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Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

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Journal of Integrative Plant biology 2024年第7期66卷 1408-1426页

作者： Tianhao Zhang Wenjing Peng Hua Xiao Shuo Cao Zhuyifu Chen Xiangnian Su Yuanyuan Luo Zhongjie Liu Yanling Peng Xiping Yang Guo-Feng Jiang Xiaodong Xu Zhiyao Ma Yongfeng Zhou National key laboratory of Tropical Crop Breeding Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China state key laboratory for conservation and utilization of subtropical agro‐Bioresources Guangxi UniversityNanning 530004China guangxi key laboratory of Forest Ecology and conservation Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest PlantationCollege of ForestryGuangxi UniversityNanning 530004China College of Informatics Huazhong Agricultural UniversityWuhan 430070China guangxi key laboratory of sugarcane biology College of AgricultureGuangxi UniversityNanning 530004China key laboratory of Horticultural Plant biology Ministry of Education Huazhong Agricultural UniversityWuhan 430070China Zhengzhou Fruit Research Institute Chinese Academy of Agricultural SciencesZhengzhou 450009China National key laboratory of Tropical Crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural SciencesHaikou 571101China

Structural variations(SVs)are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic *** this study,we employed woolly grape(Vitis retordii),a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats,as a valuable model for examining the impact of SVs on local *** assembled a haplotype-resolved chromosomal reference genome for woolly grape,and conducted population genetic analyses based on whole-genome sequencing(WGS)data from coastal and inland *** demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal *** total,1,035 genes associated with plant adaptive regulation for salt stress,radiation,and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population,of which 37.29% and 65.26% were detected by SVs and SNPs,*** genes such as FSD2,RGA1,and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV *** study highlights the importance of SVs in local adaptation;candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.

关键词： climate change grape breeding local adaptation with gene flow salt tolerance viticulture Vitis

AcWRKY28 mediated activation of AcCPK genes confers salt tolerance in pineapple(Ananas comosus)

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Horticultural Plant Journal 2024年第2期10卷 398-412页

作者： Qiao Zhou Samaranayaka Vidana Gamage Nirosha Priyadarshani Rongjuan Qin Han Cheng Tiantian Luo Myat Hnin Wai Mohammad Aqa Mohammadi Yanhui Liu Chang Liu Hanyang Cai Xiaomei Wang Yeqiang Liu Yuan Qin Lulu Wang guangxi key lab of sugarcane biology State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesCollege of AgricultureGuangxi UniversityNanningGuangxi 530004China state key laboratory of Ecological Pest Control for Fujian and Taiwan Crops College of Life ScienceCollege of Plant ProtectionCollege of AgricultureCollege of HorticultureFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyCenter for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouFujian 350002China Pingtan Science and Technology Research Institute of Fujian Agriculture and Forestry University PingtanFujian 350400China National Education Commission BMICHColombo00700Sri Lanka Fishery Multiplication Management Station of Lijiang River Water Supply Hub Project GuilinGuangxi 541001China Horticulture Research Institute Guangxi Academy of Agricultural SciencesNanning Investigation Station of South Subtropical Fruit TreesMinistry of AgricultureNanningGuangxi 530007China

Unfavorable environmental cues severely affect crop productivity resulting in significant economic losses to farmers. In plants, multiple regulatory genes, such as the WRKY transcription factor (TF) family, modulate the expression of defense genes. However, the role of the pineapple WRKY genes is poorly understood. Here, we studied the pineapple WRKY gene, AcWRKY28, by generating AcWRKY28 over-expressing transgenic pineapple plants. Overexpression of AcWRKY28 enhanced the salt stress resistance in transgenic pineapple lines. Comparative transcriptome analysis of transgenic and wild-type pineapple plants showed that “plant-pathogen interaction” pathway genes, including 9calcium-dependent protein kinases (CPKs), were up-regulated in AcWRKY28 over-expressing plants. Furthermore, chromatin immunoprecipitation and yeast one-hybrid assays revealed AcCPK12, AcCPK3, AcCPK8, AcCPK1, and AcCPK15 as direct targets of AcWRKY28. Consistently, the study of AcCPK12 over-expressing Arabidopsis lines showed that AcCPK12 enhances salt, drought, and disease resistance. This study shows that AcWRKY28 plays a crucial role in promoting salt stress resistance by activating the expression of AcCPK genes.

