Target Amplicon Sequencing for Genotyping Genome‐Wide Single Nucleotide Polymorphisms Identified by Whole‐Genome Resequencing in Peanut

Shirasawa, Kenta; Kuwata, Chikara; Watanabe, Masao; Fukami, Masanobu; Hirakawa, Hideki; Isobe, Sachiko

doi:10.3835/plantgenome2016.06.0052

Cited by 32 publications

(30 citation statements)

References 37 publications

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“…This ratio was used to calculate divergence and to restructure the phylogenetic tree [ 35 , 36 ]. The C/T allele occurred most frequently (376; 20%) among SNP alleles, which is a consistent observation in Allium cepa [ 37 ], and similar to findings in other species including C ucumis melo [ 38 ], Brassica napus [ 39 ], and oil palm [ 40 ]. The transition/transversion ratio in this study was 2.53, which is lower than has been previously reported in wheat (1.75) [ 41 ], similar to that observed in rice (2.3) [ 42 ], and higher than observed in peanut (3.2) [ 43 ].…”

Section: Resultssupporting

confidence: 82%

SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing

et al. 2018

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Onion (Allium cepa L.) is an economically important vegetable crop around the world. Genetic and genomic research into various onion accessions will provide insights into the onion genome to enhance breeding strategies and improve crops. However, the onion’s large genome size means that studies of molecular markers are limited in onion. This study aimed to discover high quality single nucleotide polymorphisms (SNPs) from 192 onion inbred lines relating to short-day cultivation in Korea. Paired-end (PE) double digested restriction site-associated DNA sequencing (ddRAD-seq) was used to discover SNPs in onion. A total of 538,973,706 reads (25.9 GB), with an average of 2,658,491 high-quality reads, were generated using ddRAD-seq. With stringent filtering, 1904 SNPs were discovered based on onion reference scaffolds. Further, population structure and genetic relationship studies suggested that two well-differentiated sub-populations exist in onion lines. SNP-associated flanking sequences were also compared with a public non-redundant database for gene ontology and pathway analysis. To our knowledge, this is the first report to identify high-quality SNPs in onion based on reference sequences using the ddRAD-seq platform. The SNP markers identified will be useful for breeders and the research community to deepen their understanding, enhance breeding programs, and support the management of onion genomic resources.

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Section: Resultssupporting

confidence: 82%

SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing

et al. 2018

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“…Genomic DNAs extracted from leaves of each RIL and their parental lines with DNeasy Plant Mini Kit (Qiagen, Germany) were double-digested with the restriction enzymes Pst I and Msp I (Thermo Fisher Scientific, MA, United States). The ddRAD-Seq libraries were constructed as described by Shirasawa et al (2016a , b ). The libraries were sequenced on HiSeq2000 (Illumina) in paired-end mode (93-base).…”

Section: Methodsmentioning

confidence: 99%

Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.)

et al. 2018

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The aim of this study was to identify candidate resistance genes for late leaf spot (LLS) and rust diseases in peanut (Arachis hypogaea L.). We used a double-digest restriction-site associated DNA sequencing (ddRAD-Seq) technique based on next-generation sequencing (NGS) for genotyping analysis across the recombinant inbred lines (RILs) derived from a cross between a susceptible line, TAG 24, and a resistant line, GPBD 4. A total of 171 SNPs from the ddRAD-Seq together with 282 markers published in the previous studies were mapped on a genetic map covering 1510.1 cM. Subsequent quantitative trait locus (QTL) analysis revealed major genetic loci for LLS and rust resistance on chromosomes A02 and A03, respectively. Heterogeneous inbred family-derived near isogenic lines and the pedigree of the resistant gene donor, A. cardenasii Krapov. & W.C. Greg., including the resistant derivatives of ICGV 86855 and VG 9514 as well as GPBD 4, were employed for whole-genome resequencing analysis. The results indicated the QTL candidates for LLS and rust resistance were located in 1.4- and 2.7-Mb genome regions on A02 and A03, respectively. In these regions, four and six resistance-related genes with deleterious mutations were selected as candidates for LLS and rust resistance, respectively. These delimited genomic regions may be beneficial in breeding programs aimed at improving disease resistance and enhancing peanut productivity.

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“…This result is consistent with a previous report in which 8,784 SNPs were obtained from an interspecific cross between different species [ 65 ]. In intercrossing, or crossing between closely related species, even though the number of SNPs obtained by ddRAD-Seq might be small [ 66 ], WGRS has the potential to overcome this issue [ 43 ]. Therefore, lab work is no longer a limiting factor in the discovery of new genetic loci.…”

Section: Discussionmentioning

confidence: 99%

“…These methods can be successfully implemented in gene mapping, including quantitative trait locus (QTL) analysis and genome-wide association studies (GWAS), of a vast array of crops [ 32 , 34 – 38 ]. On the other hand, whole-genome resequencing (WGRS) enables prediction of the effects of sequence variants on gene function throughout the genome [ 39 – 43 ]. Therefore, a combination of RAD-Seq and WGRS analysis represents a powerful strategy for rapidly identifying candidate genes responsible for traits of interests.…”

Section: Introductionmentioning

confidence: 99%

Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies

et al. 2017

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Tomato late blight caused by Phytophthora infestans (Mont.) de Bary, also known as the Irish famine pathogen, is one of the most destructive plant diseases. Wild relatives of tomato possess useful resistance genes against this disease, and could therefore be used in breeding to improve cultivated varieties. In the genome of a wild relative of tomato, Solanum habrochaites accession LA1777, we identified a new quantitative trait locus for resistance against blight caused by an aggressive Egyptian isolate of P. infestans. Using double-digest restriction site–associated DNA sequencing (ddRAD-Seq) technology, we determined 6,514 genome-wide SNP genotypes of an F2 population derived from an interspecific cross. Subsequent association analysis of genotypes and phenotypes of the mapping population revealed that a 6.8 Mb genome region on chromosome 6 was a candidate locus for disease resistance. Whole-genome resequencing analysis revealed that 298 genes in this region potentially had functional differences between the parental lines. Among of them, two genes with missense mutations, Solyc06g071810.1 and Solyc06g083640.3, were considered to be potential candidates for disease resistance. SNP and SSR markers linking to this region can be used in marker-assisted selection in future breeding programs for late blight disease, including introgression of new genetic loci from wild species. In addition, the approach developed in this study provides a model for identification of other genes for attractive agronomical traits.

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Target Amplicon Sequencing for Genotyping Genome‐Wide Single Nucleotide Polymorphisms Identified by Whole‐Genome Resequencing in Peanut

Cited by 32 publications

References 37 publications

SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing

SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing

Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.)

Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies

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