In this study, molecular-genetic analyses were carried out to identify resistance to yellow rust (Puccinia striiformis f. sp. tritici) in soft wheat (Triticum aestivum L.) samples. Yellow rust is one of the most destructive diseases of wheat worldwide, causing significant yield losses and posing a serious threat to global food security, particularly under changing climatic conditions. The disease is also highly prevalent in Central Asian countries, including Uzbekistan and Tajikistan, where wheat is a staple crop and ensuring stable production is of strategic importance. A total of 68 wheat genotypes were examined and genotyped using 42 highly polymorphic DNA markers. Based on the obtained phenotypic and genotypic data, association analysis was performed using the TASSEL and STRUCTURE programs. To identify genetic associations, GLM (General Linear Model) and MLM (Mixed Linear Model) statistical models were applied. The analysis revealed that the following markers showed significant and reliable associations with yellow rust resistance: Barc0187 (p=0.0040), Gwm340 (p=0.0043), Barc008 (p=0.0132), and Gwm111 (p=0.0147). These markers are recommended as reliable molecular indicators for identifying yellow rust-resistant genotypes and for improving marker-assisted selection (MAS) strategies in future wheat breeding programs.

Black sapote (Diospyros digyna Jacq.) is a fruit that is rich in benefits and has high economic value. However, the sex of this plant is difficult to determine early, and data on the plant is still very limited. This qualitative quantitative research was conducted to identify the genetic diversity of black sapote based on RAPD marker to determine the sex of black sapote plants. The sample used consisted of seven black sapote accessions with sample codes including P, M1, M2, M3, F1, F2, and F3. This research consists of several stages, namely DNA extraction and PCR amplification using six RAPD primers (OPA 02, OPA 05, OPA 08, OPA 09, OPC 09, and OPD 15), including electrophoresis to visualize amplified DNA. Data were analyzed using NTSYS 2.02 software and dendogram were obtained using the UPGMA method in the SAHN function. The results of the analysis showed that the polymorphism resulting from the seven black sapote accessions ranged from 50–80%, with PIC (Polymorphic Information Content) values ranging from 0.28–0.50. The closest related accessions are M1 with F2, while accession P with F2 has the highest genetic diversity. The OPA 02 primer with a band measuring 380 bp can be used as a putative marker in the determination of the female sex and hermaphrodite of black sapote plants.

Genetic diversity among 20 Azerbaijani grape (Vitis vinifera L.) accessions was assessed using 10 Inter-Simple Sequence Repeat (ISSR) markers to elucidate relationships among samples and identify a convenient marker for determining genetic diversity. Based on the polymorphic information parameters such as PIC, EMR, MI, and RP were critically analyzed for utilizing these ISSR primers for genetic variability and 4 ISSR (UBC 811, UBC 812, UBC 815, UBC 857) markers were selected for future germplasm management. The total number of identified bands varied between 2-5. The maximum PIC value was observed in UBC 857 (0.478). Among genotypes, Ag oval kishmish and Yumru kishmish cultivars had the closest genetic similarity index (0.913), while Ag oval kishmish and Marandi, Yerli Muskat and Yabani uzum 1, Yerli Muskat and Yumru kishmish cultivars had the most distant genetic similarity index (0.406). These findings highlight both the complexity of grapevine genetic structure and the value of ISSR markers for detecting non-obvious relationships.

Amylose content is a key factor affecting the eating and cooking qualities of rice. In our previous study, protein disulfide isomerase like 1-1 (PDIL1-1) on chromosome 11 was a candidate gene for amylose content (AC) trait. Based on whole genome sequencing, polymorphisms were identified between Dodamssal and Hwayeong on PDIL1-1. In this study, the association of PDIL1-1 on AC was characterized. Haplotype analysis of 79 KNU accessions highlighted the presence of allelic patterns identifiable by the sequence variants between Dodamssal and Hwayeong. Identified SNPs and InDel were used to develop gene-based molecular markers for PDIL1-1. The 29 F₂ plants and 160 Korean japonica cultivars were classified into two and three groups, respectively, based on the G/A SNP at position -4973180 and ATTCG/G at position -4974161. Our findings revealed that the G/A SNP at position -4973180 of PDIL1-1 plays a role in regulating the AC in japonica rice. This suggested that PDIL1-1 would be useful for fine-tuning the rice AC. To our knowledge, no studies of the allelic variation of the PDIL1-1 gene regulating AC have been reported worldwide. Furthermore, no research had reported the development of PDIL1-1 gene-based molecular markers.

