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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

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ORPA:a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes

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Journal of Genetics and Genomics 2024年第3期51卷 352-358页

作者： Guiqi Bi Xinxin Luan Jianbin Yan Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518124China Zhengzhou Research Base State Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan 450001China

Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually,a process that can be time-consuming and prone to errors.The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations.The processing of a large number of sequences,however,remains a time-consuming task.To conquer this challenge,we develop a speedy and efficient method called Organelle genomes for Phylogenetic analysis(ORPA).ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST,completing the task just in 1 min.With increasing data volume,the efficiency of ORPA is even more pronounced,over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes.The phylogenetic tree outputs from ORPA are equivalent to HomBlocks,indicating its outstanding efficiency.Due to its speed and accuracy,ORPA can identify species-level evolutionary conflicts,providing valuable insights into evolutionary cognition.

关键词： Ultrafast alignment Organelle phylogenomics Phylogenomic conflict Efficient pipeline Multiple sequence alignment pipeline

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Improving error-correcting capability in DNA digital storage via soft-decision decoding

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National Science Review 2024年第2期11卷 135-144页

作者：丁璐璐伍世刚候志浩李阿伦许亚苹冯虎潘玮华阮珏 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 Guangdong Provincial Key laboratory of Plant Molecular Breeding State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural University

Error-correcting codes(ECCs) employed in the state-of-the-art DNA digital storage(DDS) systems suffer from a trade-off between error-correcting capability and the proportion of redundancy. To address this issue, in this study, we introduce soft-decision decoding approach into DDS by proposing a DNA-specific error prediction model and a series of novel strategies. We demonstrate the effectiveness of our approach through a proof-of-concept DDS system based on Reed-Solomon(RS) code, named as Derrick. Derrick shows significant improvement in error-correcting capability without involving additional redundancy in both in vitro and in silico experiments, using various sequencing technologies such as Illumina, Pac Bio and Oxford Nanopore Technology(ONT). Notably, in vitro experiments using ONT sequencing at a depth of 7× reveal that Derrick, compared with the traditional hard-decision decoding strategy, doubles the error-correcting capability of RS code, decreases the proportion of matrices with decoding-failure by 229-fold, and amplifies the potential maximum storage volume by impressive 32 388-fold. Also, Derrick surpasses ‘state-of-the-art' DDS systems by comprehensively considering the information density and the minimum sequencing depth required for complete information recovery. Crucially, the soft-decision decoding strategy and key steps of Derrick are generalizable to other ECCs' decoding algorithms.

关键词： DNA digital storage (DDS) error-correcting code (ECC) soft-decision decoding error-correcting capability storage volume

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Characterization of the pheromone receptors in Mythimna loreyi reveals the differentiation of sex pheromone recognition in Mythimna species

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Insect Science 2024年第1期31卷 173-185页

作者： Chan Wang Lei Liu Tian-Yu Huang Yu Zhang Yang Liu Gui-Rong Wang State Key laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina Guangdong laboratory of Lingnan Modern agriculture ShenzhenGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina School of Forestry Northeast Forestry UniversityHarbinChina Key laboratory of Biohazard Monitoring Green Prevention and Control for Artificial GrasslandMinistry of Agriculture and Rural AffairsInstitute of Grassland Research of Chinese Academy of Agricultural SciencesInner Mongolia HohhotChina

Pheromone receptors(PRs)are key proteins in the molecular mechanism of pheromone recognition,and exploring the functional differentiation of PRs between closely related species helps to understand the evolution of moth mating systems.Pheromone components of the agricultural pest Mythimna loreyi have turned into(Z)-9-tetradecen-1-yl acetate(Z9-14:OAc),(Z)-7-dodecen-1-yl acetate(Z7-12:OAc),and(Z)-11-hexadecen-1-yl acetate,while the composition differs from that of M.separata in the genus Mythimna.To understand the molecular mechanism of pheromone recognition,we sequenced and analyzed antennal transcriptomes to identify 62 odorant receptor(OR)genes.The expression levels of all putative ORs were analyzed using differentially expressed gene analysis.Six candidate PRs were quantified and functionally characterized in the Xenopus oocytes system.MlorPR6 and MlorPR3 were determined to be the receptors of major and minor components Z9-14:OAc and Z7-12:OAc.MlorPR1 and female antennae(FA)-biased MlorPR5 both possessed the ability to detect pheromones of sympatric species,including(Z,E)-9,12-tetradecadien-1-ol,(Z)-9-tetradecen-1-ol,and(Z)-9-tetradecenal.Based on the comparison of PR functions between M.loreyi and M.separata,we analyzed the differentiation of pheromone recognition mechanisms during the evolution of the mating systems of 2 Mythimna species.

