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

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

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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.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Genome sequence, Simple sequence repeats, Molecular breeding, Peanut (Arachis hypogaea L.)
Subjects: Mandate crops > Groundnut
Others > Oilseeds
Others > Genetics and Genomics
Others > Food and Nutrition
Others > Food Security
Others > Legume Crops
Depositing User: Mr Arun S
Date Deposited: 06 Nov 2019 06:08
Last Modified: 06 Nov 2019 06:12
Official URL:
Acknowledgement: UNSPECIFIED
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