eprintid: 10095
rev_number: 10
eprint_status: archive
userid: 1305
dir: disk0/00/01/00/95
datestamp: 2017-07-18 06:34:29
lastmod: 2018-04-26 09:21:31
status_changed: 2017-07-18 06:34:29
type: article
metadata_visibility: show
creators_name: Zhao, C
creators_name: Qiu, J
creators_name: Agarwal, G
creators_name: Wang, J
creators_name: Ren, X
creators_name: Xia, H
creators_name: Guo, B
creators_name: Ma, C
creators_name: Wan, S
creators_name: Bertioli, D J
creators_name: Varshney, R K
creators_name: Pandey, M K
creators_name: Wang, X
icrisatcreators_name: Agarwal, G
icrisatcreators_name: Varshney, R K
icrisatcreators_name: Pandey, M K
affiliation: Biotechnology Research Center, Shandong Academy of Agricultural Sciences and Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology (Jinan)
affiliation: College of Life Sciences, Shandong Normal University (Jinan)
affiliation: United States Department of Agriculture – Agricultural Research Service, Crop Protection and Management Research Unit (Tifton)
affiliation: ICRISAT (Patancheru)
affiliation: Center for Applied Genetic Technologies, University of Georgia (Athens)
country: China
country: USA
country: India
title: Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea)
ispublished: pub
subjects: s1.3
subjects: s2.13
divisions: CRPS3
full_text_status: public
keywords: Wild peanut, genome sequence, microsatellites, molecular markers, quantitative trait locus (QTL), Peanut, SSRs
note: This study was supported by National High Tech Project
(2013AA102602), Shandong Province Agricultural Crop
Breeding Project (2016LZGC025), Agricultural Scientific and
Technological Innovation Project of Shandong Academy of
Agricultural Sciences (CXGC2016B02) and Young Talents
Training Program of Shandong Academy of Agricultural
Sciences. We would also like to thank the members of the
International Peanut Genome Initiative (IPGI) and the Peanut
Genome Consortium (PGC) for the support and work for the
IPGI, and for the financial support for IPGI. The authors are
also thankful to Bill & Melinda Gates Foundation (Tropical
Legumes III), MARS Chocolate Inc., and The Peanut Foundation
for financial assistance.
abstract: Despite several efforts in the last decade toward development of simple sequence repeat (SSR) markers in peanut, there is still a need for more markers for conducting different genetic and breeding studies. With the effort of the International Peanut Genome Initiative, the availability of reference genome for both the diploid progenitors of cultivated peanut allowed us to identify 135,529 and 199,957 SSRs from the A (Arachis duranensis) and B genomes (Arachis ipaensis), respectively. Genome sequence analysis showed uneven distribution of the SSR motifs across genomes with variation in parameters such as SSR type, repeat number, and SSR length. Using the flanking sequences of identified SSRs, primers were designed for 51,354 and 60,893 SSRs with densities of 49 and 45 SSRs per Mb in A. duranensis and A. ipaensis, respectively. In silico PCR analysis of these SSR markers showed high transferability between wild and cultivated Arachis species. Two physical maps were developed for the A genome and the B genome using these SSR markers, and two reported disease resistance quantitative trait loci (QTLs), qF2TSWV5 for tomato spotted wilt virus (TSWV) and qF2LS6 for leaf spot (LS), were mapped in the 8.135 Mb region of chromosome A04 of A. duranensis. From this genomic region, 719 novel SSR markers were developed, which provide the possibility for fine mapping of these QTLs. In addition, this region also harbors 652 genes and 49 of these are defense related genes, including two NB-ARC genes, three LRR receptor-like genes and three WRKY transcription factors. These disease resistance related genes could contribute to resistance to viral (such as TSWV) and fungal (such as LS) diseases in peanut. In summary, this study not only provides a large number of molecular markers for potential use in peanut genetic map development and QTL mapping but also for map-based gene cloning and molecular breeding.
date: 2017-07
date_type: published
publication: Frontiers in Plant Science
volume: 8
number: 1209
publisher: Frontiers Media
pagerange: 1-12
id_number: 10.3389/fpls.2017.01209
refereed: TRUE
issn: 1664-462X
official_url: http://dx.doi.org/10.3389/fpls.2017.01209
related_url_url: https://scholar.google.co.in/scholar?hl=en&q=Genome-Wide+Discovery+of+Microsatellite+Markers+from+Diploid+Progenitor+Species%2C+Arachis+duranensis+and+A.+ipaensis%2C+and+Their+Application+in+Cultivated+Peanut+%28A.+hypogaea%29&btnG=
related_url_type: pub
citation:   Zhao, C and Qiu, J and Agarwal, G and Wang, J and Ren, X and Xia, H and Guo, B and Ma, C and Wan, S and Bertioli, D J and Varshney, R K and Pandey, M K and Wang, X  (2017) Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea).  Frontiers in Plant Science, 8 (1209).  pp. 1-12.  ISSN 1664-462X     
document_url: http://oar.icrisat.org/10095/1/fpls-08-01209.pdf