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The octoploid strawberry (Fragaria × ananassa Duch.) is one of the most important horticultural crops in the world. However, few genomic studies have been performed in this plant due to its polyploidy nature and complex genome. In this work, we developed diallelic single-nucleotide polymorphism (SNP) markers using next-generation resequencing data and high-resolution melting (HRM) analysis. We also constructed a genetic linkage map using an F1 segregating population derived from a cross between two cultivars, F. × ananassa ‘Sulhyang’ and ‘Senga-sengana’. A previous study revealed 20,848 SNP positions that can be developed into HRM markers. In this study, 576 SNP-based and 34 simple sequence repeat (SSR)-based HRM markers were developed using 832 newly designed and 461 previously reported primer sets, respectively. In addition, a strawberry genetic linkage map covering a total genetic distance of 1504.7 cM and consisting of 759 loci on 35 linkage groups was constructed. The linkage groups were assigned to corresponding chromosomes using the informative SSR-based markers and a BLAST search to the diploid strawberry genome, Fragaria vesca ver. 2.0.a1. Furthermore, the genome-wide HRM markers were applied to analyze the homozygosity of the inbred strawberry line ‘Wongyo 3115’, which showed a homozygosity of 96.6%. This marker and map information will be useful for future genomic and genetic research of the octoploid strawberry.

Watermelon (Citrulluslanatus) is an economically important fruit crop worldwide. Gummy stem blight (GSB) is one of the most damaging diseases encountered during watermelon cultivation. In the present study, we identified quantitative trait loci (QTLs) associated with GSB resistance in an F2 population derived from a cross between maternal-susceptible line ‘920533’ (C. lanatus) and the paternal-resistant line ‘PI 189225’ (C. amarus). The resistance of 178 F2 plants was assessed by two different evaluation methods, including leaf lesion (LL) and stem blight (SB). To analyze the QTLs associated with GSB resistance, a linkage map was constructed covering a total genetic distance of 1070.2 cM. QTL analysis detected three QTLs associated with GSB resistance on chromosome 8 and 6. Among them, two QTLs, qLL8.1 and qSB8.1 on chromosome 8 identified as major QTLs, explaining 10.5 and 10.0% of the phenotypic variations localizing at same area and sharing the same top markers for both LL and SB traits, respectively. A minor QTL, qSB6.1, explains 9.7% of phenotypic variations detected on chromosome 6 only for the SB trait. High-throughput markers were developed and validated for the selection of resistant QTLs using watermelon accessions, and commercial cultivars. Four potential candidate genes were predicted associated with GSB resistance based on the physical location of flanking markers on chromosome 8. These findings will be helpful for the development of watermelon cultivars resistant to GSB.

A yellow inbred line (SP3B) and a red doubled haploid line (H6) were used to produce a F2 mapping population of onion (Allium cepa L.). Initially, insertion/deletion and cleaved amplified polymorphic sequence markers were developed based on polymorphisms in the reference transcriptome. To improve efficiency of marker development, RNA-seq was carried out to identify single nucleotide polymorphisms (SNPs) between parental lines. High-quality SNPs were selected via customized screening process, and 344 high resolution melting (HRM) markers were developed. In addition, 161 HRM markers were developed based on the SNPs detected using genotyping-by-sequencing. A linkage map consisting of 652 molecular markers distributed in eight linkage groups was constructed. The total length of the linkage map was 749.8 cM, and the average interval between markers was 1.91 cM, the highest resolution among onion linkage maps reported so far. All eight linkage groups were assigned to onion chromosomes by identifying the common homologous loci in other linkage maps. Four major loci (C, I, R, and L) determining onion bulb colors were located on separate chromosomes. Analysis of ‘Santero’, a F1 cultivar resistant to downy mildew, revealed that the length of the chromosome fragment introgressed from Allium roylei, harboring the resistance gene estimated at 27.6 cM at the end of chromosome 3. The high-resolution linkage map constructed in this study and chromosomal locations of major qualitative loci will be used to design an effective selection strategy for onion breeding programs.

