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Smart Breeding Platform:A web-based tool for high-throughput population genetics,phenomics,and genomic selection

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Molecular Plant 2024年第5期17卷 677-681页

作者： Huihui Li Xin Li Peng Zhang Yingwei Feng Junri Mi Shang Gao Lele Sheng Mohsin Ali Zikun Yang Liang Li Wei Fang Wensheng Wang Qian Qian Fei Gu Wenbin Zhou State key laboratory of crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China Nanfan Research Institute CAASSanyaHainan 572024China DAMO Academy Alibaba GroupHangzhou 310023China Hupan Lab Hangzhou 310023China Yazhouwan National laboratory No.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China State key laboratory of Rice Biology China National Rice Research InstituteHangzhouZhejiang 310006China

Dear Editor,In the era of big data and artificial intelligence,"smart breeding"has become a broad conceptual framework encompassing the paradigm shift of crop breeding to relying on analysis of high-throughput population genetics and phenomics data to conduct genomic selection,allowing identification and optimal use of the genetic potential in crop species(Xiao et al.,2022;Xu et al.,2022;Wang et al.,2023).Most existing tools for analyzing high-throughput breeding data require extensive computational power,complex installation processes,and command-line expertise and are therefore challenging and inconvenient for the majority of researchers and breeders(Brandies and Hogg,2021).

关键词： breeding artificial breed

Genes controlling grain chalkiness in rice

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The crop Journal 2024年第4期12卷 979-991页

作者： Luo Chen Xiumei Li Minhua Zheng Rui Hu Jingfang Dong Lingyan Zhou Wuge Liu Dilin Liu Wu Yang Rice Research Institute Guangdong Academy of Agricultural SciencesGuangdong Key Laboratory of New Technology in Rice BreedingGuangdong Rice Engineering LaboratoryKey Laboratory of Genetics and Breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province)Ministry of Agriculture and Rural AffairsGuangzhou 510640GuangdongChina College of Agriculture and Biology Zhongkai University of Agriculture and EngineeringGuangzhou 510225GuangdongChina Guangdong Provincial key laboratory for crop Germplasm Resources Preservation and Utilization Agro-biological Gene Research CenterGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

With rising living standards,there is an increasing demand for high-quality *** quality is mainly defined by milling quality,appearance quality,cooking and eating quality,and nutrition *** them,chalkiness is a key trait for appearance quality,which adversely affects cooking and eating quality,head rice yield,and commercial ***,chalkiness is undesirable,and reducing chalkiness is a major goal in rice quality ***,chalkiness is a complex trait jointly influenced by genetic and environmental factors,making its genetic study and precision improvement a huge *** the rapid development of molecular techniques,much knowledge has been gained about the genes and molecular networks involved in chalkiness *** present review describes the major environmental factors affecting chalkiness and summarizes the quantitative trait loci(QTL)associated with *** than 150 genes related to chalkiness formation have been *** functions of the genes regulating chalkiness,primarily those involved in starch synthesis,storage protein synthesis,transcription regulation,organelle development,grain shape regulation,and hightemperature response,are ***,we identify the challenges associated with genetic improvement of chalkiness and suggest potential ***,the review offers insight into the molecular dynamics of chalkiness and provides a strong basis for the future breeding of high-quality rice varieties.

关键词： Rice Grain quality Chalkiness QTL identification Gene

Suppressing a mitochondrial calcium uniporter activates the calcium signaling pathway and promotes cell elongation in cotton

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The crop Journal 2024年第2期12卷 411-421页

作者： Yujia Duan Xiaoguang Shang Ruiping Tian Weixi Li Xiaohui Song Dayong Zhang Wangzhen Guo State key laboratory of crop Genetics&Germplasm Enhancement and Utilization Nanjing Agricultural UniversityNanjing 210095JiangsuChina Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application Nanjing Agricultural UniversityNanjing 210095JiangsuChina