Phytophthora sojae is a soil-borne oomycete that causes both pre- and post-emergence damping-off disease in soybean that are present in poorly drained soils. Phytophthora root and stem rot of soybean has become an emerging threat to soybean production in South Korea as soybean cultivation in paddy fields has increased recently. The cultivar Daewon was identified as a genetic source for resistance to P. sojae isolate 2457; moreover, a 573 kb resistance locus was previously mapped on chromosome 3 via linkage analysis using Daepung × Daewon recombinant inbred line (RIL) population. This study aimed to develop a gene-based molecular marker associated with P. sojae resistance using single nucleotide polymorphisms (SNPs) at this locus. Three sets of single nucleotide amplified polymorphism (SNAP) markers were initially designed based on genic SNPs in the identified genomic region. Of these, the marker SNAP-Set2 successfully worked for allele-specific amplification for the respective Daepung and Daewon, as well as 20 RILs derived from crosses of the two cultivars. To validate this marker, 11 soybean germplasms were randomly selected and genotyped, which resulted in reliable allele-specific amplification that agreed with the 180 K Axiom^® SoyaSNP array data. Phenotypic evaluation of the 20 RILs and the 11 germplasms subsequently demonstrated that Daepung-type and Daewon-type for the SNAP-Set2 are both associated with susceptibility and resistance to P. sojae isolate 2457. The availability of a molecular marker linked to this resistance locus would expedite the use of this valuable resistance allele in soybean breeding programs for increased resistance to P. sojae.

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• Genetic structuring associated with Ganoderma boninense resistance in oil palm revealed by multivariate marker analysis of the EgLCC24 gene
  Rokhana Faizah, Turhadi Turhadi, Delvi Maretta, Sri Wening, Yogesh K. Ahlawat, Ajaya K. Biswal
  Physiological and Molecular Plant Pathology.2026; 144: 103243.     CrossRef
• Identification and genetic analysis of candidate genes for resistance against Phytophthora sojae in soybean using a genome-wide association study
  Hye Rang Park, Su Vin Heo, Beom Kyu Kang, Hyoseob Seo, Eunsoo Lee, Jihee Park, Yun Woo Jang, Jeong Hyun Seo, Girim Park, Jun Hoi Kim, Yeong Hoon Lee, Won Young Han, Myung Chul Seo, Ji-Ung Jeung
  Frontiers in Plant Science.2025;[Epub]     CrossRef
• Development of a molecular marker for the Pi1 gene based on the association of the SNAP protocol with the touch-up gradient amplification method
  Klaus Konrad Scheuermann, Adriana Pereira
  Journal of Microbiological Methods.2023; 214: 106845.     CrossRef

The anaerobic germination 1 (AG1) locus, which confers tolerance to the anaerobic germination of rice seed, has been previously identified and a gel-based InDel DNA marker developed for marker-assisted selection (MAS). However, there is a need for marker development for high-throughput genotyping in order to increase the breeding efficiency. Single nucleotide polymorphisms (SNPs)-based Kompetitive Allele Specific PCR (KASP) markers enable high-accuracy and high-throughput analyses for the genotyping of AG1 locus. In the present study, we developed one AG1 InDel-specific and four flanking KASP markers, which can be used as the foreground and recombination markers, respectively, for the AG1 locus. Of those, three KASP markers developed were validated with Dasan-AG1 (BC₃F₂) segregating lines; the AG1 InDel-specific KASP marker was 100% consistent with the existing AG1 gel-based marker, while the two flanking markers showed 70.3 and 66.7 percent consistency to the AG1 gel-based marker, respectively. In addition, the five KASP markers developed were further used to genotype 78 Korean and 95 foreign rice varieties. The genotyping results with 172 varieties revealed that most of the Korean varieties possessed the AG1 locus; however, a wide variation was observed in the foreign varieties for AG1 locus. Hence, the KASP markers developed for AG1 locus show promise as useful tools for expediting the breeding of varieties tolerant to anaerobic germination stress via high-throughput genotyping.

