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BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice

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Journal of Integrative plant Biology 2024年第9期66卷 1966-1982页

作者： Zhen Li Junhua Ye Qiaoling Yuan Mengchen Zhang Xingyu Wang Jing Wang Tianyi Wang Hongge Qian Xinghua Wei Yaolong Yang Lianguang Shang Yue Feng China National Center for Rice Improvement State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhou 310006China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China

Tiller angle is a key agricultural trait that establishes plant architecture,which in turn strongly affects grain yield by influencing planting density in *** shoot gravity response plays a crucial role in the regulation of tiller angle in rice,but the underlying molecular mechanism is largely ***,we report the identification of the BIG TILLER ANGLE2(BTA2),which regulates tiller angle by controlling the shoot gravity response in ***-of-function mutation of BTA2 dramatically reduced auxin content and affected auxin distribution in rice shoot base,leading to impaired gravitropism and therefore a big tiller ***2 interacted with AUXIN RESPONSE FACTOR7(ARF7)to modulate rice tiller angle through the gravity signaling *** BTA2 protein was highly conserved during *** variation in the BTA2 promoter of indica cultivars harboring a less expressed BTA2 allele caused lower BTA2 expression in shoot base and thus wide tiller angle during rice *** of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting *** findings thus uncovered the BTA2-ARF7 module that regulates tiller angle by mediating the shoot gravity *** work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.

关键词： auxin domestication gravity response rice tiller angle

A near-complete cucumber reference genome assembly and Cucumber-DB,a multi-omics database

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Molecular plant 2024年第8期17卷 1178-1182页

作者： Jiantao Guan Han Miao Zhonghua Zhang Shaoyun Dong Qi Zhoul Xiaoping Liu Diane M.Beckles Xingfang Gul Sanwen Huang Shengping Zhang State key laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina Engineering laboratory of Genetic Improvement of Horticultural crops of Shandong Province College of HorticultureQingdao Agricultural UniversityQingdao266109China Department of plant Sciences University of CaliforniaDavisOne Shield AvenueDavisCA95616USA

Dear Editor,Cucumber(Cucumis sativus)is a key vegetable crop and an essential model for genetics and genomics research in Cucurbitaceae,especially in studies on plant sex determination and vascular *** the first sequenced genome among vegetable crops,the cucumber reference genome has been a crucial genetic resource for comparative genomics and genetic ***,the latest version of the cucumber *** Long reference genome(CLv3.0),generated using PacBio long-reads data,is *** a predicted genome size of 350-367 Mb,CLv3.0 encompasses only 226.2 Mb,leaving 72 gaps and over 120 Mb of unknown *** low assembly completeness(approximately 62%)is primarily due to the high proportion(~30%)of heterochromatic satellite and rDNA sequences in cucumber,substantially higher than that observed in many other species such as Arabidopsis,rice,maize,and watermelon,where it is less than 5%(Han et al.,2008;Huang et al.,2009;Li et al.,2019).

关键词： crops incomplete cucumber

Next Generation Nutrition: Genomic and Molecular Breeding Innovations for Iron and Zinc Biofortification in Rice

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Rice science 2024年第5期31卷 526-544,I0029,I0030页

作者： Kunhikrishnan Hemalatha DHANYALAKSHMI Reshma MOHAN Sasmita BEHERA Uday Chand JHA Debashis MOHARANA Ahalya BEHERA Sini THOMAS Preman Rejitha SOUMYA Rameswar Prasad SAH Radha BEENA Department of plant physiology College of AgriculturePadannakkadKerala Agricultural UniversityKerala 671314India Department of plant physiology College of AgricultureVellayaniKerala Agricultural UniversityKerala 695522India crop Improvement Division India Council of Agricultural Research-National Rice Research InstituteOdisha 7530006India Department of plant Breeding and genetics Indian Institute of Pulse ResearchKanpur 208024India Department of plant physiology College of AgricultureKumarakomKerala Agricultural UniversityKerala 686563India

Global efforts to address malnutrition and hidden hunger, particularly prevalent in low- and middle-income countries, have intensified, with a focus on enhancing the nutritional content of staple crops like rice. Despite serving as a staple for over half of the world's population, rice falls short in meeting daily nutritional requirements, especially for iron(Fe) and zinc(Zn). Genetic resources, such as wild rice species and specific rice varieties, offer promising avenues for enhancing Fe and Zn content. Additionally, molecular breeding approaches have identified key genes and loci associated with Fe and Zn accumulation in rice grains. This review explores the genetic resources and molecular mechanisms underlying Fe and Zn accumulation in rice grains. The functional genomics involved in Fe uptake, transport, and distribution in rice plants have revealed key genes such as OsFRO1, OsIRT1, and OsNAS3. Similarly, genes associated with Zn uptake and translocation, including OsZIP11 and OsNRAMP1, have been identified. Transgenic approaches, leveraging transporter gene families and genome editing technologies, offer promising avenues for enhancing Fe and Zn content in rice grains. Moreover, strategies for reducing phytic acid(PA) content, a known inhibitor of mineral bioavailability, have been explored, including the identification of low-PA mutants and natural variants. The integration of genomic information, including whole-genome resequencing and pan-genome analyses, provides valuable insights into the genetic basis of micronutrient traits and facilitates targeted breeding efforts. functional genomics studies have elucidated the molecular mechanisms underlying Fe uptake and translocation in rice. Furthermore, transgenic and genome editing techniques have shown promise in enhancing Fe and Zn content in rice grains through the manipulation of key transporter genes. Overall, the integration of multi-omics approaches holds significant promise for addressing global malnutri