关键词： antennal transcriptome Mythimna loreyi pheromone receptor sex pheromone Xenopus oocyte

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Enhancing sheepgrass through genomic exploration and targeted editing

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Science China(Life Sciences) 2024年第3期67卷 629-630页

作者： Miao Sun Sanwen Huang Yao Zhou Key laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing 100093China State Key laboratory of Tropical Crop Breeding Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China State Key laboratory of Tropical Crop Breeding Chinese Academy of Tropical Agricultural SciencesHaikou 571101China

The growth of grass industry is essential for meeting human needs for proteins and sustaining grassland ecosystems(Bengtsson et al., 2019). Leymus chinensis, also known as sheepgrass, is a perennial Triticeae forage r... 详细信息

关键词： grassland sheep ecosystems

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The evolution and diurnal expression patterns of photosynthetic pathway genes of the invasive alien weed,Mikania micrantha

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Journal of Integrative agriculture 2024年第2期23卷 590-604页

作者： Kangkang Wang Mengjiao Jin Jingjing Li Yesong Ren Zaiyuan Li Xinghai Ren Cong Huang Fanghao Wan Wanqiang Qian Bo Liu Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China State Key laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China Shenzhen Research Institute of Henan University Shenzhen 518000China

Mikania micrantha is a fast-growing global invasive weed species that causes severe damage to natural ecosystems and very large economic losses of forest and crop production.It has advantages in photosynthesis,including a similar net photosynthetic rate as C4 plants and a higher carbon fixation capacity.We used a combination of genomics and transcriptomics approaches to study the evolutionary mechanisms and circadian expression patterns of M.micrantha.In M.micrantha,16 positive selection genes focused on photoreaction and utilization of photoassimilates.In different tissues,98.1%of the genes associated with photoresponse had high expression in stems,and more than half of the genes of the C4 cycle had higher expression in stems than in leaves.In stomatal opening and closing,2 genes of carbonic anhydrase(CAs)had higher expression at 18:00 than at 8:00,and the slow anion channel 1(SLAC1)and high-leaf-temperature 1 kinase(HT1)genes were expressed at low levels at 18:00.In addition,genes associated with photosynthesis had higher expression levels at 7:00 and 17:00.We hypothesized that M.micrantha may undergo photosynthesis in the stem and flower organs and that some stomata of the leaves were opening at night by CO_(2)signals.In addition,its evolution may attenuate photoinhibition at high light intensities,and enhance more efficient of photosynthesis during low light intensity.And the tissue-specific photosynthetic types and different diurnal pattern of photosynthetic-related genes may contribute to its rapid colonization of new habitats of M.micrantha.

关键词： invasion plant Mikania micrantha photosynthesis stomata stem

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Identification of an odorant receptor responding to sex pheromones in Spodoptera frugiperda extends the novel type-I PR lineage in moths

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Insect Science 2024年第2期31卷 489-502页

作者： Sai Zhang Emmanuelle Jacquin-Joly Nicolas Montagne Fang Liu Yang Liu Guirong Wang College of Horticulture and Plant Protection Yangzhou UniversityYangzhouChina State Key laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBejingChina Institute of Ecology and En vironmental Sciences of Paris INRAESorbonne UniversityCNRSIRDUPECUniversity of ParisVersaillesFrance Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina

moths,pheromone receptors(PRs)are crucial for intraspecific sexual communication between males and females.Moth PRs are considered as an ideal model for studying the evolution of insect PRs,and a large number of PRs have been identified and functionally characterized in different moth species.Moth PRs were initially thought to fall into a single monophyletic clade in the odorant receptor(OR)family,but recent studies have shown that ORs in another lineage also bind type-I sex pheromones,which indicates that type-I PRs have multiple independent origins in the Lepidoptera.In this study,we investigated whether ORs of the pest moth Spodoptera frugiperda belonging to clades closely related to this novel PR lineage may also have the capacity to bind type-I pheromones and serve as male PRs.Among the 7 ORs tested,only 1(SfruOR23)exhibited a male-biased expression pattern.Importantly,in vitro functional characterization showed that SfruOR23 could bind several type-I sex pheromone compounds with Z-9-tetradecenal(Z9-14:Ald),a minor component found in female sex pheromone glands,as the optimal ligand.In addition,SfruOR23 also showed weak responses to plant volatile organic compounds.Altogether,we characterized an S.frugiperda PR positioned in a lineage closely related to the novel PR clade,indicating that the type-I PR lineage can be extended in moths.

