Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection
| Autor: | Hakeem A. Ajeigbe, S.G. Mohammed, Clay Sneller, Adamu Mani Isa, Abdulwahab S. Shaibu, Jackline Chepkoech, Babu N. Motagi, Zainab L. Miko, Mercy Chepngetich |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
Linkage disequilibrium Drought tolerance groundnut Introgression Genomics Biology 01 natural sciences Genome Genetic analysis marker-assisted selection lcsh:Agriculture 03 medical and health sciences marker-trait association dartseq physiological traits 030304 developmental biology Genetics 0303 health sciences lcsh:S food and beverages Marker-assisted selection Genetic marker Agronomy and Crop Science linkage disequilibrium 010606 plant biology & botany |
| Zdroj: | Agronomy, Vol 10, Iss 2, p 192 (2020) Agronomy Volume 10 Issue 2 |
| ISSN: | 2073-4395 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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