Extensive Structural Variations Between Mitochondrial Genomes of CMS and Normal Peppers (Capsicum Annuum L.) Revealed by Complete Nucleotide Sequencing

Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. Results: We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (psi atp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and psi atp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. Conclusions: Although large portion of sequence context was shared by mitochondrial genomes of CMS and male-fertile pepper lines, extensive genome rearrangements were detected. CMS candidate genes located on the edges of highly-rearranged CMS-specific DNA regions and near to repeat sequences. These characteristics were detected among CMS-associated genes in other species, implying a common mechanism might be involved in the evolution of CMS-associated genes.Golden Seed ProjectMinistry of Agriculture, Food and Rural Affairs (MAFRA)Ministry of Oceans and Fisheries (MOF)Rural Development Administration (RDA)Korea Forest Service (KFS)Vegetable Breeding Research Center through the R&D Convergence Center Support Program, Ministry of Agriculture, Food and Rural Affairs (MAFRA) Republic of Korea 710001-07Molecular Bioscience

Breeding of Sweet Shinhong pepper by Marker-assisted backcrossing (MABC)

Capsinoids is unique compound of pepper, which have similar biological effect to apsaicinoids like anticancer and anti-obesity. However, because the characteristic of capsinoids is non-pungency contrary to capsaicinoids, it has been studied to investigate genetic factor related to biosynthesis of capsinoids and to breed pepper variety producing capsinoids. Two pathway are known to be involved in capsaicinoids synthesis, phenylpropanoid and valine pathway. Capsinoids biosynthesis pathway is common to capsaicinoids, but putative-aminotransferase (pAMT) gene mutation in phenylpropanoid pathway cause capsinoids production instead of capsaicinoids. SNU11-001 which have pAMT gene mutation produce high level of capsinoids and Shinhong is Korean chili pepper. In previous research, pAMT mutation in SNU11-001 have been introgressed to Shinhong to breed novel Shinhong pepper containing high contents of capsinoids by Marker-Assisted Backcrossing (MABC) method. Recessive homozygous pAMT allele was selected by genotyping with KASP marker for foreground selection and 8 to 10 plants which recovered by Shinhong genome highly were selected by Fluidigm high-throughput genotyping analysis. Shinhong C × SNU11-001 (SSHC) BC2F1-40 was selected by MABC with 198 SNP markers and recovery rate was 96.3%. In this study, MABC of SNU11-001 × Shinhong C (SSHC) BC3F1 and SNU11-001 × Shinhong B (SSHB) BC2F1 was proceeded. 202 and 102 markers were used for background selection, respectively. 10 SSHC BC3F1 progenies showed the highest recovery rate, 99.5%. The range of recovery rate in SSHB BC2F1 was 89.6 to 96.7%. SSHC BC2F2 was from self-crossing of SSHC BC2F1-40 and several pamt/pamt plants were selected. We will develop SSHB BC2F2 line which have pAMT mutation allele and high recovery rate of Shinhong B. This SSHB BC2F2 progeny will have cytoplasmic male sterility by being crossed with Shinhong A. Finally we will be able to breed sweet Shinhong F1 hybrid containing high level of capsinoids.OAIID:RECH_ACHV_DSTSH_NO:A201625343RECH_ACHV_FG:RR00200003ADJUST_YN:EMP_ID:A076900CITE_RATE:FILENAME:20161027_원예학회 포스터_장시영(ARC2-1).pdfDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:FILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/e1d431a8-f997-43db-85e2-5ccb8e76020e/linkCONFIRM:

Fine mapping and identification of candidate genes for the sy-2 locus in a temperature-sensitive chili pepper (Capsicum chinense)

Key message The sy-2 temperature-sensitive gene from Capsicum chinense was fine mapped to a 138.8-kb region at the distal portion of pepper chromosome 1. Based on expression analyses, two putative F-box genes were identified as sy-2 candidate genes. Abstract Seychelles-2 (sy-2) is a temperature-sensitive natural mutant of Capsicum chinense, which exhibits an abnormal leaf phenotype when grown at temperatures below 24 °C. We previously showed that the sy-2 phenotype is controlled by a single recessive gene, sy-2, located on pepper chromosome 1. In this study, a high-resolution genetic and physical map for the sy-2 locus was constructed using two individual F2 mapping populations derived from a cross between C. chinense mutant sy-2 and wild-type No. 3341. The sy-2 gene was fine mapped to a 138.8-kb region between markers SNP 5-5 and SNP 3-8 at the distal portion of chromosome 1, based on comparative genomic analysis and genomic information from pepper. The sy-2 target region was predicted to contain 27 genes. Expression analysis of these predicted genes showed a differential expression pattern for ORF10 and ORF20 between mutant and wild-type plants; with both having significantly lower expression in sy-2 than in wild-type plants. In addition, the coding sequences of both ORF10 and ORF20 contained single nucleotide polymorphisms (SNPs) causing amino acid changes, which may have important functional consequences. ORF10 and ORF20 are predicted to encode F-box proteins, which are components of the SCF complex. Based on the differential expression pattern and the presence of nonsynonymous SNPs, we suggest that these two putative F-box genes are most likely responsible for the temperature-sensitive phenotypes in pepper. Further investigation of these genes may enable a better understanding of the molecular mechanisms of low temperature sensitivity in plants.OAIID:RECH_ACHV_DSTSH_NO:T201625254RECH_ACHV_FG:RR00200001ADJUST_YN:EMP_ID:A076900CITE_RATE:3.9FILENAME:TAG(2016) Fine mapping and identification of candidate genes for sy2.pdfDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:YFILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/c773c8d3-fc79-496f-af60-fa1b9b2e214e/linkCONFIRM:

