Male sterility is used to mass-produce F₁ hybrid seeds in pepper (Capsicum annuum L.). In particular, the development of genetic male sterility (GMS)-linked molecular markers may play a crucial role in hybrid breeding of pepper. To date, approximately 20 GMS genes have been identified in pepper. Among these, several molecular markers for the ms₃ gene have been developed in previous studies; however, they are not completely linked and thus have limitations for use in selection. Therefore, in the present study, we aimed to develop molecular markers for ms₃ selection using single-nucleotide polymorphism (SNP)-based high-resolution melting (HRM) analysis. Chi-square test was conducted using three F₂ segregating populations, and the results confirmed a 3:1 segregation ratio between male-fertile and male-sterile plants. A total of 128 primer sets were designed by selecting SNPs near the ms₃ gene, and 25 HRM markers were successfully developed. Using 420 individuals from the F₂ segregating population ‘GMS3,’ a high-density genetic linkage map of pepper chromosome 1 was constructed, with eight HRM markers found to be co-segregated with the ms₃ gene. Subsequent experiments using various plant materials validated these eight markers, ultimately identifying two HRM markers, HRM119655681 and HRM135273656, for the final selection. These two markers showed co-segregation between the phenotype and genotype of ms₃ across all plant materials used in the study. The markers developed in this study are expected to be effective for maternal line development and large-scale F₁ hybrid seed production using ms₃ in pepper.

Grape (Vitis vinifera L.) is a perennial fruit tree with high heterozygosity, consisting of 38 chromosomes (2n=38), and it takes a long time for grape seedlings to grow into fruit-bearing trees. Therefore, it is difficult to study grape genetics and breeding strategies. However, it has recently become possible to discover many SNPs through whole genome resequencing or genotyping-by-sequencing (GBS) analysis. In this study, we aimed to develop high-resolution melting (HRM) markers from the detected SNPs and construct a genetic linkage map using HRM markers. In a previous study, 2,553 SNPs were identified using GBS analysis. In this study, 1,336 SNPs were used to design primer sets for HRM analysis. The developed HRM markers were used for construction of a genetic linkage map in an F₁ segregating population consisting of 192 individuals from a cross between ‘Tano Red’ (V. labrusca×V. vinifera) and ‘Ruby Seedless’ (V. vinifera). A total of 805 polymorphic HRM markers were developed, of which 363 were mapped onto the genetic linkage map of grape, with a total length of 1,453.5 cM consisting of 19 chromosomes. This SNP-based genetic linkage map and HRM markers can be used for QTL identification and marker development for important fruit traits of grape.

The color and functionality of paprika fruits (Capsicum annuum L.) are important factors that determine consumption preferences. Paprika contains a large amount of functional phytochemicals, such as carotenoids and polyphenols. In this study, the total polyphenol content by total phenol content (TPC) assay, antioxidant activity by 2,2’-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and ferric reducing antioxidant power (FRAP), and total red pigment content by American spice trade association (ASTA) color were evaluated in a total of 93 commercial cultivars and germplasms of red paprika. In results, the total polyphenol content, antioxidant activity by ABTS and FRAP, and total red pigment content ranged from 6.35-11.84 mg GAE⋅g^-1 dry weight (DW), 19.80-44.84 mg trolox⋅g^-1 DW, 8.82-31.06 mg trolox⋅g^-1 DW, and 5.30-75.03 ASTA value, respectively. For each trait, there were 2, 31, 16, and 44 germplasms, respectively, which were higher than those of the commercial cultivars. The correlation analysis between the total polyphenol content and antioxidant activity (ABTS and FRAP) showed highly positive correlations, with r=0.69 and r=0.75, respectively. In contrast, the ASTA values showed very low negative correlations with ABTS (r=-0.15) and FRAP (r=-0.26). These results imply that the antioxidant activity in paprika was largely affected by the total polyphenol content but was hardly affected by the ASTA value. Accessions 30, 31, and 56 were selected with high red pigment content, and accessions 5, 21, 24, and 26 had high antioxidant activity as well as high polyphenol content. These germplasms will be useful for the development of new paprika varieties with high red pigment content or high antioxidant activity.