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• KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance
  Bhawna Dipta, Salej Sood, Vikas Mangal, Vinay Bhardwaj, Ajay Kumar Thakur, Vinod Kumar, Brajesh Singh
  Molecular Biology Reports.2024;[Epub]     CrossRef
• Development and Validation of Kompetitive Allele-Specific Polymerase Chain Reaction Markers for Seed Protein Content in Soybean
  Shuangzhe Li, Chenyijun Guo, Xuezhen Feng, Jing Wang, Wenjing Pan, Chang Xu, Siming Wei, Xue Han, Mingliang Yang, Qingshan Chen, Jinxing Wang, Limin Hu, Zhaoming Qi
  Plants.2024; 13(24): 3485.     CrossRef
• KASP mapping of QTLs for yield components using a RIL population in Basmati rice (Oryza sativa L.)
  Hamza Ashfaq, Reena Rani, Naila Perveen, Allah Ditta Babar, Umer Maqsood, Muhammad Asif, Katherine A. Steele, Muhammad Arif
  Euphytica.2023;[Epub]     CrossRef
• Development of SNP Marker Set to Select Varieties Tolerant to Multiple Abiotic Stresses in Rice
  Jung-Woo Lee, Jung-Seok Oh, Soo-Cheul Yoo
  Plant Breeding and Biotechnology.2023; 11(3): 208.     CrossRef
• Gene-Based Allele Specific Marker for Resistance to Phytophthora sojae in Soybean (Glycine max L.)
  Young Eun Jang, Sungwoo Lee
  Plant Breeding and Biotechnology.2021; 9(2): 164.     CrossRef

Chinese jujube (Ziziphus jujuba Mill.) is an economically important species with over 4,000 years of cultivation history. Cultivar classification and phylogenetic relationship of jujube have been controversial due to the lack of data related to species origin and cultivation. In this study, inter simple sequence repeat (ISSR) markers were used to analyze the genetic characteristics and relationships of Korean and Chinese jujube cultivars. The amplification of genomic DNA of the 32 accessions using 11 primers yielded 149 amplified bands, of which 141 were polymorphic. The amplification of 22 jujube cultivars generated 76 bands, 40 of which were polymorphic, suggesting that many polymorphic bands appeared in the outgroup. The mean genetic similarity index (GSI) of the cultivars was 0.835; Bokjo, Geumseong, Wolchul, and Mudeung cultivars showed the highest GSI of 1, and Sandonglizao and Xiaolizao had the lowest GSI of 0.658. The cluster analysis resolved Indian jujube (Z. mauritiana Lam.) and Paliurus ramosissimus Poir. in a basal Group I, sour jujube 2 (Z. acidojujuba C.Y. Cheng & M.J. Liu) and Damaya formed Group II, Dabailing and Daguazao were clustered in Group III, and the remaining accessions formed Group IV. The Korean cultivars and Korean native varieties showed genetic uniformity and were close to some Chinese cultivars. Accordingly, exploration of domestic and foreign genetic resources should be supplemented with survey of characteristics of collected material for genetic resources management and breeding of elite lines.

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• Genetic diversity analysis of pomelo germplasm resources based on leaf phenotype and SCoT markers
  Xiaoqi Duan, Faisal Hayat, Ziqi Lei, Haocheng Ruan, Wenzhao Lin, Panfeng Tu, Caiqin Li, Wenpei Song, Yongquan Li, Juan Li, Lubin Zhang, Guohua Li, Ruifeng Ma, Wentao Gou, Gensheng Xiao, Qin Wang, Qiansong Wang
  Scientia Horticulturae.2025; 346: 114174.     CrossRef

The SUBMERGENCE 1 (SUB1) locus, conferring tolerance to complete inundation, was identified, and gel-based DNA markers, AEX1 and GnS2, were previously developed for marker-assisted breeding (MAB). However, a high throughput and high specific method, at low cost, is still required to detect Sub1 alleles. Kompetitive Allele Specific PCR (KASP) markers enable high throughput analysis for a large number of seeds, as well as detection of both alleles, in a single reaction. In this study, we developed KASP markers that can distinguish specific alleles at Sub1A loci based on single nucleotide polymorphisms (SNPs). Marker validations were carried out by genotyping of a segregating population with the developed KASP markers. The results from KASP assay and gel-based marker analysis were consistent for Sub1A alleles. KASP markers developed for Sub1A would be helpful due to high accuracy, low cost, and a high throughput genotyping feature in MAB.

