Rapid identification of QTLs underlying resistance to <Emphasis Type="Italic">Cucumber mosaic virus</Emphasis> in pepper (<Emphasis Type="Italic">Capsicum frutescens</Emphasis>)

Key message

Next-generation sequencing enabled a fast discovery of QTLs controlling CMV resistant in pepper. The gene CA02g19570 as a possible candidate gene of qCmr2.1 was identified for resistance to CMV in pepper.

Abstract

Cucumber mosaic virus (CMV) is one of the most important viruses infecting pepper, but the genetic basis of CMV resistance in pepper is elusive. In this study, we identified a candidate gene for CMV resistance QTL, qCmr2.1 through SLAF-seq. Segregation analysis in F₂, BC₁ and F_2:3 populations derived from a cross between two inbred lines ‘PBC688’ (CMV-resistant) and ‘G29’ (CMV-susceptible) suggested quantitative inheritance of resistance to CMV in pepper. Genome-wide comparison of SNP profiles between the CMV-resistant and CMV-susceptible bulks constructed from an F₂ population identified two QTLs, designated as qCmr2.1 on chromosome 2 and qCmr11.1 on chromosome 11 for resistance to CMV in PBC688, which were confirmed by InDel marker-based classical QTL mapping in the F₂ population. As a major QTL, joint SLAF-seq and traditional QTL analysis delimited qCmr2.1 to a 330 kb genomic region. Two pepper genes, CA02g19570 and CA02g19600, were identified in this region, which are homologous with the genes LOC104113703, LOC104248995, LOC102603934 and LOC101248357, which were predicted to encode N-like protein associated with TMV-resistant in Solanum crops. Quantitative RT-PCR revealed higher expression levels of CA02g19570 in CMV resistance genotypes. The CA02g19600 did not exhibit obvious regularity in expression patterns. Higher relative expression levels of CA02g19570 in PBC688 and F₁ were compared with those in G29 during days after inoculation. These results provide support for CA02g19570 as a possible candidate gene of qCmr2.1 for resistance to CMV in pepper.

     

QTL mapping of anthracnose (<Emphasis Type="Italic">Colletotrichum</Emphasis> spp.) resistance in a cross between <Emphasis Type="Italic">Capsicum annuum</Emphasis> and <Emphasis Type="Italic">C. chinense</Emphasis>

Anthracnose fruit rot is an economically important disease that affects pepper production in Indonesia. Strong resistance to two causal pathogens, Colletotrichum gloeosporioides and C. capsici, was found in an accession of Capsicum chinense. The inheritance of this resistance was studied in an F₂ population derived from a cross of this accession with an Indonesian hot pepper variety (Capsicum annuum) using a quantitative trait locus (QTL) mapping approach. In laboratory tests where ripe fruits were artificially inoculated with either C. gloeosporioides or C. capsici, three resistance-related traits were scored: the infection frequency, the true lesion diameter (averaged over all lesions that actually developed), and the overall lesion diameter (averaged over all inoculation points, including those that did not develop lesions). One main QTL was identified with highly significant and large effects on all three traits after inoculation with C. gloeosporioides and on true lesion diameter after inoculation with C. capsici. Three other QTL with smaller effects were found for overall lesion diameter and true lesion diameter after inoculation with C. gloeosporioides, two of which also had an effect on infection frequency. Interestingly, the resistant parent carried a susceptible allele for a QTL for all three traits that was closely linked to the main QTL. The results with C. capsici were based on less observations and therefore less informative. Although the main QTL was shown to have an effect on true lesion diameter after inoculation with C. capsici, no significant QTL were identified for overall lesion diameter or infection frequency.     

Induced androgenesis of <Emphasis Type="Italic">Capsicum frutescens</Emphasis> L.

The aim of the research was to make a preliminary determination of the effectiveness of the induction of haploids in Capsicum frutescens L. In order to induce androgenesis red and yellow fruit forms of species were used, each bred by the researchers on their own. The experiment was performed in October. Anther cultures were conducted according to a modified method developed by Dumas et al. (1981) for C. annuum L. The anthers were laid on CP medium containing 0.01 mg dm⁻³ 2.4-D and 0.01 mg dm⁻³ kinetin, with the addition of 0.5 g dm⁻³ of activated carbon and 5 mg×dm⁻³ of silver nitrate, solidified with 8 g dm⁻³ of agar. The cultures were incubated in the dark at 35 deg C for 8 days. Next they were transferred to 25 deg C under a 12-hour photoperiod. After 14 days of induction, anthers were transferred to R₁ medium supplemented with 0.1 mg dm⁻³ kinetin. Obtained embryos were subsequently transplanted onto V₃ hormone-free medium and well growing plants were planted in greenhouses. The efficiency of androgenesis for both C. frutescens L. forms was relatively low and it did not exceed 5%. The ploidy level of the resulting plants was determined by flow-cytometric analysis. The regenerants consisted of about equal numbers of haploids and diploids. Additionally, among plants regenerated from anthers of yellow fruit forms, two mixoploids were observed.     

