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OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State Key Laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such ***,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 *** this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 *** transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 *** of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and *** addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and *** also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this *** OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower *** together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing *** ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

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Partnering crops with root-associated microbes for soil health and agricultural sustainability

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Pedosphere 2024年第1期34卷 26-29页

作者： Cunhu WANG Yongjia ZHONG Hong LIAO root Biology Center College of Resources and EnvironmentFujian Agriculture and Forestry UniversityFuzhou 350002China

Increasing global demand for food presents a significant challenge to maintaining soil health and sustainable production of agricultural crops. As plant root-associated microbial fitness is greatly impacted by community growth, development, and nutrient acquisition, the cultivation of functional assembly of root-associated microbes may provide solutions for achieving food security while maintaining healthy soils. Here, we propose a four-part strategy to promote soil health and agricultural productivity by partnering crops with root-associated microbes.

关键词： crops soil agricultural

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Soybean(Glycine max)rhizosphere organic phosphorus recycling relies on acid phosphatase activity and specific phosphorusmineralizing-related bacteria in phosphate deficient acidic soils

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Journal of Integrative Agriculture 2024年第5期23卷 1685-1702页

作者： Qianqian Chen Qian Zhao Baoxing Xie Xing Lu Qi Guo Guoxuan Liu Ming Zhou Jihui Tian Weiguo Lu Kang Chen Jiang Tian Cuiyue Liang root Biology Center State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesCollege of Natural Resources and EnvironmentSouth China Agricultural UniversityGuangzhou 510642China College of Natural Resources and Environment South China Agricultural UniversityGuangzhou 510642China Henan Academy of crops Molecular Breeding Henan Academy of Agricultural SciencesZhengzhou 450002China

Bacteria play critical roles in regulating soil phosphorus(P) cycling. The effects of interactions between crops and soil P-availability on bacterial communities and the feedback regulation of soil P cycling by the bacterial community modifications are poorly understood. Here, six soybean(Glycine max) genotypes with differences in P efficiency were cultivated in acidic soils with long-term sufficient or deficient P-fertilizer treatments. The acid phosphatase(AcP) activities, organic-P concentrations and associated bacterial community compositions were determined in bulk and rhizosphere soils. The results showed that both soybean plant P content and the soil AcP activity were negatively correlated with soil organic-P concentration in P-deficient acidic soils. Soil P-availability affected the ɑ-diversity of bacteria in both bulk and rhizosphere soils. However, soybean had a stronger effect on the bacterial community composition, as reflected by the similar biomarker bacteria in the rhizosphere soils in both P-treatments. The relative abundance of biomarker bacteria Proteobacteria was strongly correlated with soil organic-P concentration and AcP activity in low-P treatments. Further high-throughput sequencing of the phoC gene revealed an obvious shift in Proteobacteria groups between bulk soils and rhizosphere soils, which was emphasized by the higher relative abundances of Cupriavidus and Klebsiella, and lower relative abundance of Xanthomonas in rhizosphere soils. Among them, Cupriavidus was the dominant phoC bacterial genus, and it was negatively correlated with the soil organic-P concentration. These findings suggest that soybean growth relies on organic-P mineralization in P-deficient acidic soils, which might be partially achieved by recruiting specific phoCharboring bacteria, such as Cupriavidus.

关键词： organic phosphorus acid phosphatase soybean bacterial community phoC-harboring bacteria rhizosphere

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Melatonin mitigates cold-induced damage to pepper seedlings by promoting redox homeostasis and regulating antioxidant profiling

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Horticultural Plant Journal 2024年第2期10卷 532-544页

作者： Muhammad Ahsan Altaf Yuanyuan Hao Huangying Shu Weiheng Jin Chuhao Chen Lin Li Yu Zhang Muhammad Ali Mumtaz Huizhen Fu Shanhan Cheng Guopeng Zhu Zhiwei Wang Key Laboratory for Quality Regulation of Tropical Horticultural crops of Hainan Province Sanya Nanfan Research InstituteHainan UniversitySanyaHainan 572025China Key Laboratory for Quality Regulation of Tropical Horticultural crops of Hainan Province School of HorticultureHainan UniversityHaikouHainan 570228China Hainan Yazhou Bay Seed Laboratory SanyaHainan 572025China