The bulb onion (Allium cepa L.), one of the most important vegetables worldwide, contains various functional compounds such as quercetin, allicin, and flavonoids. Red onions are rich in anthocyanins, a flavonoid that is a functional phytochemical with antioxidative and anticancer activities. In the previous study, two quantitative trait loci (QTLs) (qAC4.1 and qAC4.2) controlling the anthocyanin content were identified on chromosome 4 in an F₂ population derived from a cross between A. cepa ‘SP3B’ and ‘H6’. In this study, we developed single nucleotide polymorphism-based high-resolution melting (HRM) markers linked to QTLs qAC4.1 and qAC4.2. In addition, we constructed a new genetic linkage map of chromosome 4 using HRM markers and performed a QTL analysis. The QTL qAC4.1 was false, while qAC4.2 was a major QTL. The QTL peak position, logarithm of the odds value, and phenotypic variance explained of qAC4.2 was 53.6 cM, 7.45, and 22.51%, respectively. Four HRM markers (AC4.2_65336.1_1123-HRM, AC4.2_53230.3_454-HRM, AC4.2_11999.1_756-HRM, and AC4.2_14596.1_345-HRM) within the QTL region of qAC4.2 were developed in this study. The average anthocyanin content of B (homozygous paternal) genotypes was higher than that of A (homozygous maternal) and H (heterozygous) genotypes for all markers. Consequently, these markers will be useful for marker-assisted selection to develop onion cultivars with high anthocyanin content.

Citations

Citations to this article as recorded by  

• Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion
  Yanwei Li, Yumeng Huo, Yanyan Yang, Zhenbao Wang, Yaling Sun, Bingjiang Liu, Xiong Wu
  Frontiers in Plant Science.2023;[Epub]     CrossRef
• Construction of Genetic Linkage Map in Grape ‘Tano Red’ (Vitis labrusca×V. vinifera)בRuby Seedless’ (V. vinifera) F1 Population Using SNP Markers
  Seung Hyeon Joung, Dongjun Im, Youn Young Hur, Jundae Lee
  Korean Journal of Breeding Science.2022; 54(4): 260.     CrossRef
• Development of an In Vivo Bioassay Method on Leaf Blight of Onion Caused by Stemphylium vesicarium
  Jin Ju Lee, Yong Ho Choi, Hun Kim, Jin-Cheol Kim, Gyung Ja Choi
  The Korean Journal of Pesticide Science.2022; 26(1): 83.     CrossRef

Watermelon (Citrullus lanatus) is an economically important vegetable crop all over the world, which has functional compounds such as lycopene and citrulline. Gummy stem blight caused by Didymella bryoniae is one of the most devastative diseases in watermelon. Single nucleotide polymorphisms (SNPs), which are genetic variations occurring between individuals with respect to a single base, were often used to construct genetic linkage maps and develop molecular markers linked to a variety of horticultural traits and resistance to several diseases. In this study, we developed high-resolution melting (HRM) markers based on SNPs generated from NGS resequencing of two parents in watermelon. Plant materials were C. lanatus ‘920533’ (female and susceptible parent), C. amarus ‘PI 189225’ (male and resistant parent), and their F₁ and F₂ progenies. A total of 13.6 Gbp (‘920533’) and 13.1 Gbp (‘PI 189225’) of genomic sequences were obtained using NGS analysis. A total of 6.09 million SNPs between ‘920533’ and ‘PI 189225’ were detected, and 354,860 SNPs were identified as potential HRM primer sets. From these, a total of 330 primer sets for HRM analysis were designed. As a result, a total of 61 HRM markers that have polymorphic melting curves were developed. These HRM markers can be used for the construction of SNP-based linkage maps and for the analysis of quantitative trait loci (QTLs) related to gummy stem blight resistance.

Citations

Citations to this article as recorded by  

• Development of gene-based markers for black fruit color traits based on GBS-GWAS analysis of tomato germplasms
  Yeweon An, Jaegyun An, Yongtaek Jeon, Yunjeong Park, Hyunhee An, Bohyun Ki, Yeonhee Choi, Jonggwon Song, Jundae Lee
  Horticulture, Environment, and Biotechnology.2025; 66(6): 1675.     CrossRef
• Identification of a novel locus C2 controlling canary yellow flesh color in watermelons
  Girim Park, Durre Shahwar, Gaeun Jang, Jagyeong Shin, Gibeom Kwon, Younjae Kim, Chang Oh Hong, Bingkui Jin, Hoytaek Kim, Oakjin Lee, Younghoon Park
  Frontiers in Genetics.2023;[Epub]     CrossRef
• QTL Mapping for Gummy Stem Blight Resistance in Watermelon (Citrullus spp.)
  Eun Su Lee, Do-Sun Kim, Sang Gyu Kim, Yun-Chan Huh, Chang-Gi Back, Ye-Rin Lee, Muhammad Irfan Siddique, Koeun Han, Hye-Eun Lee, Jundae Lee
  Plants.2021; 10(3): 500.     CrossRef
• Characterization of Watermelon (Citrullus lanatus) Accessions Introduced from USDA
  Kyung Jun Lee, Jung-Ro Lee, Gyu-Taek Cho, Myoung-Jae Shin, Seong-Hoon Kim, Sookyeong Lee, Sea-Hee Han, Do Yoon Hyun
  Korean Journal of Breeding Science.2019; 51(4): 357.     CrossRef

