An international initiative has been started to conduct comprehensive genome-wide association studies (GWAS) using three peanut germplasm sets from ICRISAT, the USA, and China totaling 710 accessions. Phenotypic data has been collected for 22 to 50 traits including disease resistance, drought tolerance, yield, and quality from multiple locations. This initiative aims to (i) identify marker-trait associations through GWAS, (ii) identify superior accessions for use in breeding, and (iii) make phenotyping and genotyping data available to breeders. The collaborative effort is expected to accelerate peanut improvement.

1. Inclusive Market-Oriented Development (IMOD) –
our approach to bringing prosperity in the drylands.
ICRISAT is a member of the CGIAR Consortium.
RK Varshney1*, L Froencike2, MK Pandey1, SN Nayak1, HD Upadhyaya1, A Rathore1, B Liao3, N Barkley4, B Guo5,
MVC Gowda6, C Holbrook7, TB Brenneman8, RS Bhat6, C Chen9, J Damicone10, MD Burrow11, T Isleib12, L Dean12,
ML Wang4, V Vadez1, S Jackson13, RW Michelmore2
1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; 2University of California, Davis, USA; 3CAAS Oil Crops
Research Institute, Wuhan, China; 4USDA-Plant Genetic Resources Conservation Unit, Griffin, USA; 5Crop Protection and Management Research Unit,
USDA-ARS, Tifton, USA; 6University of Agricultural Sciences, Dharwad, India; 7Crop Breeding, USDA-ARS, Tifton, USA; 8Coastal Plain Experiment Station,
UGA, Tifton, USA; 9Auburn University, Auburn, USA; 10Oklahoma State University, Stillwater, USA; 11Texas AgriLife Research, Texas A & M System, Lubbock,
USA; 12North Carolina State University, Raleigh, USA; 13University of Georgia, Athens, USA; *Address for correspondence: r.k.varshney@cgiar.org
Financial support from the Peanut
Foundation and the CGIAR Generation
Challenge Programme (GCP) is gratefully
acknowledged.
This work has been undertaken as part of the
CGIAR Research Program on Grain
Legumes.
An international initiative to conduct comprehensive
genome-wide association studies (GWAS) for an array of
agronomic traits in peanut
 Compiling, curating and analyzing scattered phenotyping
data on three important collections of the world (ICRISAT,
USA and China)
 Population structure and linkage disequilibrium decay
using GBS genotyping data
 Genome-wide association analysis for identification of
marker-trait associations (MTAs)
 Data, results and molecular tools made available to peanut
research community
An international initiative has been started to undertake a comprehensive genome-wide association studies (GWAS) in three
different germplasm sets i.e. the reference set (300 genotypes) consisting of global mini core collection (184 accessions) of ICRISAT, the US
mini-core collection (112 accessions) and the Chinese mini-core collection (298 accessions). The phenotypic data have been collected for
22 to 50 traits including resistance to diseases, aflatoxin contamination, tolerance to drought and salinity, and several agronomic (yield,
100-seed weight) and nutritional quality traits in several seasons at multiple locations. This initiative plans to compile and curate available
phenotypic data, generate high-density genotyping data based on sequencing, conduct comprehensive statistical analysis, estimate
diversity features and undertake GWAS for traits of importance to breeders using all three germplasm sets. In summary, this initiative is
expected to provide: (i) sequence-based markers and haplotypes associated with traits of agronomic importance, (ii) accessions with
superior alleles for their use as donors in breeding programmes, and (iii) breeders-friendly databases for phenotyping and genotyping data.
Besides, the collaborative spirit of peanut research community will add momentum to peanut improvement.
Abstract
Acknowledgements
Summary Distribution of genotypes of global peanut
reference collection from 48 countries
GWAS analysis for marker-trait associations Germplasm sets and traits characterized
Collections Traits characterized
US minicore collection
Disease resistance Early leaf spot, late leaf spot, tomato spotted wilt virus,
nematode and preharvest aflatoxin contamination, Sclerotinia
and pepper spot, Rhizoctonia limb rot
Morphological
descriptors
Above and below ground descriptor data, U.S. descriptors,
percent shell out
Abiotic stress Tolerance to heat stress and drought stress
Fatty acid
components
Oil content, fatty acids, flavonoid, resveratrol, amino acids,
tocopherols, folic acid
Global minicore collection/ reference set (ICRISAT)
Disease resistance Aspergillus, early leaf spot, late leaf spot, rust resistance,
groundnut rosette disease
Oil and nutritional
quality
Oil content, oleic acid, oleic/linoleic acid ratio, protein
content, zinc content, iron content
Physiological
traits
Emergence, first flowering, D13C, leaf dry weight, leaf area,
specific leaf area, total leaf area, total leaf weight, SPAD
chlorophyll meter reading, leaf length, leaf weight, leaf width,
R/S ratio, rate of water loss, root length, root volume, root
weight, shelling percentage, shoot length, shoot weight, total
dry matter, total dry mass/leaf area, SMK percentage, harvest
index, haulm weight, days to flower, days to mature
Yield and
components traits
Plant number, plant height, pod length, pod width, pods /
plant, primary branching, pod weight, seed length, seed
weight, seed width, test weight, yield /plant, plot yield
Chinese mini-core collection
Morphological
descriptors
Plant height, length of first branch, total branching number,
number of branches with pods, leaflet length, leaflet width,
distance between apical and basilar leaflets, petiole length
Yield and
component traits
Number of primary, secondary and tertiary branches, pods /
plant, pod length, pod width, seed length, seed width, 100-pod
weight, seed weight of 100-pod, 100-seed weight, shelling
percentage and pod yield / plant
Expected outcome
GWAS
Linked
markers
Molecular
breeding
Peanut
improvement