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• Identification of KASP-SNP markers correlated with both growth and hypoxia tolerance traits in blunt snout bream (Megalobrama amblycephala)
  Yanluo Zhuo, Han Wang, Guanghai Dong, Huihu Wang, Guodong Zheng, Shuming Zou
  Aquaculture.2025; 608: 742745.     CrossRef
• Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1
  Md Ibrahim Khalil, Md Mahmudul Hassan, Swadesh Chandra Samanta, Abul Kashem Chowdhury, Md Zahid Hassan, Nasar Uddin Ahmed, Uzzal Somaddar, Sharmistha Ghosal, Arif Hasan Khan Robin, Ujjal Kumar Nath, Mohammad Golam Mostofa, David J. Burritt, Chien Van Ha,
  Plant Physiology and Biochemistry.2024; 206: 108224.     CrossRef
• KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance
  Bhawna Dipta, Salej Sood, Vikas Mangal, Vinay Bhardwaj, Ajay Kumar Thakur, Vinod Kumar, Brajesh Singh
  Molecular Biology Reports.2024;[Epub]     CrossRef
• Development of SNP Marker Set to Select Varieties Tolerant to Multiple Abiotic Stresses in Rice
  Jung-Woo Lee, Jung-Seok Oh, Soo-Cheul Yoo
  Plant Breeding and Biotechnology.2023; 11(3): 208.     CrossRef
• Development of Kompetitive Allele Specific PCR Markers for Anaerobic Germination 1 Locus in Rice
  Jung-Woo Lee, Joong Hyoun Chin, Soo-Cheul Yoo
  Plant Breeding and Biotechnology.2021; 9(1): 20.     CrossRef

The
objective
of this study was to develop high-throughput SNP or SNP-based markers by re-sequencing of two peanut cultivars, ‘K-Ol’ and ‘Pungan’. The whole genome re-sequencing for the two cultivars was performed to produce sequences of 35.3 × 10⁹ bp with 350 × 10⁶ reads and 32.0 × 10⁹ bp with 318 × 10⁶ reads, respectively. As compared with the peanut reference genome, the distribution of homozygous and heterozygous SNPs on each chromosome showed very similar patterns between ‘K-Ol’ and ‘Pungan’, and most of them were in intergenic-region regardless of the peanut cultivars and reference genome type. The SNPs identified between the two peanut cultivars were evenly distributed across chromosomes of peanut diploid A and B reference genomes. It indicated that these SNPs could be available to construct a genetic map using the segregating population derived from a cross between ‘K-Ol’ and ‘Pungan’. Total 61 CAPS marker were developed and tested for their availability. Of the CAPS markers, 60 CAPS markers produced normal PCR products and 18 out of them presented polymorphism among 6 peanut varieties. Results of the present study could provide useful genetic resources to facilitate marker-assisted selection for breeding programs as well as germplasm screening for peanut.

