Genome-wide association study of resistance to anthracnose in pepper (Capsicum chinense) germplasm.

BACKGROUND: Anthracnose is a fungal disease caused by Colletotrichum spp. that has a significant impact on worldwide pepper production. Colletotrichum scovillei is the most common pathogenic anthracnose-causing species in the Republic of Korea. RESULTS: The resistances of 197 pepper (Capsicum chinense) accessions deposited in Korea's National Agrobiodiversity Center were evaluated for their response against the virulent pathogens Colletotrichum acutatum isolate 'KSCa-1' and C. scovillei isolate 'Hana') in the field and in vitro methods for three consecutive years (2018 to 2020). The severity of the disease was recorded and compared between inoculation methods. Six phenotypically resistant pepper accessions were selected based on three years of disease data. All of the selected resistant pepper accessions outperformed the control resistant pepper in terms of resistance (PI 594,137). A genome-wide association study (GWAS) was carried out to identify single nucleotide polymorphisms (SNPs) associated with anthracnose resistance. An association analysis was performed using 53,518 SNPs and the disease score of the 2020 field and in vitro experiment results. Both field and in vitro experiments revealed 25 and 32 significantly associated SNPs, respectively. These SNPs were found on all chromosomes except Ch06 and Ch07 in the field experiment, whereas in the in vitro experiment they were found on all chromosomes except Ch04 and Ch11. CONCLUSION: In this study, six resistant C. chinense accessions were selected. Additionally, in this study, significantly associated SNPs were found in a gene that codes for a protein kinase receptor, such as serine/threonine-protein kinase, and other genes that are known to be involved in disease resistance. This may strengthen the role of these genes in the development of anthracnose resistance in Capsicum spp. As a result, the SNPs discovered to be strongly linked in this study can be used to identify a potential marker for selecting pepper material resistant to anthracnose, which will assist in the development of resistant varieties.

Pepper Mild Mottle Virus: An Infectious Pathogen in Pepper Production and a Potential Indicator of Domestic Water Quality.

Pepper (Capsicum spp.; Family: Solanaceae; 2n = 24) is an important crop cultivated worldwide for the consumption of its fresh and dried processed fruits. Pepper fruits are used as raw materials in a wide variety of industrial processes. As a multipurpose vegetable crop, there is a need to increase the yield. However, yield productivity of pepper is severely constrained by infectious plant pathogens, including viruses, bacteria, fungi, and oomycetes. The pepper mild mottle virus (PMMoV) is currently one of the most damaging pathogens associated with yield losses in pepper production worldwide. In addition to impacts on pepper productivity, PMMoV has been detected in domestic and aquatic water resources, as well as in the excreta of animals, including humans. Therefore, PMMoV has been suggested as a potential indicator of domestic water quality. These findings present additional concerns and trigger the need to control the infectious pathogen in crop production. This review provides an overview of the distribution, economic impacts, management, and genome sequence variation of some isolates of PMMoV. We also describe genetic resources available for crop breeding against PMMoV.

Genome-Wide Association Study of Resistance to Phytophthora capsici in the Pepper (Capsicum spp.) Collection.

One of the most serious pepper diseases is Phytophthora blight, which is caused by Phytophthora capsici. It is crucial to assess the resistance of pepper genetic resources to Phytophthora blight, understand the genetic resistances, and develop markers for selecting resistant pepper materials in breeding programs. In this study, the resistance of 342 pepper accessions to P. capsici was evaluated. The disease severity score method was used to evaluate the phenotypic responses of pepper accessions inoculated with the KCP7 isolate. A genome-wide association study (GWAS) was performed to identify single nucleotide polymorphisms (SNPs) linked to P. capsici (isolate KCP7) resistance. The pepper population was genotyped using the genotype-by-sequencing (GBS) method, and 45,481 SNPs were obtained. A GWAS analysis was performed using resistance evaluation data and SNP markers. Significantly associated SNPs for P. capsici resistance at 4 weeks after inoculation of the GWAS pepper population were selected. These SNPs for Phytophthora blight resistance were found on all chromosomes except Chr.05, Chr.09, and Chr.11. One of the SNPs found on Chr.02 was converted into a high-resolution melting (HRM) marker, and another marker (QTL5-1) from the previous study was applied to pepper accessions and breeding lines for validation and comparison. This SNP marker was selected because the resistance phenotype and the HRM marker genotype matched well. The selected SNP was named Chr02-1126 and was located at 112 Mb on Chr.02. The Chr02-1126 marker predicted P. capsici resistance with 78.5% accuracy, while the QTL5-1 marker predicted resistance with 80.2% accuracy. Along with the marker for major quantitative traits loci (QTLs) on Chr.05, this Chr02-1126 marker could be used to accurately predict Phytophthora blight resistance in pepper genetic resources. Therefore, this study will assist in the selection of resistant pepper plants in order to breed new phytophthora blight-resistant varieties.

Nutritional Metabolites of Red Pigmented Lettuce (Lactuca sativa) Germplasm and Correlations with Selected Phenotypic Characters.