Crown rot caused by Phytophthora cactorum is one of several serious, widespread diseases that cause problems in strawberry (Fragaria × ananassa Duch.) cultivation. In this study, we aimed to identify a strawberry resistant to P. cactorum through bioassay. A total of 104 wild and cultivated strawberry accessions, including ‘Sulhyang’ and ‘Akihime’, were inoculated with an isolate of P. cactorum, ‘PC151111’. A zoospore suspension was used with a density of approximately 10⁶ zoospores·mL^-1. Three strawberry seedlings were tested three times independently. The disease index was scored on a scale from 0–4 through symptom observation while the inoculated plants were incubated at 25±3°C under 16 h/8 h (light/dark) conditions for three weeks. The results showed that the mean disease index varied from 0.78–3.78, and the ‘Pechika’ and ‘Kaorino’ cultivars were highly resistant to P. cactorum, with mean disease indexes of 0.78 and 0.89, respectively. These cultivars will be useful resources in breeding strawberries resistant to crown rot.

An allo-octoploid strawberry (Fragaria × ananassa Duch.) is one of the most important vegetable crops in Korea. However, there were few genomic researches of strawberry due to polyploidy and complexity of its genome. In this study, we aimed to construct a genetic linkage map of strawberry using single nucleotide polymorphism (SNP) markers that were developed through a next-generation sequencing (NGS) analysis. Two strawberry varieties, ‘Sulhyang’ and ‘Senga-sengana’, were used as a maternal and a paternal parent, respectively, and their F1 generation consisting of 94 individuals was used for construction of a genetic linkage map. A total of 19.0 Gbp (‘Sulhyang’) and 21.8 Gbp (‘Senga-sengana’) of genomic sequences were obtained through NGS analysis. Subsequently, approximately 87,000 SNPs were identified and 1,154 primer sets for high-resolution melting (HRM) analysis were designed through bioinformatic analysis. In result, a total of 224 polymorphic HRM markers were developed and 205 markers were mapped on the genetic linkage map of strawberry, which total length was 800.8 cM and the number of linkage groups were 30. This SNP-based genetic linkage map and the 224 SNP markers will be very helpful for the genomic and genetic researches of allo-octoploid strawberry.

Citations

Citations to this article as recorded by  

• Phenotypic Characteristics of Quantitative Traits in an Everbearing Strawberry F₁ Population
  Iyeong Choi, Young Hun Lee
  Plant Breeding and Biotechnology.2025;[Epub]     CrossRef
• QTL Mapping for Resistance to Bacterial Wilt Caused by Two Isolates of Ralstonia solanacearum in Chili Pepper (Capsicum annuum L.)
  Saeyoung Lee, Nidhi Chakma, Sunjeong Joung, Je Min Lee, Jundae Lee
  Plants.2022; 11(12): 1551.     CrossRef
• Chromosome Level Assembly of Homozygous Inbred Line ‘Wongyo 3115’ Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)
  Hye-Eun Lee, Abinaya Manivannan, Sun Yi Lee, Koeun Han, Jun-Geol Yeum, Jinkwan Jo, Jinhee Kim, Il Rae Rho, Ye-Rin Lee, Eun Su Lee, Byoung-Cheorl Kang, Do-Sun Kim
  Frontiers in Plant Science.2021;[Epub]     CrossRef
• A pentaploid-based linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination
  Thomas M. Davis, Yilong Yang, Lise L. Mahoney, Daniel C. Frailey
  Horticulture Research.2020;[Epub]     CrossRef
• Diallelic SNP marker development and genetic linkage map construction in octoploid strawberry (Fragaria × ananassa) through next-generation resequencing and high-resolution melting analysis
  Ye Rin Lee, Jinhee Kim, Sun Yi Lee, Jundae Lee
  Horticulture, Environment, and Biotechnology.2020; 61(2): 371.     CrossRef
• Identification of QTLs Controlling α-Glucosidase Inhibitory Activity in Pepper (Capsicum annuum L.) Leaf and Fruit Using Genotyping-by-Sequencing Analysis
  Doie Park, Geleta Dugassa Barka, Eun-Young Yang, Myeong-Cheoul Cho, Jae Bok Yoon, Jundae Lee
  Genes.2020; 11(10): 1116.     CrossRef
• High density linkage map construction and QTL mapping for runner production in allo-octoploid strawberry Fragaria × ananassa based on ddRAD-seq derived SNPs
  Mohammad Rashed Hossain, Sathishkumar Natarajan, Hoy-Taek Kim, Denison Michael Immanuel Jesse, Cheol-Gyu Lee, Jong-In Park, Ill-Sup Nou
  Scientific Reports.2019;[Epub]     CrossRef