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We have a limited number of landraces and only a few of them have been used in breeding programs. In the Korean peninsula, maize was introduced before the middle of the 16th century and cultivated widely thereafter. Over 3000 Korean maize landraces have been collected and deposited in the Genebank of the National Agrobiodiversity Center, Korea, which is about a half of total maize germplasm stored in the Genebank. The majority of Korean maize accessions have been maintained as local landraces, implying the preservation of diverse morphological traits with a wide range of variation. However, there has been a few studies for discovering phenotypic characteristics of the Korean maize landraces. We collected phenotype data of 2699 maize germplasm which can be divided by geographic origin (Korean or overseas) and breeding progress (landraces or breeding lines). Principal component analysis demonstrated that the phenotypic variations of the collected maize germplasm were largely explained by flowering time, kernel yields, and stalk diameter traits. From the phenotype data analysis, 276 accessions were selected as a core collection. We also investigated endosperm phenotypes for the core collection and found novel multilayer aleurone germplasms. This indicates that Korean landraces have maintained the original genetic variation which has largely been lost during the modern breeding programs. These findings suggest that the core collection could be a valuable resource for understating and exploiting maize germplasm.

This study investigated carotenoid content and fruit color variation in 306 pepper accessions from diverse Capsicum species. Red-fruited accessions were predominant (245 accessions), followed by orange (35) and yellow (20). Carotenoid profiles varied significantly across accessions, with capsanthin showing the highest mean concentration (239.12 μg/g), followed by β-cryptoxanthin (63.70 μg/g) and zeaxanthin (63.25 μg/g). Total carotenoid content ranged from 7.09 to 2566.67 μg/g, emphasizing the diversity within the dataset. Correlation analysis revealed complex relationships between carotenoids, with strong positive correlations observed between total carotenoids and capsanthin (r = 0.94 ***), β-cryptoxanthin (r = 0.87 ***), and zeaxanthin (r = 0.84 ***). Principal component analysis (PCA) identified two distinct carotenoid groups, accounting for 67.6% of the total variance. A genome-wide association study (GWAS) identified 91 significant single nucleotide polymorphisms (SNPs) associated with fruit color (15 SNPs) and carotenoid content (76 SNPs). These SNPs were distributed across all chromosomes, with varying numbers on each. Among individual carotenoids, α-carotene was associated with 28 SNPs, while other carotenoids showed different numbers of associated SNPs. Candidate genes encoding diverse proteins were identified near significant SNPs, potentially contributing to fruit color variation and carotenoid accumulation. These included pentatricopeptide repeat-containing proteins, mitochondrial proton/calcium exchangers, E3 ubiquitin-protein ligase SINAT2, histone–lysine N-methyltransferase, sucrose synthase, and various enzymes involved in metabolic processes. Seven SNPs exhibited pleiotropic effects on multiple carotenoids, particularly β-cryptoxanthin and capsanthin. The findings of this study provide insights into the genetic architecture of carotenoid biosynthesis and fruit color in peppers, offering valuable resources for targeted breeding programs aimed at enhancing the nutritional and sensory attributes of pepper varieties.

This study was conducted to identify resistant pepper accessions against the destructive disease bacterial wilt (BW) caused by Ralstonia solanacearum. A total of 338 pepper (Capsicum species) germplasms collected from different countries and deposited in the National Agrobiodiversity Genebank, Rural Development Administration (RDA), Republic of Korea, were evaluated. The evaluated accessions comprise samples from five distinct species: Capsicum annuum (213), Capsicum baccatum (47), Capsicum chinense (45), Capsicum frutescens (31), and Capsicum chacoense (2). Disease severity scores were recorded over four consecutive weeks and showed an increase in severity from initial inoculation to the end of the evaluation period. A strong correlation was observed between week 1 and 2, as well as between week 3 and 4. Ten resistant pepper accessions were identified. All selected accessions consistently exhibited low disease scores ranging from 0 to 1 throughout the observation period. These accessions belong to C. chinense (2), C. annuum (6), C. chacoense (1), and C. frutescens (1). Accessions such as IT236738 (C. chinense) and IT283498 (C. chinense) were demonstrated to have high resistance, showing no symptoms over all four weeks. Other accessions belonging to C. annuum (IT247232 and IT236340) and C. chacoense (IT158713) maintained a disease score of 0 (no symptoms) for the first three consecutive weeks; however, they developed symptoms with a score of 1 in the fourth week. Other important characteristics of the resistant materials were evaluated, including carotenoids and fruit characteristics. These accessions have important traits beyond resistance to the destructive pepper disease. They will serve as promising resources for breeding resistant pepper varieties against BW to enhance productivity.

