eprintid: 11405
rev_number: 12
eprint_status: archive
userid: 3170
dir: disk0/00/01/14/05
datestamp: 2020-03-18 09:27:48
lastmod: 2020-03-18 09:27:48
status_changed: 2020-03-18 09:27:48
type: article
metadata_visibility: show
creators_name: Shaibu, A S
creators_name: Sneller, C
creators_name: Motagi, B N
creators_name: Chepkoech, J
creators_name: Chepngetich, M
creators_name: Miko, Z L
creators_name: Isa, A M
creators_name: Ajeigbe, H A
creators_name: Mohammed, S G
creators_gender: Female
icrisatcreators_name: Motagi, B N
icrisatcreators_name: Ajeigbe, H A
affiliation: Department of Agronomy, Bayero University, (Kano)
affiliation: The National Engineering Laboratory for Crop Molecular Breeding, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, (Beijing)
affiliation: Department of Horticulture and Crop Science, The Ohio State University, (Wooster)
affiliation: ICRISAT (Kano)
affiliation: Department of Genetics and Plant Breeding, Agriculture College, Vijayapur , University of Agricultural Sciences, (Dharwad)
affiliation: Integrated Genotyping Service and Support platform, Bioscience for East and Central Africa, International Livestock Institute, (Nairobi)
affiliation: Department of Animal Science, Usmanu Danfodiyo University, (Sokoto)
affiliation: Centre for Dryland Agriculture, Bayero University, (Kano)
country: Nigeria
country: China
country: USA
country: India
country: Kenya
title: Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection
ispublished: pub
subjects: s1.3
subjects: s2.12
subjects: s2.13
subjects: s2.17
subjects: s355
divisions: CRPS1
full_text_status: public
keywords: DArTseq, Groundnut, Linkage disequilibrium, Marker-assisted selection, Marker-trait association, Physiological traits
note: 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.
abstract: 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.
date: 2020-02
date_type: published
publication: Agronomy (TSI)
volume: 10
number: 2
publisher: MDPI
pagerange: 2-14
id_number: doi:10.3390/agronomy10020192
refereed: TRUE
issn: 2073-4395
official_url: https://doi.org/10.3390/agronomy10020192
related_url_url: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=10.3390%2Fagronomy10020192&btnG=
related_url_type: pub
citation:   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     
document_url: http://oar.icrisat.org/11405/1/agronomy-10-00192.pdf