关键词： Pineapple AcWRKY AcCPK Transcription factor Salt stress ChIP

DNA methylation in poultry:a review

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Journal of Animal Science and Biotechnology 2024年第2期15卷 509-518页

作者： Xing Ju Zhijun Wang Danfeng Cai Semiu Folaniyi Bello Qinghua Nie state key laboratory for conservation and utilization of subtropical agro‑Bioresources Lingnan Guangdong Laboratory of AgricultureCollege of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdong 510642China Guangdong Provincial key lab of agro‑Animal Genomics and Molecular Breeding and key lab of Chicken Genetics Breeding and ReproductionMinistry of AgricultureGuangzhouGuangdong 510642China College of Animal Science and Technology Zhejiang Agriculture and Forestry University666 Wusu RoadLin’an 311300China

As an important epigenetic modification,DNA methylation is involved in many biological processes such as animal cell differentiation,embryonic development,genomic imprinting and sex chromosome *** DNA methylation sequencing becomes more sophisticated,it becomes possible to use it to solve more zoological *** paper reviews the characteristics of DNA methylation,with emphasis on the research and application of DNA methylation in poultry.

关键词： CpG islands Differentially methylated genes Differentially methylated regions DNA methylation Poultry

Breeding maize of ideal plant architecture for high-density planting tolerance through modulating shade avoidance response and beyond

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Journal of Integrative Plant biology 2024年第5期66卷 849-864页

作者： Fereshteh Jafari Baobao Wang Haiyang Wang Junjie Zou Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China Graduate School of Chinese Academy of Agricultural Sciences Beijing 100081China National Nanfan Research Institute CAASSanya 572025China state key laboratory for conservation and utilization of subtropical agro-Bioresources College of Life SciencesSouth China AgriculturalUniversityGuangzhou 510642China

Maize is a major staple crop widely used as food,animal feed,and raw materials in industrial ***-density planting is a major factor contributing to the continuous increase of maize ***,high planting density usually triggers a shade avoidance response and causes increased plant height and ear height,resulting in lodging and yield *** plant height and ear height,more erect leaf angle,reduced tassel branch number,earlier flowering,and strong root system architecture are five key morphological traits required for maize adaption to high-density *** this review,we summarize recent advances in deciphering the genetic and molecular mechanisms of maize involved in response to high-density *** also discuss some strategies for breeding advanced maize cultivars with superior performance under high-density planting conditions.

关键词： flowering time high-density planting leaf angle maize plant architecture plant height/ear height root architecture tasselbranch

sRNAminer:多功能的植物小RNA分析工具

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Science Bulletin 2024年第6期69卷 784-791页

作者：李冠良陈程杰陈佩珂 Blake C.Meyers 夏瑞 state key laboratory for conservation and utilization of subtropical agro-Bioresources College of HorticultureSouth China Agricultural UniversityGuangzhou 510640China Guangdong laboratory for Lingnan Modern Agriculture South China Agricultural UniversityGuangzhou 510640China key laboratory of biology and Germplasm Enhancement of Horticultural Crops in South China Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhou 510640China Center Saint LouisMO 63132USA Division of Plant Science and Technology University of Missouri-ColumbiaColumbiaMO 65211USA

