Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection

Shaibu, A S and Sneller, C and Motagi, B N and Chepkoech, J and Chepngetich, M and Miko, Z L and Isa, A M and Ajeigbe, H A and Mohammed, S G (2020) Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection. Agronomy (TSI), 10 (2). pp. 2-14. ISSN 2073-4395

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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.

Item Type: Article
Divisions: Research Program : West & Central Africa
Uncontrolled Keywords: DArTseq, Groundnut, Linkage disequilibrium, Marker-assisted selection, Marker-trait association, Physiological traits
Subjects: Mandate crops > Groundnut
Others > Oilseeds
Others > Genetics and Genomics
Others > Food and Nutrition
Others > Legume Crops
Depositing User: Mr Arun S
Date Deposited: 18 Mar 2020 09:27
Last Modified: 18 Mar 2020 09:27
Official URL:
Acknowledgement: 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.
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