Selection of atrazine-resistant plants by <Emphasis Type="Italic">in vitro</Emphasis> mutagenesis in pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis>)

The effects of atrazine on cotyledon cultures of Capsicum annuum (L.) cv. G₄ were investigated with a view of establishing a system for in vitro selection of resistant mutants. At low levels of herbicide produced little growth inhibition, some chlorophyll loss occurred associated with the production of albino shoots. At 20 mg l⁻¹ atrazine bleaching was more pronounced and was accompanied by the development of necrotic spots; however, efficient bleaching was associated with severe suppression of growth. Mutagenized cotyledon explants resulted in production of herbicide-resistant plants on medium containing selective levels of sucrose (0.5%) and atrazine (20 mg l⁻¹). Differential morphogenetic responses were observed when the levels of sucrose (0.5–5%) were altered. Shoot regeneration was maximum in 2 sucrose and the regenerating ability decreased with a further increase in sucrose concentration (3%–5%). However, lowering of sucrose concentration from 2 to 0.5% caused complete bleaching of explants and permitted the selection of herbicide-resistant plants. Complete atrazine-resistant plantlets were obtained after rooting of regenerated green shoots on rooting medium containing 10 mg l⁻¹atrazine, 1.0 mg l⁻¹IAA and 0.5% sucrose. Leaf-segment assay of differentiated plants revealed that all regenerants were resistant to the atrazine. Reciprocal crosses between atrazine-resistant and -sensitive plants showed a non-Mendelian transmission of resistance trait.     

Anther culture in pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.) in vitro

Pepper (Capsicum annuum L.) is an important vegetable crop that can be improved using plant tissue culture and biotechnology. However, it is difficult to develop appropriate breeding material by in vitro cultivation in this species. Haploid plant production is useful in the breeding programs to facilitate recovery of recessive mutations and unique genetic recombinations. In embryogenesis, haploid formation from pollen in anther culture is a scientifically advanced, but controversial system. Various techniques for haploid plant regeneration are used to establish an efficient double haploid production method. The purpose of this article is to summarize, through comparison, results in pepper anther culture, problems associated with work in this field, and the influence of critical factors for successful embryo formation and plantlet development.     

<Emphasis Type="Italic">In vitro</Emphasis> flowering of <Emphasis Type="Italic">Perilla frutescens</Emphasis>

This study investigated the factors affecting in vitro flowering of Perilla frutescens. The shoots regenerated from cotyledonary and hypocotyl explants cultured on Murashige and Skoog (MS) medium supplemented with benzyladenine (BA) and indole-3-acetic acid, each at 0.5 mg l⁻¹, were excised and transferred to MS medium containing 30 g l⁻¹ of sucrose, 8.25 g l⁻¹ of ammonium nitrate, and 1.0 mg l⁻¹ of BA. After 40 d of culture, 86.2% of shoots flowered and most of which self-fertilized in vitro and produced mature fruits with viable seeds. These seeds were germinated and plants were grown to maturity and flowered in soil under greenhouse conditions. The in vitro flowering system reported in this study may facilitate rapid breeding of P. frutescens and offers a model system for studying the physiological mechanism of flowering.     

<Emphasis Type="Italic">In vitro</Emphasis> fruiting and seed set of <Emphasis Type="Italic">Capsicum annuum</Emphasis> L. CV. Sweet banana

Summary Plantlets of Capsicum annuum L. ev. Sweet Banana regenerated via somatic embryogenesis from immature zygotic embryos were capable of producing flower, fruit, and seed when cultured in small tissue culture containers. In vitro floral buds were first formed on plantlets that grew on plantlet development medium [agar-gelled Murashige and Skoog (MS) basal medium containing 1 mgl⁻¹ (5.3 μM) α-naphthaleneacetic acid (NAA)] in a growth room at 22°C and continuous illumination. However, floral buds rarely developed further into mature flowers. This problem was overcome using the vented autoclavable plant tissue culture containers. In vitro fruit formation and ripening was observed when liquid half-strength MS basal medium supplemented with 5 μg ml⁻¹ silver thiosulfate, 1 mg l⁻¹ (5.3 μM) NAA, and 3% sucrose was added to the surface of the plantlet development medium. Hand-pollination improved fruit set. Further research in needed to determine why the pepper seeds formed in vitro failed to germinate.     