Small RNAs(sRNAs),found extensively in plants,play an essential role in plant growth and *** various sRNA analysis tools have been developed for plants,the use of most of them depends on programming and command-line environments,which is a challenge for many wet-lab ***,current sRNA analysis tools mostly focus on the analysis of certain type of sRNAs and are resource-intensive,normally demanding an immense amount of time and effort to learn the use of numerous tools or scripts and assemble them into a workable pipeline to get the final ***,we present sRNAminer,a powerful stand-alone toolkit with a user-friendly interface that integrates all common functions for the analysis of three major types of plant sRNAs:microRNAs(miRNAs),phased small interfering RNAs(phasiRNAs),and heterochromatic siRNAs(hc-siRNAs).We constructed a curated or"golden"set of MIRNA and PHAS loci,which was used to assess the performance of sRNAminer in comparison to other existing *** results showed that sRNAminer outperformed these tools in multiple aspects,highlighting its *** addition,to enable an efficient evaluation of sRNA annotation results,we developed Integrative Genomics Viewer(IGV)-sRNA,a modified genome browser optimized from IGV and we incorporated it as a functional module in ***-sRNA can display a wealth of sRNA-specific features,enabling a more comprehensive understanding of sRNA *** and IGV-sRNA are both platform-independent software that can be run under all operating *** are now freely available at https://***/kli28/sRNAminer and https://***/CJchen/IG V-sRNA.

关键词： sRNAminer sRNA analysis miRNA PhasiRNA hc-siRNA IGV-sRNA

Manganese toxicity-induced chlorosis in sugarcane seedlings involves inhibition of chlorophyll biosynthesis

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The Crop Journal 2022年第6期10卷 1674-1682页

作者： Shu Yang Guizhi Ling Qiuyue Li Ke Yi Xinlian Tang Muqing Zhang Xiaofeng Li state key laboratory for conservation and utilization of subtropical agro-bioresources/guangxi key laboratory for sugarcane biology College of AgricultureGuangxi UniversityNanning 530004GuangxiChina Institute for New Rural Development Guangxi UniversityNanning 530004GuangxiChina

Manganese(Mn)toxicity-induced leaf chlorosis limits crop production in acidic soils,but its underlying mechanisms remain *** effects of excessive Mn on chlorophyll(Chl)biosynthesis in sugarcane(Saccharum officinarum L.)leaves were *** Mn treatment,Chl concentration decreased with Mn accumulation and chlorosis appeared in expanding *** that,levels of the initial Chl precursor 5-aminolevulinic acid(ALA)and its downstream intermediates decreased,whereas magnesium-protoporphyrin IX monomethyl ester(MgPME)*** of Mn in leaves downregulated the ALA biosynthetic gene GluTR(encoding glutamyl-tRNA reductase)and MgPME conversion gene MgPMEC(encoding MgPME cyclase),upregulated the ALA biosynthesis inhibitor FLU(encoding FLUORESCENT),but had no significant effect on the expression of other Chl biosynthetic *** above Mn-induced changes of Chl precursors and expression of corresponding genes commenced before the Chl decline and leaf chlorosis,and were reversed by ALA ***,excessive Mn-induced chlorosis in sugarcane is mediated by a Chl-biosynthesis disorder resulting from the inhibition of ALA synthesis and MgPME conversion.

关键词： sugarcane Manganese toxicity Chlorosis Chlorophyll biosynthesis Gene expression

Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum

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Journal of Integrative Agriculture 2022年第11期21卷 3230-3244页

作者： LIU Lei WANG Heng-bo LI Yi-han CHEN Shu-qi WU Ming-xing DOU Mei-jie QI Yi-yin FANG Jing-ping ZHANG Ji-sen Center for Genomics and Biotechnology Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of GeneticsFujian Agriculture and Forestry UniversityFuzhouFujian 350002P.R.China state key lab for conservation and utilization of subtropical agro-biological resources&guangxi key lab for sugarcane biology Guangxi UniversityNanning 530004P.R.China College of Life Sciences Fujian Normal UniversityFuzhou 350007P.R.China