关键词： odorant receptor pheromone receptor lineage sex pheromone Spodoptera frugiperda

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Combining genome-wide association study and transcriptome analysis to identify molecular markers and genetic basis of population-asynchronous ovarian development in Coilia nasus

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Zoological Research 2024年第3期45卷 491-505页

作者： Yue Yu Shi-Ming Wan Cheng-You Huang Shuang-Meng Zhang Ai-Li Sun Jun-Qi Liu Shun-Yao Li Yong-Fu Zhu Shu-Xin Gu Ze-Xia Gao College of Fisheries Hubei Hongshan Laboratory/Key Lab of Freshwater Animal BreedingMinistry of Agriculture and Rural Affairs/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationHuazhong Agricultural UniversityWuhanHubei 430070China laboratory for Marine Biology and Biotechnology Qingdao Marine Science and Technology CenterQingdaoShandong 266237China Wuhan Hengyuxin Technology Breeding Professional Cooperative WuhanHubei 430117China Hubei Provincial Aquatic Science Research Institute WuhanHubei 430208China Zhenjiang Jiangzhiyuan Fishery Technology Co. Ltd.ZhenjiangJiangsu 212213China

Coilia nasus,a migratory fish species found in the middle and lower reaches of the Yangtze River and along offshore areas of China,possesses considerable aquacultural and economic potential.However,the species faces challenges due to significant variation in the gonadal development rate among females,resulting in inconsistent ovarian maturation times at the population level,an extended reproductive period,and limitations on fish growth rate due to ovarian prematurity.In the present study,we combined genome-wide association study(GWAS)and comparative transcriptome analysis to investigate the potential single nucleotide polymorphisms(SNPs)and candidate genes associated with population-asynchronous ovarian development in C.nasus.Genotyping of the female population based on whole-genome resequencing yielded 2120695 high-quality SNPs,39 of which were suggestively associated with ovarian development.Of note,a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified,with cpne5a determined as the causal gene of the peak.Therefore,single-marker and haplotype association analyses were performed on cpne5a,revealing four genetic markers(P0.9)significantly associated with the phenotype.Comparative transcriptome analysis of precociously and normally maturing individuals screened out 29 and 426 overlapping differentially expressed genes in the brain and ovary,respectively,between individuals of different body sizes.Integrating the GWAS and transcriptome analysis results,this study identified genes and pathways related to hypothalamic-pituitary-gonadal axis hormone secretion,extracellular matrix,angiogenesis,and gap junctions involved in population-asynchronous ovarian development.The insights gained from this study provide a basis for a deeper understanding of the molecular mechanisms underlying ovarian development in fish and may facilitate the genetic breeding of C.nasus strains exhibiting population-synchronous ovarian development in the future.

关键词： Coilia nasus GWAS Transcriptome Ovarian development SNP

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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

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genome-wide analysis of Panonychus citrimicro RNAs witha focus on potential insecticidal activity of 4 micro RNAs toeggs and nymphs

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Insect Science 2024年第2期31卷 354-370页

作者： Chuan-Zhen Li Yu-Hang Liu Deng Pan Meng-Hao Xia Qiang Zhang Yu-Chuang Li Guo-Rui Yuan Jin-Jun Wang Wei Dou Key laboratory of Entomology and Pest Control Engineering College of Plant ProtectionAcademy of Agricultural SciencesSouthwestUniversityChongqingChina Key laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River(ministry of Education) Academy of Agricultural SciencesSouthwest UniversityChongqingChina

Panonychus citriMcGregor(Acari:Tetranychidae),a destructive citrus pest,causes considerable annual economic losses due to its short lifespan and rapid resistancedevelopment.MicroRNA(miRNA)-induced RNA interference is a promising approachfor pest control because of endogenous regulation of pest growth and development.Tosearch for miRNAs with potential insecticidal activity inP.citri,genome-wide analysis ofmiRNAs at different developmental stages was conducted,resulting in the identificationof 136 miRNAs,including 73 known and 63 novel miRNAs.A total of 17 isomiRNAsand 12 duplicated miRNAs were characterized.MiR-1 and miR-252-5p were identified asreference miRNAs forP.citriandTetranychus urticae.Based on differential expressionanalysis,treatments with miR-let-7a and miR-315 mimics and the miR-let-7a antagomirsignificantly reduced the egg hatch rate and resulted in abnormal egg development.Over-expression or downregulation of miR-34-5p and miR-305-5p through feeding significantlydecreased the adult eclosion rate and caused molting defects.The 4 miRNAs,miR-let-7a,miR-315,miR-34-5p,and miR-305-5p,had important regulatory functions and insectici-dal properties in egg hatching and adult eclosion.In general,these data advance our un-derstanding of miRNAs in mite biology,which can assist future studies on insect-specificmiRNA-based green pest control technology.

关键词： growth and development microRNAs Panonychus citri referencemiRNAs regulation small RNA libraries

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