Genome-wide detection of markers associated with early leaf spot and pod weight in groundnut using SNP and DArT markers

Shaibu, Abdulwahab S.; Miko, Zainab L.; Ajeigbe, H A; Mohammed, Salisu; Usman, A.; Muhammad, Muhammad S.; Umar, Muhammad; Ahmed, H. O.; Adnan, Adnan A.; Sneller, Clay

doi:10.1080/15427528.2020.1846102

Cited by 4 publications

(2 citation statements)

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“…A number of studies by linkage and association mappings have been conducted on leaf spot diseases in groundnut ( Pasupuleti et al., 2013 ; Pandey et al., 2014 ; Zhang et al., 2020a ; Shaibu et al., 2021 ). However, most of the reported genomic regions/markers are not consistent due to population specific or environment sensitivity ( Patil et al., 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, seven and five major QTL for ELS and LLS have been detected and reported on chromosomes 2 and 3, respectively ( Chu et al., 2019 ). In addition, Shaibu et al. (2021) detected 25 SNPs for ELS in mini-core collection of 168 accessions in Nigeria by efficient mixed-model association (EMMA) and compression mixed linear model (CMLM).…”

Section: Introductionmentioning

confidence: 99%

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Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm

Oteng‐Frimpong

Karikari²,

Sie³

et al. 2023

Front. Plant Sci.

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Early leaf spot (ELS) and late leaf spot (LLS) diseases are the two most destructive groundnut diseases in Ghana resulting in ≤ 70% yield losses which is controlled largely by chemical method. To develop leaf spot resistant varieties, the present study was undertaken to identify single nucleotide polymorphism (SNP) markers and putative candidate genes underlying both ELS and LLS. In this study, six multi-locus models of genome-wide association study were conducted with the best linear unbiased predictor obtained from 294 African groundnut germplasm screened for ELS and LLS as well as image-based indices of leaf spot diseases severity in 2020 and 2021 and 8,772 high-quality SNPs from a 48 K SNP array Axiom platform. Ninety-seven SNPs associated with ELS, LLS and five image-based indices across the chromosomes in the 2 two sub-genomes. From these, twenty-nine unique SNPs were detected by at least two models for one or more traits across 16 chromosomes with explained phenotypic variation ranging from 0.01 - 62.76%, with exception of chromosome (Chr) 08 (Chr08), Chr10, Chr11, and Chr19. Seventeen potential candidate genes were predicted at ± 300 kbp of the stable/prominent SNP positions (12 and 5, down- and upstream, respectively). The results from this study provide a basis for understanding the genetic architecture of ELS and LLS diseases in African groundnut germplasm, and the associated SNPs and predicted candidate genes would be valuable for breeding leaf spot diseases resistant varieties upon further validation.

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