Abstract 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.

This study utilized a diverse Capsicum accessions (5658) sourced from various species and geographical regions, deposited at the National Agrobiodiversity Center, Genebank. We employed 19 SNP markers through a Fluidigm genotyping system and screened these accessions against eight prevalent diseases of pepper. This study revealed accessions resistant to individual diseases as well as those exhibiting resistance to multiple diseases, including bacterial spot, anthracnose, powdery mildew, phytophthora root rot, and potyvirus. The C. chacoense accessions were identified as resistant materials against bacterial spot, anthracnose, powdery mildew, and phytophthora root rot, underscoring the robust natural defense mechanisms inherent in the wild Capsicum species and its potential uses as sources of resistance for breeding. C. baccatum species also demonstrated to be a promising source of resistance to major pepper diseases. Generally, disease-resistant germplasm has been identified from various Capsicum species. Originating from diverse locations such as Argentina, Bolivia, and the United Kingdom, these accessions consistently demonstrated resistance, indicating the widespread prevalence of disease-resistant traits across varied environments. Additionally, we selected ten pepper accessions based on their resistance to multiple diseases, including CMV, Phytophthora root rot, potyviruses, and TSWV, sourced from diverse geographical regions like Hungary, Peru, the United States, and the Netherlands. This comprehensive analysis provides valuable insights into disease resistance in Capsicum, crucial for fostering sustainable agricultural practices and advancing crop improvement through breeding strategies.

Leaf mustard, characterized by its purple/red/green leaves with a green/white midrib, is known for its thick, tender, and spicy leaves with a unique taste and flavor. There were only a few studies reported on leaf mustard for its morphological and biochemical traits from Korea. A total of 355 leaf mustard accessions stored at the GenBank of the National Agrobiodiversity Center were evaluated for 25 agro-morphological traits and seven intact glucosinolates (GSLs). The accessions showed a wide variation in terms of most of the traits. The quantitative agro-morphological traits varied from 16.0 (leaf length) to 48.7% (petiole width) of the coefficient of variation (CV). The highest variation was observed in glucoiberin (299.5%, CV), while the total GSL showed a CV of 66.1%. Sinigrin, followed by gluconapin and gluconasturtiin, was the most abundant GSL, accounting for as high as 75% of the total GSLs, while glucobrassicanapin and glucoiberin were the least abundant, contributing 0.7% and 0.1% on average, respectively. Sinigrin had a positive significant correlation with all GSLs but gluconasturtiin, while glucobarbarin and gluconasturtiin were highly positively correlated to each other, but least correlated with other GSLs. The leaf length was negatively correlated with sinigrin and glucoiberin. The width of the petiole showed a positive correlation with gluconapin, glucobrassicanapin, and glucobrassicin, while the length of the petiole had a negative correlation with sinigrin, glucobrassicanapin, glucoiberin, glucobrassicin, and the total GSLs. A higher width of the midrib was associated with higher contents of gluconapin, glucobrassicanapin, and glucobrassicin. A PCA analysis based on the agro-morphological traits showed that the first and second principal components accounted for 65.2% of the overall variability. Accessions that form a head tend to exhibit a longer leaf length, a larger plant weight, a thicker midrib, and higher widths of the midrib, petiole, and leaf. The GSLs showed inconsistent inter-and intra-leaf variation. Accessions that identified for various traits in their performance, such as, for example, Yeosu66 and IT259487 (highest total glucosinolates) and IT228984 (highest plant weight), would be promising lines for developing new varieties.

