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OsTHA8 encodes a pentatricopeptide repeat protein required for RNA editing and splicing during rice chloroplast development OsTHA8编码水稻叶绿体发育过程中RNA编辑和剪接所需的五肽重复蛋白
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.04.009
Yanwei Wang , Yu Duan , Pengfei Ai
{"title":"OsTHA8 encodes a pentatricopeptide repeat protein required for RNA editing and splicing during rice chloroplast development","authors":"Yanwei Wang ,&nbsp;Yu Duan ,&nbsp;Pengfei Ai","doi":"10.1016/j.cj.2023.04.009","DOIUrl":"https://doi.org/10.1016/j.cj.2023.04.009","url":null,"abstract":"<div><p>In higher plants, the chloroplast is the most important organelle for photosynthesis and for numerous essential metabolic processes in the cell. Although many genes involved in chloroplast development have been identified, the mechanisms underlying such development are not fully understood. In this study, a rice (<em>Oryza sativa</em>) mutant exhibiting pale green color and seedling lethality was isolated from a mutant library. The mutated gene was identified as an ortholog of <em>THA8</em> (<em>thylakoid assembly 8</em>) in <em>Arabidopsis</em> and maize. This gene is designated as <em>OsTHA8</em> hereafter. OsTHA8 showed a typical pentatricopeptide repeat (PPR) characteristic of only four PPR motifs. Inactivation of OsTHA8 led to a deficiency in chloroplast development in the rice seedling stage. <em>OsTHA8</em> was expressed mainly in young leaves and leaf sheaths. The OsTHA8 protein was localized to the chloroplast. Loss of function of OsTHA8 weakened the editing efficiency of <em>ndhB-611</em>/<em>737</em> and <em>rps8-182</em> transcripts under normal conditions. Y2H and BiFC indicated that OsTHA8 facilitates RNA editing by forming an editosome with multiple organellar RNA editing factor (OsMORF8) and thioredoxin z (OsTRXz), which function in RNA editing in rice chloroplasts. Defective OsTHA8 impaired chloroplast ribosome assembly and resulted in reduced expression of PEP-dependent genes and photosynthesis-related genes. Abnormal splicing of the chloroplast gene <em>ycf3</em> was detected in <em>ostha8</em>. These findings reveal a synergistic regulatory mechanism of chloroplast biogenesis mediated by RNA, broaden the function of the PPR family, and shed light on the RNA editing complex in rice.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49845246","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":null,"pages":null},"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
Improving maize growth and development simulation by integrating temperature compensatory effect under plastic film mulching into the AquaCrop model 将地膜覆盖下的温度补偿效应纳入AquaCrop模型改进玉米生长发育模拟
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.05.008
Chao Zhang , Jiying Kong , Min Tang , Wen Lin , Dianyuan Ding , Hao Feng
{"title":"Improving maize growth and development simulation by integrating temperature compensatory effect under plastic film mulching into the AquaCrop model","authors":"Chao Zhang ,&nbsp;Jiying Kong ,&nbsp;Min Tang ,&nbsp;Wen Lin ,&nbsp;Dianyuan Ding ,&nbsp;Hao Feng","doi":"10.1016/j.cj.2023.05.008","DOIUrl":"https://doi.org/10.1016/j.cj.2023.05.008","url":null,"abstract":"<div><p>Temperature compensatory effect, which quantifies the increase in cumulative air temperature from soil temperature increase caused by mulching, provides an effective method for incorporating soil temperature into crop models. In this study, compensated temperature was integrated into the AquaCrop model to investigate the capability of the compensatory effect to improve assessment of the promotion of maize growth and development by plastic film mulching (PM). A three-year experiment was conducted from 2014 to 2016 with two maize varieties (spring and summer) and two mulching conditions (PM and non-mulching (NM)), and the AquaCrop model was employed to reproduce crop growth and yield responses to changes in NM, PM, and compensated PM. A marked difference in soil temperature between NM and PM was observed before 50 days after sowing (DAS) during three growing seasons. During sowing–emergence and emergence–tasseling, the increase in air temperature was proportional to the compensatory coefficient, with spring maize showing a higher compensatory temperature than summer maize. Simulation results for canopy cover (CC) were generally in good agreement with the measurements, whereas predictions of aboveground biomass and grain yield under PM indicated large underestimates from 60 DAS to the end of maturity. Simulations of spring maize biomass and yield showed general increase based on temperature compensation, accompanied by improvement in modeling accuracy, with RMSEs decreasing from 2.5 to 1.6 t ha<sup>−1</sup> and from 4.1 t to 3.4 t ha<sup>−1</sup>. Improvement in biomass and yield simulation was less pronounced for summer than for spring maize, implying that crops grown during low-temperature periods would benefit more from the compensatory effect. This study demonstrated the effectiveness of the temperature compensatory effect to improve the performance of the AquaCrop model in simulating maize growth under PM practices.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49803756","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
