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OsBLS6.2: A rice bacterial leaf streak resistance gene identified by GWAS and RNA-seq OsBLS6.2:通过 GWAS 和 RNA-seq 鉴定的水稻细菌性叶斑病抗性基因
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-12-01 DOI: 10.1016/j.cj.2023.08.007
Huabin Xie , Chunzi Lin , Wenyu Lu , Zhikai Han , Danhong Wei , Xing Huo , Tianjiao Li , Jian Zhang , Yongqiang He , Chun Chen , Hui Wang , Tao Guo , Jiafeng Wang
{"title":"OsBLS6.2: A rice bacterial leaf streak resistance gene identified by GWAS and RNA-seq","authors":"Huabin Xie ,&nbsp;Chunzi Lin ,&nbsp;Wenyu Lu ,&nbsp;Zhikai Han ,&nbsp;Danhong Wei ,&nbsp;Xing Huo ,&nbsp;Tianjiao Li ,&nbsp;Jian Zhang ,&nbsp;Yongqiang He ,&nbsp;Chun Chen ,&nbsp;Hui Wang ,&nbsp;Tao Guo ,&nbsp;Jiafeng Wang","doi":"10.1016/j.cj.2023.08.007","DOIUrl":"10.1016/j.cj.2023.08.007","url":null,"abstract":"<div><p>Bacterial leaf streak (BLS), caused by <em>Xanthomonas oryzae</em> pv<em>. oryzicola</em> (<em>Xoc</em>), is a bacterial disease affecting rice production in Asia and Africa, whose severity is expected to increase with climate change. Identification of new quantitative-trait loci (QTL) or resistance genes for BLS resistance is essential for developing resistant rice. A genome-wide association study to identify QTL associated with BLS resistance was conducted using phenotypic and genotypic data from 429 rice accessions. Of 47 QTL identified, 45 were novel and two co-localized with previously reported QTL or genes conferring BLS resistance. <em>qBLS6.2</em> on chromosome 6 explained the greatest phenotypic variation. Combined analysis of differential expression and annotations of predicted genes near <em>qBLS6.2</em> based on haplotype and disease phenotype identified <em>OsBLS6.2</em> (<em>LOC_Os06g02960</em>) as a candidate gene for <em>qBLS6.2</em>. <em>OsBLS6.2</em> knockout plants showed higher resistance to <em>Xoc</em> than wild-type plants. Many other candidate genes for resistance to <em>Xoc</em> were identified.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"11 6","pages":"Pages 1862-1871"},"PeriodicalIF":6.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214514123001186/pdfft?md5=2ca67f6b7845f9d0dd3ae4b326577a08&pid=1-s2.0-S2214514123001186-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134995507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution 棉花线粒体基因组的组装和系统进化分析有助于深入了解棉花的进化史
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-12-01 DOI: 10.1016/j.cj.2023.05.004
Yanlei Feng , Yukang Wang , Hejun Lu , Jun Li , Delara Akhter , Fang Liu , Ting Zhao , Xingxing Shen , Xiaobo Li , James Whelan , Tianzhen Zhang , Jianping Hu , Ronghui Pan
{"title":"Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution","authors":"Yanlei Feng ,&nbsp;Yukang Wang ,&nbsp;Hejun Lu ,&nbsp;Jun Li ,&nbsp;Delara Akhter ,&nbsp;Fang Liu ,&nbsp;Ting Zhao ,&nbsp;Xingxing Shen ,&nbsp;Xiaobo Li ,&nbsp;James Whelan ,&nbsp;Tianzhen Zhang ,&nbsp;Jianping Hu ,&nbsp;Ronghui Pan","doi":"10.1016/j.cj.2023.05.004","DOIUrl":"10.1016/j.cj.2023.05.004","url":null,"abstract":"<div><p>Cotton is a major crop that provides the most important renewable textile fibers in the world. Studies of the taxonomy and evolution of cotton species have received wide attentions, not only due to cotton’s economic value but also due to the fact that <em>Gossypium</em> is an ideal model system to study the origin, evolution, and cultivation of polyploid species. Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation. Whereas, with only a few mitogenomes assembled in the cotton genus <em>Gossypium</em>, our knowledge about their roles in cotton evolution and speciation is still scarce. To close this gap, here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades (A–G, K, and AD genomes) and 5 cotton relatives using short and long sequencing reads. Systematic analyses uncovered a high level of mitochondrial gene sequence conservation, abundant sequence repeats and many insertions of foreign sequences, as well as extensive structural variations in cotton mitogenomes. The sequence repeats and foreign sequences caused significant mitogenome size inflation in <em>Gossypium</em> and its close relative <em>Kokia</em> in general, while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content, RNA editing, and gene expression level. Interestingly, we further revealed the specific presence and expression of two novel mitochondrial open reading frames (ORFs) in lint-fiber cotton species. Finally, these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"11 6","pages":"Pages 1782-1792"},"PeriodicalIF":6.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214514123000752/pdfft?md5=3c2a66969442433e8a54dbea4fb9d85e&pid=1-s2.0-S2214514123000752-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133496766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Regulation of soybean stem growth habit: A ten-year progress report 大豆茎干生长习性的调控:十年进展报告