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• Optimization of commercial SNP arrays and the generation of a high-efficiency GenoBaits Peanut 10K panel
  Yaran Zhao, Y. M. Nevame Adedze, Jiahui Dong, Renxu Zhang, Songan Zheng, Haofa Lan, Yurong Li, Song Liu, Yanfen Xu, Jianan Zhang
  Scientific Reports.2025;[Epub]     CrossRef
• Identification of QTL Associated With Luteolin Content in Peanut (Arachis hypogaea L.) Shells
  Kunyan Zou, Minjae Choi, Jeong‐Dong Lee, Kyung Do Kim, Hyeon Do Lim, Ki‐Seung Kim, Tae‐Hwan Jun
  Plant Breeding.2025; 144(1): 1.     CrossRef
• Genome-wide association and RNA-seq analyses reveal genes linked to salt stress in peanut (Arachis hypogaea L.)
  Kunyan Zou, Yang Jae Kang, Bo-Keun Ha, Kyung Do Kim, Ki-Seung Kim, Tae-Hwan Jun
  Frontiers in Plant Science.2025;[Epub]     CrossRef
• Designing future peanut: the power of genomics-assisted breeding
  Ali Raza, Hua Chen, Chong Zhang, Yuhui Zhuang, Yasir Sharif, Tiecheng Cai, Qiang Yang, Pooja Soni, Manish K. Pandey, Rajeev K. Varshney, Weijian Zhuang
  Theoretical and Applied Genetics.2024;[Epub]     CrossRef
• Genome-Wide Association Study of Leaf Chlorophyll Content Using High-Density SNP Array in Peanuts (Arachis hypogaea L.)
  Kunyan Zou, Ki-Seung Kim, Dongwoo Kang, Min-Cheol Kim, Jungmin Ha, Jung-Kyung Moon, Tae-Hwan Jun
  Agronomy.2022; 12(1): 152.     CrossRef
• Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.)
  Kunyan Zou, Ki-Seung Kim, Kipoong Kim, Dongwoo Kang, Yu-Hyeon Park, Hokeun Sun, Bo-Keun Ha, Jungmin Ha, Tae-Hwan Jun
  Genes.2020; 12(1): 2.     CrossRef
• Resveratrol, total phenolic and flavonoid contents, and antioxidant potential of seeds and sprouts of Korean peanuts
  Bishnu Adhikari, Sanjeev Kumar Dhungana, Muhammad Waqas Ali, Arjun Adhikari, Il-Doo Kim, Dong-Hyun Shin
  Food Science and Biotechnology.2018; 27(5): 1275.     CrossRef

Resource plants are important and have strong potential for a variety of utilities as crops or pharmaceutical materials. However, most resource plants remain wild and thus their utility for breeding and biotechnology is limited. Molecular markers are useful to initiate genetic study and molecular breeding for these understudied resource plants. We collected various wild collections of Peucedanum japonicum which is indigenous resource plants utilized as oriental medicine and leafy vegetables in Korea. In this study, we produced two independent whole genome sequences (WGSs) from two collections and identified large scale polymorphic simple sequence repeat (pSSR) based on our pipeline to develop SSR markers based on comparison of two WGSs. We identified a total of 452 candidate pSSR contigs. To confirm the accuracy and utility of pSSR, we designed ten SSR primer pairs and successfully applied those to seven collections of P. japonicum. The WGS and pSSR candidates identified in this study will be useful resource for genetic research and breeding purpose for the valuable resource plant, P. japonicum.

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• Complete plastid and 45S rDNA sequences allow authentication of Liriope platyphylla and Ophiopogon japonicus
  Yeonjeong Lee, Hyun-Seung Park, Jae-Hyeon Jeon, Jee Young Park, Seung Hyun Kim, Jungmoo Huh, Sunmin Woo, Do-Won Jeong, Tae-Jin Yang
  Current Plant Biology.2022; 30: 100244.     CrossRef
• De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of Scutellaria L. Species
  Hakjoon Choi, Wan Seok Kang, Jin Seok Kim, Chang-Su Na, Sunoh Kim
  Current Issues in Molecular Biology.2021; 43(3): 2177.     CrossRef

Rice varieties developed through the inter-specific crosses between Asian (Oryza sativa L.) and African cultivated rice (O. glaberrima Steud.) have contributed to yield enhancement of African rice. However, the genetic diversity and genetic structure of the African varieties have rarely been reported. In this study, we characterized 40 rice varieties including rice released in Africa based on eleven yield related agronomic traits and 96 single nucleotide polymorphism (SNP) markers. They were grouped into three categories based on the cluster analysis using agronomic traits. Meanwhile, they were grouped into two distinct clusters, indica- and japonica-type, based on the genetic distance using 96 SNP markers. CG14, which belongs to O. glaberrima, was found to be an admixture type between indica and japonica. The number of secondary branches (SBs) was the only agronomic trait which was significantly different between two groups. The results of this study provide basic agronomic and genomic information of cultivated and tested rice varieties for Africa, that would be helpful for further rice varietal improvement in Africa.

