CaDMR1 Cosegregates with QTL Pc5.1 for Resistance to Phytophthora capsici in Pepper (Capsicum annuum)

Rehrig, William Z.; Ashrafi, Hamid; Hill, Theresa; Prince, James P.; Deynze, Allen Van

doi:10.3835/plantgenome2014.03.0011

Cited by 54 publications

(56 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…From GBS, 1704 SNP markers were aligned to the CM334 reference genome. After filtering out SNPs with >50% missing data and SNPs that did not segregate with Mendelian ratios (1:1 for RIL), 318 markers including 22 SNP markers [13 markers from the pepper P. capsici study of Rehrig et al (2014)] were selected for map construction and QTL analysis ( Fig. 3 and Supplemental Table S1).…”

Section: Genotype-by-sequencing and Map Constructionmentioning

confidence: 99%

Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (Capsicum annuum)

et al. 2018

Self Cite

View full text Add to dashboard Cite

Bell pepper ( L.) is a group of fruit vegetables that has large variation in fruit shape, fruit size, and horticultural traits. Using unadapted sources of germplasm to bring in novel alleles while maintaining favorable quality and horticultural traits is challenging for breeding in pepper. A genetic map with 318 loci from genotype-by-sequencing (GBS) and single nucleotide polymorphism assays was generated from a recombinant inbred line population derived from a cultivated bell-type 'Maor' and a landrace highly resistant to , 'Criollo de Morelos-334'. Forty-nine quantitative trait loci (QTLs) were detected for fruit, leaf, and horticultural traits with the scantwo permutation and stepwiseqtl methods from R/qtl. With the availability of a pepper reference genome and GBS data, candidate genes for pepper organ size and other horticultural traits were predicted. , , and genes were candidate genes for controlling organ sizes on chromosome 1, 2, and 3, respectively. Two candidate genes controlling trichome formation in pepper are located at chromosome 10: and . The locus on chromosome 10, which encodes a member of the R2R3 MYB-domain family of proteins, has a function in anthocyanin accumulation. These QTL results and the candidate genes for each trait emphasize the genetic basis of the important traits for breeding with unadapted parents in bell pepper.

show abstract

Section: Genotype-by-sequencing and Map Constructionmentioning

confidence: 99%

Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (Capsicum annuum)

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…Recently, CaDMR1 , a candidate gene that encodes a homoserine kinase, was reported to be highly associated with the major QTL Pc5.1 [22]. Additionally, a single nucleotide polymorphism marker (SNP) on chromosome 5, Phyto5NBS1, was reported to be highly associated with resistant/susceptible traits against low virulence P. capsici strains [23].…”

Section: Introductionmentioning

confidence: 99%

Identification and Expression Analysis of Candidate Genes Associated with Defense Responses to Phytophthora capsici in Pepper Line “PI 201234”

Wang

Liu

Guo

et al. 2015

IJMS

View full text Add to dashboard Cite

Phytophthora capsici (Leonian), classified as an oomycete, seriously threatens the production of pepper (Capsicum annuum). Current understanding of the defense responses in pepper to P. capsici is limited. In this study, RNA-sequencing analysis was utilized to identify differentially expressed genes in the resistant line “PI 201234”, with 1220 differentially expressed genes detected. Of those genes, 480 were up-regulated and 740 were down-regulated, with 211 candidate genes found to be involved in defense responses based on the gene annotations. Furthermore, the expression patterns of 12 candidate genes were further validated via quantitative real-time PCR (qPCR). These genes were found to be significantly up-regulated at different time points post-inoculation (6 hpi, 24 hpi, and 5 dpi) in the resistant line “PI 201234” and susceptible line “Qiemen”. Seven genes were found to be involved in cell wall modification, phytoalexin biosynthesis, symptom development, and phytohormone signaling pathways, thus possibly playing important roles in combating exogenous pathogens. The genes identified herein will provide a basis for further gene cloning and functional verification studies and will aid in an understanding of the regulatory mechanism of pepper resistance to P. capsici.

show abstract

“…The two assemblies have a similar number of genes annotated, ∼34– 35 thousand, with overlapping and assembly specific genes placed on pseudomolecules (Kim et al, 2014; Qin et al, 2014). These genome assemblies and annotations will allow us to determine the physical positions of genes and QTLs and thus identify overlapping QTLs and candidate genes within QTL intervals (Rehrig et al, 2014).…”

mentioning

confidence: 99%

Regions Underlying Population Structure and the Genomics of Organ Size Determination in Capsicum annuum

Hill

Chunthawodtiporn²,

Ashrafi³

et al. 2017

The Plant Genome

Self Cite

View full text Add to dashboard Cite

Fruits, as an important part of the human diet, have been under strong selection during domestication. In general, continued directed selection has led to varieties having larger fruit with greater shape variation and tremendous increases in fruit mass. Common cultivated peppers (Capsicum annuum L.) are found in a wide range of sizes and shapes. Analysis of genetic relatedness and population structure has shown that the large-fruited, nonpungent types have reduced diversity and comprise a highly structured group. To explore this population structure, a statistical method for detecting fixation within subpopulations was applied to a set of 21 pungent and 19 nonpungent lines that represent the pepper breeding germplasm. We have identified 17 blocks within the pepper genome that are conserved among nonpungent large-fruited varieties. To determine if these regions were fixed by selection on fruit size or pungency, quantitative trait loci (QTLs) from seven studies along with capsaicin biosynthesis genes and homologs of organ size regulatory genes were mapped onto the current pepper genome assembly. Of the 17 fixed regions, 14 overlapped with fruit size or shape QTLs. There were seven putative organ size regulators and seven capsaicin biosynthetic genes within these regions. This work defines genomic regions that underly structure within the nonpungent pepper germplasm and QTLs or genes that may have been selected for during the development of large-fruited nonpungent pepper varieties.

show abstract

CaDMR1 Cosegregates with QTL Pc5.1 for Resistance to Phytophthora capsici in Pepper (Capsicum annuum)

Cited by 54 publications

References 80 publications

Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (Capsicum annuum)

Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (Capsicum annuum)

Identification and Expression Analysis of Candidate Genes Associated with Defense Responses to Phytophthora capsici in Pepper Line “PI 201234”

Regions Underlying Population Structure and the Genomics of Organ Size Determination in Capsicum annuum

Contact Info

Product

Resources

About