An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum)

Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there are few studies on QTL mapping of horticultural traits in pepper (Capsicum spp.) due to the lack of high-density molecular maps and the sequence information. In this study, an ultra-high-density map and 120 recombinant inbred lines (RILs) derived from a cross between C. annuum 'Perennial' and C. annuum 'Dempsey' were used for QTL mapping of horticultural traits. Parental lines and RILs were resequenced at 18x and 1x coverage, respectively. Using a sliding window approach, an ultra-high-density bin map containing 2,578 bins was constructed. The total map length of the map was 1,372 cM, and the average interval between bins was 0.53 cM. A total of 86 significant QTLs controlling 17 horticultural traits were detected. Among these, 32 QTLs controlling 13 traits were major QTLs. Our research shows that the construction of bin maps using low-coverage sequence is a powerful method for QTL mapping, and that the short intervals between bins are helpful for fine-mapping of QTLs. Furthermore, bin maps can be used to improve the quality of reference genomes by elucidating the genetic order of unordered regions and anchoring unassigned scaffolds to linkage groups.OAIID:RECH_ACHV_DSTSH_NO:T201625248RECH_ACHV_FG:RR00200001ADJUST_YN:EMP_ID:A076900CITE_RATE:5.267FILENAME:DNA research(2016) An ultra high density bin map facilitates high throughput QTL mapping in pepper.pdfDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:YFILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/56a2d8bc-c985-47f7-a01c-70d1a2f88513/linkCONFIRM:

Fine mapping of Restorer-of-fertility in pepper (Capsicum annuum L.) identified a candidate gene encoding a pentatricopeptide repeat (PPR)-containing protein

Key message Using fine mapping techniques, the genomic region co-segregating with Restorer-of-fertility (Rf) in pepper was delimited to a region of 821 kb in length. A PPR gene in this region, CaPPR6, was identified as a strong candidate for Rf based on expression pattern and characteristics of encoding sequence. Abstract Cytoplasmic-genic male sterility (CGMS) has been used for the efficient production of hybrid seeds in peppers (Capsicum annuum L.). Although the mitochondrial candidate genes that might be responsible for cytoplasmic male sterility (CMS) have been identified, the nuclear Restorer-of-fertility (Rf) gene has not been isolated. To identify the genomic region co-segregating with Rf in pepper, we performed fine mapping using an Rf-segregating population consisting of 1068 F2 individuals, based on BSA-AFLP and a comparative mapping approach. Through six cycles of chromosome walking, the co-segregating region harboring the Rf locus was delimited to be within 821 kb of sequence. Prediction of expressed genes in this region based on transcription analysis revealed four candidate genes. Among these, CaPPR6 encodes a pentatricopeptide repeat (PPR) protein with PPR motifs that are repeated 14 times. Characterization of the CaPPR6 protein sequence, based on alignment with other homologs, showed that CaPPR6 is a typical Rf-like (RFL) gene reported to have undergone diversifying selection during evolution. A marker developed from a sequence near CaPPR6 showed a higher prediction rate of the Rf phenotype than those of previously developed markers when applied to a panel of breeding lines of diverse origin. These results suggest that CaPPR6 is a strong candidate for the Rf gene in pepper.OAIID:RECH_ACHV_DSTSH_NO:T201625308RECH_ACHV_FG:RR00200001ADJUST_YN:EMP_ID:A076900CITE_RATE:3.9FILENAME:TAG(2016) Fine mapping of Rf in pepper.pdfDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:YFILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/8c5822f8-5600-4a60-a386-0529e2f49934/linkCONFIRM:

Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Abstract Background Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato. Results For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation. Conclusions Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family

FASCICULATE regulates plant architecture including cluster flower and plant height in pepper (Capsicum annuum)