This study assessed the influence of exogenous ME in the mitigation of cold damage in pepper seedlings. Melatonin(ME) is a dynamic molecule that helps plants cope with stress in several ways. Cold stress(CS) is one of the most important environmental factors that restrict plant growth and yield. Pepper(Capsicum annuum L.) is a valuable commercial crop, highly sensitive to CS. Thus, identifying an efficient strategy to mitigate cold damage is critical for long-term pepper production. For this purpose, the roots of pepper seedlings were pretreated with ME(5 μmol · L^(-1)) and exposed to CS for 7 d. The results indicated that CS suppressed pepper growth, hampered photosynthetic capacity, and damaged root architecture in pepper plants. In contrast, the production of reactive oxygen species(ROS), malondialdehyde(MDA), electrolyte leakage(EL), proline, and soluble sugars were enhanced in plants under CS. ME(5 μmol · L^(-1)) pretreatment reduced the negative effects of CS by recovering plant growth, root traits, gas exchange elements, and pigment molecules compared to CS control treatment. Furthermore, ME application efficiently reduced oxidative stress markers [hydrogen peroxide(H_(2)O_(2)), superoxide ion(O_(2)^(·-)), EL, and MDA] while increasing proline and soluble sugar content in pepper leaves. ME application combined with CS further increased antioxidant enzymes and related gene expression. Collectively, our results confirmed the mitigating potential of ME supplementation for CS by maintaining pepper seedling growth,improving the photosynthesis apparatus, regulating pigments, and osmolyte content.

关键词： Pepper Melatonin Cold stress Antioxidant enzyme root trait

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Mulching with plastic film improved the root quality of summersown sweet potato(Ipomoea batatas(L).Lam.)in northern China

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Journal of Integrative Agriculture 2019年第5期18卷 982-991页

作者： HOU Fu-yun DONG Shun-xu XIE Bei-tao ZHANG Hai-yan LI Ai-xian WANG Qing-mei Crop Research Institute Shandong Academy of Agricultural Sciences/Scientific Observation and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai RegionMinistry of Agriculture and Rural Affairs

The root quality of sweet potato cultivated during the summer season is poor in northern China;thus,this study was conducted to determine whether root quality could be improved through mulching with plastic film(MPF).The effect of MPF on root starch and its composition,the activity of starch synthesis enzymes,and other quality-related parameters were investigated in two purple flesh sweet potato cultivars,Jishu 18 and Ayamurasaki(Aya).The results indicated that root dry matter,anthocyanin content,adenosine triphosphate(ATP),and starch content were higher in both cultivars under the MPF treatment than those under the control *** root adenosine diphosphate glucose pyrophosphorylase/uridine diphosphate glucose pyrophosphorylase(ADPGPPase/UDPGPPase)activity and adenosine triphosphatease(ATPase)activity were increased using ***,under the MPF treatment,the amylose content,soluble sugar content,and granule-bound synthase(GBSS)activity increased in Jishu 18 but decreased in Aya,and the amylopectin content,protein content,and soluble starch synthase(SSS)activity decreased in Jishu 18 but increased in ***,MPF seems benifit to improve the quality of sweet potato,but the effects of this treatment condition may be dependent on the cultivar.

关键词： mulching with plastic film summer-sown sweet potato root quality starch

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Horticultural Plant Journal 2022年第3期8卷 369-380页

作者： Yumeng Niu Guangcun Li Yinqiao Jian Shaoguang Duan Ju Liu Jianfei Xu Liping Jin Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropsMinistry of Agriculture and Rural AffairsBeijing 100081China

