@article{icrisat11405,
           month = {February},
           title = {Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection},
       publisher = {MDPI},
            year = {2020},
          author = {A S Shaibu and C Sneller and B N Motagi and J Chepkoech and M Chepngetich and Z L Miko and A M Isa and H A Ajeigbe and S G Mohammed},
           pages = {2--14},
          volume = {10},
            note = {We acknowledged the IGSS for some bioinformatics analysis and data interpretation. We also acknowledge the support of ICRISAT, Kano Station, Nigeria, for the ?eld phenotyping.},
         journal = {Agronomy (TSI)},
          number = {2},
        keywords = {DArTseq, Groundnut, Linkage disequilibrium, Marker-assisted selection, Marker-trait association, Physiological traits},
             url = {http://oar.icrisat.org/11405/},
        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 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 (p {\ensuremath{<}} 0.05 and r2 {\ensuremath{>}} 0.2) and 3.14\% of the pairs were in complete LD. The MTAs studies revealed 20 significant MTAs (p {\ensuremath{<}} 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.}
}