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Unveiling a half-century mystery of molecular bases for three-line hybrid rice breeding system

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Journal of Integrative Plant Biology 2024年第1期66卷 3-6页

作者： Xiaoming Zheng qian qian State Key Laboratory of Crop Gene Resources and Breeding Chinese Academy of Agricultural SciencesBeijing 100081China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya 572024China

Rice(Oryza sativa L.)isa staplecropforhalf theworld's Ipopulation and an important contributor to world food security.The discovery and application of cytoplasmic male sterility(CMS)and fertility restoration(Rf)genetic materials have allowed the production of three-line hybrid rice(Kim and Zhang,2018),successfully harnessing heterosis in crops.Three major CMS and/or Rf systems are commonly used to produce three-line hybrid rice:Wild Abortive(CMS-WA),Boroll(CMS-BT),and Honglian(CMS-HL).Among these,the CMS-WA system is the most widely employed(Sattari et al.,2007;Chen and Liu,2014;Huang et al.,2014).Several Rf genes from different CMS systems have been cloned in rice,including Rf4 for CMS-WA(Tang et al.,2014),Rf1a and Rf1b for CMS-BT(Wang et al.,2006),Rf5,and Rf6 for CMS-HL(Huet al.,2012;Huang et al.,2015),and Rf19for CMS-FA(Jiang et al.,2022).A molecular mechanism and evolutionary model for the CMS-WA gene WA352c have also been reported(Luo et al.,2013;Tang et al.,2017).

关键词： breeding fertility Wild

Molecular Mechanism of Rice Necrotic Lesion for Optimized Yield and Disease Resistance

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Rice science 2024年第3期31卷 285-299页

作者： HOU Xinyue WANG Yuping qian qian REN Deyong State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Rice Research InstituteSichuan Agricultural UniversityChengdu 611130China

How to balance rice resistance and yield is an important issue in rice breeding.Plants with mutated necrotic lesion genes often have persistent broad-spectrum resistance,but this broad-spectrum resistance usually comes at the expense of yield.Currently,many necrotic lesion mutants in rice have been identified,and these genes are involved in disease resistance pathways.This review provides a detailed introduction to the characteristics,classification,and molecular mechanisms of necrotic lesion formation.Additionally,we review the molecular regulatory pathways of genes involved in rice disease resistance.Concurrently,we summarize the relationship between resistance and yield in rice using newly developed gene editing methods.We discuss a rational and precise breeding strategy to better utilize molecular design technology for breeding disease-resistant and high-yield rice varieties.

关键词： rice necrotic lesion regulation mechanism high yield high resistance

Grow rice under sunshine of Xizang/Tibet:promise and challenges

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Journal of Genetics and Genomics 2024年第3期51卷 265-267页

作者： Chunkun Fan Xiaoming Zheng Qingbo Yuan Tao Wang qian qian Qingyun Bu Fan Chen Agricultural Institute Xizang Academy of Agricultural and Animal Husbandry ScienceLasaXizang 850032China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of AgriculturalSciencesBeijing 100081China Sanya National Research Institute of Breeding in Hainan Chinese Academy of Agricultural SciencesBeijing 572000China Yazhouwan National Laboratory SanyaHainan 572704China Chengdu Institute of Biology Chinese Academy of SciencesChengduSichuan 610041China Northeast Institute of Geography and Agroecology Chinese Academy of SciencesHarbinHeilongjiang 150081China

Xizang,previously known as Tibet,is located in the southwest region of China and is the highest region of the Qinghai-Tibet Plateau(QzP),with an average altitude of over 4000 m.With the development of modern agriculture,the grain productivity in Xizang has been effectively improved.The total annual grain production has increased from 558,700 tons in 1988 to 1044,000 tons in 2018(Xizang Statistical Year Book).

关键词： sunshine Tibet southwest

Rice AGL1 determines grain size and sterile lemma identity

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The Crop Journal 2024年第2期12卷 630-634页

作者： Haiping Yu An Wang Guangheng Zhang Guojun Dong Longbiao Guo qian qian Deyong Ren State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006ZhejiangChina Hainan Yazhou Bay Seed Laboratory Sanya 572024HainanChina National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024HainanChina

The grass spikelet is a unique inflorescence structure that determines grain size.Although many genetic factors have been well characterized for grain size and glume development,the underlying molecular mechanisms in rice are far from established.Here,we isolated rice gene,AGL1 that controlled grain size and determines the fate of the sterile lemma.Loss of function of AGL1 produced larger grains and reduced the size of the sterile lemma.Larger grains in the agl1 mutant were caused by a larger number of cells that were longer and wider than in the wild type.The sterile lemma in the mutant spikelet was converted to a rudimentary glume-like organ.Our findings showed that the AGL1(also named LAX1)protein positively regulated G1 expression,and negatively regulated NSG1 expression,thereby affecting the fate of the sterile lemma.Taken together,our results revealed that AGL1 played a key role in negative regulation of grain size by controlling cell proliferation and expansion,and supported the opinion that rudimentary glume and sterile lemma in rice are homologous organs.