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-12-01 DOI: 10.1016/j.cj.2023.08.002
Shang-Shang Xiong , Dan-Dan Guo , Zhao Wan , Le Quan , Wen-Tian Lu , Yongguo Xue , Baohui Liu , Hong Zhai
{"title":"Regulation of soybean stem growth habit: A ten-year progress report","authors":"Shang-Shang Xiong ,&nbsp;Dan-Dan Guo ,&nbsp;Zhao Wan ,&nbsp;Le Quan ,&nbsp;Wen-Tian Lu ,&nbsp;Yongguo Xue ,&nbsp;Baohui Liu ,&nbsp;Hong Zhai","doi":"10.1016/j.cj.2023.08.002","DOIUrl":"10.1016/j.cj.2023.08.002","url":null,"abstract":"<div><p>Stem growth habit dictates plant architecture and influences flowering and podding (seed setting), making it an essential morphological and breeding agronomic trait of soybean (<em>Glycine max</em>). Stem growth habit in soybean is affected by photoperiod and environment and is determined by genetic variation at major genes. Classical genetic analysis identified two critical loci, designated <em>Determinacy 1</em> (<em>Dt1</em>) and <em>Determinacy 2</em> (<em>Dt2</em>). <em>Dt1</em> is an ortholog of <em>Arabidopsis thaliana</em> TERMINAL FLOWER1 (TFL1) and specifies an indeterminate stem growth habit, whereas <em>Dt2</em> specifies a semi-determinate growth habit. MADS-box proteins, including Dt2, SUPPRESSOR OF OVEREXPRESSION OF CO1 (GmSOC1) and MADS-box genes downregulated by E1 (<em>GmMDE</em>), repress <em>Dt1</em> expression. Photoreceptors encoded by the <em>E3</em> and <em>E4</em> loci regulate the expression of soybean <em>FLOWERING LOCUS T</em> (<em>GmFT</em>) orthologs via circadian clock genes and E1, and GmFTs compete with Dt1 to regulate stem growth habit. Study of the molecular mechanism underlying the regulation of stem growth habit in soybean has focused on the repression of <em>Dt1</em> expression. Here we provide an overview of progress made in elucidating the genetic and molecular bases of stem growth habit in soybean, with emphasis on the molecular components responsible for integrating photoperiodic flowering and stem growth habit.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"11 6","pages":"Pages 1642-1648"},"PeriodicalIF":6.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214514123001125/pdfft?md5=ad0bdc36fcc037fe0ef2eff98376e7ba&pid=1-s2.0-S2214514123001125-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135248171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
The miR5810/OsMRLP6 regulatory module affects rice seedling photosynthesis miR5810/OsMRLP6 调控模块影响水稻幼苗的光合作用
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-12-01 DOI: 10.1016/j.cj.2023.08.004
Weiwei Gao , Mingkang Li , Huaping Cheng , Kuaifei Xia , Mingyong Zhang
{"title":"The miR5810/OsMRLP6 regulatory module affects rice seedling photosynthesis","authors":"Weiwei Gao ,&nbsp;Mingkang Li ,&nbsp;Huaping Cheng ,&nbsp;Kuaifei Xia ,&nbsp;Mingyong Zhang","doi":"10.1016/j.cj.2023.08.004","DOIUrl":"10.1016/j.cj.2023.08.004","url":null,"abstract":"<div><p>Photosynthesis affects crop growth and yield. The roles of microRNAs (miRNAs) in photosynthesis are little known. In the present study, the role of the OsNF-YB7<em>–OsMIR5810–OsMRLP6</em> regulatory module in photosynthesis was investigated. The malectin-like protein gene <em>OsMRLP6</em> was identified as a target gene of osa-miR5810 (miR5810). Overexpression in rice of miR5810 or down-expression of <em>OsMRLP6</em> resulted in reduced expression of genes involved in chloroplast development and photosynthesis and decreased net photosynthetic rate, finally leading to lower shoot biomass and grain yield. Down-expression of miR5810 and overexpression of <em>OsMRLP6</em> showed the opposite effect. Overexpression of transcription factor <em>OsNF-YB7</em> elevated expression of <em>OsMIR5810</em> in rice seedlings by binding to its promoter. The OsNF-YB7<em>–OsMIR5810–OsMRLP6</em> regulatory module affects photosynthesis to mediate growth and grain yield.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"11 6","pages":"Pages 1686-1695"},"PeriodicalIF":6.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214514123001149/pdfft?md5=8b8359e5a947d0689a88bde2a9209388&pid=1-s2.0-S2214514123001149-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135389975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