Introgression of QTL from Aegilops tauschii enhances yield-related traits in common wheat 灰山羊草QTL导入提高普通小麦产量相关性状的研究
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.05.001
Feifei Ma , Ranzhe Li , Guanghui Guo, Fang Nie, Lele Zhu, Wenjuan Liu, Linlin Lyu, Shenglong Bai, Xinpeng Zhao, Zheng Li, Dale Zhang, Hao Li, Suoping Li, Yun Zhou, Chun-Peng Song
{"title":"Introgression of QTL from Aegilops tauschii enhances yield-related traits in common wheat","authors":"Feifei Ma ,&nbsp;Ranzhe Li ,&nbsp;Guanghui Guo,&nbsp;Fang Nie,&nbsp;Lele Zhu,&nbsp;Wenjuan Liu,&nbsp;Linlin Lyu,&nbsp;Shenglong Bai,&nbsp;Xinpeng Zhao,&nbsp;Zheng Li,&nbsp;Dale Zhang,&nbsp;Hao Li,&nbsp;Suoping Li,&nbsp;Yun Zhou,&nbsp;Chun-Peng Song","doi":"10.1016/j.cj.2023.05.001","DOIUrl":"https://doi.org/10.1016/j.cj.2023.05.001","url":null,"abstract":"<div><p>To break the narrow diversity bottleneck of the wheat D genome, a set of <em>Aegilops tauschii</em>-wheat introgression (A-WI) lines was developed by crossing <em>Ae. tauschii</em> accession T015 with common wheat elite cultivar Zhoumai 18 (Zhou18). A high-density genetic map was constructed based on Single Nucleotide Polymorphism (SNP) markers and 15 yield-related traits were evaluated in 11 environments for detecting quantitative trait loci (QTL). A total of 27 environmentally stable QTL were identified in at least five environments, 20 of which were derived from <em>Ae. tauschii</em> T015, explaining up to 24.27% of the phenotypic variations. The major QTL for kernel length (KL), <em>QKl-2D.5</em>, was delimited to a physical interval of approximately 2.6 Mb harboring 52 candidate genes. Three Kompetitive Allele Specific PCR (KASP) markers were successfully developed based on nonsynonymous nucleotide mutations of candidate gene <em>AetT093_2Dv1G100900.1</em> and showed that A-WI lines with the T015 haplotype had significantly longer KL than the Zhou18 haplotype across all 11 environments. Four primary valuable A-WIs with good trait performance and carrying yield-related QTL were selected for breeding improvement. The results will facilitate the efficient transfer of beneficial genes from <em>Ae. tauschii</em> into wheat cultivars to improve wheat yield and other traits.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49803760","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: 1
Fine mapping of a major QTL qHYF_B06 for peanut yield 花生产量主效QTL qHYF_B06的精细定位
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.04.004
Yongqing Yang, Qiao Su, Yurong Li, Zengshu Cheng, Yahui Song, Xinxin Jin, Jin Wang
{"title":"Fine mapping of a major QTL qHYF_B06 for peanut yield","authors":"Yongqing Yang,&nbsp;Qiao Su,&nbsp;Yurong Li,&nbsp;Zengshu Cheng,&nbsp;Yahui Song,&nbsp;Xinxin Jin,&nbsp;Jin Wang","doi":"10.1016/j.cj.2023.04.004","DOIUrl":"https://doi.org/10.1016/j.cj.2023.04.004","url":null,"abstract":"<div><p>High yield is a major objective for peanut (<em>Arachis hypogaea</em> L.) breeding worldwide. However, fewer yield-related quantitative trait loci (QTL) have been reported in peanut than in other staple food crops such as rice (<em>Oryza sativa</em>), wheat (<em>Triticum aestivum</em>), and maize (<em>Zea mays</em>). This study aimed to identify stable major-effect QTL associated with pod yield per plant, hundred-pod weight for double-seeded pods, hundred-seed weight, shelling percentage, and pod number per plant, allowing us to predict candidate genes by means of transcriptome and genome sequencing. To this end, we used a population of recombinant inbred lines comprising 192 F<sub>9:11</sub> families derived from a JH6 × KX01-6 cross to construct a high-resolution genetic map (1705.7 cM) consisting of 2273 polymorphic SNPs, with 0.75 cM (on average) between adjacent SNPs. We identified two high-confidence, yield-related QTL, <em>qHYF_A08</em> and <em>qHYF_B06</em>, explaining 5.78%–31.40% of phenotypic variation and with LOD values of 5.10–24.48, in six environments. <em>qHYF_A08</em> mainly