eprintid: 9191
rev_number: 12
eprint_status: archive
userid: 1305
dir: disk0/00/00/91/91
datestamp: 2015-12-22 09:25:28
lastmod: 2016-08-19 04:04:11
status_changed: 2015-12-22 09:25:28
type: article
metadata_visibility: show
creators_name: Hong, Y
creators_name: Pandey, M K
creators_name: Liu, Y
creators_name: Chen, X
creators_name: Liu, H
creators_name: Varshney, R K
creators_name: Liang, X
creators_name: Huang, S
icrisatcreators_name: Varshney, R K
affiliation: Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences (Guangzhou)
affiliation: School of Life Sciences, Sun Yat-Sen University (Guangzhou)
affiliation: ICRISAT (Patancheru)
affiliation: College of Agriculture, South China Agricultural University (Guangzhou)
affiliation: School of Plant Biology and Institute of Agriculture, The University of Western Australia (Crawley)
country: China
country: India
country: Australia
title: Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis
ispublished: pub
subjects: s1.3
subjects: s2.13
divisions: D3
crps: crp1.5
full_text_status: public
keywords: SNPs, Peanut, Tetraploid, High resolution melting (HRM), Polymorphism
note: This research was funded by grants from National Natural Science Foundation of China (No. 31271767), Natural Science Foundation of Guangdong (No. S2013020012647), Pearl River Science and Technology Nova of Guangzhou (No. 2013J2200088), International Science & Technology Cooperation Program of Guangdong Province (No. 2013B050800021), Agricultural Science and Technology Program of Guangdong (2013B020301014), and supported by the earmarked fund for Modern Agro-industry Technology Research System (CARS-14). The founders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We declare no conflict of interests.
abstract: The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.
date: 2015-12-02
date_type: published
publication: Frontiers in Plant Science
volume: 06
number: 1068
publisher: Frontiers
pagerange: 01-10
id_number: 10.3389/fpls.2015.01068
refereed: TRUE
issn: 1664-462X
official_url: http://dx.doi.org/10.3389/fpls.2015.01068
related_url_url: https://scholar.google.com/scholar?q=Identification+and+Evaluation+of+Single-Nucleotide+Polymorphisms+in+Allotetraploid+Peanut+%28Arachis+hypogaea+L.%29+Based+on+Amplicon+Sequencing+Combined+with+High+Resolution+Melting+%28HRM%29+Analysis&btnG=&hl=en&as_s
related_url_type: pub
citation:   Hong, Y and Pandey, M K and Liu, Y and Chen, X and Liu, H and Varshney, R K and Liang, X and Huang, S  (2015) Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis.  Frontiers in Plant Science, 06 (1068).  01-10.  ISSN 1664-462X     
document_url: http://oar.icrisat.org/9191/1/fpls-06-01068.pdf