著者

Kenta Shirasawa Daijiro Harada Hideki Hirakawa Sachiko Isobe Chittaranjan Kole

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20146, (Released:2021-04-06)

被引用文献数

20

---

Genome sequence analysis in higher plants began with the whole-genome sequencing of Arabidopsis thaliana. Owing to the great advances in sequencing technologies, also known as next-generation sequencing (NGS) technologies, genomes of more than 300 plant species have been sequenced to date. Long-read sequencing technologies, together with sequence scaffolding methods, have enabled the synthesis of chromosome-level de novo genome sequence assemblies, which has further allowed comparative analysis of the structural features of multiple plant genomes, thus elucidating the evolutionary history of plants. However, the quality of the assembled chromosome-level sequences varies among plant species. In this review, we summarize the status of chromosome-level assemblies of 114 plant species, with genome sizes ranging from 125 Mb to 16.9 Gb. While the average genome coverage of the assembled sequences reached up to 88.7%, the average coverage of chromosome-level pseudomolecules was 72.9%. Thus, further improvements in sequencing technologies and scaffolding, and data analysis methods, are required to establish gap-free telomere-to-telomere genome sequence assemblies. With the forthcoming new technologies, we are going to enter into a new genomics era where pan-genomics and the >1,000 or >1 million genomes’ project will be routine in higher plants.

著者

Yusaku Uga

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20118, (Released:2021-01-06)

被引用文献数

41

---

Roots are essential organs for capturing water and nutrients from the soil. In particular, root system architecture (RSA) determines the extent of the region of the soil where water and nutrients can be gathered. As global climate change accelerates, it will be important to improve belowground plant parts, as well as aboveground ones, because roots are front-line organs in the response to abiotic stresses such as drought, flooding, and salinity stress. However, using conventional breeding based on phenotypic selection, it is difficult to select breeding lines possessing promising RSAs to adapted to abiotic stress because roots remain hidden underground. Therefore, new breeding strategies that do not require phenotypic selection are necessary. Recent advances in molecular biology and biotechnology can be applied to the design-oriented breeding of RSA without phenotypic selection. Here I summarize recent progress in RSA ideotypes as “design” and RSA-related gene resources as “materials” that will be needed in leveraging these technologies for the RSA breeding. I also highlight the future challenges to design-oriented breeding of RSA and explore solutions to these challenges.

著者

Shota Teramoto Yusaku Uga

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.21053, (Released:2022-02-09)

被引用文献数

7

---

Root system architecture (RSA) determines unevenly distributed water and nutrient availability in soil. Genetic improvement of RSA, therefore, is related to crop production. However, RSA phenotyping has been carried out less frequently than above-ground phenotyping because measuring roots in the soil is difficult and labor intensive. Recent advancements have led to the digitalization of plant measurements; this digital phenotyping has been widely used for measurements of both above-ground and RSA traits. Digital phenotyping for RSA is slower and more difficult than for above-ground traits because the roots are hidden underground. In this review, we summarized recent trends in digital phenotyping for RSA traits. We classified the sample types into three categories: soil block containing roots, section of soil block, and root sample. Examples of the use of digital phenotyping are presented for each category. We also discussed room for improvement in digital phenotyping in each category.

著者

Yu Takahashi Hiroo Nasu Seiji Nakayama Norihiko Tomooka

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.22074, (Released:2023-04-27)

被引用文献数

3

---

Domestication of azuki bean and soybean has enabled them to acquire non-dormant seeds, non-shattering pods, and larger seed size. Seed remains of the Jomon period recently discovered at archeological sites in the Central Highlands of Japan (6,000–4,000 BP) suggest that the use of azuki bean and soybean and their increase in seed size began earlier in Japan than in China and Korea; molecular phylogenetic studies indicate that azuki bean and soybean originated in Japan. Recent identification of domestication genes indicate that the domestication traits of azuki bean and soybean were established by different mechanisms. Analyses of domestication related genes using DNA extracted from the seed remains would reveal further details about their domestication processes.

