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Fine mapping of Rf5 region for a sorghum fertility restorer gene and microsynteny analysis across grass species. 高粱育性恢复基因Rf5区的精细定位及禾草种间微共生性分析。
IF 2.4 4区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2022-04-01 Epub Date: 2022-03-10 DOI: 10.1270/jsbbs.21057
Atsushi Kiyosawa, Jun-Ichi Yonemaru, Hiroshi Mizuno, Hiroyuki Kanamori, Jianzhong Wu, Hiroyuki Kawahigashi, Kazumi Goto

Cytoplasmic male sterility (CMS) is widely used to control pollination in the production of commercial F1 hybrid seed in sorghum. So far, 6 major fertility restorer genes, Rf1 to Rf6, have been reported in sorghum. Here, we fine-mapped the Rf5 locus on sorghum chromosome 5 using descendant populations of a 'Nakei MS-3A' × 'JN43' cross. The Rf5 locus was narrowed to a 140-kb region in BTx623 genome (161-kb in JN43) with 16 predicted genes, including 6 homologous to the rice fertility restorer Rf1 (PPR.1 to PPR.6). These 6 homologs have tandem pentatricopeptide repeat (PPR) motifs. Many Rf genes encode PPR proteins, which bind RNA transcripts and modulate gene expression at the RNA level. No PPR genes were detected at the Rf5 locus on the corresponding homologous chromosome of rice, foxtail millet, or maize, so this gene cluster may have originated by chromosome translocation and duplication after the divergence of sorghum from these species. Comparison of the sequences of these genes between fertile and CMS lines identified PPR.4 as the most plausible candidate gene for Rf5.

细胞质雄性不育(CMS)被广泛应用于高粱商业化F1杂交种子生产中的授粉控制。迄今为止,在高粱中已报道了6个主要的育性恢复基因Rf1 ~ Rf6。在这里,我们利用“Nakei MS-3A”דJN43”杂交的后代群体,对高粱5号染色体上的Rf5位点进行了精细定位。在BTx623基因组中,Rf5位点被缩小到140-kb (JN43为161-kb),有16个预测基因,其中6个与水稻育性恢复基因Rf1 (PPR.1 ~ PPR.6)同源。这6个同源物具有串联五肽重复(PPR)基序。许多Rf基因编码PPR蛋白,这些蛋白结合RNA转录物并在RNA水平上调节基因表达。在水稻、谷子和玉米的相应同源染色体Rf5位点均未检测到PPR基因,因此该基因簇可能是高粱与这些物种分化后染色体易位和重复产生的。将这些基因序列在可育系和不育系之间进行比较,确定PPR.4是Rf5最可能的候选基因。
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引用次数: 0
Allelic variation and genetic diversity of HMW glutenin subunits in Chinese wheat (Triticum aestivum L.) landraces and commercial cultivars. 中国小麦(Triticum aestivum L.)地方品种和商品品种HMW谷蛋白亚基的等位基因变异和遗传多样性
IF 2.4 4区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2022-04-01 Epub Date: 2022-02-02 DOI: 10.1270/jsbbs.21076
Xiaofang Wang, Ruilian Song, Yue An, Haiyi Pei, Song Gao, Daokun Sun, Xifeng Ren

Wheat landraces have abundant genetic variation at the Glu-1 loci, which is desirable germplasms for genetic enhancement of modern wheat varieties, especially for quality improvement. In the current study, we analyzed the allelic variations of the Glu-1 loci of 597 landraces and 926 commercial wheat varieties from the four major wheat-growing regions in China using SDS-PAGE. As results, alleles Null, 7+8, and 2+12 were the dominant HMW-GSs in wheat landraces. Compared to landraces, the commercial varieties contain higher frequencies of high-quality alleles, including 1, 7+9, 14+15 and 5+10. The genetic diversity of the four commercial wheat populations (alleles per locus (A) = 7.33, percent polymorphic loci (P) = 1.00, effective number of alleles per locus (Ae) = 2.347 and expected heterozygosity (He) = 0.563) was significantly higher than that of the landraces population, with the highest genetic diversity found in the Southwestern Winter Wheat Region population. The genetic diversity of HMW-GS is mainly present within the landraces and commercial wheat populations instead of between populations. The landraces were rich in rare subunits or alleles may provide germplasm resources for improving the quality of modern wheat.