explained the variation in shelling percentage, whereas <em>qHYF_B06</em> explained variation in hundred-pod weight and hundred-seed weight and accounted for 8.77%–31.40% of the variation in effective pod number per plant, pod number per plant, and shelling percentage. We narrowed down <em>qHYF_B06</em> to an 890-kb interval using an advanced mapping population. Transcriptome and genome analyses revealed that only Arahy.129FS0 and Arahy.3R9A5K in the candidate mapping interval were differentially expressed between JH6 and KX01-6, with substantial structural variations in their promoter and coding regions. Genotypes of 208 peanut accessions determined using a diagnostic CAPS marker suggested that the two haplotypes of Arahy.3R9A5K were highly associated with hundred-seed weight and hundred-pod weight; this diagnostic CAPs marker could therefore be useful for selecting high-yielding lines during peanut breeding. Overall, our results provide valuable information for cloning alleles with favorable effects on peanut yield.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49845244","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
Changes in concentrations and transcripts of plant hormones in wheat seedling roots in response to Fusarium crown rot 小麦根尖镰刀菌冠腐病对根系植物激素浓度和转录的影响
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.01.006
Yutian Gao , Xuejun Tian , Weidong Wang , Xiangru Xu , Yuqing Su , Jiatian Yang , Shuonan Duan , Jinlong Li , Mingming Xin , Huiru Peng , Qixin Sun , Chaojie Xie , Jun Ma
{"title":"Changes in concentrations and transcripts of plant hormones in wheat seedling roots in response to Fusarium crown rot","authors":"Yutian Gao ,&nbsp;Xuejun Tian ,&nbsp;Weidong Wang ,&nbsp;Xiangru Xu ,&nbsp;Yuqing Su ,&nbsp;Jiatian Yang ,&nbsp;Shuonan Duan ,&nbsp;Jinlong Li ,&nbsp;Mingming Xin ,&nbsp;Huiru Peng ,&nbsp;Qixin Sun ,&nbsp;Chaojie Xie ,&nbsp;Jun Ma","doi":"10.1016/j.cj.2023.01.006","DOIUrl":"https://doi.org/10.1016/j.cj.2023.01.006","url":null,"abstract":"<div><p>Fusarium crown rot (FCR) is a soilborne disease causing severe yield losses in many wheat-growing areas of the world. Diseased plants show browning and necrosis of roots and stems causing white heads at maturity. Little is known about the molecular processes employed by wheat roots to respond to the disease. We characterized morphological, transcriptional and hormonal changes in wheat seedling roots following challenge with <em>Fusarium pseudograminearum</em> (<em>Fp</em>), the main pathogen of FCR. The pathogen inhibited root development to various extents depending on plants’ resistance level. Many genes responsive to FCR infection in wheat roots were enriched in plant hormone pathways. The contents of compounds involved in biosynthesis and metabolism of jasmonic acid, salicylic acid, cytokinin and auxin were drastically changed in roots at five days post-inoculation. Presoaking seeds in methyl jasmonate for 24 h promoted FCR resistance, whereas presoaking with cytokinin 6-benzylaminopurine made plants more susceptible. Overexpression of <em>TaOPR3</em>, a gene involved in jasmonic acid biosynthesis, enhanced plant resistance as well as root and shoot growth during infection.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49883484","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: 1
Trehalose: A sugar molecule involved in temperature stress management in plants 海藻糖:一种在植物中参与温度胁迫管理的糖分子
1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.09.010
Ali Raza, Savita Bhardwaj, Md Atikur Rahman, Pedro García-Caparrós, Madiha Habib, Faisal Saeed, Sidra Charagh, Christine H Foyer, Kadambot H.M. Siddique, Rajeev K. Varshney
{"title":"Trehalose: A sugar molecule involved in temperature stress management in plants","authors":"Ali Raza, Savita Bhardwaj, Md Atikur Rahman, Pedro García-Caparrós, Madiha Habib, Faisal Saeed, Sidra Charagh, Christine H Foyer, Kadambot H.M. Siddique, Rajeev K. Varshney","doi":"10.1016/j.cj.2023.09.010","DOIUrl":"https://doi.org/10.1016/j.cj.2023.09.010","url":null,"abstract":"","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136153972","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
Development of plant cytosine base editors with the Cas12a system 利用Cas12a系统开发植物胞嘧啶碱基编辑器
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.03.002
Huanhuan Wang , Jing Liang , Like Chen , Bufang Deng , Dongfang Gu , Xiaoshuang Liu , Shan Jin , Rongfang Xu , Ruiying Qin , Yitong Zhu , Liangxia Zhao , Dourong Kou , Yanjun Chen , Yingli Jiang , Juan Li , Pengcheng Wei
