Inhwa Yeam

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.

Infection processes of xylem‑colonizing pathogenic bacteria: possible explanations for the scarcity of qualitative disease resistance genes against them in crops

Key messageDisease resistance against xylem-colonizing pathogenic bacteria in crops.AbstractPlant pathogenic bacteria cause destructive diseases in many commercially important crops. Among these bacteria, eight pathogens, Ralstonia solanacearum, Xanthomonas oryzae pv. oryzae, X. campestris pv. campestris, Erwinia amylovora, Pantoea stewartii subsp. stewartii, Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. actinidiae, and Xylella fastidiosa, infect their host plants through different infection sites and paths and eventually colonize the xylem tissues of their host plants, resulting in wilting symptoms by blocking water flow or necrosis of xylem tissues. Noticeably, only a relatively small number of resistant cultivars in major crops against these vascular bacterial pathogens except X. oryzae pv. oryzae have been found or generated so far, although these pathogens threaten productivity of major crops. In this review, we summarize the lifestyles of major xylem-colonizing bacterial pathogens and then discuss the progress of current research on disease resistance controlled by qualitative disease resistance genes or quantitative trait loci against them. Finally, we propose infection processes of xylem-colonizing bacterial pathogens as one of possible reasons for why so few qualitative disease resistance genes against these pathogens have been developed or identified so far in crops.

Molecular marker development and genetic diversity exploration by RNA-seq in Platycodon grandiflorum.

Platycodon grandiflorum, generally known as the bellflower or balloon flower, is the only species in the genus Platycodon of the family Campanulaceae. Platycodon plants have been traditionally used as a medicinal crop in East Asia for their antiphlogistic, antitussive, and expectorant properties. Despite these practical uses, marker-assisted selection and molecular breeding in platycodons have lagged due to the lack of genetic information on this genus. In this study, we performed RNA-seq analysis of three platycodon accessions to develop molecular markers and explore genetic diversity. First, genic simple sequence repeats (SSRs) were retrieved and compared; dinucleotide motifs were the most abundant repeats (39%-40%) followed by trinucleotide (25%-31%), tetranucleotide (1.5%-1.9%), and pentanucleotide (0.3%-1.0%) repeats. The result of in silico SSR analysis, three SSR markers were detected and showed possibility to distinguish three platycodon accessions. After several filtering procedures, 180 single nucleotide polymorphisms (SNPs) were used to design 40 cleaved amplified polymorphic sequence (CAPS) markers. Twelve of these PCR-based markers were validated as highly polymorphic and utilized to investigate genetic diversity in 21 platycodon accessions collected from various regions of South Korea. Collectively, the 12 markers yielded 35 alleles, with an average of 3 alleles per locus. Polymorphism information content (PIC) values ranged from 0.087 to 0.693, averaging 0.373 per locus. Since platycodon genetics have not been actively studied, the sequence information and the DNA markers generated from our research have the potential to contribute to further genetic improvements, genomic studies, and gene discovery in this genus.

Current advances and prospectus of viral resistance in horticultural crops

Viruses are a major threat causing massive yield loss and economical damage to crop production worldwide. Through complex evolutionary processes, plants encounter and overcome viral infection by developing effective resistance mechanisms. Over the past decade, remarkable progress has been made in understanding the nature of plant resistance to viruses at the molecular level. This review summarizes the major resistance strategies that plants use to prevent viral infection. Recent investigations suggest that antiviral RNA silencing is the most prevalent defense strategy in plants. Other forms of resistance include R gene-mediated resistance and host factor-related recessive resistance. Naturally occurring resistances arise and are maintained in numerous virus-plant pathosystems based mainly on arms-race relationships and the cost-efficiency of resistance acquisition. In addition to the current status of the known resistance mechanisms, this review discusses the future prospectus for the practical application of plant resistances that influence resistance durability in agricultural ecosystems. Such applications include molecular breeding strategies using advanced molecular marker systems and the utilization of trans- or cis- genetics via the acquisition of engineered disease resistances.

Allelic relationships at the pvr1 locus in Capsicum annuum

Diseases caused by members of the Potyviridae family currently threaten pepper crops (Capsicum annuum L.) worldwide. A series of monogenic recessive resistance genes that control potyvirus resistance at the pvr1 locus in Capsicum species are widely known and used in pepper breeding programs, each allele with a differential resistance spectrum affecting a distinct range of viral strains across three viruses, Tobacco etch virus (TEV), Pepper mottle virus and Potato virus Y. In this study, we systematically analyzed the resistant spectra, and the level of the resistance each allele confers using a set of pepper genotypes homozygous or heterozygous for the following alleles; Pvr1+, pvr1, pvr11 and pvr12. The resistance alleles at the pvr1 locus show recessive inheritance when combined with a susceptible allele in F1 progenies. However, our results show that resistance in this system is, in fact, not always fully recessive and establish a hierarchy of allelic interactions We identified the resistance phenotype in F1 progenies generated by combining a complete resistant allele with an incomplete resistance allele against TEV strains implying that the resistance alleles at the pvr1 shows dominant inheritance when combined with an incomplete resistance allele. Resistance alleles against TEV-HAT, pvr1 and pvr12, show dominance inheritance when each is combined with pvr11. The resistance allele, pvr1, shows dominance inheritance when combined with pvr12 against TEV-N. These results clarify the allelic relationship between resistance alleles at the pvr1 locus displaying different resistance spectra, and will assist breeders to select the preferred combinations of the resistance alleles to obtain durable resistance against multiple potyviral strains.