A dynamic regulation of nitrogen on floret primordia development in wheat 氮对小麦小花原基发育的动态调控
1区 农林科学
Crop Journal Pub Date : 2023-11-01 DOI: 10.1016/j.cj.2023.10.009
Zhen Zhang, Yujing Li, Yuxun Wu, Xiaoyu Zheng, Xiaolei Guo, Wan Sun, Zhencai Sun, Zhimin Wang, Yinghua Zhang
{"title":"A dynamic regulation of nitrogen on floret primordia development in wheat","authors":"Zhen Zhang, Yujing Li, Yuxun Wu, Xiaoyu Zheng, Xiaolei Guo, Wan Sun, Zhencai Sun, Zhimin Wang, Yinghua Zhang","doi":"10.1016/j.cj.2023.10.009","DOIUrl":"https://doi.org/10.1016/j.cj.2023.10.009","url":null,"abstract":"Nitrogen (N) fertilization is critical for spike and floret development, which affects the number of fertile florets per spike (NFFs). However, the physiological regulation of the floret development process by N fertilization is largely unknown. A high temporal-resolution investigation of floret primordia number and morphology, dry matter, and N availability was conducted under three N fertilization levels: 0 (N0), 120 (N1) and 240 (N2) kg ha−1. Interestingly, fertile florets at anthesis stage were determined by those floret primordia with meiotic ability at booting stage: meiotic ability was a threshold that predicted whether a floret primordium became fertile or abortive florets. Because the developmental rate of the 4th floret primordium in the central spikelet was accelerated and then they acquired meiotic ability, the NFFs increased gradually as N application increased, but the increase range decreased under N2. There were no differences in spike N concentration among treatments, but leaf N concentration was increased in the N1 and N2 treatments. Correspondingly, dry matter accumulation and N content of the leaf and spike in the N1 and N2 treatments was increased as compared to N0. Clearly, optimal N fertilization increased leaf N availability and transport of assimilates to spikes, and allowed more floret primordia to acquire meiotic ability and become fertile florets, finally increasing NFFs. There was no difference in leaf N concentration between N1 and N2 treatment, whereas soil N concentration at 0-60 cm soil layers was higher in N2 than in N1 treatment, implying that there was still some N fertilization that remained unused. Therefore, improving the leaf’s ability to further use N fertilizer is vital for greater NFFs.","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"50 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135566238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Remote sensing of quality traits in cereal and arable production systems: A review 谷物和耕地生产系统品质性状的遥感研究进展
1区 农林科学
Crop Journal Pub Date : 2023-11-01 DOI: 10.1016/j.cj.2023.10.005
Zhenhai Li, Chengzhi Fan, Yu Zhao, Xiuliang Jin, Raffaele Casa, Wenjiang Huang, Xiaoyu Song, Gerald Blasch, Guijun Yang, James Taylor, Zhenhong Li
{"title":"Remote sensing of quality traits in cereal and arable production systems: A review","authors":"Zhenhai Li, Chengzhi Fan, Yu Zhao, Xiuliang Jin, Raffaele Casa, Wenjiang Huang, Xiaoyu Song, Gerald Blasch, Guijun Yang, James Taylor, Zhenhong Li","doi":"10.1016/j.cj.2023.10.005","DOIUrl":"https://doi.org/10.1016/j.cj.2023.10.005","url":null,"abstract":"Cereal is an essential source of calories and protein for the global population. Accurately predicting cereal quality before harvest is highly desirable in order to optimise management for farmers, grading harvest and categorised storage for enterprises, future trading prices, and policy planning. The use of remote sensing data with extensive spatial coverage demonstrates some potential in predicting crop quality traits. Many studies have also proposed models and methods for predicting such traits based on multi-platform remote sensing data. In this paper, the key quality traits that are of interest to producers and consumers are introduced. The literature related to grain quality prediction was analyzed in detail, and a review was conducted on remote sensing platforms, commonly used methods, potential gaps, and future trends in crop quality prediction. This review recommends new research directions that go beyond the traditional methods and discusses grain quality retrieval and the associated challenges from the perspective of remote sensing data.","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"23 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135713893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rice–wheat comparative genomics: Gains and gaps 稻麦比较基因组学:进展与差距