Pepper (Capsicum spp.) is one of the most important crops worldwide. The fruits of Capsicum species are known to contain high amounts of vitamins and carotenoids, and they have health-promoting properties. In this study, a total of 513 pepper accessions belonging to two Capsicum species, C. annuum and C. frutescens, were investigated for their morphological characteristics and contents of phytochemicals including carotenoids, β-carotene, vitamin C, capsaicinoids, and total soluble solids. The results revealed wide variations in morphological traits and phytochemical contents between the accessions and across species. In addition, the association of fruit color and orientation with phytochemical contents was evaluated; the results indicated that germplasm with yellow-colored and pendant-oriented fruits could be important due to their high vitamin C levels. Multivariate analysis of the agro-morphological and phytochemical parameters revealed that Capsicum germplasm were clearly distinguished according to species. Furthermore, cluster analysis showed that germplasms belonged to three groups, and six genotypes were determined as being good genetic resources with high health-promoting phytochemical contents. Especially, vitamin C content was positively correlated with fruit diameter, weight, and wall thickness. Our findings revealed morphological and phytochemical characteristics potentially useful for breeding programs.

Rapid changes in agricultural environments caused by global warming pose a major challenge to food production and safety. Common wheat (Triticum aestivum) is a hexaploid plant (AABBDD) that shares large numbers of quantitative traits and resistance genes with B and D genomes of Aegilops species, which are responsible for several metabolic functions and biosynthetic processes, particularly in plant adaptation to biotic as well as abiotic stresses. Comparatively, the abundance of the Aegilops gene pool is much higher than that of Triticum. Therefore, we used four universal DNA barcodes for plants (ITS2, matK, rbcL, and psbM-petN) to construct a phylogenetic tree to classify the genus Aegilops. Fourteen species were distinguished among a total of 17 representative species. Aegilops biuncialis, Aegilops juvenalis, and Aegilops umbellulata could not be grouped into any of the clusters in the phylogenetic tree, indicating that these three species could not be distinguished by four DNA barcodes. Therefore, from 2408 SNPs obtained using genotyping by sequencing (GBS), we manually screened 30 SNPs that could be potentially used to classify these three species. The results of gene flow and genetic differentiation index (Fst) showed that the genetic differentiation among the three species was small, and there was bidirectional horizontal gene transfer between the three species, which was consistent with our results that the three species were difficult to classify by DNA barcode.

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.

Eggplant is one of the most economically and nutritionally important vegetables worldwide. The study of the association of phenotypic traits with genetic factors is vital for the rapid and efficient identification and selection of eggplant genetic resources for breeding purposes with desired traits. The eggplant resources (587) collected from different countries, including Korea, were used for establishing the core collection. A total of 288 accessions were selected from 587 Solanum accessions based on 52 single nucleotide polymorphisms (SNPs) markers together with 17 morphological traits. This core collection was further used to analyze the genetic associations of eggplant morphological variations. A large variation was found among the evaluated eggplant accessions for some agro-morphological traits. Stem prickles and leaf prickles showed a significant positive correlation (r = 0.83***), followed by days to flowering and days to maturity (r = 0.64***). A total of 114,981 SNPs were filtered and used for phylogenetic tree analysis, population structure analysis, and genome-wide association study (GWAS). Among the agro-morphological traits, significantly associated SNPs were found for six traits. A total of 377 significantly associated SNPs with six agro-morphological traits were identified. These six traits and the number of SNPs were: days to maturity (51), flower size (121), fruit width (20), harvest fruit color (42), leaf prickles (38), and stem prickles (105). The largest fraction of significant SNPs (11.94%) was obtained on chromosome Ch01, followed by Ch07 and Ch06 with 11.67% and 10.08%, respectively. This study will help to develop markers linked to the most important agro-morphological traits of eggplant genetic resources and support the selection of desirable traits for eggplant breeding programs.