小麦地方品种在Glu-1位点具有丰富的遗传变异,是现代小麦品种遗传改良特别是品质改良的理想种质。本研究利用SDS-PAGE分析了中国四大小麦产区597个地方小麦品种和926个商品小麦品种的Glu-1位点的等位基因变异。结果表明,Null、7+8和2+12等位基因是小麦地方品种的优势等位基因。商品品种的1、7+9、14+15、5+10等优质等位基因频率高于地方品种。4个商品小麦群体的遗传多样性(每位点等位基因数(A) = 7.33,多态性位点百分比(P) = 1.00,每位点有效等位基因数(Ae) = 2.347,期望杂合度(He) = 0.563)均显著高于地方小麦群体,其中西南冬麦区群体的遗传多样性最高。高分子量小麦的遗传多样性主要存在于地方小麦和商品小麦群体内部,而不是群体之间。这些地方品种具有丰富的稀有亚基或等位基因,可为提高现代小麦品质提供种质资源。
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引用次数: 2
Erratum: Comparative QTL mapping for male sterility of cultivated strawberry (Fragaria × ananassa Duch.) using different reference genome sequences. 不同参考基因组序列对栽培草莓(Fragaria × ananassa Duch.)雄性不育性的比较QTL定位。
IF 2.4 4区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2022-04-01 DOI: 10.1270/jsbbs.20151e
Takuya Wada, Hiyori Monden, Sachiko Isobe, Kenta Shirasawa, Takayuki Sueyoshi, Chiharu Hirata, Miyuki Mori, Shiro Nagamatsu, Yoshiki Tanaka

[This corrects the article DOI: 10.1270/jsbbs.20151.].

[这更正了文章DOI: 10.1270/jsbbs.20151.]。
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引用次数: 0
Development of a plant conveyance system using an AGV and a self-designed plant-handling device: A case study of DIY plant phenotyping. 使用AGV和自行设计的植物处理装置的植物运输系统的开发:DIY植物表型的案例研究。
IF 2.4 4区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2022-03-01 Epub Date: 2022-02-17 DOI: 10.1270/jsbbs.21070
Takanari Tanabata, Kunihiro Kodama, Takuyu Hashiguchi, Daisuke Inomata, Hidenori Tanaka, Sachiko Isobe

Plant phenotyping technology has been actively developed in recent years, but the introduction of these technologies into the field of agronomic research has not progressed as expected, in part due to the need for flexibility and low cost. "DIY" (Do It Yourself) methodologies are an efficient way to overcome such obstacles. Devices with modular functionality are critical to DIY experimentation, allowing researchers flexibility of design. In this study, we developed a plant conveyance system using a commercial AGV (Automated Guided Vehicle) as a case study of DIY plant phenotyping. The convey module consists of two devices, a running device and a plant-handling device. The running device was developed based on a commercial AGV Kit. The plant-handling device, plant stands, and pot attachments were originally designed and fabricated by us and our associates. Software was also developed for connecting the devices and operating the system. The run route was set with magnetic tape, which can be easily changed or rerouted. Our plant delivery system was developed with low cost and having high flexibility, as a unit that can contribute to others' DIY' plant research efforts as well as our own. It is expected that the developed devices will contribute to diverse phenotype observations of plants in the greenhouse as well as to other important functions in plant breeding and agricultural production.

近年来,植物表型技术得到了积极的发展,但由于对灵活性和低成本的需求,将这些技术引入农艺研究领域并没有取得预期的进展。“DIY”(自己动手)方法是克服这些障碍的有效方法。具有模块化功能的设备对DIY实验至关重要,允许研究人员灵活设计。在这项研究中,我们开发了一种植物运输系统,使用商用AGV(自动导引车)作为DIY植物表型的案例研究。输送模块由两个装置组成,一个运行装置和一个物料搬运装置。该运行装置是在商用AGV套件的基础上开发的。植物处理装置、植物支架和花盆附件最初是由我们和我们的同事设计和制造的。还开发了用于连接设备和操作系统的软件。运行路线是用磁带设置的,可以很容易地改变或重新路由。我们的植物输送系统开发成本低,灵活性高,作为一个单元,可以为其他“DIY”植物研究工作做出贡献,也可以为我们自己的研究工作做出贡献。期望所研制的装置将有助于温室植物表型的多样化观察,并在植物育种和农业生产中发挥其他重要作用。
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引用次数: 3
Improving the efficiency of plant root system phenotyping through digitization and automation. 通过数字化和自动化提高植物根系表型分型效率。
IF 2.4 4区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2022-03-01 Epub Date: 2022-02-09 DOI: 10.1270/jsbbs.21053
Shota Teramoto, Yusaku Uga

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.

