Abstract
Key message
The identified 30 functional nucleotide polymorphisms or genic SNP markers would offer essential information for marker-assisted breeding in groundnut.
Abstract
A genome-wide association study (GWAS) on component traits of LLS resistance in an eight-way multiparent advance generation intercross (MAGIC) population of groundnut in the field and in a light chamber (controlled conditions) was performed via an Affymetrix 48 K single-nucleotide polymorphism (SNP) ‘Axiom Arachis’ array. Multiparental populations with high-density genotyping enable the detection of novel alleles. In total, five quantitative trait loci (QTLs) with marker − log10(p value) scores ranging from 4.25 to 13.77 for the incubation period (IP) and six QTLs with marker − log10(p value) scores ranging from 4.33 to 10.79 for the latent period (LP) were identified across the A- and B-subgenomes. A total of 62 markers‒trait associations (MTAs) were identified across the A- and B-subgenomes. Markers for LLS scores and the area under the disease progression curve (AUDPC) recorded for plants in the light chamber and under field conditions presented − log10 (p value) scores ranging from 4.22 to 27.30. The highest number of MTAs (six) was identified on chromosomes A05, B07 and B09. Out of a total of 73 MTAs, 37 and 36 MTAs were detected in subgenomes A and B, respectively. Taken together, these results suggest that both subgenomes have equal potential genomic regions contributing to LLS resistance. A total of 30 functional nucleotide polymorphisms or genic SNP markers were detected, among which eight genes were found to encode leucine-rich repeat (LRR) receptor-like protein kinases and putative disease resistance proteins. These important SNPs can be used in breeding programmes for the development of cultivars with improved disease resistance.
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Data availability
The data sets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.
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The research reported here was financially supported by OPEC Fund for International Development (OFID) with grant number 13161, and was conducted under CGIAR Research Program on Grain Legumes and Dryland Cereals (CRP-GLDC).
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APW recorded the phenotypic data, done GWAS analysis and prepared the manuscript. SY helped in GWAS analysis. KPV, VPC, HKS, MPD and VSS were involved in experiment design and manuscript revising. DBD and SG helped in recording the phenotypic data. AKV analysed the phenotypic data. JP conceptualized and supervised the whole study and provided assistance for manuscript preparation.
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Wankhade, A.P., Chimote, V.P., Viswanatha, K.P. et al. Genome-wide association mapping for LLS resistance in a MAGIC population of groundnut (Arachis hypogaea L.). Theor Appl Genet 136, 43 (2023). https://doi.org/10.1007/s00122-023-04256-7
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DOI: https://doi.org/10.1007/s00122-023-04256-7