Early tuberization,a short period from stolon occurrence to tuber formation,is one of the major characteristics of a good early-maturing potato cultivar,while the regulatory mechanism of tuberization time(TT)is still *** this study,two tetraploid cultivars,Zhongshu 3(Z3)and Zhongshu 18(Z18),with short and long TT respectively,were examined to reveal regulatory genes related to TT using RNA sequencing of tissue samples taken during stolon occurrence,stolon swelling and tuber *** analysis showed that the gene expression patterns at the stolon swelling and tuber formation stages were significantly different from those at stolon occurrence in both Z3 and ***,we screened the differentially expressed genes(DEGs)at stolon swelling and tuber formation and compared them to those at stolon occurrence.A total of 3085 DEGs were specifically identified and analyzed according to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment,and DEGs involved in starch and sucrose metabolism,plant hormone signal transduction and plant circadian clock were significantly *** circadian clock genes were significantly differentially expressed between Z3 and Z18,revealing an important role for the plant circadian pathway in regulating ***,three candidate genes,StGI,StPRR and StEFM involved in circadian regulation and significantly differentially expressed between Z3 and Z18,were discovered and confirmed by *** results provide valuable information for understanding the regulatory mechanisms of potato TT and represent a step toward breeding early-maturing potato cultivars.

关键词： Potato tuberization time Transcriptome analysis Circadian rhythm genes

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Screening Landraces for Additional Sources of Field Resistance to Cassava Mosaic Disease and Green Mite for Integration into the Cassava Improvement program

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Journal of Integrative Plant Biology 2008年第3期50卷 311-318页

作者： Adebola Raji Oluseyi Ladeinde Alfred Dixon root and tuber program International Institute of Tropical Agriculture (IITA) Ibadan Nigeria Department of Plant Breeding and Seed Technology University of Agriculture Abeokuta Nigeria

Twelve cassava landraces were evaluated for sources of resistance genes to diseases and pests of major economic importance in Africa. The objective was to assess their levels of field resistance to mosaic disease （ACMD）, bacterial blight （CBB）, anthracnose （CAD）, and green mite （CGM）, compared to TMS30572, an elite cultivar widely adopted in Africa. Considerable genotypic variation was observed among cultivars for resistance to ACMD and CGM but not for CBB and CAD. The lowest mean incidence of 12% and severity of 1.8 on a scale of 1-5 for ACMD was recorded for Atu, a landrace with farmer acceptable qualities. In comparison, the improved cultivar, TMS 30572, had a mean disease incidence of 72% and a severity score of 2.8. Another landrace, MS-20 had the lowest CGM damage score （2.1） while TMS 30572 emerged as one of the susceptible cultivars with a damage score of 3. Additional sources of resistance to ACMD and CGM that may possibly be better than the popular improved cultivar, TMS 30572, were identified in this study. These could serve as novel sources of additional genes to complement existing resources for elite cassava breeding in Africa.

关键词： anthracnose bacterial blight green mite landraces mosaic disease resistance

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Damage and Control Suggestions for the Emerging Disease Coffee root Rot

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Plant Diseases and Pests 2024年第4期15卷 13-16页

作者： Xingfei FU Guiping LI Faguang HU Institute of Tropical and Subtropical Cash crops Yunnan Academy of Agricultural SciencesBaoshan 678000China

[Objectives]The paper was to elucidate the symptoms,morphological characteristics,etiological factors,and current extent of damage associated with coffee root rot disease.[Methods]The symptoms,morphological characteristics,and etiological factors associated with coffee root rot disease were systematically observed,described,and *** assessment of damage was carried out using a specialized investigative methodology.[Results]The application of bottom fertilizer containing Fusarium incarnatum facilitated the pathogen's entry through root wounds during transplantation,resulting in the development of water-soaked depression lesions in the affected *** infection significantly reduced the number of lateral roots in coffee plants,leading to symptoms such as wilting,withering,and ultimately,the death of the aboveground *** exhibited three distinct types of spore morphology:macroconidia,which were sickle-shaped;mesoconidia,which were spindle-shaped;and microconidia,which were *** incidence rate of the disease in the affected region reached 100%,with a disease index exceeding 91,indicating severe damage.[Conclusions]This study serves as a valuable reference for the prevention and management of the emerging disease known as coffee root rot.