1区 农林科学
Crop Journal Pub Date : 2023-11-01 DOI: 10.1016/j.cj.2023.10.008
Akila Wijerathna-Yapa, Ruchi Bishnoi, Buddhini Ranawaka, Manu Maya Magar, Hafeez Ur Rehman, Swati G. Bharad, Michal T. Lorenc, Vinita Ramtekey, Sasha Gohar, Charu Lata, Md. Harun-Or-Rashid, Maryam Razzaq, Muhammad Sajjad, Bhoja R. Basnet
{"title":"Rice–wheat comparative genomics: Gains and gaps","authors":"Akila Wijerathna-Yapa, Ruchi Bishnoi, Buddhini Ranawaka, Manu Maya Magar, Hafeez Ur Rehman, Swati G. Bharad, Michal T. Lorenc, Vinita Ramtekey, Sasha Gohar, Charu Lata, Md. Harun-Or-Rashid, Maryam Razzaq, Muhammad Sajjad, Bhoja R. Basnet","doi":"10.1016/j.cj.2023.10.008","DOIUrl":"https://doi.org/10.1016/j.cj.2023.10.008","url":null,"abstract":"Rice and wheat provide nearly 40% of human calorie and protein requirements. They share a common ancestor and belong to the Poaceae (grass) family. Characterizing their genetic homology is crucial for developing new cultivars with enhanced traits. Several wheat genes and gene families have been characterized based on their rice orthologs. Rice–wheat orthology can identify genetic regions that regulate similar traits in both crops. Rice–wheat comparative genomics can identify candidate wheat genes in a genomic region identified by association or QTL mapping, deduce their putative functions and biochemical pathways, and develop molecular markers for marker-assisted breeding. A knowledge of gene homology facilitates the transfer between crops of genes or genomic regions associated with desirable traits by genetic engineering, gene editing, or wide crossing.","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135670216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max 大豆品种中黄13号的端粒到端粒基因组组装
1区 农林科学
Crop Journal Pub Date : 2023-11-01 DOI: 10.1016/j.cj.2023.10.003
Anqi Zhang, Tangchao Kong, Baiquan Sun, Shizheng Qiu, Jiahe Guo, Shuyong Ruan, Yu Guo, Jirui Guo, Zhishuai Zhang, Yue Liu, Zheng Hu, Tao Jiang, Yadong Liu, Shuqi Cao, Shi Sun, Tingting Wu, Huilong Hong, Bingjun Jiang, Maoxiang Yang, Xiangyu Yao, Yang Hu, Bo Liu, Tianfu Han, Yadong Wang
{"title":"A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max","authors":"Anqi Zhang, Tangchao Kong, Baiquan Sun, Shizheng Qiu, Jiahe Guo, Shuyong Ruan, Yu Guo, Jirui Guo, Zhishuai Zhang, Yue Liu, Zheng Hu, Tao Jiang, Yadong Liu, Shuqi Cao, Shi Sun, Tingting Wu, Huilong Hong, Bingjun Jiang, Maoxiang Yang, Xiangyu Yao, Yang Hu, Bo Liu, Tianfu Han, Yadong Wang","doi":"10.1016/j.cj.2023.10.003","DOIUrl":"https://doi.org/10.1016/j.cj.2023.10.003","url":null,"abstract":"Soybean (Glycine max) stands as a globally significant agricultural crop, and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history. Nevertheless, previous soybean genome assemblies have harbored gaps and incompleteness, which have constrained in-depth investigations into soybean. Here, we present Telomere-to-Telomere (T2T) assembly of the Chinese soybean cultivar Zhonghuang 13 (ZH13) genome, termed ZH13-T2T, utilizing PacBio Hifi and ONT ultralong reads. We employed a multi-assembler approach, integrating Hifiasm, NextDenovo, and Canu, to minimize biases and enhance assembly accuracy. The assembly spans 1,015,024,879 bp, effectively resolving all 393 gaps that previously plagued the reference genome. Our annotation efforts identified 50,564 high-confidence protein-coding genes, 707 of which are novel. ZH13-T2T revealed longer chromosomes, 421 not-aligned regions (NARs), 112 structure variations (SVs), and a substantial expansion of repetitive element compared to earlier assemblies. Specifically, we identified 25.67 Mb of tandem repeats, an enrichment of 5S and 48S rDNAs, and characterized their genotypic diversity. In summary, we deliver the first complete Chinese soybean cultivar T2T genome. The comprehensive annotation, along with precise centromere and telomere characterization, as well as insights into structural variations, further enhance our understanding of soybean genetics and evolution.","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"9 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135410126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
