Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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

Abdulwahab Shaibu
* ORCID logo ,
Clay Sneller
,
Babu Motagi
,
Jackline Chepkoech
,
Mercy Chepngetich
,
Zainab Miko
,
Adamu Isa
,
Hakeem Ajeigbe
,
Sanusi Mohammed
Version 1 : Received: 11 July 2019 / Approved: 12 July 2019 / Online: 12 July 2019 (11:42:33 CEST)

A peer-reviewed article of this Preprint also exists.

Shaibu, A.S.; Sneller, C.; Motagi, B.N.; Chepkoech, J.; Chepngetich, M.; Miko, Z.L.; Isa, A.M.; Ajeigbe, H.A.; Mohammed, S.G. Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection. Agronomy 2020, 10, 192. Shaibu, A.S.; Sneller, C.; Motagi, B.N.; Chepkoech, J.; Chepngetich, M.; Miko, Z.L.; Isa, A.M.; Ajeigbe, H.A.; Mohammed, S.G. Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection. Agronomy 2020, 10, 192.

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.

Keywords

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

Subject

Biology and Life Sciences, Agricultural Science and Agronomy

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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