Development of SNP-Based Molecular Markers by Re-Sequencing Strategy in Peanut

Abstract

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT The objective of this study was to develop high-throughput SNP or SNP-based markers by re-sequencing of two peanut cultivars, 'K-Ol' and 'Pungan'. The whole genome re-sequencing for the two cultivars was performed to produce sequences of 35.3 × 10 9 bp with 350 × 10 6 reads and 32.0 × 10 9 bp with 318 × 10 6 reads, respectively. As compared with the peanut reference genome, the distribution of homozygous and heterozygous SNPs on each chromosome showed very similar patterns between 'K-Ol' and 'Pungan', and most of them were in intergenic-region regardless of the peanut cultivars and reference genome type. The SNPs identified between the two peanut cultivars were evenly distributed across chromosomes of peanut diploid A and B reference genomes. It indicated that these SNPs could be available to construct a genetic map using the segregating population derived from a cross between 'K-Ol' and 'Pungan'. Total 61 CAPS marker were developed and tested for their availability. Of the CAPS markers, 60 CAPS markers produced normal PCR products and 18 out of them presented polymorphism among 6 peanut varieties. Results of the present study could provide useful genetic resources to facilitate marker-assisted selection for breeding programs as well as germplasm screening for peanut.

Resveratrol, total phenolic and flavonoid contents, and antioxidant potential of seeds and sprouts of Korean peanuts

“…Nutrient content of four peanut cultivars have also been reported. Pungan seeds are rich in luteolin and have good composition of fatty acids [33]. Akwang seeds contain vitamins and a high ratio of oleic and linoleic acid which is considered good fatty acid composition from health perspective [34].…”

The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm

“…It is categorized as an accurate and high-performance genotyping device (Lochlainn et al 2011). HRM was developed on sweet cherry (Ganopoulos et al 2013), rice (Zhu et al 2013), cotton (Ghatage and Das 2016), and peanut (Kim et al 2017). Moreover, HRM has been developed for rapid identification of genotypes and mutations induced by CRISPR/ Cas9 mutagenesis in rice (Li et al 2018).…”

Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.)

“…Cultivated peanut is allotetraploid (2n = 4× = 40, AABB) with a genome size of 2800 Mb/1C and the genome composition of cultivated peanut was shown to have derived from a recent hybridization of A. duranensis (A subgenome) and A. ipaensis (B subgenome) [ 23 , 24 , 25 , 26 ]. As the polyploidization event occurred recently, the genetic diversity of cultivated peanut is extremely low [ 27 ]. Peanut subgenomes are very closely related [ 28 , 29 ] and have an estimated repetition rate of 64% [ 1 ], which makes the assembly of peanut genome sequences extremely difficult [ 1 , 26 , 30 ].…”

“…In 2005, pyrosequencing technology was implemented using large-scale parallel sequencing or deep sequencing, revolutionizing next generation sequencing (NGS) technology and biological genomic research [ 33 ]. In the past decade, NGS technology made significant progress, and the cost of sequencing dropped sharply [ 27 ]. In addition, there have been innovative improvements in the productivity and accuracy of sequencing data.…”

“…In recent work, high-throughput genotyping was conducted using NGS technology through double-digest restriction-site-associated DNA sequencing (ddRADseq), a total of 14,663 SNPs were developed, and a genetic linkage map based on SNPs was constructed using 1765 SNP markers in 166 F9 RIL population from a cross between Zhonghua 5 and ICGV86699 [ 37 ]. Numerous SNP and cleaved amplified polymorphic sequence (CAPS) markers were developed from the re-sequencing of two Korean peanut germplasms of K-Ol and Pungan, which indicates that the molecular marker information can provide valuable guidance and information for peanut breeding programs [ 27 ].…”