RPNet: Rice plant counting after tillering stage based on plant attention and multiple supervision network RPNet:基于植株关注和多重监督的水稻分蘖期后植株计数网络
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.04.005
Xiaodong Bai , Susong Gu , Pichao Liu , Aiping Yang , Zhe Cai , Jianjun Wang , Jianguo Yao
{"title":"RPNet: Rice plant counting after tillering stage based on plant attention and multiple supervision network","authors":"Xiaodong Bai ,&nbsp;Susong Gu ,&nbsp;Pichao Liu ,&nbsp;Aiping Yang ,&nbsp;Zhe Cai ,&nbsp;Jianjun Wang ,&nbsp;Jianguo Yao","doi":"10.1016/j.cj.2023.04.005","DOIUrl":"https://doi.org/10.1016/j.cj.2023.04.005","url":null,"abstract":"<div><p>Rice is a major food crop and is planted worldwide. Climatic deterioration, population growth, farmland shrinkage, and other factors have necessitated the application of cutting-edge technology to achieve accurate and efficient rice production. In this study, we mainly focus on the precise counting of rice plants in paddy field and design a novel deep learning network, RPNet, consisting of four modules: feature encoder, attention block, initial density map generator, and attention map generator. Additionally, we propose a novel loss function called RPloss. This loss function considers the magnitude relationship between different sub-loss functions and ensures the validity of the designed network. To verify the proposed method, we conducted experiments on our recently presented URC dataset, which is an unmanned aerial vehicle dataset that is quite challenged at counting rice plants. For experimental comparison, we chose some popular or recently proposed counting methods, namely MCNN, CSRNet, SANet, TasselNetV2, and FIDTM. In the experiment, the mean absolute error (MAE), root mean squared error (RMSE), relative MAE (rMAE) and relative RMSE (rRMSE) of the proposed RPNet were 8.3, 11.2, 1.2% and 1.6%, respectively, for the URC dataset. RPNet surpasses state-of-the-art methods in plant counting. To verify the universality of the proposed method, we conducted experiments on the well-know MTC and WED datasets. The final results on these datasets showed that our network achieved the best results compared with excellent previous approaches. The experiments showed that the proposed RPNet can be utilized to count rice plants in paddy fields and replace traditional methods.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"11 5","pages":"Pages 1586-1594"},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49883481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
SimET: An open-source tool for estimating crop evapotranspiration and soil water balance for plants with multiple growth cycles SimET:一个用于估计具有多个生长周期的植物的作物蒸散和土壤水分平衡的开源工具
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.03.008
Minguo Liu, Mei Yang, Huimin Yang
{"title":"SimET: An open-source tool for estimating crop evapotranspiration and soil water balance for plants with multiple growth cycles","authors":"Minguo Liu,&nbsp;Mei Yang,&nbsp;Huimin Yang","doi":"10.1016/j.cj.2023.03.008","DOIUrl":"https://doi.org/10.1016/j.cj.2023.03.008","url":null,"abstract":"<div><p>Accurate estimation of crop evapotranspiration (ETc) and soil water balance, which is vital for optimizing water management strategy in crop production, can be performed by simulation. But existing software has many deficiencies, including complex operation, limited scalability, lack of batch processing, and a single ETc model. Here we present simET, an open-source software package written in the R programming language. Many concepts involved in crop ETc simulation are condensed into functions in the package. It includes three widely used crop ETc models built on these functions: the single-crop coefficient, double-crop coefficient, and Shuttleworth–Wallace models, along with tools for preparing model data and comparing estimates. SimET supports ETc simulation in crops with repeated growth cycles such as alfalfa, a perennial forage crop that is cut multiple times annually.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"11 5","pages":"Pages 1579-1585"},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49803754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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