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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 Epub Date: 2023-04-18 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
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 Epub Date: 2023-06-05 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":"11 5","pages":"Pages 1353-1367"},"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
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 Epub Date: 2023-05-24 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":"11 5","pages":"Pages 1533-1540"},"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
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 Epub Date: 2023-05-29 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":"11 5","pages":"Pages 1521-1532"},"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
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 Epub Date: 2023-07-06 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":"11 5","pages":"Pages 1559-1568"},"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
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":"134 1","pages":"0"},"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
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 Epub Date: 2023-02-24 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":"11 5","pages":"Pages 1441-1450"},"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
Puccinia triticina effector protein Pt_21 interacts with wheat thaumatin-like protein TaTLP1 to inhibit its antifungal activity and suppress wheat apoplast immunity 小麦Puccinia triticina效应蛋白Pt_21与小麦thaumatin样蛋白TaTLP1相互作用抑制其抗真菌活性并抑制小麦质外体免疫
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 Epub Date: 2023-05-29 DOI: 10.1016/j.cj.2023.04.006
Fei Wang , Songsong Shen , Zhongchi Cui , Shitao Yuan , Ping Qu , Hui Jia , Linshuo Meng , Xiaoyu Hao , Daqun Liu , Lisong Ma , Haiyan Wang
{"title":"Puccinia triticina effector protein Pt_21 interacts with wheat thaumatin-like protein TaTLP1 to inhibit its antifungal activity and suppress wheat apoplast immunity","authors":"Fei Wang ,&nbsp;Songsong Shen ,&nbsp;Zhongchi Cui ,&nbsp;Shitao Yuan ,&nbsp;Ping Qu ,&nbsp;Hui Jia ,&nbsp;Linshuo Meng ,&nbsp;Xiaoyu Hao ,&nbsp;Daqun Liu ,&nbsp;Lisong Ma ,&nbsp;Haiyan Wang","doi":"10.1016/j.cj.2023.04.006","DOIUrl":"https://doi.org/10.1016/j.cj.2023.04.006","url":null,"abstract":"<div><p><em>Puccinia triticina</em> (<em>Pt</em>), as the causal agent of wheat leaf rust, employs a plethora of effector proteins to modulate wheat immunity for successful colonization. Understanding the molecular mechanisms underlying <em>Pt</em> effector-mediated wheat susceptibility remains largely unexplored. In this study, an effector Pt_21 was identified to interact with the apoplast-localized wheat thaumatin-like protein TaTLP1 using a yeast two-hybrid assay and the Pt_21-TaTLP1 interaction was characterized. The interaction between Pt_21 and TaTLP1 was validated by <em>in vivo</em> co-immunoprecipitation assay. A TaTLP1 variant, TaTLP1<sup>C71A</sup>, that was identified by the site-directed mutagenesis failed to interact with Pt_21. Pt_21 was able to suppress Bax-mediated cell death in leaves of <em>Nicotiana benthamiana</em> and inhibit TaTLP1-mediated antifungal activity. Furthermore, infiltration of recombinant protein Pt_21 into leaves of transgenic wheat line overexpressing <em>TaTLP1</em> enhanced the disease development of leaf rust compared to that in wild-type leaves. These findings demonstrate that Pt_21 suppresses host defense response by directly targeting wheat TaTLP1 and inhibiting its antifungal activity, which broadens our understanding of the molecular mechanisms underlying <em>Pt</em> effector-mediated susceptibility in wheat.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"11 5","pages":"Pages 1431-1440"},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49803786","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 and transcriptome sequencing reveal candidate genes conferring all-stage resistance to stripe rust on chromosome arm 1AL in Chinese wheat landrace AS1676 精细定位和转录组测序揭示了中国小麦地方品种AS1676染色体臂1AL上具有抗条锈病全阶段抗性的候选基因
IF 6.6 1区 农林科学
Crop Journal Pub Date : 2023-10-01 Epub Date: 2023-06-22 DOI: 10.1016/j.cj.2023.04.011
Xiu Yang , Yunfeng Jiang , Xianghai Yu , Haipeng Zhang , Yuqi Wang , Fangnian Guan , Li Long , Hao Li , Wei Li , Qiantao Jiang , Jirui Wang , Yuming Wei , Jian Ma , Houyang Kang , Pengfei Qi , Qiang Xu , Meng Deng , Yazhou Zhang , Youliang Zheng , Yonghong Zhou , Guoyue Chen
{"title":"Fine mapping and transcriptome sequencing reveal candidate genes conferring all-stage resistance to stripe rust on chromosome arm 1AL in Chinese wheat landrace AS1676","authors":"Xiu Yang ,&nbsp;Yunfeng Jiang ,&nbsp;Xianghai Yu ,&nbsp;Haipeng Zhang ,&nbsp;Yuqi Wang ,&nbsp;Fangnian Guan ,&nbsp;Li Long ,&nbsp;Hao Li ,&nbsp;Wei Li ,&nbsp;Qiantao Jiang ,&nbsp;Jirui Wang ,&nbsp;Yuming Wei ,&nbsp;Jian Ma ,&nbsp;Houyang Kang ,&nbsp;Pengfei Qi ,&nbsp;Qiang Xu ,&nbsp;Meng Deng ,&nbsp;Yazhou Zhang ,&nbsp;Youliang Zheng ,&nbsp;Yonghong Zhou ,&nbsp;Guoyue Chen","doi":"10.1016/j.cj.2023.04.011","DOIUrl":"https://doi.org/10.1016/j.cj.2023.04.011","url":null,"abstract":"<div><p>Stripe rust, caused by <em>Puccinia striiformis</em> f. sp. <em>tritici</em> (<em>Pst</em>), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against <em>Pst</em> race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F<sub>7</sub> recombinant inbred line (RIL) population lacking the <em>Yr18</em> gene, a near-isogenic line (NIL) population was developed to map the resistance gene. An all-stage resistance gene, <em>YrAS1676</em>, was identified on chromosome arm 1AL via bulked-segregant exome-capture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between <em>KA1A_485.36</em> and <em>KA1A_490.13</em>, spanning 485.36–490.13 Mb on 1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to <em>Pst</em> race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of <em>YrAS1676</em>. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with <em>Pst</em> challenge, the <em>YrAS1676</em> genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that <em>YrAS1676</em> has potential use in wheat stripe rust resistance breeding.</p></div>","PeriodicalId":10790,"journal":{"name":"Crop Journal","volume":"11 5","pages":"Pages 1501-1511"},"PeriodicalIF":6.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49803761","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
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 Epub Date: 2023-06-21 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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