关键词： Abnormal grain and sterile lemma 1 Oryza sativa Grain size Rudimentary glume

Carotenoid isomerase regulates rice tillering and grain productivity by its biosynthesis pathway

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Journal of Integrative Plant Biology 2024年第2期66卷 172-175页

作者： Chaoqing Ding Zhengji Shao Yuping Yan Guangheng Zhang Dali Zeng Li Zhu Jiang Hu Zhenyu Gao Guojun Dong qian qian Deyong Ren State Key Laboratory of Rice Biology and Breeding ChinaNational Rice Research InstituteHangzhou 310006China

Tillers are unique inflorescence-like branches in grasses,and their number determines the panicle number,plant architecture,and yield(Shang et al.,2021).Tiller formation mainly undergoes axillary meristem(AM)initiation and tiller bud outgrowth(Wang et al.,2018;Yan et al.,2023).The rice(Oryza sativa)KNOX gene OSH1 is expressed in AMs,and an osh1 mutant produces fewer tillers(Tanaka et al.,2015).

关键词： sativa Oryza panicle

Simultaneous production of high-frequency synthetic apomixis with high fertility and improved agronomic traits in hybrid rice

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Molecular Plant 2024年第1期17卷 4-7页

作者： Mengqiu Song Wumei Wang Chun Ji Shengnan Li Wei Liu Xiaoyu Hul Anhui Feng Shuang Ruan Shiyun Du Huan Wang Kui Dai Longbiao Guo qian qian Hongqi Si Xingming Hu College of Agronomy Anhui Agricultural UniversityHefeiAnhui 230036China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhouZhejiang 310006China Rice Research Institute Anhui Academy of Agricultural SciencesHefeiAnhui 230031China Jiangxi Modern Seed Industry Co.NanchangJiangxi 330026China

Dear Editor,Utilization of heterosis is fundamental to modern agricultural improvement and contributes significantly to food security and agricultural development(Ouyang et al.,2022).However,heterosis of F,hybrids cannot be stably inherited.Apomixis,or asexual reproduction through seeds,offers the potential for the fixation of heterosis in F,hybrids and the formation of clonal offspring,which could have considerable implications for plant breeding and agriculture(Schmidt,2020).But naturally occurring apomixis has never been found in major crops.Recently,synthetic apomixis has been successfully generated by inducing incomplete meiotic development combined with parthenogenesis development to produce cloned rice(Oryza sativa)seeds(Khanday et al.,2019;Wang et al.,2019;Vernet et al.,2022;Wei et al.,2023).

关键词： sativa fertility breeding

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

Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National Science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie qian qian Lianguang Shang 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 Sciences Institute of Wetland Agriculture and Ecology Shandong Academy of Agricultural Sciences State Key Laboratory of Rice Biology China National Rice Research Institute National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National Laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

A centromere map based on super pan-genome highlights the structure and function of rice centromeres

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Journal of Integrative Plant Biology 2024年第2期66卷 196-207页

作者： Yang Lv Congcong Liu Xiaoxia Li Yueying Wang Huiying He Wenchuang He Wu Chen Longbo Yang Xiaofan Dai Xinglan Cao Xiaoman Yu Jiajia Liu Bin Zhang Hua Wei Hong Zhang Hongge qian Chuanlin Shi Yue Leng Xiangpei Liu Mingliang Guo Xianmeng Wang Zhipeng Zhang Tianyi Wang Bintao Zhang qiang Xu Yan Cui qianqian Zhang Qiaoling Yuan Noushin Jahan Jie Ma Xiaoming Zheng Yongfeng Zhou qian qian Longbiao Guo Lianguang Shang State Key Laboratory of Rice Biology China 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 518120China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya City 572024China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary factors.Rice centromeres are crucial for chromosome segregation,and contain some unreported genes.Due to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is needed.We constructed a high-quality centromere map based on the rice super pangenome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.We showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary patterns.We also revealed that long terminal repeats(LTRs),especially young Gypsy-type LTRs,are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution.Furthermore,high-quality genome assembly and complete telomere-to-telomere(T2T)reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging.We investigated the association between structural variations and gene expression in the rice centromere.A centromere gene,OsMAB,which positively regulates rice tiller number,was further confirmed by expression quantitative trait loci,haplotype analysis and clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein9 methods.By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres,our finding will facilitate future research on centromere biology and crop improvement.

关键词： centromere super pan-genome CentoO satellite repeat rice