{"title":"Development of plant cytosine base editors with the Cas12a system","authors":"Huanhuan Wang ,&nbsp;Jing Liang ,&nbsp;Like Chen ,&nbsp;Bufang Deng ,&nbsp;Dongfang Gu ,&nbsp;Xiaoshuang Liu ,&nbsp;Shan Jin ,&nbsp;Rongfang Xu ,&nbsp;Ruiying Qin ,&nbsp;Yitong Zhu ,&nbsp;Liangxia Zhao ,&nbsp;Dourong Kou ,&nbsp;Yanjun Chen ,&nbsp;Yingli Jiang ,&nbsp;Juan Li ,&nbsp;Pengcheng Wei","doi":"10.1016/j.cj.2023.03.002","DOIUrl":"https://doi.org/10.1016/j.cj.2023.03.002","url":null,"abstract":"<div><p>Base editors of the Cas9 system have been widely used for precise nucleotide substitution in crops. In this study, Cas12a was applied to construct plant cytosine base editors (CBEs). The main elements of Cas12a-CBEs were engineered and their efficiency was evaluated in stably transformed rice cells. An optimized ttCas12a-hyA3Bctd editor, consisting of a LbCas12a variant carrying catalytic inactive D832A and temperature-tolerance D156R double mutations, a truncated human APOBEC3B deaminase, a human RAD51 single-stranded DNA-binding domain, and double copies of UGI, outperformed other Cas12a-CBEs in base editing efficiency. In T<sub>0</sub> transgenic rice plants, ttCas12a-hyA3Bctd edited an average of 42.01% and a maximum of 68.75% of lines at six genomic targets. A-to-G conversions were generated in rice by an adenine base editor with a similar architecture to the optimized CBE. Our results provide preliminary evidence for the feasibility of robust and efficient plant Cas12a base editing systems, which could be useful for precise crop breeding.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49845241","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
Multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysis 多组学数据集揭示了通过多光谱成像分析鉴定的苜蓿硬种子的显著物理和生理休眠
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.03.003
Xuemeng Wang , Han Zhang , Rui Song, Ming Sun, Ping Liu, Peixin Tian, Peisheng Mao, Shangang Jia
{"title":"Multiple omics datasets reveal significant physical and physiological dormancy in alfalfa hard seeds identified by multispectral imaging analysis","authors":"Xuemeng Wang ,&nbsp;Han Zhang ,&nbsp;Rui Song,&nbsp;Ming Sun,&nbsp;Ping Liu,&nbsp;Peixin Tian,&nbsp;Peisheng Mao,&nbsp;Shangang Jia","doi":"10.1016/j.cj.2023.03.003","DOIUrl":"https://doi.org/10.1016/j.cj.2023.03.003","url":null,"abstract":"<div><p>Physical dormancy (PY) commonly present in the seeds of higher plants is believed to be responsible for the germination failure by impermeable seed coat in hard seeds of legume species, instead of physiological dormancy (PD). In this study, a non-destructive approach involving multispectral imaging was used to successfully identify hard seeds from non-hard seeds in <em>Medicago sativa</em>, with accuracy as high as 96.8%–99.0%. We further adopted multiple-omics strategies to investigate the differences of physiology, metabolomics, methylomics, and transcriptomics in alfalfa hard seeds, with non-hard seeds as control. The hard seeds showed dramatically increased antioxidants and 125 metabolites of significant differences in non-targeted metabolomics analysis, which are enriched in the biosynthesis pathways of flavonoids, lipids and hormones, especially with significantly higher ABA, a hormone known to induce dormancy. In our transcriptomics results, the enrichment pathway of “response to abscisic acid” of differential expressed genes (DEG) supported the key role of ABA in metabolomics results. The methylome analysis identified 54,899, 46,216 and 54,452 differential methylation regions for contexts of CpG, CHG and CHH, and 344 DEGs might be regulated by hypermethylation and hypomethylation of promoter and exon regions, including four ABA- and JA-responsive genes. Among 8% hard seeds in seed lots, 24.5% still did not germinate after scarifying seed coat, and were named as non-PY hard seeds. Compared to hard seeds, significantly higher contents of ABA/IAA and ABA/JA were identified in non-PY hard seeds, which indicated the potential presence of PD. In summary, the significantly changed metabolites, gene expressions, and methylations all suggested involvement of ABA responses in hard seeds, and germination failure of alfalfa hard seeds was caused by combinational dormancy (PY + PD), rather than PY alone.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49845242","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: 3
SPP-extractor: Automatic phenotype extraction for densely grown soybean plants SPP提取器:密生大豆植株表型的自动提取
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 DOI: 10.1016/j.cj.2023.04.012
Wan Zhou , Yijie Chen , Weihao Li , Cong Zhang , Yajun Xiong , Wei Zhan , Lan Huang , Jun Wang , Lijuan Qiu
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