Mitochondrial calcium uniporter(MCU)is a conserved calcium ion(Ca^(2+))transporter in the mitochondrial inner membrane of eukaryotic *** MCU proteins regulate Ca^(2+)flow and modulate plant cell development remain largely ***,we identified the gene GhMCU4 encoding a MCU protein that negatively regulates plant development and fiber elongation in cotton(Gossypium hirsutum).GhMCU4expressed constitutively in various tissues with the higher transcripts in elongating fiber *** of GhMCU4 in cotton significantly elevated the plant height and root *** calcium signaling pathway was significantly activated and calcium sensor genes,including Ca^(2+)dependent modulator of interactor of constitutively active ROP(GhCMI1),calmodulin like protein(GhCML46),calciumdependent protein kinases(GhCPKs),calcineurin B-like protein(GhCBLs),and CBL-interacting protein kinases(GhCIPKs),were dramatically upregulated in GhMCU4-silenced *** processes were preferentially enriched,and genes related to regulation of transcription were upregulated in GhMCU4-silenced *** contents of Ca^(2+)and H_(2)O_(2)were significantly increased in roots and leaves of GhMCU4-silenced *** length and Ca^(2+)and H_(2)O_(2)contents in fibers were significantly increased in GhMCU4-silenced *** study indicated that GhMCU4 plays a negative role in regulating cell elongation in cotton,thus expanding understanding in the role of MCU proteins in plant growth and development.

关键词： Calcium signaling Hydrogen peroxide Metabolic processed Gossypium hirsutum

Unveiling the evolutionary dynamics of microR NA-targeted plant laccase genes

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Science China Life Sciences 2024年

作者： Rui-Rui He Meng-Qi Lei Yan-Zhao Feng Jiao Xue Yu-Chan Zhang Yue-Qin Chen Yang Yu Guangdong Provincial key laboratory of Plant Stress Biology State Key Laboratory for Biocontrol School of Life Science Sun Yat-Sen University Guangdong key laboratory of crop Germplasm Resources Preservation and Utilization Agro-biological Gene Research Center Guangdong Academy of Agricultural Sciences

Dear Editor,MicroRNAs (miRNAs) are small noncoding RNA molecules that play crucial roles in the regulation of gene *** have been extensively studied in various organisms, including plants,where they have been found to be involved in diverse biological processes,such as development, growth, and response to environmental stresses. Plant miRNAs achieve their regulatory functions by binding to the m RNA of target genes and modulating their expression levels.

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Large porewater exchange reshapes saltmarsh carbon and greenhouse gas budgets on local and global scales

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Science China Earth Sciences 2024年第7期67卷 2195-2209页

作者： Xiaogang CHEN Isaac RSANTOS Lucheng ZHAN Yu Yan YAU Yan ZHANG Ling LI key laboratory of Coastal Environment and Resources of Zhejiang Province School of EngineeringWestlake UniversityHangzhou 310024China Department of Marine Sciences University of GothenburgGothenburg 41319Sweden College of water Conservancy and Hydropower Engineering Hohai UniversityNanjing 210024China

Saltmarshes are carbon-rich ecosystems that play a role in climate regulation by efficiently sequestrating atmospheric CO_(2).Climate change is a major threat to saltmarshes and will impact saltmarsh carbon ***,porewater-derived carbon outwelling emerges as a crucial pathway for carbon sequestration,but it has been largely overlooked in ***,we assessed the drivers of dissolved carbon exports and greenhouse gas emissions in a saltmarsh and placed those observations into a global *** our study site,porewater exchange(PEX)was the major process controlling dissolved carbon and greenhouse gas *** our results with 33 other studies in saltmarshes worldwide,porewater-derived carbon fluxes were equivalent to~48% of average global saltmarsh primary productivity and 2.2 times greater than global organic carbon ***,our local observations and global upscaling demonstrate the major role played by PEX in saltmarsh carbon *** part of dissolved inorganic carbon returns to the atmosphere as CO_(2),the remaining bicarbonate fraction is stored in the ocean over long time *** findings strengthen global blue carbon assessments and build arguments for the use of saltmarshes as nature-based solutions for global climate change.

关键词： Coastal carbon Global carbon budget Carbon neutrality Nature-based solutions Coastal wetlands Submarine groundwater discharge

Natural variation of an autophagy-family gene among rice subspecies affects grain size and weight

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The crop Journal 2024年第1期12卷 121-132页

作者： Shiying Huang Peng Wang Caijing Li Qingwen Zhou Tao Huang Yicong Cai Qin Cheng Hui Wang Qi Zhong Zhihao Chen Liping Chen Haohua He Jianmin Bian key laboratory of crop Physiology Ecology and Genetic BreedingMinistry of Education.Jiangxi Agricultural UniversityNanchang 330045JiangxiChina Weill Cornell Medical Immunology and Microbiology1300 York AvenueBox 62New YorkNY 10065USA

Elucidating the genetic basis of natural variation in grain size and weight among rice varieties can help breeders develop high-yielding *** identified a novel gene,GW3a(Grain Weight 3a)(LOC_Os03g27350),that affects rice grain size and ***3a mutants showed higher total starch content and dry matter accumulation than the wild type(WT),Nipponbare,suggesting that GW3a negatively regulates grain size and ***,our study found that GW3a interacted with OsATG8 by cleaving it,suggesting that GW3a may be involved in the assembly of autophagosomes and starch degradation in *** haplotype analysis of GW3a showed functional differences between indica and japonica *** together,we conclude that GW3a is expressed in the autophagosome pathway regulating starch metabolism in rice,affecting yield-related traits,such as grain size,grain weight and thousand grain weight(TGW).Our findings also shed new light on autophagy-mediated yield trait regulation,proposing a possible strategy for the genetic improvement of high-yield germplasm in rice.

关键词： Grain size GW3a Autophagy Starch content

Identification of Highly Repetitive Enhancers with Long-range regulation Potential in Barley via STARR-seq

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 107-120页

作者： Wanlin Zhou Haoran Shi Zhiqiang Wang Yuxin Huang Lin Ni Xudong Chen Yan Liu Haojie Li Caixia Li Yaxi Liu State key laboratory of crop Gene Exploration and Utilization in Southwest China Sichuan Agricultural UniversityChengdu 611130China Triticeae Research Institute Sichuan Agricultural UniversityChengdu 611130China Chengdu Academy of Agricultural and Forestry Sciences Chengdu 611130China

Enhancers are DNA sequences that can strengthen transcription ***,the global identification of plant enhancers is complicated due to uncertainty in the distance and orientation of enhancers,especially in species with large *** this study,we performed self-transcribing active regulatory region sequencing(STARR-seq)for the first time to identify enhancers across the barley genome.A total of 7323 enhancers were successfully identified,and among 45 randomly selected enhancers,over 75%were effective as validated by a dual-luciferase reporter assay system in the lower epidermis of tobacco ***,up to 53.5%of the barley enhancers were repetitive sequences,especially transposable elements(TEs),thus reinforcing the vital role of repetitive enhancers in gene *** the common active mark H3K4me3 and repressive mark H3K27me3 were abundant among the barley STARR-seq *** addition,the functional range of barley STARR-seq enhancers seemed much broader than that of rice or maize and extended to±100 kb of the gene body,and this finding was consistent with the high expression levels of genes in the *** study specifically depicts the unique features of barley enhancers and provides available barley enhancers for further utilization.

关键词： Barley Enhancer Transposable element Gene expression Repetitive sequence

Two types of coumarins-specific enzymes complete the last missing steps in pyran- and furanocoumarins biosynthesis

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Acta Pharmaceutica Sinica B 2024年第2期14卷 869-880页

作者： Yucheng Zhao Yuedong He Liangliang Han Libo Zhang Yuanzheng Xia Fucheng Yin Xiaobing Wang Deqing Zhao Sheng Xu Fei Qiao Yibei Xiao Lingyi Kong Department of Resources Science of Traditional Chinese Medicines School of Traditional Chinese Pharmacyand State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing 210009China College of Bioscience and Biotechnology Hunan Agricultural UniversityChangsha 410128China Jiangsu key laboratory of Bioactive Natural Product Research and State key laboratory of Natural Medicines Department of Natural Medicinal ChemistryChina Pharmaceutical UniversityNanjing 210009China key laboratory of crop Gene Resources and Germplasm Enhancement in Southern China Ministry of AgricultureTropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural SciencesHaikou 517317China Institute of Botany Jiangsu Province and Chinese Academy of SciencesNanjing 210014China Department of Pharmacology School of Pharmacyand State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing 210009China

Pyran-and furanocoumarins are key representatives of tetrahydropyrans and tetrahydrofurans,respectively,exhibiting diverse physiological and medical ***,the biosynthetic mechanisms for their core structures remain poorly *** we combined multiomics analyses of biosynthetic enzymes in Peucedanum praeruptorum and in vitro functional verification and identified two types of key enzymes critical for pyran and furan ring biosynthesis in *** included three distinct *** prenyltransferases(PpPT1e3)responsible for the prenylation of the simple coumarin skeleton 7 into linear or angular precursors,and two novel CYP450 cyclases(PpDC and PpOC)crucial for the cyclization of the linear/angular precursors into either tetrahydropyran or tetrahydrofuran *** analyses of cyclases indicated that acid/base-assisted epoxide ring opening contributed to the enzyme-catalyzed tetrahydropyran and tetrahydrofuran ring *** possible acid/base-assisted catalytic mechanisms of the identified cyclases were theoretically investigated and assessed using site-specific *** identified two possible acidic amino acids Glu303 in PpDC and Asp301 in PpOC as vital in the catalytic *** study provides new enzymatic tools in the epoxide formation/epoxide-opening mediated cascade reaction and exemplifies how plants become chemically diverse in terms of enzyme function and catalytic process.

关键词： Tetrahydropyrans Tetrahydrofurans Baldwin rules Coumarins CYP450cyclase

Transcription factor OsWRKY11 induces rice heading at low concentrations but inhibits rice heading at high concentrations

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Journal of Integrative Plant Biology 2024年第7期66卷 1385-1407页

作者： Lirong Zhao Yunwei Liu Yi Zhu Shidie Chen Yang Du Luyao Deng Lei Liu Xia Li Wanqin Chen Zhiyu Xu Yangyang Xiong You Ming Siyu Fang Ligang Chen Houping Wang Diqiu Yu CAS key laboratory of Tropical Plant Resources and Sustainable use Xishuangbanna Tropical Botanical GardenThe Chinese Academy of SciencesMengla 666303China College of Life Sciences University of Chinese Academy of SciencesBeijing 101408China State key laboratory for Conservation and Utilization of Bio‐resources in Yunnan Yunnan UniversityKunming 650500China School of Life Sciences Yunnan UniversityKunming 650500China Southwest United Graduate School Yunnan UniversityKunming 650092China

The heading date of rice is a crucial agronomic characteristic that influences its adaptability to different regions and its productivity *** the involvement of WRKY transcription factors in various biological processes related to development,the precise mechanisms through which these transcription factors regulate the heading date in rice have not been well *** present study identified OsWRKY11 as a WRKY transcription factor which exhibits a pivotal function in the regulation of the heading date in rice through a comprehensive screening of a clustered regularly interspaced palindromic repeats(CRISPR)-CRISPR-associated nuclease 9 mutant library that specifically targets the WRKY genes in *** heading date of oswrky11 mutant plants and OsWRKY11-overexpressing plants was delayed compared with that of the wild-type plants under short-day and long-day *** investigation revealed that OsWRKY11 exerts dual effects on transcriptional promotion and suppression through direct and indirect DNA binding,*** normal conditions,OsWRKY11 facilitates flowering by directly inducing the expression of OsMADS14 and *** presence of elevated levels of OsWRKY11 protein promote formation of a ternary protein complex involving OsWRKY11,Heading date 1(Hd1),and Days to heading date 8(DTH8),and this complex then suppresses the expression of Ehd1,which leads to a delay in the heading *** investigation revealed that a mild drought condition resulted in a modest increase in OsWRKY11 expression,promoting ***,under severe drought conditions,a significant upregulation of OsWRKY11 led to the suppression of Ehd1 expression,ultimately causing a delay in heading *** findings uncover a previously unacknowledged mechanism through which the transcription factor OsWRKY11 exerts a dual impact on the heading date by directly and indirectly binding to the promoters of target genes.

关键词： heading date OsWRKY11 rice transcription factors