Inclusive Market-Oriented Development (IMOD) –our approach to bringing prosperity in the drylands.

ICRISAT is a member of the CGIAR Consortium.

Manish K Pandey1, Hari D Upadhyaya1, Abhishek Rathore1, Vincent Vadez1, MS Sheshashayee2, Manda

Sriswathi1, Mansee Govil1, Ashish Kumar1,3, MVC Gowda4, Shivali Sharma1, Falalou Hamidou1, V Anil Kumar1,

Pawan Khera1,5, Ramesh S Bhat4, Aamir W Khan1, Sube Singh1, Hongjie Li6, Emmanuel Monyo7, H L Nadaf4,

Ganapati Mukari4, Scott Jackson8, Baozhu Guo5, Xuanqiang Liang9, Rajeev K Varshney1,*

1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; 2University of Agricultural Sciences, GKVK,

Bangalore, India; 3Jawahar Lal Nehru Krishi Vishwa Vidyalaya, Jabalpur, India; 4University of Agricultural Sciences, Dharwad, India; 5Crop

Protection and Management Research Unit, USDA-ARS, Tifton, USA; 6ShangDong Shofine Seed Technology Co Ltd, Jining, China; 6International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya; 8The University of Georgia, Athens, USA; 9Crop

Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China; *Address for correspondence: r.k.varshney@cgiar.org

Genome-wide association studies in 50 agronomic traits in peanut using the ‘reference set’ comprising 300 genotypes from 48 countries of the semi-arid tropics of the world

Abstract

Acknowledgements

Summary

S. No. Traits MTAs P value range PVE % range

Disease resistance

1 Aspergillus (ASP) 1 9.68E-07 24.69

2 Groundnut rosette disease (GRD) 31 5.25E-20 − 7.66E-07 10.25−39.29

3 Late leaf spot (LLS) 1 1.54E-06 18.10

4 Early leaf spot (ELS) 6 4.21E-07 − 7.59E-08 9.18−10.99

Quality and nutrition

5 Oil content (OC) 25 3.18E-10 − 1.70E-06 5.84−40.37

6 Oleic acid (OLE) 2 2.47E-06 16.42

7 Oleic/linoleic acid ratio (OLR) 22 1.52E-12 − 1.95E-06 13.67−47.45

8 Zinc content (ZC) 1 8.62E-07 15.63

9 Protein content (PC) 11 8.62E-08 − 2.14E-06 11.63−36.09

10 Sound mature kernel % (SMK%) 3 8.13E-08 − 2.11E-06 22.21−29.02

Physiological and yield component

11 Leaf length (LLN) 30 6.67E-08 − 1.26E-06 12.48−21.61

12 Harvest index (HI) 41 7.35E-17 − 2.12E-06 5.81−31.80

13 Root volume (RTVOL) 1 6.16E-07 39.59

14 Root water loss (RWL) 2 8.28E-07 − 6.11E-08 11.60 −13.66

15 Haulm weight (HLMWT) 6 3.59E-07 − 1.42E-06 10.16−12.44

16 SPAD chlorophyll meter reading (SCMR) 127 1.27E-10 − 2.12E-06 7.78−18.27

17 Seed length (SDL) 9 1.04E-06 − 2.78E-07 11.81−13.29

18 Shelling percentage (ShP) 2 8.15E-08 − 1.99E-06 34.43−36.45

19 Shoot weight (ShWT) 2 5.03E-07 − 1.82E-06 10.38−12.13

20 Specific leaf area (SLA) 3 2.48E-07 − 2.09E-06 8.72−19.54

21 Seed width (SDWD) 3 1.82E-07 − 1.39E-06 14.91−30.09

22 Seed weight (SDWT) 5 7.89E-08 − 2.16E-06 12.73−26.08

23 Total leaf area (TLA) 3 1.17E-07 − 2.03E-06 13.07−15.52

24 Total leaf weight (TLWT) 2 1.17E-06 − 1.20E-06 10.03−10.25

25 Pod yield 33 4.55E-08 − 2.16E-06 9.74−37.36

Traits under well watered and drought stress

26 Harvest index_drought stress 36 2.97E-10 − 1.95E-06 8.95−85.40

27 Harvest index_well watered 11 2.35E-10 − 1.40E-06 8.83−39.29

28 Haulm weight_drought stress 10 3.56E-12 − 1.77E-06 9.34−32.26

29 Haulm weight_well watered 10 1.01E-10 − 2.09E-06 8.93−21.25

30 Leaf area_well watered 1 1.77E-06 9.89

31 Leaf area_drought stress 1 8.16E-07 19.84

32 Leaf dry weight_drought stress 4 8.43E-07 − 1.24E-06 9.73−19.09

33 SCMR_drought stress 10 1.05E-07 − 1.91E-06 8.24−12.42

34 SCMR_well watered 16 8.05E-10 − 2.12E-06 9.23−14.31

35 Seed weight_drought stress 7 3.20E-22 − 9.03E-08 12.63−90.09

36 Seed weight_well watered 46 7.33E-33 − 1.93E-06 10.32−88.90

Total 524 7.33E-33 − 1.32E-06 5.81−90.09

Global / base collection

Composite

collection

Core

collection

Multiseason and multilocation evaluation

518 component traits for 50 traits

Reference set (304 genotypes)Wild, landraces and breeding lines

Association analysis Marker-trait associations

Molecular ID based on SSRs for all the genotypes of peanut reference set

Low PIC for DArTs (0.16) than SSRs (0.71)

Population structure identified three subgroups (K = 3) based on SSRs

LD decay of 15 cM in peanut genome based on SSRs

524 MTAs identified for 36 traits with PVE % ranging from 5.81 to 90.09

Financial support from the Peanut Foundation (USA) 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.

A high-resolution genotyping (4,957 polymorphic DArT features and 154 SSRs) and multiple season phenotyping data for

50 important agronomic, disease and quality traits were generated on the ‘reference set’ of peanut. These data were subjected to

comprehensive analyses for allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA)

in the ‘reference set’. The DArT markers (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information

content (PIC) than SSR markers (22.21 alleles /locus, 0.715 PIC). Multi-allelic SSRs identified three sub-groups while the LD simulation

trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15-20 cM. Association analysis resulted in

identification of 524 highly significant MTAs (pvalue >2.1x10-6) with wide phenotypic variance range (5.81-90.09%) for 36 traits. These

MTAs upon validation may be deployed in genomics-assisted breeding for developing improved peanut cultivars with enhanced

resistance/tolerance to different stress and higher pod yield with improved oil/ seed/ nutritional quality. These results have been

published recently in detail in the PLOS ONE journal (PLoS ONE, 9(8):e105228, DOI:10.1371/journal.pone.0105228).

Phenotyping Disease resistance

Quality and nutritional

Physiological and yield

component

Traits under well watered and

drought stress

LD decay based on SSR markers

DArT : 4,597

SSR : 154

Population structure and association analysis

Genome-wide distribution of marker-trait

associations

(a) Grouping based on SSR and DArT markers

(b) Principle co-ordinate analysis based on SSR

and DArT markers

(c) Population structure at different K values

(d) Three subgroups based on mean Fst values

Global distribution of genotypes containing

linked-marker allele(s) for different traits

Population structure