Lettuce is an important dietary source of bioactive phytochemicals. Screening and identification of the health beneficial metabolites and evaluating the relationships with phenotypic characters can help consumers adjust their preferences for lettuce plant types. Thus, we explored the major health-beneficial individual metabolites and antioxidant potential of 113 red pigmented lettuce leaf samples. A UV-Vis spectrophotometer and UPLC-DAD-QTOF/MS (TQ/MS) instruments were used for the identification and quantification of metabolites and antioxidant activity accordingly. The metabolites were quantified against their corresponding external standards. The contents of metabolites varied significantly among lettuce samples. Cyanidin 3-O-(6″-O-malonyl)glucoside (4.7~5013.6 µg/g DW), 2,3-di-O-caffeoyltartaric acid (337.1~19,957.2 µg/g DW), and quercetin 3-O-(6″-O-malonyl)glucoside (45.4~31,121.0 µg/g DW) were the most dominant in red pigmented lettuce samples among anthocyanins, hydroxycinnamoyl derivatives, and flavonols, respectively. Lettuces with dark and very dark red pigmented leaves, circular leaf shape, a strong degree of leaf undulation, and highly dense leaf incisions were found to have high levels of flavonoids and hydroxycinnamoyl derivatives. Principal component analysis was used to investigate similarities and/or differences between samples, and the partial least square discriminant analysis classified them into known groups. The key variables that contributed highly were determined. Our report provides critical data on the bioactive constituents of red pigmented lettuce to breeders developing varieties with enhanced bioactive compounds and to nutraceutical companies developing nutrient dense foods and pharmaceutical formulations.

Glucosinolate Content in Brassica Genetic Resources and Their Distribution Pattern within and between Inner, Middle, and Outer Leaves.

Glucosinolates (GSLs) are sulfur-containing secondary metabolites naturally occurring in Brassica species. The purpose of this study was to identify the GSLs, determine their content, and study their accumulation patterns within and between leaves of kimchi cabbage (Brassica rapa L.) cultivars. GSLs were analyzed using UPLC-MS/MS in negative electron-spray ionization (ESI-) and multiple reaction monitoring (MRM) mode. The total GSL content determined in this study ranged from 621.15 to 42434.21 µmolkg-1 DW. Aliphatic GSLs predominated, representing from 4.44% to 96.20% of the total GSL content among the entire samples. Glucobrassicanapin (GBN) contributed the greatest proportion while other GSLs such as glucoerucin (ERU) and glucotropaeolin (TRO) were found in relatively low concentrations. Principal component analysis (PCA) yielded three principal components (PCs) with eigenvalues ≥ 1, altogether representing 74.83% of the total variation across the entire dataset. Three kimchi cabbage (S/No. 20, 4, and 2), one leaf mustard (S/No. 26), and one turnip (S/No. 8) genetic resources were well distinguished from other samples. The GSL content varied significantly among the different positions (outer, middle, and inner) of the leaves and sections (top, middle, bottom, green/red, and white) within the leaves. In most of the samples, higher GSL content was observed in the proximal half and white sections and the middle layers of the leaves. GSLs are regarded as allelochemicals; hence, the data related to the patterns of GSLs within the leaf and between leaves at a different position could be useful to understand the defense mechanism of Brassica plants. The observed variability could be useful for breeders to develop Brassica cultivars with high GSL content or specific profiles of GSLs.

Fruit Morphology, Citrulline, and Arginine Levels in Diverse Watermelon (Citrullus lanatus) Germplasm Collections.

Watermelon (Citrullus lanatus) is a non-seasonal, economically important, cucurbit cultivated throughout the world, with Asia as a continent contributing the most. As part of the effort to diversify watermelon genetic resources in the already cultivated group, this study was devoted to providing baseline data on morphological quality traits and health-beneficial phytonutrients of watermelon germplasm collections, thereby promoting watermelon research and cultivation programs. To this end, we reported morphological traits, citrulline, and arginine levels of watermelon genetic resources obtained from the gene bank of Agrobiodiversity Center, Republic of Korea, and discussed the relationships between each. Diverse characteristics were observed among many of the traits, but most of the genetic resources (>90%) were either red or pink-fleshed. Korean originated fruits contained intermediate levels of soluble solid content (SSC) while the USA, Russian, Tajikistan, Turkmenistan, Taiwan, and Uruguay originated fruits had generally the highest levels of soluble solids. The citrulline and arginine contents determined using the High Performance Liquid Chromatography (HPLC) method ranged from 6.9 to 52.1 mg/g (average, 27.3 mg/g) and 1.8 to 21.3 mg/g (average, 9.8 mg/g), respectively. The citrulline content determined using the Citrulline Assay Kit ranged from 6.5 to 42.8 mg/g (average, 27.0 mg/g). Resources with high citrulline and arginine levels contained low SSC, whereas red- and pink-colored flesh samples had less citrulline compared to yellow and orange.

Identification and quantification of selected metabolites in differently pigmented leaves of lettuce (Lactuca sativa L.) cultivars harvested at mature and bolting stages.