根系结构(RSA)决定了土壤中水分和养分的不均匀分布。因此,RSA的遗传改良与作物生产有关。然而,RSA表型分析比地上表型分析进行得少,因为测量土壤中的根是困难和劳动密集型的。最近的进展导致了植物测量的数字化;这种数字表型已广泛用于地上和RSA性状的测量。RSA的数字表型比地上性状的表型更慢,更困难,因为根隐藏在地下。在这篇综述中,我们总结了RSA性状的数字表型的最新趋势。我们将样品类型分为三类:含根的土壤块、土壤块段和根样。使用数字表型的例子,提出了每个类别。我们还讨论了在每个类别中数字表型的改进空间。
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引用次数: 5
Recent applications of metabolomics in plant breeding. 代谢组学在植物育种中的最新应用。
IF 2.4 4区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2022-03-01 Epub Date: 2022-02-03 DOI: 10.1270/jsbbs.21065
Nozomu Sakurai

Metabolites play a central role in maintaining organismal life and in defining crop phenotypes, such as nutritional value, fragrance, color, and stress resistance. Among the 'omes' in biology, the metabolome is the closest to the phenotype. Consequently, metabolomics has been applied to crop improvement as method for monitoring changes in chemical compositions, clarifying the mechanisms underlying cellular functions, discovering markers and diagnostics, and phenotyping for mQTL, mGWAS, and metabolite-genome predictions. In this review, 359 reports of the most recent applications of metabolomics to plant breeding-related studies were examined. In addition to the major crops, more than 160 other crops including rare medicinal plants were considered. One bottleneck associated with using metabolomics is the wide array of instruments that are used to obtain data and the ambiguity associated with metabolite identification and quantification. To further the application of metabolomics to plant breeding, the features and perspectives of the technology are discussed.

代谢物在维持生物生命和确定作物表型(如营养价值、香味、颜色和抗逆性)方面发挥着核心作用。在生物学的“基因组”中,代谢组是最接近表型的。因此,代谢组学已被应用于作物改良,作为监测化学成分变化的方法,阐明细胞功能的机制,发现标记和诊断,以及mQTL、mGWAS和代谢物基因组预测的表型。本文综述了代谢组学在植物育种相关研究中的最新应用报道359篇。除主要作物外,还考虑了包括稀有药用植物在内的160多种其他作物。与使用代谢组学相关的一个瓶颈是用于获取数据的各种仪器以及与代谢物鉴定和量化相关的模糊性。为了进一步将代谢组学技术应用于植物育种,本文对代谢组学技术的特点和发展前景进行了探讨。
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引用次数: 8
Development of a high-throughput field phenotyping rover optimized for size-limited breeding fields as open-source hardware. 开发一个高通量的田间表型漫游器,优化大小有限的育种领域作为开源硬件。
IF 2.4 4区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2022-03-01 Epub Date: 2022-02-08 DOI: 10.1270/jsbbs.21059
Ken Kuroki, Kai Yan, Hiroyoshi Iwata, Kentaro K Shimizu, Toshiaki Tameshige, Shuhei Nasuda, Wei Guo

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.

表型是植物育种中的一个关键过程,特别是在育种计划中对简化选择过程的需求日益增加时。由于人工表型分析效率有限,近年来由于传感器和图像处理技术的进步,高通量表型分析方法得到了推广。然而,在日本和其他亚洲国家普遍存在的规模有限的育种领域,在田间引入大型机械或在田间飞行无人驾驶飞行器是具有挑战性的。在这项研究中,我们开发了一种基于地面的高通量田间表型探测车,即使没有特殊设施,也可以很容易地将其引入田间,而不考虑田间的规模和位置。我们还将野外漫游车的硬件开源,使其系统对公众开放,便于修改,这样任何人都可以以低成本建造一个自己使用的。实地探测车的试运行表明,它可以收集植物的详细遥感图像并根据图像进行定量分析。结果表明,本研究开发的田间探测车可以实现高效的植物表型分析,特别是在小范围的育种领域。
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引用次数: 0
Model-based plant phenomics on morphological traits using morphometric descriptors. 基于模型的植物形态特征表型组学研究。
IF 2.4 4区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2022-03-01 Epub Date: 2022-02-17 DOI: 10.1270/jsbbs.21078
Koji Noshita, Hidekazu Murata, Shiryu Kirie

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.