Diabetes mellitus, a group of metabolic disorders characterized by hyperglycemia, is one of the most serious and common diseases around the world and is associated with major complications such as diabetic neuropathy, retinopathy, and cardiovascular diseases. A widely used treatment for non-insulin-dependent diabetes is &alpha, glucosidase inhibitors (AGIs) such as acarbose, which hinders hydrolytic cleavage of disaccharides and retard glucose absorption. The ability to inhibit &alpha, glucosidase activity has been reported in leaf and fruit of pepper (Capsicum annuum L.). In this study, we aimed to identify quantitative trait loci (QTLs) controlling &alpha, glucosidase inhibitory activity (AGI activity) in pepper leaf and fruit using enzyme assay and genotyping-by-sequencing (GBS) analysis. The AGI activity at three stages of leaf and one stage of fruit development was analyzed by 96 F2 individuals. GBS analysis identified 17,427 SNPs that were subjected to pepper genetic linkage map construction. The map, consisting of 763 SNPs, contained 12 linkage groups with a total genetic distance of 2379 cM. QTL analysis revealed seven QTLs (qAGI1.1, qAGI11.1, qAGI5.1, qAGI9.1, qAGI12.1, qAGI5.2, and qAGI12.2) controlling AGI activity in pepper leaf and fruit. The QTLs for AGI activity varied by plant age and organ. This QTL information is expected to provide a significant contribution to developing pepper varieties with high AGI activity.

Anthocyanins, the pigmented flavonoids responsible for red and blue colors in horticultural products, promote human health by preventing cancers and lowering the risk of cardiovascular disease. Red onions contain several cyanidin- and peonidin-based anthocyanins. In this study, we constructed a single-nucleotide polymorphism (SNP)-based genetic linkage map in an F2 segregating population derived from a cross between the inbred line &lsquo, SP3B&rsquo, (yellow bulb) and the doubled haploid line &lsquo, H6&prime, (red bulb) to identify quantitative trait loci (QTLs) for total anthocyanin content of onion bulbs using a genotyping-by-sequencing (GBS) analysis based on a reference gene set. A total of 101.9 Gbp of raw sequences were generated using an Illumina HiSeq 2500 system and a total of 1625 SNP loci were identified with the criteria of three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 319 GBS-based SNP loci and 34 high-resolution melting (HRM) markers was constructed with eight linkage groups and a total genetic distance of 881.4 cM. In addition, the linkage groups were assigned to corresponding chromosomes by comparison with the reference genetic map OH1&times, 5225 through marker development based on common transcripts. The analysis revealed one major QTL, qAS7.1, for anthocyanin synthesis and two significant QTLs, qAC4.1 and qAC4.2, for anthocyanin content. The QTL qAS7.1, located on chromosome 7 with a phenotypic variation of 87.61%, may be a dihydroflavonol 4-reductase (DFR) gene that determines whether the bulb color is red or yellow. The QTLs qAC4.1 and qAC4.2 are separately positioned on chromosome 4 with R2 values of 19.43% and 26.28%, respectively. This map and QTL information will contribute to marker development and breeding for high anthocyanin content in bulb onion.

The genomic region cosegregating with the genic male-sterile ms 1 gene of Capsicum annuum L. was delimited to a region of 869.9 kb on chromosome 5 through fine mapping analysis. A strong candidate gene, CA05g06780, a homolog of the Arabidopsis MALE STERILITY 1 gene that controls pollen development, was identified in this region. Genic male sterility caused by the ms 1 gene has been used for the economically efficient production of massive hybrid seeds in paprika (Capsicum annuum L.), a colored bell-type sweet pepper. Previously, a CAPS marker, PmsM1-CAPS, located about 2–3 cM from the ms 1 locus, was reported. In this study, we constructed a fine map near the ms 1 locus using high-resolution melting (HRM) markers in an F2 population consisting of 1118 individual plants, which segregated into 867 male-fertile and 251 male-sterile plants. A total of 12 HRM markers linked to the ms 1 locus were developed from 53 primer sets targeting intraspecific SNPs derived by comparing genome-wide sequences obtained by next-generation resequencing analysis. Using this approach, we narrowed down the region cosegregating with the ms 1 gene to 869.9 kb of sequence. Gene prediction analysis revealed 11 open reading frames in this region. A strong candidate gene, CA05g06780, was identified; this gene is a homolog of the Arabidopsis MALE STERILITY 1 (MS1) gene, which encodes a PHD-type transcription factor that regulates pollen and tapetum development. Sequence comparison analysis suggested that the CA05g06780 gene is the strongest candidate for the ms 1 gene of paprika. To summarize, we developed a cosegregated marker, 32187928-HRM, for marker-assisted selection and identified a strong candidate for the ms 1 gene.

