title: Genomewide association studies for 50 agronomic traits in peanut using the 'reference set' comprising 300 genotypes from 48 countries of the semi-arid tropics of the world.
abstract: Peanut is an important and nutritious agricultural commodity and a livelihood of many small-holder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with on-going genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, high-resolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the 'reference set' of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three sub-groups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15-20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (p value > 2.1 × 10-6) with wide phenotypic variance (PV) range (5.81-90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Manish K
authors.initials: MK
authors.lastname: Pandey
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Abhishek
authors.initials: A
authors.lastname: Rathore
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Vincent
authors.initials: V
authors.lastname: Vadez
authors.affiliation: Department of Crop Physiology, University of Agricultural Sciences (UAS), Bangalore, Karnataka, India.
authors.forename: M S
authors.initials: MS
authors.lastname: Sheshshayee
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Manda
authors.initials: M
authors.lastname: Sriswathi
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Mansee
authors.initials: M
authors.lastname: Govil
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India; Plant Pathology, Jawahar Lal Nehru Krishi Vishwa Vidyalaya (JNKVV), Jabalpur, Madhya Pradesh, India.
authors.forename: Ashish
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Genetics and Plant Breeding, University of Agricultural Sciences (UAS), Dharwad, Karnataka, India.
authors.forename: M V C
authors.initials: MV
authors.lastname: Gowda
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Shivali
authors.initials: S
authors.lastname: Sharma
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Sahelian Center, Niamey, Niger.
authors.forename: Falalou
authors.initials: F
authors.lastname: Hamidou
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: V Anil
authors.initials: VA
authors.lastname: Kumar
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Pawan
authors.initials: P
authors.lastname: Khera
authors.affiliation: Department of Biotechnology, University of Agricultural Sciences (UAS), Dharwad, Karnataka, India.
authors.forename: Ramesh S
authors.initials: RS
authors.lastname: Bhat
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Aamir W
authors.initials: AW
authors.lastname: Khan
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Sube
authors.initials: S
authors.lastname: Singh
authors.affiliation: ShanDong Shofine Seed Technology Co Ltd, Jining, Shandong, China.
authors.forename: Hongjie
authors.initials: H
authors.lastname: Li
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Monyo
authors.affiliation: Department of Genetics and Plant Breeding, University of Agricultural Sciences (UAS), Dharwad, Karnataka, India.
authors.forename: H L
authors.initials: HL
authors.lastname: Nadaf
authors.affiliation: Department of Genetics and Plant Breeding, University of Agricultural Sciences (UAS), Dharwad, Karnataka, India.
authors.forename: Ganapati
authors.initials: G
authors.lastname: Mukri
authors.affiliation: Center for Applied Genetic Technologies, The University of Georgia (UGA), Athens, Georgia, United States of America.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: Crop Protection and Management Research Unit, US Department of Agriculture-Agricultural Research Service (USDA-ARS), Tifton, Georgia, United States of America.
authors.forename: Baozhu
authors.initials: B
authors.lastname: Guo
authors.affiliation: Crop Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, Guangdong, China.
authors.forename: Xuanqiang
authors.initials: X
authors.lastname: Liang
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D010367:Arachis / Q000235:genetics*; D016000:Cluster Analysis; D018556:Crops, Agricultural / Q000235:genetics; D017343:Genes, Plant; D024861:Genetic Enhancement; D055106:Genome-Wide Association Study / Q000592:standards*; D005838:Genotype; D006824:Hybridization, Genetic; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D012015:Reference Standards; D014329:Tropical Climate