Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (<i>Arachis hypogaea</i> L.) Mini Core Collection
2020
Abdulwahab S. Shaibu | Clay Sneller | Babu N. Motagi | Jackline Chepkoech | Mercy Chepngetich | Zainab L. Miko | Adamu M. Isa | Hakeem A. Ajeigbe | Sanusi G. Mohammed
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 3249 diversity array technology sequencing (DArTSeq) markers for a genetic analysis of 125 ICRISAT groundnut mini core collection evaluated in 2015 and 2017 for genome-wide marker-trait association for some physiological traits and to determine the magnitude of linkage disequilibrium (LD). Marker-trait association (MTA) analysis, probability values, and percent variation modelled by the markers were calculated using the GAPIT package via the KDCompute interface. The LD analysis showed that about 36% of loci pairs were in significant LD (<i>p</i> < 0.05 and <i>r</i><sup>2</sup> > 0.2) and 3.14% of the pairs were in complete LD. The MTAs studies revealed 20 significant MTAs (<i>p</i> < 0.001) with 11 markers. Four MTAs were identified for leaf area index, 13 for canopy temperature, one for chlorophyll content and two for normalized difference vegetation index. The markers explained 20.8% to 6.6% 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. This could be due to a common ancestor of the A and B genome which explains the linkage detected between markers lying on different chromosomes. 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 after further validation.
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