BACKGROUND: Identification and screening of cultivars rich in bioactive phytoconstituents can be potentially useful to make nutrient-dense dishes and in medicinal formulations. In this study, we have identified, characterized and quantified caffeoylquinic acids, dicaffeoylquinic acid, dicaffeoyltartaric acid, kaempferol conjugates, quercetin malonylglucoside, sesquiterpene lactones, and cyanidin in 22 lettuce cultivars at mature and bolting stages using UPLC-PDA-Q-TOF-HDMS, UPLC, and HPLC. RESULTS: The composition and contents of the studied metabolites and antioxidant activity varied significantly and depend on leaf color, cultivar type and stage of maturity. The main phenolic acid components of lettuce were quinic and tartaric acid derivatives, whereas kaempferol derivatives were the dominant flavonoids. The sum of the content of phenolic acids ranged from 18.3 to 54.6 mg/100 g DW and 15.5 to 54.6 mg/100 g DW, whereas the sum of the contents of flavonoids ranged from 9.2 to 25.9 mg/100 g DW and 14.9 to 83.0 mg/100 g DW in mature and bolting stage cultivars, respectively. The content of cyanidin, lactucin, lactucopicrin, and ABTS radical antioxidant activity were in the range of 0.3 to 9.7 (mature stage) and 0.5 to 10.2 mg/g DW (bolting stage), 1.8 to 41.9 (mature stage) and 9.7 to 213.0 (bolting stage) µg/g DW, 9.9 to 344.8 (mature stage) and 169.2 to 3888.2 (bolting stage) µg/g DW, and 12.1 to 29.0 (mature stage) and 15.7 to 30.3 (bolting stage) mg TE/g DW, respectively. The principal component analysis (PCA) showed that the green and red pigmented lettuce cultivars were grouped to the negative and positive sides of PC1, respectively, while the green/red pigmented cultivars were distributed throughout the four quadrants of the PCA plots with no prominent grouping. The loading plot showed that phenolic acids, flavonoids, and cyanidin are the most potent contributors to the radical scavenging activity of lettuce extracts. CONCLUSIONS: Lettuce at the bolting stage accumulate relatively high amount of sesquiterpene lactones (SLs), quercetin malonylglucoside (QMG), methylkaempferol glucuronide (MKGR), kaempferol malonylglucoside (KMG), and 3-O-caffeoylquinic acid (3-CQA) compared to the mature stage. Higher amount of phytoconstituents were found to be accumulated in the red pigmented lettuce leaves compared to the green lettuce leaves. In addition, the contents of most of the metabolites in lettuce seem to increase with age of the leaves. The presence of the two bitter SLs, lactucin and lactucopicrin, in significantly high amount in lettuce leaves at bolting stage could diminish consumer acceptance. However, alternatively, these leaves could be utilized by nutraceutical companies working to recover these compounds.

QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum.

Capsaicinoids are unique compounds produced only in peppers (Capsicum spp.). Several studies using classical quantitative trait loci (QTLs) mapping and genomewide association studies (GWAS) have identified QTLs controlling capsaicinoid content in peppers; however, neither the QTLs common to each population nor the candidate genes underlying them have been identified due to the limitations of each approach used. Here, we performed QTL mapping and GWAS for capsaicinoid content in peppers using two recombinant inbred line (RIL) populations and one GWAS population. Whole-genome resequencing and genotyping by sequencing (GBS) were used to construct high-density single nucleotide polymorphism (SNP) maps. Five QTL regions on chromosomes 1, 2, 3, 4 and 10 were commonly identified in both RIL populations over multiple locations and years. Furthermore, a total of 109 610 SNPs derived from two GBS libraries were used to analyse the GWAS population consisting of 208 C. annuum-clade accessions. A total of 69 QTL regions were identified from the GWAS, 10 of which were co-located with the QTLs identified from the two biparental populations. Within these regions, we were able to identify five candidate genes known to be involved in capsaicinoid biosynthesis. Our results demonstrate that QTL mapping and GBS-GWAS represent a powerful combined approach for the identification of loci controlling complex traits.

Evaluation of Resistance to Ralstonia solanacearum in Tomato Genetic Resources at Seedling Stage.

Bacterial wilt of tomatoes caused by Ralstonia solanacearum is a devastating disease that limits the production of tomato in Korea. The best way to control this disease is using genetically resistant tomato plant. The resistance degree to R. solanacearum was evaluated for 285 tomato accessions conserved in the National Agrobiodiversity Center of Rural Development Administration. These accessions of tomato were originated from 23 countries. Disease severity of tomato accessions was investigated from 7 days to 14 days at an interval of 7 days after inoculation of R. solanacearum under greenhouse conditions. A total of 279 accessions of tomato germplasm were susceptible to R. solanacearum, resulting in wilt and death in 70 to 90% of these plants. Two tomato accessions were moderately resistant to R. solanacearum. Only four accessions showed high resistance against R. solanacearum. No distinct symptom of bacterial wilt appeared on the resistant tomato germplasms for up to 14 days after inoculation of R. solanacearum. Microscopy of resistant tomato stems infected with R. solanacearum revealed limited bacterial spread with thickening of pit membrane and gum production. Therefore, these four resistant tomato germplasms could be used in tomato breeding program against bacterial wilt.