关键词： biofortification grain quality iron phytic acid rice zinc

Generation of selectable marker-free soft transgenic rice with transparent kernels by downregulation of SSSⅡ-2

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The crop Journal 2020年第1期8卷 53-61页

作者： Zhihao Xu Meimei Yu Youwei Yin Cenwen Zhu Wen Ji Changquan Zhang Qianfeng Li Honggen Zhang Shuzu Tang Hengxiu Yu Qiaoquan Liu jiangsu key laboratory of crop genetics and physiology Key Laboratory of Plant Functional Genomics of the Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingJiangsu Co-Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou University

The amylose content(AC) of rice endosperm starch varies from 0 to 35%,and is associated with rice cooking and eating *** rice has low AC,generally between 6% and 15%,and its eating quality is high whether it is consumed hot or ***,the appearance quality of current soft rice cultivars needs to be improved,especially opaque *** genetic engineering has improved some agronomic traits of soft rice varieties,but not endosperm *** the present study,a RNAi construct of the soluble starch synthase Ⅱ-2(SSSⅡ-2) and the hygromycin phosphotransferase(HPT) gene were introduced into an elite japonica rice variety,Kangtiaowuyunjing(KWY8) by *** selectable marker-free(SMF) transgenic lines were obtained,and SSSⅡ-2 expression was significantly downregulated in selected transgenic lines,resulting in lower AC of the *** physicochemical properties of the transgenic rice kernels,including gel consistency(GC) and rapid visco analyzer(RVA) profile,differed significantly from those of wild-type rice and were similar to those of a soft rice variety,Nanjing 46(NJ46).These findings indicate that the cooking,eating,and processing qualities of transgenic rice are comparable to those of ***,the transgenic rice endosperm retained a transparent appearance under low-moisture ***,SMF SSSⅡ-2 RNAi rice provides a resource for breeding soft rice with transparent endosperm.

关键词： Rice(Oryza sativa L.) SSSⅡ-2 RNAi Starch quality SMF transgenic lines

Prospect of the QTL-qSB-9^(Tq) utilized in molecular breeding program of japonica rice against sheath blight

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Journal of genetics and genomics 2008年第8期35卷 499-505页

作者： Shimin Zuo Li Zhang Hui Wang Yuejun Yin Yafang Zhang Zongxiang Chen Yuyin Ma Xuebiao Pan key laboratory of crop genetics and physiology of jiangsu Province Yangzhou University Yangzhou 225009 China key laboratory of plant functional genomics of Ministry of Education Yangzhou University Yangzhou 225009 China

The major QTL-qSB-9^Tq conferring partial resistance to rice （Oryza sativa L.） sheath blight （Rhizoctonia solani Kvhn） has been verified on chromosome 9 of the indica rice cultivar, Teqing. In this study, the prospect of this QTL utilized in molecular breeding program of japonica rice for sheath blight resistance was investigated. Most of the japonica rice cultivars showed lower level of sheath blight resistance than the indica rice cultivars. At the corresponding site of qSB-9^Tq, nine typical japonica rice cultivars from different ecological regions or countries proved to possess the susceptible allele（s）. Introgression of qSB-9^Tq into these cultivars enhanced their resistance level by decreasing sheath blight score of 1.0 （0.5-1.3）, which indicated that qSB-9^Tq had a large potential in strengthening the resistance of japonica rice to sheath blight. The use of the three molecular markers, which were polymorphic between Teqing and many japonica rice cultivars, promotes the application of qSB-9^Tq in a concrete molecular breeding program.

关键词： rice (Oryza sativa L.) japonica cultivar sheath blight QTL molecular breeding

Weed biology andmanagement in the multi-omics era:Progress and perspectives

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plant Communications 2024年第4期5卷 16-35页

作者： Ke Chen Haona Yang Di Wu Yajun Peng Lei Lian Lianyang Bai Lifeng Wang key laboratory of Indica Rice genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley Ministry of Agriculture and Rural AffairsHunan Rice Research InstituteHunan Academy of Agricultural SciencesChangsha 410125China State key laboratory of Hybrid Rice Hunan Academy of Agricultural SciencesChangsha 410125China Longping Branch College of BiologyHunan UniversityChangsha 410125China Huangpu Research Institute of Longping Agricultural Science and Technology Guangzhou 510715China Hunan Weed Science key laboratory Hunan Agricultural Biotechnology Research InstituteHunan Academy of Agricultural SciencesChangsha 410125China Qingdao Kingagroot Compounds Co.Ltd Qingdao 266000China

Weeds pose a significant threat to crop production,resulting in substantial yield *** addition,they possess robust weedy traits that enable them to survive in extreme environments and evade human *** recent years,the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy *** this review,we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology,including the origins of weed spe-cies,weed classification,and the underlying genetic and molecular bases of important weedy traits such as crop–weed interactions,adaptability to different environments,photoperiodicflowering responses,and herbicide *** addition,we discuss limitations to the application of multi-omics techniques in weed science,particularly compared with their extensive use in model plants and *** this regard,we provide a forward-looking perspective on the future application of multi-omics technologies to weed science *** powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy *** resulting advances will facilitate the development of sustainable and highly effective weed management strategies,promoting greener practices in agriculture.

关键词： weeds multi-omics weed management genomics RNA-seq

Genetic analysis and molecular mapping of a presenescing leaf gene psll in rice （Oryza sativa L.）

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Chinese Science Bulletin 2006年第24期51卷 2986-2992页

作者： WANG dun WU Shujun ZHOU Yong ZHOU Lihui XU Jiefen HU Jing FANG Yunxia GU Minghong LIANG Guohua key laboratory of the Ministry of Education for plant functional genomics/jiangsu key laboratory for crop genetics and physiology Yangzhou University Yangzhou 225009 China

A rice psl1 (presenescing leaf) mutant was obtained from a japonica variety Zhonghua 11 via radiation of 60Co-γ in M2 generation. Every leaf of the mutant began to wither after it reached the big-gest length,while the leaves of the wild variety could keep green for 25―35 d. In this study,genetic analysis and gene mapping were carried out for the mutant identified. The SSR marker analysis showed that the mutant was controlled by a single recessive gene (psl1) located on chromosome 2. Fine mapping of the psl1 locus was conducted with 34 new STS markers developed around psl1 anchored region based on the sequence diversity between Nippon-bare and 93-11. The psl1 was further mapped be-tween two STS markers,STS2-19 and STS2-26,with genetic distances of 0.43 and 0.11 cM,respectively,while cosegregated with STS2-25. A BAC contig was found to span the psl1 locus,the region being delim-ited to 48 kb. This result was very useful for cloning of the psl1 gene.

关键词： psIl基因水稻叶片早衰遗传分析分子图谱

Genetic mapping of quantitative trait loci in crops

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The crop Journal 2017年第2期5卷 175-184页

作者： Yang Xu Pengcheng Li Zefeng Yang Chenwu Xu jiangsu provincial key laboratory of crop genetics and physiology/Co-Innovation Center for Modern Production Technology of Grain crops Key Laboratory of Plant Functional Genomics of Ministry of Education Yangzhou University Yangzhou 225009 China

Dissecting the genetic architecture of complex traits is an ongoing challenge for *** complementary approaches for genetic mapping,linkage mapping and association mapping have led to successful dissection of complex traits in many crop *** of these methods detect quantitative trait loci(QTL) by identifying marker–trait associations,and the only fundamental difference between them is that between mapping populations,which directly determine mapping resolution and *** on this difference,we first summarize in this review the advances and limitations of family-based mapping and natural population-based mapping instead of linkage mapping and association *** then describe statistical methods used for improving detection power and computational speed and outline emerging areas such as large-scale meta-analysis for genetic mapping in *** the era of next-generation sequencing,there has arisen an urgent need for proper population design,advanced statistical strategies,and precision phenotyping to fully exploit high-throughput genotyping.

关键词： Family-based mapping Natural population-based mapping Mixed linear model MAGIC population Meta-analysis Genotyping by sequencing

Molecular evolution and functional divergence of HAK potassium transporter gene family in rice(Oryza sativa L.)

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Journal of genetics and genomics 2009年第3期36卷 161-172页

作者： Zefeng Yang Qingsong Gao Changsen Sun Wenjuan Li Shiliang Gu Chenwu Xu jiangsu provincial key laboratory of crop genetics and physiology Key Laboratory of Plant Functional Genomics of Ministry of Education Yangzhou University Yangzhou 225009 China School of Life Sciences Taizhou University Linhai 317000 China

The high-affinity K＋（HAK） transporter gene family is the largest family in plant that functions as potassium transporter and is important for various aspects of plant life. In the present study, we identified 27 members of this family in rice genome. The phylogenetic tree divided the land plant HAK transporter proteins into 6 distinct groups. Although the main characteristic of this family was established before the origin of seed plants, they also showed some differences between the members of non-seed and seed plants. The HAK genes in rice were found to have expanded in lineage-specific manner after the split of monocots and dicots, and both segmental duplication events and tandem duplication events contributed to the expansion of this family. functional divergence analysis for this family provided statistical evidence for shifted evolutionary rate after gene duplication. Further analysis indicated that both point mutant with positive selection and gene conversion events contributed to the evolution of this family in rice.

关键词： HAK potassium transporter gene family rice functional divergence gene conversion positive selection