Jundae Lee

New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

BackgroundTransposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.ResultsWe report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.ConclusionsOur study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.

Phase-coherent conduction in mesoscopic normal-metal/superconductor hybrid junctions

In this paper we report about the transport properties of mesoscopic normal-metal/superconductor (NS) hybrid systems with two different junction layouts. One is a junction fabricated by overlaying S on N wire and the other with S sandwiched between two N wires, forming an NSN structure. At zero bias all the junctions exhibited a sharp decrease of dV=dI; which is believed to arise from the interference between the disorder-scattered and the Andreev-reflected quasiparticles. A small magnetic field corresponding to one flux quantum through the normal metal region, applied in parallel with the NS junction, easily suppressed the anomalous zero-bias conductance enhancement for the sandwich-junction sample. This high sensitivity to a small magnetic field observed in our systems of mesoscopic NS junctions in a diffusive-transport regime directly confirms the electron‐holeinterference origin of the zero-bias anomaly. q 2000 Published by Elsevier Science Ltd. All rights reserved.

The complete chloroplast genome sequence of Capsicum chinense Jacq. (Solanaceae)

Abstract Capsicum chinense is one of the domesticated pepper species and well known for its distinctive pungency. The complete chloroplast genome sequence of C. chinense was generated by de novo assembly using next generation sequencing data. The chloroplast genome is 156 807 bp long, containing large single-copy region of 87 290 bp and small single-copy region of 17 911 bp separated by a pair of inverted repeats of 25 803 bp. A total of 113 genes were predicted including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenomic analysis revealed that C. chinense chloroplast genome was most closely related to Capsicum annuum var. glabriusculum (American bird pepper), a wild progenitor of C. annuum.

QTL mapping of resistance to the Cucumber mosaic virus P1 strain in pepper using a genotyping-by-sequencing analysis

Cucumber mosaic virus (CMV), a member of the Cucumovirus genus in the family Bromoviridae, is a frequently occurring virus in pepper worldwide. A broad host range, which includes many weed species and a large number of insects, means it is difficult to control CMV in the field. CMV resistance has been reported in Capsicum spp. In Korea, the C. annuum ‘Bukang’ cultivar is resistant to the CMVFNY and CMVKorean strains; however, a new strain (CMVP1) is able to infect the resistant cultivars. Therefore, it is necessary to pursue CMVP1 resistance in pepper breeding. In this study, we surveyed the quantitative trait loci (QTL) for resistance to CMVP1 using a single-seed-descent (SSD) F3 segregating population derived from a cross between a resistant line, ‘A1’, and a susceptible line, ‘2602.’ A total of 174 plants were evaluated for resistance to CMVP1 at 30 days after mechanical inoculation, with phenotypes confirmed by reverse transcription PCR. The number of resistant and susceptible plants was 88 and 86, respectively. Of these, 96 individuals including 48 resistant lines and 48 susceptible lines were used for a genotyping-by-sequencing (GBS) analysis. Approximately 19,000 single-nucleotide polymorphism (SNP) genotypes were obtained. Using the SNP data, a pepper genetic linkage map consisting of 906 SNP markers was constructed. The map showed 12 linkage groups with a total linkage distance of 1,272.9 cM. QTL analysis using a composite interval mapping (CIM) method revealed that two QTLs, cmvP1-5.1 and cmvP1-10.1, located on chromosomes 5 and 10, respectively, had R2 (coefficient of determination) values of 17.81% and 22.78%. This information will be helpful for developing SNP markers linked to CMVP1-resistant QTLs and for developing new CMVP1-resistant pepper cultivars.

Symptom and Resistance of Cultivated and Wild Capsicum Accessions to Tomato Spotted Wilt Virus

Agricultural Microbiology Division, National Academy of Agricultural Science, Suwon 441-707, Korea(Received on November 22, 2010; Accepted on March 7, 2011)One hundred Capsicum accessions were screened for symptomatic response and resistance to Tomato spottedwilt virus-pb1 (TSWV-pb1). Symptom and its severity rating were checked by visual observation at 9, 12, 14,and 45 days after inoculation, respectively. Enzyme-linked immune-sorbent assay was performed all testedindividuals on non-inoculated upper leaves after the third rating to indentify viral infection. Leaf curling waspredominant in almost susceptible individuals of each accession. Stem necrosis was most frequent in wildspecies while yellowing in commercial hybrids and Korean land race cultivars. Ring spot, a typical symptomof TSWV, was rarely detected in some of a few accessions. Different levels of resistance to TSWV-pb1 wereobserved among the tested accessions. High level of resistance was detected in 4 commercial cultivars of Kpc-35, -36, -57, and -62, and 8 wild species of PBI-11, C00105, PBC076, PBC280, PBC426, PBC495, PBC537, andPI201238 through seedling test by mechanical inoculation. Keywords : Chili pepper, Resistance, Tomato, Tomato spotted wilt virus 토마토반점위조바이러스(Tomato spotted wilt virus;TSWV)는 Bunyaviridae과 Tospovirus속으로 분류되는 구형 바이러스로 꽃노랑총채벌레(Frankliniella occidentalis)에 의해 주로 전반된다(Whitfield 등, 2005). 1919년에 호주의 토마토에서 처음 발생한 이후 TSWV는 하와이, 브라질, 유럽의 여러 국가, 남아프리카공화국 등에서 보고되었으며(조 등, 2005), 국내에서는 2003년에 충남 예산신안면 파프리카 재배 농가에서 최초로 발생하였다(Choi등, 2010). 이후 강원도 지역을 포함한 총 23개 지역에서발생하였고, 고추와 토마토뿐만 아니라 국화, 콩 등에도감염하여 지속적으로 관찰해야 할 주요 바이러스로 인식되고 있다(Choi 등, 2010). 우리나라에 발생하는 TSWV는 식물 종류별, 발생 지역별 병원성 분화가 일어나는 것으로 확인되어 각 작물 별 저항성 유전자원 확보가 매우중요한 것으로 보고되었다(조 등, 2009). 한편, 국내에서는 TSWV 발생현황과 바이러스에 대한특성 연구가 주로 보고 되었으나 외국에서는 TSWV 저항성 연구가 활발하게 수행되었다. Capsicum chinensePI159236과 PI152225에서는 단일 우성 유전자인 Tsw 이보고되었으며, 이와 연관 분자 표지도 개발되어 실제 상업 육종에 이용되고 있다(Boiteux와 Avila, 1994; Boiteux,1995). 비록 Tsw 유전자가 도입된 상용 파프리카가 판매되고 있지만, 1992년부터 브라질(Boiteux와 Nagata, 1992),루이지아나(Hobbs 등, 1994), 이탈리아(Roggero 등, 2002),스페인(Margaria 등, 2004), 호주(Sharman와 Persley, 2006)에서는 Tsw 저항성을 극복하는 새로운 TSWV 계통이 보