title: Development and Evaluation of a High Density Genotyping 'Axiom_Arachis' Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut.
abstract: Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array 'Axiom_Arachis' with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for other diploids (A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi). Genotyping of the groundnut 'Reference Set' containing 300 genotypes identified 44,424 polymorphic SNPs and genetic diversity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array 'Axiom_Arachis' with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Manish K
authors.initials: MK
authors.lastname: Pandey
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.|University of Georgia (UGA), Tifton, USA.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Agarwal
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Sandip M
authors.initials: SM
authors.lastname: Kale
authors.affiliation: University of Georgia (UGA), Tifton, USA.
authors.forename: Josh
authors.initials: J
authors.lastname: Clevenger
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Spurthi N
authors.initials: SN
authors.lastname: Nayak
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Manda
authors.initials: M
authors.lastname: Sriswathi
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Annapurna
authors.initials: A
authors.lastname: Chitikineni
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia (UGA), Athens, USA.
authors.forename: Carolina
authors.initials: C
authors.lastname: Chavarro
authors.affiliation: Crops Research Institute (CRI), Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Chen
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Manish K
authors.initials: MK
authors.lastname: Vishwakarma
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia (UGA), Athens, USA.
authors.forename: Soraya
authors.initials: S
authors.lastname: Leal-Bertioli
authors.affiliation: Crops Research Institute (CRI), Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China.
authors.forename: Xuanqiang
authors.initials: X
authors.lastname: Liang
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia (UGA), Athens, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Bertioli
authors.affiliation: Crop Protection and Management Research Unit, USDA-ARS, Tifton, USA.
authors.forename: Baozhu
authors.initials: B
authors.lastname: Guo
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia (UGA), Athens, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: University of Georgia (UGA), Tifton, USA.
authors.forename: Peggy
authors.initials: P
authors.lastname: Ozias-Akins
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.|The University of Western Australia, Crawley, Australia.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D010367:Arachis / Q000235:genetics* / Q000254:growth & development*; D001947:Breeding; D005787:Gene Frequency / Q000235:genetics; D018745:Genome, Plant; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012015:Reference Standards; D013045:Species Specificity