In this study, 226 Capsicum chinense genetic resources were analyzed using high-performance liquid chromatography and a spectrophotometer to measure and compare their carotenoid content and American Spice Trade Association (ASTA) color values, respectively. The total carotenoid content and ASTA values of the 226 pepper genetic resources were found to be in the range of 7.04–2430.85 mg/100 g dry weight (DW) and 0–221.32, respectively. Capsanthin, capsorubin, lutein, zeaxanthin, antheraxanthin, violaxanthin, α-carotene, β-carotene, and β-cryptoxanthin were the individual carotenoids studied. The average content of each carotenoid (n = 226) in mg/100 g DW was as follows: capsanthin (325.77), antheraxanthin (136.34), capsorubin (82.36), β-carotene (59.11), violaxanthin (46.54), zeaxanthin (43.21), α-carotene (13.91), β-cryptoxanthin (9.67), and lutein (2.72). A strong positive correlation was observed between total carotenoid content and ASTA value (r = 0.965). Likewise, the individual carotenoid content and ASTA value revealed a strong correlation, such as antheraxanthin (r = 0.964), capsanthin (r = 0.946), and capsorubin (r = 0.858). Three genetic resources with a total carotenoid content above 2000 mg/100 g DW were obtained, such as IT261426 (2430.85 mg/100 g DW), IT183657 (2077.55 mg/100 g DW), and IT261213 (2062.54 mg/100 g DW). The findings of this study will assist in the selection of genetic resources with high carotenoid content and ASTA value that can be used to develop and breed new pepper varieties. Also, detailed results of ASTA value correlation with carotenoids in C. chinense genetic resources are provided.

Pepper (Capsicum spp.) fruit-related traits are critical determinants of quality. These traits are controlled by quantitatively inherited genes for which marker-assisted selection (MAS) has proven insufficiently effective. Here, we evaluated the potential of genomic selection, in which genotype and phenotype data for a training population are used to predict phenotypes of a test population with only genotype data, for predicting fruit-related traits in pepper. We measured five fruit traits (fruit length, fruit shape, fruit width, fruit weight, and pericarp thickness) in 351 accessions from the pepper core collection, including 229 Capsicum annuum, 48 Capsicum baccatum, 48 Capsicum chinense, 25 Capsicum frutescens, and 1 Capsicum chacoense in 4 years at two different locations and genotyped these accessions using genotyping-by-sequencing. Among the whole core collection, considering its genetic distance and sexual incompatibility, we only included 302 C. annum complex (229 C. annuum, 48 C. chinense, and 25 C. frutescens) into further analysis. We used phenotypic and genotypic data to investigate genomic prediction models, marker density, and effects of population structure. Among 10 genomic prediction methods tested, Reproducing Kernel Hilbert Space (RKHS) produced the highest prediction accuracies (measured as correlation between predicted values and observed values) across the traits, with accuracies of 0.75, 0.73, 0.84, 0.83, and 0.82 for fruit length, fruit shape, fruit width, fruit weight, and pericarp thickness, respectively. Overall, prediction accuracies were positively correlated with the number of markers for fruit traits. We tested our genomic selection models in a separate population of recombinant inbred lines derived from two parental lines from the core collection. Despite the large difference in genetic diversity between the training population and the test population, we obtained moderate prediction accuracies of 0.32, 0.34, 0.50, and 0.48 for fruit length, fruit shape, fruit width, and fruit weight, respectively. This use of genomic selection for fruit-related traits demonstrates the potential use of core collections and genomic selection as tools for crop improvement.