著者

Yusaku Noda Ryohei Sugita Atsushi Hirose Naoki Kawachi Keitaro Tanoi Jun Furukawa Ken Naito

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.72, no.4, pp.326-331, 2022 (Released:2022-11-05)

参考文献数

16

被引用文献数

6

---

Wild species in the genus Vigna are a great resource of tolerance to various stresses including salinity. We have previously screened the genetic resources of the genus Vigna and identified several accessions that have independently evolved salt tolerance. However, many aspects of such tolerance have remained unknown. Thus, we used autoradiography with radioactive sodium (22Na+) and Inductively Coupled Plasma Mass Spectrometry (ICP-MS) to visualize and compare Na+ allocation in Vigna angularis (Willd.) Ohwi & H.Ohashi (azuki bean), Vigna nakashimae (Ohwi) Ohwi & H.Ohashi, Vigna riukiuensis (Ohwi) Ohwi & H.Ohashi, Vigna luteola (Jacq.) Benth. and Vigna marina (Burm.) Merr.. The results indicated: 1) Tolerant accessions suppress Na+ accumulation compared to azuki bean. 2) V. nakashimae and V. marina does so by accumulating higher amount of K+, whereas V. riukiuensis and V. luteola does so by other mechanisms. 3) V. luteola avoids salt-shedding by allocating excess Na+ to newly expanded leaves. As the mechanisms of the tolerant species were different, they could be piled up in a single crop via classical breeding or by genetic engineering or genome editing.

著者

Kenji Fujino Yoshihiro Kawahara Kanako O. Koyanagi Kenta Shirasawa

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20089, (Released:2021-02-17)

被引用文献数

8

---

Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and FST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido.

著者

Al Imran Malik Pasajee Kongsil Vũ Anh Nguyễn Wenjun Ou Sholihin Pao Srean MN Sheela Luis Augusto Becerra López-Lavalle Yoshinori Utsumi Cheng Lu Piya Kittipadakul Hữu Hỷ Nguyễn Hernan Ceballos Trọng Hiển Nguyễn Michael Selvaraj Gomez Pornsak Aiemnaka Ricardo Labarta Songbi Chen Suwaluk Amawan Sophearith Sok Laothao Youabee Motoaki Seki Hiroki Tokunaga Wenquan Wang Kaimian Li Hai Anh Nguyễn Văn Đồng Nguyễn Lê Huy Hàm Manabu Ishitani

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.18180, (Released:2020-03-05)

被引用文献数

70

---

In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIs), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha–1 in 1996 to 21.3 t ha–1 in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.

著者

Ken Kuroki Kai Yan Hiroyoshi Iwata Kentaro K. Shimizu Toshiaki Tameshige Shuhei Nasuda Wei Guo

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.72, no.1, pp.66-74, 2022 (Released:2022-03-08)

参考文献数

28

---

Phenotyping is a critical process in plant breeding, especially when there is an increasing demand for streamlining a selection process in a breeding program. Since manual phenotyping has limited efficiency, high-throughput phenotyping methods are recently popularized owing to progress in sensor and image processing technologies. However, in a size-limited breeding field, which is common in Japan and other Asian countries, it is challenging to introduce large machinery in the field or fly unmanned aerial vehicles over the field. In this study, we developed a ground-based high-throughput field phenotyping rover that could be easily introduced to a field regardless of the scale and location of the field even without special facilities. We also made the field rover open-source hardware, making its system available to public for easy modification, so that anyone can build one for their own use at a low cost. The trial run of the field rover revealed that it allowed the collection of detailed remote-sensing images of plants and quantitative analyses based on the images. The results suggest that the field rover developed in this study could allow efficient phenotyping of plants especially in a small breeding field.

著者

蓬原 雄三 鳥山 国士 角田 公正

出版者

Japanese Society of Breeding

雑誌

育種学雑誌 (ISSN:05363683)

巻号頁・発行日

vol.17, no.2, pp.85-90, 1967-06-25 (Released:2008-05-16)

参考文献数

9

被引用文献数

19 20

---

A new rice variety "Reimei" was obtained by gamma-ray irradiation of seed of "Fujiminori", a leading variety with long culm in north-eastern district of Japan. This new mutant variety has a characteristic of short culm, reduced by approximately 15cm as compared with the original variety.

著者

Satoshi Natsume Kaori Oikawa Chihiro Nomura Kazue Ito Hiroe Utsushi Motoki Shimizu Ryohei Terauchi Akira Abe

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.73, no.4, pp.415-420, 2023 (Released:2023-10-03)

参考文献数

19

---

DNA markers are indispensable tools in genetics and genomics research as well as in crop breeding, particularly for marker-assisted selection. Recent advances in next-generation sequencing technology have made it easier to obtain genome sequences for various crop species, enabling the large-scale identification of DNA polymorphisms among varieties, which in turn has made DNA marker design more accessible. However, existing primer design software is not suitable for designing many types of genome-wide DNA markers from next-generation sequencing data. Here, we describe the development of V-primer, high-throughput software for designing insertion/deletion, cleaved amplified polymorphic sequence, and single-nucleotide polymorphism (SNP) markers. We validated the applicability of these markers in different crops. In addition, we performed multiplex PCR targeted amplicon sequencing using SNP markers designed with V-primer. Our results demonstrate that V-primer facilitates the efficient and accurate design of primers and is thus a useful tool for genetics, genomics, and crop breeding. V-primer is freely available at https://github.com/ncod3/vprimer.

著者

Hideki Takanashi

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.73, no.1, pp.57-69, 2023 (Released:2023-04-15)

参考文献数

121

被引用文献数

6

---

Global climate change and global warming, coupled with the growing population, have raised concerns about sustainable food supply and bioenergy demand. Sorghum [Sorghum bicolor (L.) Moench] ranks fifth among cereals produced worldwide; it is a C4 crop with a higher stress tolerance than other major cereals and has a wide range of uses, such as grains, forage, and biomass. Therefore, sorghum has attracted attention as a promising crop for achieving sustainable development goals (SDGs). In addition, sorghum is a suitable genetic model for C4 grasses because of its high morphological diversity and relatively small genome size compared to other C4 grasses. Although sorghum breeding and genetic studies have lagged compared to other crops such as rice and maize, recent advances in research have identified several genes and many quantitative trait loci (QTLs) that control important agronomic traits in sorghum. This review outlines traits and genetic information with a focus on morphogenetic aspects that may be useful in sorghum breeding for grain and biomass utilization.

著者

Hiroshi Hisano Fumitaka Abe Robert E. Hoffie Jochen Kumlehn

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.21019, (Released:2021-08-27)

被引用文献数

14

---

The recent advent of customizable endonucleases has led to remarkable advances in genetic engineering, as these molecular scissors allow for the targeted introduction of mutations or even precisely predefined genetic modifications into virtually any genomic target site of choice. Thanks to its unprecedented precision, efficiency, and functional versatility, this technology, commonly referred to as genome editing, has become an effective force not only in basic research devoted to the elucidation of gene function, but also for knowledge-based improvement of crop traits. Among the different platforms currently available for site-directed genome modifications, RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) endonucleases have proven to be the most powerful. This review provides an application-oriented overview of the development of customizable endonucleases, current approaches to cereal crop breeding, and future opportunities in this field.

著者

Yoshihiro Kawahara Tomoko Endo Mitsuo Omura Yumiko Teramoto Takeshi Itoh Hiroshi Fujii Takehiko Shimada

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.19097, (Released:2020-03-05)

被引用文献数

10

---

Citrus species are some of the most valuable and widely consumed fruits globally. The genome sequences of representative citrus (e.g., Citrus clementina, C. sinensis, C. grandis) species have been released but the research base for mandarin molecular breeding is still poor. We assembled the genomes of Citrus unshiu and Poncirus trifoliata, two important species for citrus industry in Japan, using hybrid de novo assembly of Illumina and PacBio sequence data, and developed the Mikan Genome Database (MiGD). The assembled genome sizes of C. unshiu and P. trifoliata are 346 and 292 Mb, respectively, similar to those of citrus species in public databases; they are predicted to possess 41,489 and 34,333 protein-coding genes in their draft genome sequences, with 9,642 and 8,377 specific genes when compared to C. clementina, respectively. MiGD is an integrated database of genome annotation, genetic diversity, and Cleaved Amplified Polymorphic Sequence (CAPS) marker information, with these contents being mutually linked by genes. MiGD facilitates access to genome sequences of interest from previously reported linkage maps through CAPS markers and obtains polymorphism information through the multiple genome browser TASUKE. The genomic resources in MiGD (https://mikan.dna.affrc.go.jp) could provide valuable information for mandarin molecular breeding in Japan.

著者

Kotaro Akai Kenji Asano Chika Suzuki Etsuo Shimosaka Seiji Tamiya Takako Suzuki Toru Takeuchi Takehiro Ohki

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.73, no.2, pp.168-179, 2023 (Released:2023-06-06)

参考文献数

62

被引用文献数

2

---

The isolation of disease resistance genes introduced from wild or related cultivated species is essential for understanding their mechanisms, spectrum and risk of breakdown. To identify target genes not included in reference genomes, genomic sequences with the target locus must be reconstructed. However, de novo assembly approaches of the entire genome, such as those used for constructing reference genomes, are complicated in higher plants. Moreover, in the autotetraploid potato, the heterozygous regions and repetitive structures located around disease resistance gene clusters fragment the genomes into short contigs, making it challenging to identify resistance genes. In this study, we report that a de novo assembly approach of a target gene-specific homozygous dihaploid developed through haploid induction was suitable for gene isolation in potatoes using the potato virus Y resistance gene Rychc as a model. The assembled contig containing Rychc-linked markers was 3.3 Mb in length and could be joined with gene location information from the fine mapping analysis. Rychc was successfully identified in a repeated island located on the distal end of the long arm of chromosome 9 as a Toll/interleukin-1 receptor-nucleotide-binding site-leucine rich repeat (TIR-NBS-LRR) type resistance gene. This approach will be practical for other gene isolation projects in potatoes.

著者

Wakana Tanaka Takaki Yamauchi Katsutoshi Tsuda

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.73, no.1, pp.3-45, 2023 (Released:2023-04-15)

参考文献数

422

被引用文献数

13

---

The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.

著者

Ayumi Agata Motoyuki Ashikari Yutaka Sato Hidemi Kitano Tokunori Hobo

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.73, no.1, pp.86-94, 2023 (Released:2023-04-15)

参考文献数

34

被引用文献数

1

---

Rice panicle architecture displays remarkable diversity in branch number, branch length, and grain arrangement; however, much remains unknown about how such diversity in patterns is generated. Although several genes related to panicle branch number and panicle length have been identified, how panicle branch number and panicle length are coordinately regulated is unclear. Here, we show that panicle length and panicle branch number are independently regulated by the genes Prl5/OsGA20ox4, Pbl6/APO1, and Gn1a/OsCKX2. We produced near-isogenic lines (NILs) in the Koshihikari genetic background harboring the elite alleles for Prl5, regulating panicle rachis length; Pbl6, regulating primary branch length; and Gn1a, regulating panicle branching in various combinations. A pyramiding line carrying Prl5, Pbl6, and Gn1a showed increased panicle length and branching without any trade-off relationship between branch length or number. We successfully produced various arrangement patterns of grains by changing the combination of alleles at these three loci. Improvement of panicle architecture raised yield without associated negative effects on yield-related traits except for panicle number. Three-dimensional (3D) analyses by X-ray computed tomography (CT) of panicles revealed that differences in panicle architecture affect grain filling. Importantly, we determined that Prl5 improves grain filling without affecting grain number.

著者

Yusaku Noda Ryohei Sugita Atsushi Hirose Naoki Kawachi Keitaro Tanoi Jun Furukawa Ken Naito

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.22012, (Released:2022-08-30)

被引用文献数

6

---

Wild species in the genus Vigna are a great resource of tolerance to various stresses including salinity. We have previously screened the genetic resources of the genus Vigna and identified several accessions that have independently evolved salt tolerance. However, many aspects of such tolerance have remained unknown. Thus, we used autoradiography with radioactive sodium (22Na+) and Inductively Coupled Plasma Mass Spectrometry (ICP-MS) to visualize and compare Na+ allocation in Vigna angularis (Willd.) Ohwi & H.Ohashi (azuki bean), Vigna nakashimae (Ohwi) Ohwi & H.Ohashi, Vigna riukiuensis (Ohwi) Ohwi & H.Ohashi, Vigna luteola (Jacq.) Benth. and Vigna marina (Burm.) Merr.. The results indicated: 1) Tolerant accessions suppress Na+ accumulation compared to azuki bean. 2) V. nakashimae and V. marina does so by accumulating higher amount of K+, whereas V. riukiuensis and V. luteola does so by other mechanisms. 3) V. luteola avoids salt-shedding by allocating excess Na+ to newly expanded leaves. As the mechanisms of the tolerant species were different, they could be piled up in a single crop via classical breeding or by genetic engineering or genome editing.

著者

Koji Noshita Hidekazu Murata Shiryu Kirie

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.21078, (Released:2022-02-17)

被引用文献数

3

---

The morphological traits of plants contribute to many important functional features such as radiation interception, lodging tolerance, gas exchange efficiency, spatial competition between individuals and/or species, and disease resistance. Although the importance of plant phenotyping techniques is increasing with advances in molecular breeding strategies, there are barriers to its advancement, including the gap between measured data and phenotypic values, low quantitativity, and low throughput caused by the lack of models for representing morphological traits. In this review, we introduce morphological descriptors that can be used for phenotyping plant morphological traits. Geometric morphometric approaches pave the way to a general-purpose method applicable to single units. Hierarchical structures composed of an indefinite number of multiple elements, which is often observed in plants, can be quantified in terms of their multi-scale topological characteristics using topological data analysis. Theoretical morphological models capture specific anatomical structures, if recognized. These morphological descriptors provide us with the advantages of model-based plant phenotyping, including robust quantification of limited datasets. Moreover, we discuss the future possibilities that a system of model-based measurement and model refinement would solve the lack of morphological models and the difficulties in scaling out the phenotyping processes.

著者

Hirokazu Takahashi Christophe Pradal

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.71, no.1, pp.109-116, 2021 (Released:2021-02-25)

参考文献数

68

被引用文献数

30

---

As plants cannot relocate, they require effective root systems for water and nutrient uptake. Root development plasticity enables plants to adapt to different environmental conditions. Research on improvements in crop root systems is limited in comparison with that in shoots as the former are difficult to image. Breeding more effective root systems is proposed as the “second green revolution”. There are several recent publications on root system architecture (RSA), but the methods used to analyze the RSA have not been standardized. Here, we introduce traditional and current root-imaging methods and discuss root structure phenotyping. Some important root structures have not been standardized as roots are easily affected by rhizosphere conditions and exhibit greater plasticity than shoots; moreover, root morphology significantly varies even in the same genotype. For these reasons, it is difficult to define the ideal root systems for breeding. In this review, we introduce several types of software to analyze roots and identify important root parameters by modeling to simplify the root system characterization. These parameters can be extracted from photographs captured in the field. This modeling approach is applicable to various legacy root data stored in old or unpublished formats. Standardization of RSA data could help estimate root ideotypes.

著者

Katsuhiko Sumitomo Kenta Shirasawa Sachiko N. Isobe Hideki Hirakawa Akiho Harata Masato Kawabe Masafumi Yagi Masaaki Osaka Miyuki Kunihisa Fumiya Taniguchi

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20063, (Released:2021-03-25)

被引用文献数

6

---

White rust caused by Puccinia horiana Henn. adversely affects chrysanthemum (Chrysanthemum morifolium Ramat.) production. The breeding of resistant varieties is effective in controlling the disease. Here we aimed to develop DNA markers for the strong resistance to P. horiana. We conducted a linkage analysis based on the genome-wide association study (GWAS) method. We employed a biparental population for the GWAS, wherein the single nucleotide polymorphism (SNP) allele frequency could be predicted. The population was derived from crosses between a strong resistant “Southern Pegasus” and a susceptible line. The GWAS used simplex and double-simplex SNP markers selected out of SNP candidates mined from ddRAD-Seq data of an F1 biparental population. These F1 individuals segregated in a 1:1 ratio of resistant to susceptible. Twenty-one simplex SNPs were significantly associated with P. horiana resistance in “Southern Pegasus” and generated one linkage group. These results show the presence of a single resistance gene in “Southern Pegasus”. We identified the nearest SNP marker located 2.2 cM from P. horiana resistance locus and demonstrated this SNP marker-resistance link using an independent population. This is the first report of an effective DNA marker linked to a gene for P. horiana resistance in chrysanthemum.