Pepper EST database: comprehensive <Emphasis Type="Italic">in silico</Emphasis> tool for analyzing the chili pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis>) transcriptome

Background  

There is no dedicated database available for Expressed Sequence Tags (EST) of the chili pepper (Capsicum annuum), although the interest in a chili pepper EST database is increasing internationally due to the nutritional, economic, and pharmaceutical value of the plant. Recent advances in high-throughput sequencing of the ESTs of chili pepper cv. Bukang have produced hundreds of thousands of complementary DNA (cDNA) sequences. Therefore, a chili pepper EST database was designed and constructed to enable comprehensive analysis of chili pepper gene expression in response to biotic and abiotic stresses.     

<Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated genetic transformation of <Emphasis Type="Italic">Perilla frutescens</Emphasis>

A reproducible plant regeneration and an Agrobacterium tumefaciens-mediated genetic transformation protocol were developed for Perilla frutescens (perilla). The largest number of adventitious shoots were induced directly without an intervening callus phase from hypocotyl explants on MS medium supplemented with 3.0 mg/l 6-benzylaminopurine (BA). The effects of preculture and extent of cocultivation were examined by assaying -glucuronidase (GUS) activity in explants infected with A. tumefaciens strain EHA105 harboring the plasmid pIG121-Hm. The highest number of GUS-positive explants were obtained from hypocotyl explants cocultured for 3 days with Agrobacterium without precultivation. Transgenic perilla plants were regenerated and selected on MS basal medium supplemented with 3.0 mg/l BA, 125 mg/l kanamycin, and 500 mg/l carbenicillin. The transformants were confirmed by PCR of the neomycin phosphotransferase II gene and genomic Southern hybridization analysis of the hygromycin phosphotransferase gene. The frequency of transformation from hypocotyls was about 1.4%, and the transformants showed normal growth and sexual compatibility by producing progenies.     

Isolation and characterization of the cytoplasmic male sterility-associated <Emphasis Type="Italic">orf456</Emphasis> gene of chili pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.)

Cytoplasmic male sterility (CMS) in plants is known to be associated with novel open reading frames (ORFs) that result from recombination events in the mitochondrial genome. In this study Southern and Northern blot analyses using several mitochondrial DNA probes were conducted to detect the presence of differing band patterns between male fertile and CMS lines of chili pepper (Capsicum annuum L.). In the CMS pepper, a novel ORF, termed orf456, was found at the 3′-end of the coxII gene. Western blot analysis revealed the expression of an approximately 17-kDa product in the CMS line, and the intensity of expression of this protein was severely reduced in the restorer pepper line. To investigate the functional role of the ORF456 protein in plant mitochondria, we carried out two independent experiments to transform Arabidopsis with a mitochondrion-targeted orf456 gene construct by Agrobacterium-mediated transformation. About 45% of the T₁ transgenic population showed the male-sterile phenotype and no seed set. Pollen grains from semi-sterile T₁ plants were observed to have defects on the exine layer and vacuolated pollen phenotypes. It is concluded that this newly discovered orf456 may represent a strong candidate gene – from among the many CMS-associated mitochondrial genes – for determining the male-sterile phenotype of CMS in chili pepper. GenBank accession number DQ116040 (orf456 genomic sequence), DQ126683 (pepper coxII genomic sequence)     

Complete genome sequencing and analysis of <Emphasis Type="Italic">Capsicum annuum</Emphasis> varieties

Peppers (Capsicum spp.), economically important crops of the nightshade family, are used as vegetables, spices, and medicines. Bacterial wilt (BW), one of the most devastating bacterial plant diseases, causes heavy losses in many crops, including peppers. The aim of this study was to develop DNA-based molecular markers that could be used in future marker-assisted breeding for BW resistance. Genome-wide discovery of single-nucleotide polymorphisms (SNPs was achieved by comparing whole-genome resequencing data from two pepper varieties, Saengryeg 211 (susceptible to BW) and 82PR66 (resistant to BW) with the reference genome of Capsicum annuum cv. CM334. A total of 118,588,231 and 148,774,861 paired raw reads with an average length of 151 bp were recorded for Saengryeg 211 and 82PR66, respectively. Data mining revealed 6,804,889 and 4,293,534 SNPs for Saengryeg 211 and 82PR66, respectively. The SNPs, were assorted into 12 chromosomes. A total of 5,514,563 polymorphic SNPs were discovered between the two varieties, and 42,236 high-resolution melting marker primer sets were selected for use in future experiments. Our results reveal numerous DNA-based molecular markers that might be useful in molecular breeding and QTL mapping in pepper.     

