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

Qing Lu,Huifang Jiang,Xuanqiang Liang,Haofa Lan,Shijie Wen,Haiyan Liu,Haifen Li,Rajeev K Varshney,Yanbin Hong,Hao Liu,Shaoxiong Li,Guiyuan Zhou,Xingyu Li,Xiaoping Chen,Jianan Zhang

doi:10.1186/s12864-019-6148-5

Abstract

BackgroundMicrosatellites, 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.ResultsA 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.ConclusionsThe 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.

Highlights

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 Simple sequence repeats (SSR) markers, which can be used to conduct genetic analyses and molecular breeding
More SSRs were identified in subgenome B (4,414,961) than in subgenome A (3,772,653), and 141,882 SSRs were identified on the nine scaffolds of the peanut reference genome assembly (Table 1)
Analysis of SSR distribution on each chromosome revealed that the largest number of SSRs was present on chromosome A07 (538,928), followed by chromosome B09 (532,326) (Additional file 1: Table S1; Additional file 2: Figure S1)

Summary

Introduction

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 be used to conduct genetic analyses and molecular breeding. Sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map. Several hundred EST-SSR markers were developed by investigating ESTs [10, 11], and thousands of transcriptome-SSR markers were identified based on different transcriptome libraries of cultivated peanut [12,13,14]. These available SSRs were insufficient for constructing high-density genetic maps and enhancing molecular breeding [17]

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