关键词： Coffea arabica root rot Fusarium incarnatum Prevention and control New diseases

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Transcriptional regulation of MdPIN7 by MdARF19 during gravityinduced formation of adventitious root GSA in self-rooted apple stock

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Horticultural Plant Journal 2024年第5期10卷 1073-1084页

作者： Zenghui Wang Xuemei Yang Linyue Hu Wei Liu Lijuan Feng Xiang Shen Yanlei Yin Jialin Li Shandong Institute of Pomology Tai'anShandong 271000China School of Biological Science and Technology University of JinanJinanShandong 250022China State Key Laboratory of Crop Biology Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(Huanghuai Region)Ministry of AgricultureCollege of Horticulture Science and EngineeringShandong Agricultural UniversityTai'anShandong 271018China

Self-rooted apple stock is widely used for apple ***,the shallowness of the adventitious roots in self-rooted apple stock leads to poor performance in the barren orchards of *** is because of the considerable difference in the development of a gravitropic set-point angle(GSA)between self-rooted apple stock and seedling ***,it is crucial to study the molecular mechanism of adventitious root GSA in self-rooted apple stock for breeding self-rooted and deep-rooted apple rootstock *** apple auxin response factor MdARF19 functioned to establish the adventitious root GSA of self-rooted apple stock in response to gravity and auxin ***19 bound directly to the MdPIN7 promoter,activating its transcriptional expression and thus regulating the formation of the adventitious root GSA in 12-2 self-rooted apple ***,MdARF19 influenced the expression of auxin efflux carriers(MdPIN3 and MdPIN10)and the establishment of adventitious root GSA of self-rooted apple stock in response to gravity signals by direct activation of *** findings provide new information on the transcriptional regulation of MdPIN7 by auxin response factor MdARF19 in the regulation of the adventitious root GSA of self-rooted apple stock in response to gravity and auxin signals.

关键词： Apple Self-rooted stock Gravity MdARF19 MdPIN7 Gravitropic set-point angle Transcriptional regulation

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Combined application of organic fertilizer and chemical fertilizer alleviates the kernel position effect in summer maize by promoting post-silking nitrogen uptake and dry matter accumulation

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Journal of Integrative Agriculture 2024年第4期23卷 1179-1194页

作者： Lichao Zhai Lihua Zhang Yongzeng Cui Lifang Zhai Mengjing Zheng Yanrong Yao Jingting Zhang Wanbin Hou Liyong Wu Xiuling Jia Institute of Cereal and Oil crops Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Crop Cultivation Physiology and Green Production of Hebei ProvinceShijiazhuang 050035China Hebei Science and Technology Innovation Service Center Shijiazhuang 050051China Yongnian Agricultural Technology Extension Center Handan 057150China Ningjin Agricultural Technology Extension Center Xingtai 055550China

Adjusting agronomic measures to alleviate the kernel position effect in maize is important for ensuring high *** order to clarify whether the combined application of organic fertilizer and chemical fertilizer(CAOFCF)can alleviate the kernel position effect of summer maize,field experiments were conducted during the 2019 and 2020 growing seasons,and five treatments were assessed:CF,100%chemical fertilizer;OFCF1,15%organic fertilizer+85%chemical fertilizer;OFCF2,30%organic fertilizer+70%chemical fertilizer;OFCF3,45%organic fertilizer+55%chemical fertilizer;and OFCF4,60%organic fertilizer+40%chemical *** with the CF treatment,the OFCF1 and OFCF2 treatments significantly alleviated the kernel position effect by increasing the weight ratio of inferior kernels to superior kernels and reducing the weight gap between the superior and inferior *** effects were largely due to the improved filling and starch accumulation of inferior ***,there were no obvious differences in the kernel position effect among plants treated with CF,OFCF3,or OFCF4 in most *** area indexes,post-silking photosynthetic rates,and net assimilation rates were higher in plants treated with OFCF1 or OFCF2 than in those treated with CF,reflecting an enhanced photosynthetic capacity and improved postsilking dry matter accumulation(DMA)in the plants treated with OFCF1 or *** with the CF treatment,the OFCF1 and OFCF2 treatments increased post-silking N uptake by 66.3 and 75.5%,respectively,which was the major factor driving post-silking photosynthetic capacity and ***,the increases in root DMA and zeatin riboside content observed following the OFCF1 and OFCF2 treatments resulted in reduced root senescence,which is associated with an increased post-silking N *** showed that post-silking N uptake,DMA,and grain yield in summer maize were negatively correlated with the kernel position *** conclusion,the combined application of

关键词： chemical fertilizer dry mater accumulation kernel position effect N uptake organic fertilizer

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