Genetic diversity and capsaicinoids content association of Thai chili landraces analyzed by whole genome sequencing-based SNPs

Kethom, Wassana; Tongyoo, Pumipat; Mongkolporn, Orarat

doi:10.1016/j.scienta.2019.02.022

Cited by 7 publications

(3 citation statements)

References 32 publications

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“…Analysis of molecular variance further supported this differentiation, as majority of the variation (76.08 %) was attributed to the genetic differences among the populations. Previously, C. annuum was also observed to form a discrete group from other Capsicum species [ 21 , 33 ]. Nonetheless, in contrast with the observations by Pereira-Dias et al [ 21 ], we observed that the chiltepins clustered with the C. annuum in the PCA biplot.…”

Section: Discussionmentioning

confidence: 99%

Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

et al. 2021

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Background Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different traits. This study assessed genetic diversity, population structure, and linkage disequilibrium (LD) among 165 chile pepper genotypes using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Results A GBS approach identified 66,750 high-quality SNP markers with known map positions distributed across the 12 chromosomes of Capsicum. Principal components analysis revealed four distinct clusters based on species. Neighbor-joining phylogenetic analysis among New Mexico State University (NMSU) chile pepper cultivars showed two main clusters, where the C. annuum genotypes grouped together based on fruit or pod type. A Bayesian clustering approach for the Capsicum population inferred K = 2 as the optimal number of clusters, where the C. chinense and C. frutescens grouped in a single cluster. Analysis of molecular variance revealed majority of variation to be between the Capsicum species (76.08 %). Extensive LD decay (~ 5.59 Mb) across the whole Capsicum population was observed, demonstrating that a lower number of markers would be required for implementing genome wide association studies for different traits in New Mexican type chile peppers. Tajima’s D values demonstrated positive selection, population bottleneck, and balancing selection for the New Mexico Capsicum population. Genetic diversity for the New Mexican chile peppers was relatively low, indicating the need to introduce new alleles in the breeding program to broaden the genetic base of current germplasm. Conclusions Genetic diversity among New Mexican chile peppers was evaluated using GBS-derived SNP markers and genetic relatedness on the species level was observed. Introducing novel alleles from other breeding programs or from wild species could help increase diversity in current germplasm. We present valuable information for future association mapping and genomic selection for different traits for New Mexican chile peppers for genetic improvement through marker-assisted breeding.

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Section: Discussionmentioning

confidence: 99%

Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

et al. 2021

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“…Genetic diversity was analyzed by a simple matching coefficient method (Kethom et al 2019) using filtered SNPs with a call rate greater than 90% and polymorphic informative content (PIC) higher than 0.1. A dendrogram was generated by DARwin software version 6.0.13 based on the dissimilarity index (DI) using unweighted neighbor-joining with 1000-repeat bootstrap analysis.…”

Section: Tomato Germplasm Diversity Analysismentioning

confidence: 99%

Genome-wide association study revealed genetic loci for resistance to fusarium wilt in tomato germplasm

Kawicha

Tongyoo

Wongpakdee

et al. 2023

Crop Breed. Appl. Biotechnol.

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Tomato Fusarium wilt caused by Fusarium oxysporum f.sp. lycopersici (Fol) constrains tomato production worldwide. Three hundred forty tomato accessions were evaluated for Fusarium wilt resistance and single nucleotide polymorphisms (SNPs) associated with resistance. The disease resistance evaluation revealed that 15, 13, and 15 accessions were identified as Fusarium wilt resistant in Test 1, 2, and Mean data, respectively, with the disease severity index (DSI) ranging from 0-16.7%. A genome-wide association study (GWAS) identified SNPs associated with resistance. Eighteen common SNPs were detected in at least two tests and located on chromosomes 4, 6, 7, 9, and 12. Six unique significant SNPs were found in either Test 1 or 2, located on chromosomes 2, 4, and 7. Candidate genes associated with Fusarium wilt resistance were identified. Notably, two genes encoding leucine-rich repeat-like protein and diseaseresistance protein were predicted from the two unique SNPs, solDsnp10606 and solDsnp6266, respectively.

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“…The filtered SNPs with a call rate greater than 90% and polymorphic informative content (PIC) higher than .1 were analysed for genetic diversity using a simple matching coefficient method (Kethom et al, 2019). A phylogenetic dendrogram based on the dissimilarity index (DI) was generated by DARwin software version 6.0.21.…”

Section: Analysis Of Tomato Germplasm Diversitymentioning

confidence: 99%

Genetic loci associated with Fusarium wilt resistance in tomato (Solanum lycopersicum L.) discovered by genome‐wide association study

Thanyasiriwat,

Tongyoo,

Saman

et al. 2023

Plant Breeding

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Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. lycopersici (Fol), has impacted global tomato production. This study aims to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with FW resistance against different Fol isolates in tomato accessions using genome‐wide association studies (GWAS). Ninety‐four tomato accessions were evaluated for FW resistance and subjected to GWAS analysis. Broad‐spectrum tomato accessions demonstrated resistance to Fol in at least two isolates, exhibiting a disease severity index (DSI) of 0%. Thirty‐two SNP loci were significantly linked to the DSI of Fol isolates TFPK401, BK2269 and NP‐T4, clustering on chromosome 6. Among these, 12 common significant SNPs were associated with the DSI of at least two Fol isolates, while four unique SNPs were specific to TFPK401 or NP‐T4. Furthermore, candidate genes associated with disease response to Fol infection were identified within a 37.9–41 Mb region flanking the SNPs. These findings contribute to a deeper understanding of resistance mechanisms against Fol infection in tomatoes, potentially aiding the development of effective breeding strategies for Fusarium wilt resistance.

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Genetic diversity and capsaicinoids content association of Thai chili landraces analyzed by whole genome sequencing-based SNPs

Cited by 7 publications

References 32 publications

Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

Genome-wide association study revealed genetic loci for resistance to fusarium wilt in tomato germplasm

Genetic loci associated with Fusarium wilt resistance in tomato (Solanum lycopersicum L.) discovered by genome‐wide association study

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