植物的形态特征决定了植物的辐射拦截、抗倒伏、气体交换效率、个体和/或物种间的空间竞争以及抗病性等重要的功能特征。尽管随着分子育种策略的进步,植物表型技术的重要性日益增加,但其发展存在障碍,包括测量数据与表型值之间的差距,由于缺乏表征形态性状的模型而导致的低数量和低通量。在这篇综述中,我们介绍了可以用于植物形态性状表型的形态描述子。几何形态计量学方法为适用于单个单位的通用方法铺平了道路。在植物中经常观察到由无数多个元素组成的层次结构,利用拓扑数据分析可以根据其多尺度拓扑特征进行量化。理论形态模型捕捉特定的解剖结构,如果识别。这些形态描述符为我们提供了基于模型的植物表型分析的优势,包括有限数据集的稳健量化。此外,我们还讨论了基于模型的测量和模型改进系统将解决形态学模型的缺乏和扩大表型过程的困难的未来可能性。
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引用次数: 2
Digital phenotyping and data analysis for plant breeding. 植物育种的数字表型和数据分析。
IF 2.4 4区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2022-03-01 DOI: 10.1270/jsbbs.72.1
Sachiko Isobe, Seishi Ninomiya
The life sciences have entered an era of big data analy‐ sis over the last decade. This is mainly due to the largescale acquisition of genome information by the advent of next generation sequencing technologies and the develop‐ ment of data analysis technologies such as artificial intel‐ ligence. Digital technology has also been developed in plant phenotyping and has begun to be introduced into crop breeding. In contrast to genome sequencing, a variety of measurement technologies are required in plant pheno‐ typing depending on the target traits and plants. In addition, the analysis methods for the acquired data are still in the process of development, and it is difficult to choose the best method without sufficient knowledge. Therefore, this special issue features the current status of digital plant phenotyping technology and data analy‐ sis methods. There are five review and five research arti‐ cles included in this issue. The first review article gives an overview of the current status and prospects of highspeed phenotyping technology for crops. The second article describes ways of using morphometric descriptors to rep‐ resent morphological traits. The third article reviews the creation of 3D models, which is one of the most popular aspects of digital phenotyping. The fourth article reviews the available technologies for measuring roots, which is one of the most challenging traits in plant phenotyping. The fifth article is a review of metabolomics analysis, since chemical component analysis is another important part of phenotyping. The sixth to tenth articles are research papers describing the actual technology development for digital phenotyping or data analysis of plants, including the devel‐ opment of data acquisition equipment and methods for extracting necessary information through image analysis. The development of digital plant phenotyping technol‐ ogy has been driven by the convergence of biological, informatics, and engineering research fields. Many of the papers in this special issue are written by authors who are involved in engineering or information science rather than breeding science. Thus, there may be unfamiliar words that are difficult to read for the typical readers of BS. Despite this unfamiliarity, we hope that this special issue will be read by many BS readers, and will provide an opportunity to enter this new research field.
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引用次数: 0
All-around 3D plant modeling system using multiple images and its composition. 全方位三维植物建模系统,使用多图像及其组成。
IF 2.4 4区 农林科学 Q1 Agricultural and Biological Sciences Pub Date : 2022-03-01 Epub Date: 2022-02-02 DOI: 10.1270/jsbbs.21068
Nobuo Kochi, Atsushi Hayashi, Yota Shinohara, Takanari Tanabata, Kunihiro Kodama, Sachiko Isobe
In this study, we developed an all-around 3D plant modeling system that operates using images and is capable of measuring plants non-destructively without any contact. During the fabrication of this device, we selected a method capable of performing 3D model reconstruction from multiple images. We then developed an improved SfM-MVS (Structure from Motion / Multi-View-Stereo) method that enables 3D reconstruction by simply capturing images with a camera. The resulting image-based method offers a high degree of freedom because the hardware and software can comprise commercially available products, and it permits the use of one or more cameras according to the shape and size of the plant. The advantages of the image-based method are that 3D reconstruction can be conducted at any time as long as the images are already taken, and that the desired locations can be observed, measured, and analyzed from 2D images and a 3D point cloud. The device we developed is capable of 3D measurements and modeling of plants from a few millimeters to 2.4 m of height using this method. This article explains this device, the principles of its composition, and the accuracy of the models obtained from it.
在这项研究中,我们开发了一个全方位的3D植物建模系统,该系统使用图像操作,能够在没有任何接触的情况下无损地测量植物。在该装置的制造过程中,我们选择了一种能够从多个图像中进行3D模型重建的方法。然后,我们开发了一种改进的SfM-MVS(运动/多视图立体结构)方法,通过简单地用相机捕获图像来实现3D重建。由此产生的基于图像的方法提供了高度的自由度,因为硬件和软件可以由商业上可用的产品组成,并且它允许根据植物的形状和大小使用一个或多个相机。基于图像的方法的优点是,只要已经拍摄了图像,就可以随时进行3D重建,并且可以从2D图像和3D点云中观察,测量和分析所需的位置。我们开发的设备能够使用这种方法对几毫米到2.4米高的植物进行3D测量和建模。本文介绍了该装置及其组成原理,以及由此得到的模型的精度。
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引用次数: 3
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Breeding Science
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