Preprint Article Version 1 This version is not peer-reviewed

Genome Wide Association Studies for Four Physiological Traits in Groundnut (Arachis hypogaea L.) Minicore Collection

Version 1 : Received: 11 July 2019 / Approved: 12 July 2019 / Online: 12 July 2019 (11:42:33 CEST)

How to cite: Shaibu, A.; Sneller, C.; Motagi, B.; Chepkoech, J.; Chepngetich, M.; Miko, Z.; Isa, A.; Ajeigbe, H.; Mohammed, S. Genome Wide Association Studies for Four Physiological Traits in Groundnut (Arachis hypogaea L.) Minicore Collection. Preprints 2019, 2019070166 (doi: 10.20944/preprints201907.0166.v1). Shaibu, A.; Sneller, C.; Motagi, B.; Chepkoech, J.; Chepngetich, M.; Miko, Z.; Isa, A.; Ajeigbe, H.; Mohammed, S. Genome Wide Association Studies for Four Physiological Traits in Groundnut (Arachis hypogaea L.) Minicore Collection. Preprints 2019, 2019070166 (doi: 10.20944/preprints201907.0166.v1).

Abstract

In order to integrate genomics in breeding and development of drought tolerant groundnut genotypes, identification of genomic regions/genetic markers for drought surrogate traits is essential. We used SNP markers for a genetic analysis of the ICRISAT groundnut minicore collection for genome wide marker-trait association for some physiological traits and to determine the magnitude of linkage disequilibrium (LD) present in the genetic resources. The LD analysis showed that about 36% of loci pairs were in significant LD (P < 0.05 and r2 > 0.2) and 3.14% of the pairs were in complete LD. There was rapid decline in LD with distance and the LD was <0.2 at a distance of 41635 bp. The marker trait association (MTAs) studies revealed 20 significant MTAs (p <0.001) with 11 markers for leaf area index (4), canopy temperature (13), chlorophyll content (1) and NDVI (2). The markers explained 2 to 21% of the phenotypic variation observed. Most of the MTAs identified on the A subgenome were also identified on the respective homeologous chromosome on the B subgenome. The duplications of effect observed could be due to common ancestor of the A and B genome which explains the linkage detected between markers lying on different chromosomes seen in the current study. The present study identified a total of 20 highly significant marker trait associations with 11 markers for four physiological traits of importance in groundnut; LAI, CT, SCMR and NDVI. The markers identified in this study can serve as useful genomic resources to initiate marker-assisted selection and trait introgression of groundnut for drought tolerance. The identified markers in this study may be useful for marker assisted selection after further validation.

Subject Areas

DArTseq; Groundnut; Linkage disequilibrium; Marker assisted selection; Marker trait association; Physiological traits

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