The soil-borne pathogenPhytophthora capsicicauses severe destruction ofCapsicumspp. Resistance inCapsicumagainstP. capsiciis controlled by numerous minor quantitative trait loci (QTLs) and a consistent major QTL on chromosome 5. Molecular markers onCapsicumchromosome 5 have been developed to identify the predominant genetic contributor to resistance but have achieved little success. In this study, previously reported molecular markers were used to reanalyze the major QTL region on chromosome 5 (6.2 Mbp to 139.2 Mbp). Candidate resistance gene analogs (RGAs) were identified in the extended major QTL region including 14 nucleotide binding site leucine-rich repeats, 3 receptor-like kinases, and 1 receptor-like protein. Sequence comparison of the candidate RGAs was performed between twoCapsicumgermplasms that are resistant and susceptible, respectively, toP. capsici.11 novel RGA-based markers were developed through high-resolution melting analysis which were closely linked to the major QTL forP. capsiciresistance. Among the markers, CaNB-5480 showed the highest cosegregation rate at 86.9% and can be applied to genotyping of the germplasms that were not amenable by previous markers. With combination of three markers such as CaNB-5480, CaRP-5130 and CaNB-5330 increased genotyping accuracy for 61Capsicumaccessions. These could be useful to facilitate high-throughput germplasm screening and further characterize resistance genes againstP. capsiciin pepper.

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 R 2 (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.

Capsaicinoids are pungent compounds used for industrial and medical purposes including food, medicine and cosmetics. The Indian local variety ‘Bhut Jolokia’ (Capsicum chinense Jacq.) is one of the world's hottest chilli peppers. It produces more than one million Scoville heat units (SHUs) in total capsaicinoids. In this study, our goal was to identify quantitative trait loci (QTLs) responsible for the high content of capsaicin and dihydrocapsaicin in ‘Bhut Jolokia’. Capsicum annuum ‘NB1’, a Korean pepper inbred line containing 14 000 SHUs, was used as a maternal line. An F2 population derived by crossing between ‘NB1’ and ‘Bhut Jolokia’ was generated to map QTLs for capsaicinoids content. A total of 234 markers, including 201 HRM, 21 SSR, 2 CAPS and 10 gene-based markers of the capsaicinoid synthesis pathway, were mapped. The final map covered a total distance of 1175.2 cM and contained 12 linkage groups corresponding to the basic chromosome number of chilli pepper. Capsaicin and dihydrocapsaicin content were analysed in 175 F2 pepper fruits using the HPLC method. The maximum total capsaicinoids content was 1389 mg per 100g DW (dry weight), and the minimum content was 11 mg per 100g DW. Two QTLs (qcap3.1 and qcap6.1) for capsaicin content were identified on LG3 and LG6, and two QTLs (qhdc2.1 and qdhc2.2) for dihydrocapsaicin content were located on LG2. We did not detect QTLs for total capsaicinoids content. The QTL positions for capsaicin content were different from those for dihydrocapsaicin content. These results indicate that the complexity of selecting for more pungent chilli peppers must be considered in a chilli pepper breeding programme. The QTL-linked markers identified here will be helpful to develop more pungent pepper varieties from ‘Bhut Jolokia’, a very hot pepper.

Background Transposable 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. Results We 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. Conclusions Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1341-9) contains supplementary material, which is available to authorized users.

Type-2 diabetes mellitus is one of the most prevalent metabolic diseases in the world, and is characterized by hyperglycemia (i.e., high levels of glucose in the blood). Alpha-glucosidases are enzymes in the digestive tract that hydrolyze carbohydrates into glucose. One strategy that has been developed to treat type-2 diabetes is inhibition of the activity of alpha-glucosidases using synthetic drugs. However, these inhibitors are usually associated with gastrointestinal side effects. Therefore, the development of inhibitors from natural products offers an alternative option for the control of hyperglycemia. In recent years, various studies have been conducted to identify alpha-glucosidases inhibitors from natural sources such as plants, and many candidates have transpired to be secondary metabolites including alkaloids, flavonoids, phenols, and terpenoids. In this review, we focus on the alpha-glucosidases inhibitors found in common vegetable crops and the major classes of phytochemicals responsible for the inhibitory activity, and also as potential/natural drug candidates for the treatment of type-2 diabetes mellitus. In addition, possible breeding strategies for production of improved vegetable crops with higher content of the inhibitors are also described.

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.

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.