%O We acknowledged the IGSS for some bioinformatics analysis and data interpretation. We also acknowledge the support of ICRISAT, Kano Station, Nigeria, for the field phenotyping.
%K DArTseq, Groundnut, Linkage disequilibrium, Marker-assisted selection, Marker-trait association, Physiological traits
%A A S Shaibu
%A C Sneller
%A B N Motagi
%A J Chepkoech
%A M Chepngetich
%A Z L Miko
%A A M Isa
%A H A Ajeigbe
%A S G Mohammed
%I MDPI
%V 10
%L icrisat11405
%J Agronomy (TSI)
%N 2
%P 2-14
%R doi:10.3390/agronomy10020192
%D 2020
%X 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 < 0.05 and r2 > 0.2) and 3.14% of the pairs were in complete LD. The MTAs studies revealed 20 significant MTAs (p < 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.
%T Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection