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Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.)

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Relation http://oar.icrisat.org/11330/
https://doi.org/10.1186/s12864-019-6148-5
doi:10.1186/s12864-019-6148-5
 
Title Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.)
 
Creator Lu, Q
Hong, Y
Li, S
Liu, H
Li, H
Zhang, J
Lan, H
Liu, H
Li, X
Wen, S
Zhou, G
Varshney, R K
Jiang, H
Chen, X
Liang, X
 
Subject Groundnut
Oilseeds
Genetics and Genomics
Food and Nutrition
Food Security
Legume Crops
 
Description Background: Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely
distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to
conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop
worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker
development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop
genomic markers and construct a high-density physical map.
Results: A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were
distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified
SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and
nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an
average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea
varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A.
hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of
44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the
newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7,
was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed
SSR markers were located and 108 candidate genes were detected.
Conclusions: The availability of these newly developed and public SSR markers both provide a large number of
molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve
molecular breeding strategies for cultivated peanut.
 
Publisher BMC
 
Date 2019-11
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Identifier http://oar.icrisat.org/11330/1/s12864-019-6148-5.pdf
Lu, Q and Hong, Y and Li, S and Liu, H and Li, H and Zhang, J and Lan, H and Liu, H and Li, X and Wen, S and Zhou, G and Varshney, R K and Jiang, H and Chen, X and Liang, X (2019) Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.). BMC Genomics (TSI), 20 (1). pp. 1-9. ISSN 1471-2164