Single Nucleotide Polymorphism Marker Discovery from Transcriptome Sequencing for Marker-assisted Backcrossing in Capsicum

Kang, Jin‐Ho; Yang, Heng; Jeong, Hawoong; Choe, Phillip; Kwon, Jae-Hoon; Kang, Byoung−Cheorl

doi:10.7235/hort.2014.14109

Cited by 12 publications

(13 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, we used 96 alleles to survey genetic diversity. The cost of genotyping of large germplasm collection is relatively expensive, therefore based on our preliminary studies with 412 SNPs [19], 48 SNPs with high PIC values were used for diversity study. Even though most of the SNP makers used in this study had high PIC values close to 0.5, SNP markers are less powerful than SSR markers in terms of relative kinship estimation and population structure analysis [42–44] because SSR markers have higher allelic diversity than SNP markers.…”

Section: Discussionmentioning

confidence: 99%

“…A set of 48 SNP markers evenly distributed in 12 pepper chromosomes were used in this study [19] (Additional file 1: Table S1). In a preliminary study a total of 282 accessions were randomly selected from entire germplasm collection for genetic diversity study with 412 SNP markers developed by Kang et al [19].…”

Section: Methodsmentioning

confidence: 99%

“…In a preliminary study a total of 282 accessions were randomly selected from entire germplasm collection for genetic diversity study with 412 SNP markers developed by Kang et al [19]. Based on this analysis, highly polymorphic SNP markers (PIC > 0.45) were selected.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm

Lee

Jeong

et al. 2016

BMC Genet

Self Cite

View full text Add to dashboard Cite

BackgroundConservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum.ResultsTo explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (HE = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (HE = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection ‘CC240’ with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher genetic diversity (I = 0.95) and genetic evenness (J’ = 0.80), and represented a wider range of phenotypic variation (MD = 9.45 %, CR = 98.40 %).ConclusionsA total of 240 accessions were selected from 3,821 Capsicum accessions based on transcriptome-based 48 SNP markers with genome-wide distribution and 32 traits using a systematic approach. This core collection will be a primary resource for pepper breeders and researchers for further genetic association and functional analyses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0452-8) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm

Lee

Jeong

et al. 2016

BMC Genet

Self Cite

View full text Add to dashboard Cite

show abstract

“…The expression patterns of PLPK genes from various pepper genotypes were analysed using RNA-seq data from previous research [ 48 ]. The sequence reads were mapped to the pepper transcriptome database ( http://cab.pepper.snu.ac.kr ) with CLC Genomics Workbench v8.0 (CLC Bio, Aarhus, Denmark) with default parameters.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Analysis and Evolution of the Pto-Like Protein Kinase (PLPK) Gene Family in Pepper

2016

Self Cite

View full text Add to dashboard Cite

The tomato Pto gene, which encodes a serine/threonine kinase (STK) domain-containing protein, confers resistance to bacterial speck disease caused by Pseudomonas syringae pv. tomato (Pst). In this study, in vivo recognition assays using PVX constructs showed that AvrPto was specifically recognized in the pepper genotypes. This AvrPto recognition caused a nonhost hypersensitive response (HR) and localization of the PVX::AvrPto fusion protein to inoculated pepper leaf tissues, which indicates the presence of a similar Pto recognition mechanism in pepper as in tomato. However, genome-wide analysis in pepper revealed no Pto clade corresponding to that in tomato, suggesting an alternative system for Pto recognition in pepper. Nevertheless, 25 Pto-like protein kinases (PLPKs) with a highly conserved STK domain have been identified in the pepper genome. For the majority of the amino acid sites in the STK domain of Ptos and PLPKs, nonsynonymous (dN) to synonymous (dS) nucleotide substitution ratios (ω) were less than one, suggesting that purifying selection played a predominant role in the evolutionary process. However, some amino acid sites were found to be subjected to episodic positive selection in the course of evolution of Pto homologs, and, thus, different evolutionary processes might have shaped the Pto gene family in plants. Based on RNA-seq data, PLPK genes and other Pto pathway genes, such as Prf, Pti1, Pti5, and Pti6 were expressed in all tested pepper genotypes. Therefore, the nonhost HR against Pst in pepper may be due to the recognition of the AvrPto effector by a PLPK homolog, and subsequent action of downstream components of the Pto signaling pathway. However, the possibility remains that the recognition of AvrPto in pepper plants may involve activities of other receptor like kinases (RLKs). The identification of the PLPKs in this study will serve as a foundation for further efforts to understand the roles of PLPKs in nonhost resistance.

show abstract

“…The fragments were sequenced and SNP positions were selected based on the variable genotypic differences in single nucleotides. DNA fragments bearing more than 60 nucleotides coupled with at least three diallelic SNP positions were selected as SNP markers [19]. A nanofluidic genotyping system was deployed for evaluating and validating the selected putative SNP markers for their suitability in identifying heterozygous onion cultivars.…”

Section: Mining and Validation Of Putative Snpsmentioning

confidence: 99%

Varietal Identification of Open-Pollinated Onion Cultivars Using a Nanofluidic Array of Single Nucleotide Polymorphism (SNP) Markers

Lee¹,

Robin

Natarajan

et al. 2018

Agronomy

View full text Add to dashboard Cite

Onions (Allium cepa L.) are a medicinally and economically important vegetable species rich in sulphur compounds, polyphenols, and antioxidants. In Korea, most of the onion cultivars are of the open-pollinated, heterozygous, short duration, and early spring type, which are generally harvested in April. Precise varietal identification is crucially important to warrant the authenticity of supreme onion genotypes, which aid in affirming the genetic identity of breeding materials at both the breeders and farmers levels. A set of markers identified from the double-digest restriction-site associated DNA sequencing (ddRAD-seq) database of Allium cepa L. and involving single nucleotide polymorphisms (SNPs) were deployed for genotyping deoxyribonucleic acid (DNA) samples extracted from seven genetically diverse onion cultivars collected in Korea and Japan. The validation process led us to designating 43 SNPs out of 48 that unequivocally identified all seven genotypes with high statistical validity (p < 0.001). Phylogenetic relationships and varietal identity among the cultivars were ascertained by Bayesian clustering and ordination analyses. Two genotypes, Singsingball and Taegeukhwang of Korean origin, showed a greater genetic distance from the five other onion cultivars. The SNP markers deployed in this study effectively authenticated the DNA fingerprints of the early spring onion cultivars utilizing a high-throughput genotyping protocol. The method exploited in this study provides an efficient pathway of verifying genetic identity of onion genotypes for their quality control. The markers developed are highly useful in the management and conservation of elite onion breeding materials at the farmers’ level.

show abstract

Single Nucleotide Polymorphism Marker Discovery from Transcriptome Sequencing for Marker-assisted Backcrossing in Capsicum

Cited by 12 publications

References 40 publications

Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm

Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm

Genome-Wide Analysis and Evolution of the Pto-Like Protein Kinase (PLPK) Gene Family in Pepper

Varietal Identification of Open-Pollinated Onion Cultivars Using a Nanofluidic Array of Single Nucleotide Polymorphism (SNP) Markers

Contact Info

Product

Resources

About