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

Abstract

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.

Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Punica granatum L.) cv. Tunisia Genome

“…A high-density physical map with uniform genomic positions and coverage is necessary for conducting high-resolution gene/QTL mapping ( Lu et al, 2019 ). In pomegranate, however, reports on construction of SSR-based linkage map are currently lacking.…”

“…Discovery and characterization of the DNA markers spanning entire genome such as SSRs provides the foundation for trait discovery studies and molecular breeding. Following genome sequencing, genome-wide SSRs were designed for several plant species, including rice ( Zhang et al, 2007 ), soybean ( Song et al, 2010 ), Brachypodium ( Sonah et al, 2011 ), maize ( Xu et al, 2013 ), foxtail millet ( Pandey et al, 2013 ), Brassica ( Shi et al, 2014 ), cotton ( Wang et al, 2015 ), Nicotiana ( Wang et al, 2018 ), peanut ( Zhao et al, 2017 ; Lu et al, 2019 ), eggplant ( Portis et al, 2018 ), carrot ( Uncu and Uncu, 2020 ), and more recently in pomegranate ( Patil et al, 2020c ).…”

Development of Genome-wide Simple Sequence Repeat Markers from Whole-genome Sequence of Mungbean (Vigna radiata)

“…Discovery and mining of genomic SSR loci from W GS have had fruitful applications in many plant species, including soybean (Song et al, 2010), peanut (Lu et al, 2019), castor bean (Tan et al, 2014). In the present study, a total of 12, 49,774 and 11, 86, 386 perfect and imperfect SSR repeats with di-, tri-, tetra-, penta and hexanucleotide repeats equal to, or longer than 8, 5, 4, 3 and 2 repeat units were identified from the mungbean genome.…”

Advances in Crop Improvement and Delivery Research for Nutritional Quality and Health Benefits of Groundnut (Arachis hypogaea L.)

“…Availability of reference genome and high density genotyping assay are the most important milestones for understanding genome architecture, trait mapping, gene discovery, and molecular breeding (Varshney et al, 2013). The major genomic resources that have been developed in recent years include 1) reference genome of cultivated tetraploid (Bertioli et al, 2019;Chen et al, 2019;Zhuang et al, 2019); 2) reference genome of allotetraploid wild groundnut, Arachis monticola (Yin et al, 2018); 3) reference genomes of diploid progenitors of cultivated groundnut i.e., A. duranensis (Bertioli et al, 2016;Chen et al, 2016) and A. ipaensis (Bertioli et al, 2016;Lu et al, 2018); 4) "Axiom_Arachis" array, a high density genotyping assay with >58K highly informative SNPs (Pandey et al, 2017a); 5) gene expression atlas for cultivated tetraploid (Clevenger et al, 2016); 6) molecular/ genetic markers (Pandey et al, 2016;Pandey et al, 2017a;Vishwakarma et al, 2017;Zhao et al, 2017;Lu et al, 2019;Pandey et al, 2019b;Pandey et al, 2019c); and 7) diverse genetic populations such as MAGIC and nested association mapping (NAM) populations to conduct high resolution genetic mapping and breeding (Pandey et al, 2017a;Pandey et al, 2017b;Pandey et al, 2017c); and 8) trait linked diagnostic markers for use in genomics-assisted breeding (GAB) (Pandey et al, 2017c). As a result, the next-generation sequencing based trait discovery (Pandey et al, 2017b) and sequence-based breeding (Varshney et al, 2019) will enhance breeding speed and precision for greater genetic gains.…”