Allele-specific CAPS marker in a <Emphasis Type="Italic">Ve1</Emphasis> homolog of <Emphasis Type="Italic">Capsicum annuum</Emphasis> for improved selection of <Emphasis Type="Italic">Verticillium dahliae</Emphasis> resistance

Verticillium wilt (Verticillium dahliae) is an economically important disease for many high-value crops. The pathogen is difficult to manage due to the long viability of its resting structures, wide host range, and the inability of fungicides to affect the pathogen once in the plant vascular system. In chile pepper (Capsicum annuum), breeding for resistance to Verticillium wilt is especially challenging due to the limited resistance sources. The dominant Ve locus in tomato (Solanum lycopersicum) contains two closely linked and inversely oriented genes, Ve1 and Ve2. Homologs of Ve1 have been characterized in diverse plant species, and interfamily transfer of Ve1 confers race-specific resistance. Queries in the chile pepper WGS database in NCBI with Ve1 and Ve2 sequences identified one open reading frame (ORF) with homology to the tomato Ve genes. Comparison of the candidate CaVe (Capsicum annuum Ve) gene sequences from susceptible and resistant accessions revealed 16 single nucleotide polymorphisms (SNPs) and several haplotypes. A homozygous haplotype was identified for the susceptible accessions and for resistant accessions. We developed a cleaved amplified polymorphic sequence (CAPS) molecular marker within the coding region of CaVe and screened diverse germplasm that has been previously reported as being resistant to Verticillium wilt in other regions. Based on our phenotyping using the New Mexico V. dahliae isolate, the marker could select resistance accessions with 48% accuracy. This molecular marker is a promising tool towards marker-assisted selection for Verticillium wilt resistance and has the potential to improve the efficacy of chile pepper breeding programs, but does not eliminate the need for a bioassay. Furthermore, this work provides a basis for future research in this important pathosystem.     

Identification and molecular genetic mapping of <Emphasis Type="Italic">Chili veinal mottle virus</Emphasis> (ChiVMV) resistance genes in pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis>)

Chili veinal mottle virus (ChiVMV) threatens the agricultural production of peppers (Capsicum annuum) in Asia and Africa. In this study, we evaluated ChiVMV resistance in the four pepper varieties CV3, CV4, CV8, and CV9. Segregation analyses revealed that CV3 and CV8 contain the single dominant resistance gene Cvr1, and CV9 contains the single recessive resistance gene cvr4. SNP markers were developed and used to map the Cvr1 gene in CV3 to the short arm of chromosome 6 where NLR genes are clustered. In CV4 oligogenic resistance loci were detected. A genotyping-by-sequencing (GBS) combined with modified sliding window approach mapped two resistance loci, to chromosomes 6 and 10. The development of SNP markers and the resulting knowledge of genomic positioning will assist in breeding ChiVMV-resistant pepper varieties and in the fine mapping of ChiVMV resistance genes.     

A SNP-based genetic linkage map of <Emphasis Type="Italic">Capsicum baccatum</Emphasis> and its comparison to the <Emphasis Type="Italic">Capsicum annuum</Emphasis> reference physical map

Capsicum baccatum L., one of five domesticated species of Capsicum, is a valuable species in chili pepper breeding. In particular, it is a source of disease resistance against anthracnose and powdery mildew. Genetic maps and molecular markers are important to improve the efficiency of crop breeding programs. Recently, using genetic maps several researchers have identified quantitative trait loci (QTLs) for important horticultural traits and have cloned genes of interest. In this study, we constructed a genetic map of C. baccatum in an intraspecific population from a cross between ‘Golden-aji’ and ‘PI594137.’ A total of 395 high-resolution melting markers were developed based on single-nucleotide polymorphisms identified by comparing genome sequences generated through next-generation resequencing of the parents, ‘Golden-aji’ and ‘PI594137.’ The genetic linkage map contained 12 linkage groups, covered a total distance of 1056.2 cM, and had an average distance of 2.67 cM between markers. In addition, the final map was compared to the reference physical map of C. annuum ‘CM334.’ Interestingly, two major reciprocal translocations between chromosomes 3 and 5 and between chromosomes 3 and 9 were found, suggesting that these translocations might act as a genetic barrier between C. annuum and C. baccatum. Translocations between chromosomes 1 and 8 were also observed, as were previously reported in C. chinense, C. frutescens, and wild C. annuum. The synteny of other chromosomes was maintained, on the whole, except for several small inversions. The information on this genetic map will be helpful to analyze QTLs for important traits such as anthracnose resistance in C. baccatum and to study the causes of genetic barriers between C. annuum and C. baccatum.