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• Analysis of Agricultural Traits of O. sativa and O. glaberrima under Korean Climatic Conditions
  Jae-Ryoung Park, Hyun-Su Park, Jeonghwan Seo, Chang-Min Lee, Songhee Park, Mina Jin, Keon Mi Lee, Keunpyo Lee, Sukyeung Lee, Ebrima Jallow, O-Young Jeong
  Korean Journal of Breeding Science.2024; 56(2): 97.     CrossRef
• QTL Analysis of Rice Grain Size Using Segregating Populations Derived from the Large Grain Line
  Ja-Hong Lee, Jeonghwan Seo, San Mar Lar, Seong-Gyu Jang, Hongjia Zhang, Ah-Rim Lee, Fang-Yuan Cao, Na-Eun Kim, Joohyun Lee, Soon-Wook Kwon
  Agriculture.2021; 11(6): 565.     CrossRef
• Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding
  Jeonghwan Seo, Gileung Lee, Zhuo Jin, Backki Kim, Joong Hyoun Chin, Hee-Jong Koh
  Molecular Breeding.2020;[Epub]     CrossRef

Miniature transposable elements (mTEs) such as miniature inverted-repeat transposable element (MITE), terminal repeat retrotransposon in miniature, and short interspersed element are exquisite sources for marker development. mTEs are short, non-autonomous and stably inherited. The high-copy members are widely distributed into the gene rich euchromatic regions. Here, we conducted a modified transposon display (TD) for a high-copy MITE family, BraSto-2 (Bs2). The Bs2-specific primers derived from conserved sequences of Bs2 members as well as MseI adapter primers were used for polymerase chain reaction (PCR) in two Brassica rapa accessions, ‘Chiifu’ and ‘Kenshin’. The pooled PCR products were sequenced by Illumina sequencing platform instead of high-resolution gel electrophoresis. Subsequent in silico-based insertion polymorphism (IP) analysis (next-generation sequencing [NGS]-based Bs2 transposon display) was conducted, which generated more than 99 putative polymorphic insertion sites between ‘Chiifu’ and ‘Kenshin’. Among 90 successful PCR amplification, 34 showed Bs2 IP (IP-Bs2) between ‘Chiifu’ and ‘Kenshin’ accessions, 27 and seven ‘Chiifu’- and ‘Kenshin’-unique insertions, respectively. When the 90 IP-Bs2 primer sets were applied to 10 Brassica accessions, including four additional B. rapa and B. oleracea accessions, 69 (76%) showed insertion olymorphism among accessions. The IP-Bs2 were evenly distributed through all the chromosomes and provide rich polymorphism among various B. rapa and B. oleracea accessions demonstrating the usefulness of these markers for various genetic diversity and molecular breeding studies in Brassica. In addition, NGS-based TD will be applicable to various high copy transposable elements family for high throughput and rapid polymorphic marker development which will be helpful for efficient plant genomics and breeding purposes.

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• Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines
  Sampath Perumal, Nomar Espinosa Waminal, Jonghoon Lee, Hyun-Jin Koo, Boem-soon Choi, Jee Young Park, Kyounggu Ahn, Tae-Jin Yang
  Horticultural Plant Journal.2021; 7(6): 539.     CrossRef
• Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding
  Venkatesh, B. Nandini
  Molecular Biology Reports.2020; 47(4): 3155.     CrossRef

Vicia amurensis is a perennial plant found in Northern China, Japan, and Korea that plays an important role in sustainable agricultural practices due to its ability to fix atmospheric nitrogen in a symbiotic association with rhizobia. 454 sequencing technology was used to sequence the V. amurensis transcriptome which yielded 26.41 Mb from 71,197 reads as a result of 24,959 valid singletons. In addition, 1743 contigs, with the largest contig size being 3534, and 26,702 unigenes were detected. The contig distributions in three non-mutually exclusive Gene Ontology classifications and clusters of orthologous gene classes showed that differentially expressed genes were generally overrepresented in general function and prediction alone (176, 14.47%), and posttranslational modifications, protein turnover, chaperones (162, 13.32%). In total, 12,656 single nucleotide polymorphism (SNP) types were detected; these variants contained 10,585 SNPs, 1513 indels and 558 variants involving more than one nucleotide. The 2383 SNP types with high confidence differences were identified. The present study provides invaluable information on the functional genomic resources and future biological research on V. amurensis. The SNPs identified in this study will provide a material basis for future mapping and marker-assisted breeding analyses.