Gene-based molecular marker system for multiple disease resistances in tomato against Tomato yellow leaf curl virus, late blight, and verticillium wilt

Marker assisted selection (MAS) for disease resistance is widely applied in practical tomato breeding programs in the public and private sectors. Due to its commercial value and importance as a model crop, tomato has taken the lead in MAS among the horticultural crops. Tomato yellow leaf curl virus, which is transmitted by the whitefly (Bemisia tabaci), is a major threat to tomato production worldwide. The Ty1 and Ty3 resistance loci originated from Solanum chilense LA1969 and LA1932/LA2779, respectively. Recently, the gene responsible for Ty1 resistance was identified as a DFDGD-class RNA-dependent RNA polymerase and was demonstrated to be allelic with Ty3 resistance. The Ph3 resistance locus from S. pimpinellifolium (L3708), which confers incomplete resistance against a widerange of Phytophthora infestans isolates, is considered the most effective source of resistance against tomato late blight. A coiled-coil nucleotide-binding leucine-rich repeat gene on chromosome 9 was determined to be responsible for Ph3 resistance. Resistance against verticillium wilt diseases in tomato is conferred by the Ve locus that contains two closely linked, inversely oriented genes: Ve1 and Ve2. The Ve locus provides resistance against Verticillium alboatrum race 1 and encodes an extracellular leucine-rich repeat receptor-like protein class of disease resistance proteins. We developed reliable and comprehensive molecular markers based on either the single nucleotide polymorphisms or insertions/deletions directly responsible for the resistance provided by the Ty1, Ph3, and Ve1 loci. These gene-based functional molecular markers are expected to enhance the effectiveness and accuracy of MAS for disease resistance in tomato breeding programs.

Mining secreted proteins that function in pepper fruit development and ripening using a yeast secretion trap (YST)

Plant cells secrete diverse sets of constitutively- and conditionally-expressed proteins under various environmental and developmental states. Secreted protein populations, or secretomes have multiple functions, including defense responses, signaling, metabolic processes, and developmental regulation. To identify genes encoding secreted proteins that function in fruit development and ripening, a yeast secretion trap (YST) screen was employed using pepper (Capsicum annuum) fruit cDNAs. The YST screen revealed 80 pepper fruit-related genes (CaPFRs) encoding secreted proteins including cell wall proteins, several of which have not been previously described. Transient GFP-fusion assay and an in planta secretion trap were used to validate the secretion of proteins encoded by selected YST clones. In addition, RNA gel blot analyses provided further insights into their expression and regulation during fruit development and ripening. Integrating our data, we conclude that the YST provides a valuable functional genomics tool for the identification of substantial numbers of novel secreted plant proteins that are associated with biological processes, including fruit development and ripening.

Exploring natural variations in eIF4E and screening for potyviral resistance in diverse Nicotiana species

The eukaryotic translation factors, including eIF4E which plays a major role in host translation initiation by recruiting messenger RNAs to the ribosomal complex, have repeatedly been identified as host factors required for viral infection. The cDNA sequence of eIF4E and eIF(iso)4E from 16 different genotypes, including 8 Nicotiana species and 8 Nicotiana tabacum cultivars, were determined in this study. The consensus Nicotiana eIF4E cDNA is 669 nucleotides long and codes for 222 amino acids. A high level of similarity was detected among eIF4E proteins of Nicotiana species sharing over 97% nucleotide identity and 95% amino acid identity in most cases. The eIF4E from tobacco (Nicotiana tabacum) shares a protein identities of 75.7% with pepper-eIF4E, 74.3% with tomato-eIF4E, 73.4% with potato-eIF4E, 73.1% with melon-eIF4E, 72.6% with cucumber-eIF4E, 73.1% with lettuce-eIF4E, and 71.5% with pea-eIF4E. In the case of eIF(iso)4E, the cDNA is 603 nucleotides long and codes for 200 amino acids. In this study, we investigated variations which exist in eIF4E or eIF(iso)4E, and attempted to correlate the variations which exist in these translation initiation factors with the resistance phenotype against several potyviruses in Nicotiana plants. We detected amino acid substitutions at the 18 positions for eIF4E and substitutions at the 11 positions for eIF(iso)4E. We attempted to correlate the resistance against Potato virus Y (PVY) or Pepper mottle virus (PepMoV) with the natural variations detected within the Nicotiana genotypes. However, no variation responsible for the gains of potyviral resistance was detected in this study. The result suggests that the potyviral resistance observed in Nicotiana species against PVY and PepMoV was conferred by an unknown resistance factor other than eIF4E or eIF(iso)4E, unlike general potyviral resistance observed in other plant species of the Solanaceae family.