The overall plant shape is determined by genetic program. Regulation of plant architecture is an important agronomic trait for agricultural plants. Capsicum annuum MicroPep shows cluster flowers and short height. By contrast, C. annuum Jeju shows typical pepper architecture. In this study, we crossed C. annuum MicroPep and C. annuum Jeju to identify the genetic loci controlling plant architecture. A total of 117 F2 plants were genotyped using genotyping-by-sequencing (GBS) method and 2,612 single nucleotide polymorphisms (SNPs) were detected. Linked SNPs with same genotype were called as bin, and 1,731 cM bin map with 983 bins were constructed. Using bin map and the phenotype of F2 population, one locus determining MicroPep and Jeju plant shape was mapped on chromosome 6. This locus was also identified to control the plant height from quantitative trait locus (QTL) analysis, while there were 5 additional QTLs on chromosome 1 and 11 for plant height. At this locus of chromosome 6, FASCICUATE (FA) was colocalized indicating that this gene is a strong candidate for the gene controlling the cluster flower phenotype and plant height. This locus can explain 24% of total phenotypic variations. The successfully identification and characterization of FA gene can provide a chance for study of architecture in pepper.OAIID:RECH_ACHV_DSTSH_NO:A201625327RECH_ACHV_FG:RR00200003ADJUST_YN:EMP_ID:A076900CITE_RATE:FILENAME:2016 육종학회 (한고은,강민영).pdfDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:FILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/86aa7a79-ab26-4ef1-9eb5-4dbefd8194b8/linkCONFIRM:

Assessment of phenotypic variants and identification of non-pungent mutants among EMS-treated M2 population

Plant breeding needs genetic variation of economical traits to develop new, high-yielding and improved cultivars. EMS-induces mutation has been practiced to cause mutations at loci regulating economically important traits and/or to knock out the genes to elucidate their functions. The present study was under taken to induce mutations in a Capsicum annuum Micro-Pep. Micro-Pep is a small, pungent pepper generally used as ornamental purpose. The accession is convenient to use in mutation study and molecular research due to its compact growth habit, and small size. The seeds were treated with 1.3% of mutagen to induce mutation and 30% less germination percentage was observed in EMS treated seeds in comparison to control seeds. A total of 6,620 M1 plants were grown under greenhouse condition and 3996 M2 mutant lines were harvested. Among these mutants 350 lines were evaluated for novel traits. The mutants were observed with various phenotypic variants such as plant growth, habit, leaves color and shapes, flower and fruits morphology. In parallel to this, these mutants were screened for non-pungent mutants using Gibbs reagent method. In a result, 3 non-pungent mutants were identified. These mutant phenotypes and non-pungent mutants will be valuable genetic resources for identification of functional genes and molecular breeding of pepper.OAIID:RECH_ACHV_DSTSH_NO:A201625342RECH_ACHV_FG:RR00200003ADJUST_YN:EMP_ID:A076900CITE_RATE:FILENAME:2016 추계 원예학회 (이르판,한고은).pdfDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:FILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/7282a41a-5069-49ad-86bf-767a616a5875/linkCONFIRM:

Exploring resistance against Phytophthora capsici in pepper

OAIID:RECH_ACHV_DSTSH_NO:A201625325RECH_ACHV_FG:RR00200003ADJUST_YN:EMP_ID:A076900CITE_RATE:FILENAME:2016 육종학회 (이르판,한고은).pdfDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:FILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/3b8f894b-afe5-4253-b09d-9033b363540a/linkCONFIRM:

Genetic Mapping and Marker Development for the Powdery Mildew Resistance Gene PMR1 in Pepper (Capsicum annuum)

Powdery mildew (Capsicum annuum) is a major fungal disease caused by Leveillula taurica in greenhouse. Although powdery mildew resistance has a complex mode of inheritance, resistant cultivars have been steadily developed. Therefore, our objective was to map the resistance gene to powdery mildew resistance using a breeding line, C. annuum VK515 R. Based genetic analysis of an F2:3 families derived from across between the resistant parent VK515 R and a susceptible parent VK515 S, it was found that the powdery mildew resistant is controlled by a single dominant gene, PMR1. Molecular mapping revealed that the PMR1 locus is located at 1 cM genetic interval between CZ2_11628, and HRM4.1.6 markers on pepper chromosome 0. These results provide a solid foundation for map-based cloning of the PMR1 gene and development of markers for breeding powdery mildew resistant cultivars. This is the first report showing the localization of the resistance gene to powdery mildew in pepper.OAIID:RECH_ACHV_DSTSH_NO:A201625340RECH_ACHV_FG:RR00200003ADJUST_YN:EMP_ID:A076900CITE_RATE:FILENAME:2016육종학회_조진관.pptxDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:FILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/40b1853c-96b4-4c4f-b3ab-5d5c0c6ab429/linkCONFIRM: