Breeding Science最新文献_第3页

Identification of an early-heading mutant in Indonesian native rice cultivar: 'Gemdjah Beton-10'. 印度尼西亚本地水稻品种‘吉吉-白顿-10’早抽穗突变体的鉴定。

IF 1.7 4区农林科学

Breeding Science Pub Date : 2025-12-01 Epub Date: 2025-11-01 DOI: 10.1270/jsbbs.25024

Asanga D Nagalla, Ryouhei Morita, Hiroyuki Ichida, Yoriko Hayashi, Yuki Shirakawa, Kazuki Ohshiro, Tadashi Sato, Yoshimichi Fukuta, Kinya Toriyama, Hiroki Saito, Yutaka Okumoto, Tomoko Abe

{"title":"Identification of an early-heading mutant in Indonesian native rice cultivar: 'Gemdjah Beton-10'.","authors":"Asanga D Nagalla, Ryouhei Morita, Hiroyuki Ichida, Yoriko Hayashi, Yuki Shirakawa, Kazuki Ohshiro, Tadashi Sato, Yoshimichi Fukuta, Kinya Toriyama, Hiroki Saito, Yutaka Okumoto, Tomoko Abe","doi":"10.1270/jsbbs.25024","DOIUrl":"10.1270/jsbbs.25024","url":null,"abstract":"Rice is one of the world's most widely cultivated field crops and a short-day adapted plant. It possesses a complex genetic regulatory mechanism for heading date determination. Gemdjah Beton (GB) is an Indonesian rice cultivar that takes approximately 17 weeks to flower after being transplanted into a rice field in Japan. We isolated early-heading mutant line GB-10 (flowers around two to three weeks earlier than GB in the field). Under long-day (LD) conditions, GB-10 flowered approximately two weeks earlier than GB. Under short-day conditions, the heading date between GB-10 and GB plants shows no apparent difference. In agreement with the heading date, Hd3a and RFT1 expressions show around a 10-time relative transcript quantity difference under LD conditions in GB-10 compared to GB. Interestingly, Ghd7 expression was significantly reduced in GB-10, which may trigger the Hd3a and RFT1 activation. A bulk segregation analysis indicated that a single nucleotide variant on chromosome 7 was genetically linked to the early heading phenotype of GB-10 lines. Taken together, we reported the successful isolation of GB-10 as an early-heading mutant.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 5","pages":"412-420"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13129580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Low amylose content in rice lowac2 mutant is caused by a new allele of C₂H₂ zinc-finger protein that regulates pre-mRNA splicing of Wx^b. 水稻lowac2突变体直链淀粉含量低是由C2H2锌指蛋白的一个新等位基因引起的，该等位基因调节Wxb的pre-mRNA剪接。

IF 1.7 4区农林科学

Breeding Science Pub Date : 2025-12-01 Epub Date: 2025-11-01 DOI: 10.1270/jsbbs.25037

Rina Sakaguchi, Yuko Kozakura, Koume Monma, Naoko Crofts, Hiroyuki Ito, Dong-Jin Kang, Shigeki Hamada

{"title":"Low amylose content in rice lowac2 mutant is caused by a new allele of C2H2 zinc-finger protein that regulates pre-mRNA splicing of Wxb.","authors":"Rina Sakaguchi, Yuko Kozakura, Koume Monma, Naoko Crofts, Hiroyuki Ito, Dong-Jin Kang, Shigeki Hamada","doi":"10.1270/jsbbs.25037","DOIUrl":"10.1270/jsbbs.25037","url":null,"abstract":"The isolated rice mutant, designated lowac2, exhibited low amylose content. Whole-genome resequencing and single-nucleotide polymorphism (SNP) fragment analysis revealed that a mutation in the gene encoding the C2H2 zinc-finger protein in the long-arm terminal of Chromosome 6 was responsible for this low amylose phenotype. An SNP from G to A was observed in the 5' splice junction of intron11, resulting in the production of a protein lacking the C-terminal. Mutation of the C2H2 zinc-finger protein specifically affected the splicing efficiency of intron1 in Waxyb (Wxb ). This reduced the levels of granule-bound starch synthase I, which is encoded by Wxb . Mutations in lowac2 increased the mRNA expression levels of several starch biosynthetic enzymes, especially starch synthase IIa and starch branching enzyme I. This was consistent with the presence of amylopectin with reduced short glucan chains in lowac2 seeds compared to wild-type seeds. Furthermore, the crossed lines possessing a gene combination between Wxa from indica variety and lowac2 also showed a decrease in amylose content and Wxa expression; however, this did not affect splicing in Wxa . The new allele of the C2H2 zinc-finger protein found in this study affects both Wx genes differently.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 5","pages":"421-429"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13129570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification and characterization of QTLs for brown planthopper resistance from wild rice, Oryza rufipogon. 野生稻抗褐飞虱qtl的鉴定与鉴定。

IF 1.7 4区农林科学

Breeding Science Pub Date : 2025-12-01 Epub Date: 2025-11-21 DOI: 10.1270/jsbbs.25027

Hoang Nam Nguyen, Takashige Ishii, Sachiyo Sanada-Morimura, Shao-Hui Zheng, Daisuke Fujita

引用次数: 0

Detection and validation of QTLs for flowering time in morning glory. 牵牛花开花时间qtl的检测与验证。

IF 1.7 4区农林科学

Breeding Science Pub Date : 2025-12-01 Epub Date: 2025-10-15 DOI: 10.1270/jsbbs.24067

Hiroaki Katsuyama, Takuro Ito, Kyousuke Ezura, Emdadul Haque, Atsushi Hoshino, Eiji Nitasaka, Michiyuki Ono, Shusei Sato, Sachiko Isobe, Hiroyuki Fukuoka, Nobuyoshi Watanabe, Tsutomu Kuboyama

{"title":"Detection and validation of QTLs for flowering time in morning glory.","authors":"Hiroaki Katsuyama, Takuro Ito, Kyousuke Ezura, Emdadul Haque, Atsushi Hoshino, Eiji Nitasaka, Michiyuki Ono, Shusei Sato, Sachiko Isobe, Hiroyuki Fukuoka, Nobuyoshi Watanabe, Tsutomu Kuboyama","doi":"10.1270/jsbbs.24067","DOIUrl":"10.1270/jsbbs.24067","url":null,"abstract":"Japanese morning glory (Ipomoea nil), a short day plant, has been used for studying flowering times. Here, quantitative trait loci (QTL) analysis for days from sowing to flowering (DTF) of F2 between I. nil var. Tokyo Kokei Standard (TKS) and I. hederacea line var. Q65, an early flowering variety, revealed seven QTLs: QTL Ipomoea Flowering 1-7 (qIF1-7). The position of qIF3, which had the most significant effect among the seven QTLs, corresponds with that of I. nil (or I. hederacea) CONSTANS (InCO/IhCO) in the linkage map. There is a single-base InDel in the coding sequence of InCO/IhCO. The single-base deletion (SBD) causes a frame-shift mutation and loss of function in TKS allele (inco-1). I. nil accessions bearing inco-1 tend to flower early, similarly to rice varieties bearing the loss of function allele of CO ortholog, hd1. The TKS allele of qIF3 reduces DTF and corresponds with the inferred effect of inco-1. Based on the distribution of inco-1, a hypothesis was proposed that the SBD in inco-1 might have played an important role in the expansion of Japanese morning glories, originally native to the tropical regions of the Americas, into temperate Asia.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 5","pages":"339-348"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13129579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Breeding and characterization of a new sweetpotato cultivar, 'Miyaakari', with bright yellow flesh for confectionery processing. 甘薯新品种“Miyaakari”的选育和特性，具有用于糖果加工的亮黄色果肉。

IF 1.7 4区农林科学

Breeding Science Pub Date : 2025-12-01 Epub Date: 2025-10-18 DOI: 10.1270/jsbbs.25017

Keisuke Suematsu, Yumi Kai, Rie Kurata, Akira Kobayashi, Takeo Sakaigaichi, Yukari Kawata, Tetsufumi Sakai, Yasuhiro Takahata, Masaru Yoshinaga, Kenji Katayama, Toshiro Fujita

引用次数: 0

Identification and characterization of QTLs for brown planthopper resistance from wild rice, Oryza nivara (Sharma et Shastry). 野生水稻Oryza nivara （Sharma et Shastry）抗褐飞虱qtl的鉴定与鉴定。

IF 1.7 4区农林科学

Breeding Science Pub Date : 2025-12-01 Epub Date: 2025-10-25 DOI: 10.1270/jsbbs.25038

Hoang Nam Nguyen, Cuong Dinh Nguyen, Sachiyo Sanada-Morimura, Shao-Hui Zheng, Daisuke Fujita

{"title":"Identification and characterization of QTLs for brown planthopper resistance from wild rice, Oryza nivara (Sharma et Shastry).","authors":"Hoang Nam Nguyen, Cuong Dinh Nguyen, Sachiyo Sanada-Morimura, Shao-Hui Zheng, Daisuke Fujita","doi":"10.1270/jsbbs.25038","DOIUrl":"10.1270/jsbbs.25038","url":null,"abstract":"The brown planthopper (Nilaparvata lugens (Stål); BPH) is a serious insect pest of rice (Oryza sativa L.). Host plant resistance is an effective means of controlling this pest; up to date at least 46 BPH resistance genes have been identified. However, BPH can overcome resistance conferred by single resistance genes. Therefore, it is necessary to detect new and durable resistance genes. Here, we identified quantitative trait loci (QTLs) for BPH resistance from the wild rice Oryza nivara (Sharma et Shastry) IRGC 89073. Using backcrossed populations derived from IRGC 89073 × the susceptible 'Taichung 65', we detected two resistance QTLs, qBPH4 on chromosome 4 and qBPH11 on chromosome 11. qBPH11 was validated in the BC3F2 population. A near-isogenic line carrying qBPH11 showed significant resistance to BPH in antibiosis, antixenosis, MSST, and honeydew tests. These results suggest that IRGC 89073 harbors valuable genetic resources that could enhance BPH resistance in rice breeding programs, particularly through pyramiding strategies using marker-assisted selection.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 5","pages":"369-377"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13129573/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification and evaluation of important agronomic traits in 49 synthetic hexaploid wheat (AABBDD) germplasm resources grown on the Qinghai-Tibet Plateau, China. 青藏高原49个合成六倍体小麦（AABBDD）种质资源重要农艺性状鉴定与评价

IF 1.7 4区农林科学

Breeding Science Pub Date : 2025-12-01 Epub Date: 2025-11-13 DOI: 10.1270/jsbbs.25015

Shuxiang Yin, Jicheng Shen, Fahui Ye, Xia Li, Caixia Zhao, Chaobo Liu, Meixi Song, Qingxu Wang, Demei Liu, Ruijuan Liu, Shunzong Ning, Lianquan Zhang, Huaigang Zhang, Yuhu Shen, Wenjie Chen

{"title":"Identification and evaluation of important agronomic traits in 49 synthetic hexaploid wheat (AABBDD) germplasm resources grown on the Qinghai-Tibet Plateau, China.","authors":"Shuxiang Yin, Jicheng Shen, Fahui Ye, Xia Li, Caixia Zhao, Chaobo Liu, Meixi Song, Qingxu Wang, Demei Liu, Ruijuan Liu, Shunzong Ning, Lianquan Zhang, Huaigang Zhang, Yuhu Shen, Wenjie Chen","doi":"10.1270/jsbbs.25015","DOIUrl":"10.1270/jsbbs.25015","url":null,"abstract":"In this study, 49 ABD-type synthetic hexaploid wheat germplasm resources grown on the Qinghai-Tibet Plateau in 2022-2024 were measured for important agronomic traits. Clustering and principal component analyses were applied to classify and compare relevant indicators for a comprehensive evaluation. The aim was to identify outstanding synthetic hexaploid wheat germplasm and establish a new germplasm resource foundation for the breeding and improvement of new wheat varieties in the Qinghai-Tibet Plateau and other regions with similar climatic conditions. The coefficient of variation for important agronomic traits ranged from 1.63% to 22.02%, with the highest coefficients of variation observed for spike stem node length, plant height, and thousand-grain weight. Cluster analysis revealed that the 49 synthetic hexaploid wheat germplasm resources could be divided into eight major clusters. Among them, the quality traits of the accessions belonging to clusters Ⅴ exhibited excellent performance, while the accessions with outstanding yield-related traits were concentrated in clusters Ⅲ and Ⅷ. Using the gray relational analysis method for comprehensive evaluation, the five germplasm resources with the highest scores were ABD-SHW-15 (64.53), ABD-SHW-6 (64.39), ABD-SHW-5 (63.70), ABD-SHW-14 (63.18), and ABD-SHW-38 (62.33).","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 5","pages":"430-441"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13129577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Applying gradient tree boosting to QTL mapping with Shapley additive explanations. 利用Shapley加性解释将梯度树增强应用于QTL映射。

IF 1.7 4区农林科学

Breeding Science Pub Date : 2025-12-01 Epub Date: 2025-10-29 DOI: 10.1270/jsbbs.24083

Tomohiro Ishibashi, Akio Onogi

{"title":"Applying gradient tree boosting to QTL mapping with Shapley additive explanations.","authors":"Tomohiro Ishibashi, Akio Onogi","doi":"10.1270/jsbbs.24083","DOIUrl":"10.1270/jsbbs.24083","url":null,"abstract":"Mapping quantitative trait loci (QTLs) is one of the major goals of quantitative genetics; however, identifying the interactions between QTLs (i.e., epistasis) remains challenging. Recently developed machine learning methods, such as deep learning and gradient boosting, are transforming the real world. These methods could advance QTL mapping methodologies because of their high capability for capturing complex relationships among features. One problem with applying such complex models to QTL mapping is the evaluation of feature importance. In this study, XGBoost, a popular gradient tree boosting algorithm, was applied for QTL mapping in biparental populations with Shapley additive explanations (SHAPs). SHAP is a local (i.e., instance-wise) importance index with the desired properties as feature importance indices. The SHAP-assisted XGBoost (SHAP-XGB) was compared with conventional methods, including composite interval mapping (CIM), multiple interval mapping (MIM), inclusive CIM (ICIM), and BayesC, using simulations and rice heading date data. SHAP-XGB performed comparably to CIM, MIM, ICIM, and BayesC in mapping main QTL effects and was superior to MIM, ICIM, and BayesC in mapping QTL interaction effects. As SHAP can evaluate local importance, interactions between markers can be visualized by plotting SHAP interaction values for each instance (plant/line). These results illustrated the strength of SHAP-XGB in detecting and interpreting epistatic QTLs and suggest the possibility that SHAP-XGB complements conventional methods.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 5","pages":"378-391"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13129572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Visible-near infrared spectral analysis for identification of physiological and genetic features in rice. 水稻生理和遗传特征的可见-近红外光谱分析。

IF 1.7 4区农林科学

Breeding Science Pub Date : 2025-12-01 Epub Date: 2025-10-07 DOI: 10.1270/jsbbs.25018

Hinako Takehisa, Ichiro Nagaoka, Akifumi Ikehata, Yutaka Sato

{"title":"Visible-near infrared spectral analysis for identification of physiological and genetic features in rice.","authors":"Hinako Takehisa, Ichiro Nagaoka, Akifumi Ikehata, Yutaka Sato","doi":"10.1270/jsbbs.25018","DOIUrl":"10.1270/jsbbs.25018","url":null,"abstract":"Visible-near infrared hyperspectral analysis is widely used for plant characterization and evaluation of agricultural products and food quality. On the other hand, it has remained un-certain whether this technique has a sufficient potential for evaluation of biological complexity during the growth of crop plants. In the present study, using a spectrometer and hyperspectral camera placed in a laboratory environment, we carried out continuous hyperspectral profiling of leaves derived from four rice cultivars grown under two field conditions. Combined analysis with transcriptome data revealed that the hyperspectral profile had potential to predict the degree of expression of developmentally regulated genes. In addition, principal component analysis of hyperspectral imaging data made it possible to detect growth-stage dependent dynamics and to distinguish differences between subspecies as well as field conditions by selecting an adequate pretreatment method. Furthermore, we obtained hyperspectral data for brown rice grains of recombinant inbred lines derived from a cultivar with high temperature tolerance during the ripening stage and with a good grain appearance. We then performed quantitative trait locus analysis using the extracted principal component scores and trait values related to grain appearance to explore the possibility of using spectral analysis for genetic studies.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 5","pages":"349-357"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13129574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LAYLA: development of a comprehensive and cross-sample program for detecting structural variants and its application to citrus cultivars. LAYLA：一个综合性的、跨样本的柑橘结构变异检测程序的开发及其在柑橘品种上的应用。

IF 1.7 4区农林科学

Breeding Science Pub Date : 2025-12-01 Epub Date: 2025-10-28 DOI: 10.1270/jsbbs.25020

Tomoaki Watanabe, Tomoko Endo, Yoshihiro Kawahara, Kenta Shirasawa, Keisuke Nonaka, Sachiko Isobe, Takehiko Shimada, Shingo Goto, Hiroshi Fujii

{"title":"LAYLA: development of a comprehensive and cross-sample program for detecting structural variants and its application to citrus cultivars.","authors":"Tomoaki Watanabe, Tomoko Endo, Yoshihiro Kawahara, Kenta Shirasawa, Keisuke Nonaka, Sachiko Isobe, Takehiko Shimada, Shingo Goto, Hiroshi Fujii","doi":"10.1270/jsbbs.25020","DOIUrl":"10.1270/jsbbs.25020","url":null,"abstract":"Structural variants (SVs) are genomic mutations that are typically 50 bp or larger. Given their larger scale compared to single nucleotide polymorphisms and small insertions and deletions, SVs are expected to be associated with various traits in several crops and fruit species. They can also be used to identify plant cultivars. However, it is challenging to detect SVs using short-read next-generation sequencing (NGS), which, until recently, has been the mainstream method, due to its short read length compared to SVs. In recent years, long-read NGS, which generates reads exceeding the length of SVs, has made SV detection more feasible. To take advantage of this, we developed LAYLA (Large indel AnalYzer for muLti-sAmple), a pipeline program designed to comprehensively detect and visualize SVs across multiple samples using long-read data. Here, we applied LAYLA to 13 citrus founder cultivars used in Japanese breeding and Citrus unshiu Marc. We identified SVs at 59,983 positions in the reference genome. This analysis revealed both common and cultivar-specific SVs. Furthermore, we designed primers targeting nine selected SVs and conducted experimental validation, confirming the presence of SVs detected by LAYLA. In the future, LAYLA can be applied to other plant species to detect SVs.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 5","pages":"442-454"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13129578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0