SNPs from 18,980 different genes spanning 12 rice chromosomes, including 3,710 single-copy (SC) genes conserved between wheat and rice, 14,959 SC genes unique to rice, 194 agronomically important cloned rice genes and 117 multi-copy rice genes. Assays with this chip showed high success rate and reproducibility because of the SC gene based array with no sequence redundancy and cross-hybridisation problems. The usefulness of the chip in genetic diversity and phylogenetic studies of cultivated and wild rice germplasm was demonstrated. Furthermore, its efficacy was validated for analysing background recovery in improved mega rice varieties with submergence tolerance developed through marker-assisted backcross breeding.
authors.affiliation: 1] National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India [2] Rayat and Bahra Institute of Engineering and Bio-Technology, Mohali, Punjab Technical University, Jalandhar 140104, India.
authors.forename: Nisha
authors.initials: N
authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Pawan Kumar
authors.initials: PK
authors.lastname: Jayaswal
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Kabita
authors.initials: K
authors.lastname: Panda
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Paritra
authors.initials: P
authors.lastname: Mandal
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Vinod
authors.initials: V
authors.lastname: Kumar
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Balwant
authors.initials: B
authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Shefali
authors.initials: S
authors.lastname: Mishra
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Yashi
authors.initials: Y
authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Renu
authors.initials: R
authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Vandna
authors.initials: V
authors.lastname: Rai
authors.affiliation: Rayat and Bahra Institute of Engineering and Bio-Technology, Mohali, Punjab Technical University, Jalandhar 140104, India.
authors.forename: Anita
authors.initials: A
authors.lastname: Gupta
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Tilak
authors.initials: T
authors.lastname: Raj Sharma
authors.affiliation: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
authors.forename: Nagendra Kumar
authors.initials: NK
authors.lastname: Singh
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D018628:Gene Dosage; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods; D006239:Haplotypes; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D000069600:Plant Breeding; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results
chemical_list: D010940:Plant Proteins