sugarcane has a large,complex,polyploid genome that has hindered the progress of genomic research and molecular marker-assisted *** user-friendly SSR markers have attracted considerable attention owing to their ideal genetic ***,these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane *** this present study,744305and 361638 candidate SSRs were identified from the genomes of *** and ***,*** verified the reliability of the predicted SSRs by using 1200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum,including ***,***,***,and modern sugarcane *** results showed that 660 SSR markers displayed interspecific polymorphisms among these ***,100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions.A total of 320 alleles were generated using 100 polymorphic primers,with each marker ranging from two to seven *** genetic diversity analysis revealed that these accessions were distributed in four main groups,including group I(14 *** accessions),group II(two *** accessions),group III(18 modern sugarcane hybrid accessions),and group IV(five *** accessions).Experimental verification supported the reliability of the SSR markers based on genome-wide *** development of a large number of SSR markers based on wet experiments is valuable for genetic studies,including genetic linkage maps,comparative genome analysis,genome-wide association studies,and marker-assisted selection in Saccharum.

关键词： Saccharum genome-wide simple repeat sequences(SSR) microsatellite molecular markers

Sequence analysis of Erianthus arundinaceus chromosome 1 isolated by flow sorting after genomic in situ hybridization in suspension

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The Crop Journal 2022年第6期10卷 1746-1754页

作者： Shan Yang Petr Cápal Jaroslav Dolezel Xueting Li Wang Qian Zhiqiang Wang Kai Zeng Peiting Li Hongkai Zhou Rui Xia Muqing Zhang Zuhu Deng National Engineering Research Center for sugarcane&state key laboratory for conservation and utilization of subtropical agro-bioresources Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina state key laboratory for conservation and utilization of subtropical agro-bioresources&guangxi key laboratory of sugarcane biology Guangxi UniversityNanning 530004GuangxiChina Institute of Experimental Botany of the Czech Academy of Sciences Center of the Region Hanáfor Biotechnological and Agricultural ResearchOlomouc CZ-77900Czech Republic College of Coastal Agricultural Sciences Guangdong Ocean UniversityZhanjiang 524088GuangdongChina state key laboratory for conservation and utilization of subtropical agro-bioresources South China Agricultural UniversityGuangzhou 510642GuangdongChina

Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic ***,limited knowledge of the complex genome of hexaploid *** has impeded the development of required molecular *** complex genomes into single chromosomes can simplify *** flow-cytometric sorting of a single chromosome of *** in a Saccharum-Erianthus introgression line is reported.A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size.A total of 218,000 *** chromosome 1(EaC1)were sorted to>97%purity and amplified DNA was sequenced using Illumina and Pac Bio *** resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb.A total of 56.69 Mb repeat sequences were predicted,accounting for 79.1%of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59%of the *** these genes,1877(70.9%)genes were functionally *** phylogenetic relationship of *** with other species using the chromosome1 sequence revealed that *** was distantly related to Oryza sativa and Zea mays,followed by Sorghum bicolor,and was closely related to *** and Saccharum *** study provides the first insights into the characteristics of EaC1,and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.

关键词： Flow cytometry GISHIS Chromosome sorting Genome analysis sugarcane

SsRSS1 mediates salicylic acid tolerance and contributes to virulence in sugarcane smut fungus

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Journal of Integrative Agriculture 2023年第7期22卷 2126-2137页

作者： ZHANG Hao-yang YANG Yan-fang GUO Feng SHEN Xiao-rui LU Shan CHEN Bao-shan College of Agriculture/guangxi key laboratory of sugarcane biology Guangxi UniversityNanning 530004P.R.China state key laboratory for conservation and utilization of subtropical agro-Bioresources/College of Life Science and Technology Guangxi UniversityNanning 530004P.R.China Ministry and Province Co-sponsored Collaborative Innovation Center for sugarcane and Sugar Industry Guangxi UniversityNanning 530004P.R.China

sugarcane smut caused by Sporisorium scitamineum is a destructive disease responsible for significant losses in sugarcane production ***,the mechanisms underlying the pathogenicity of this fungus remain largely *** this study,we found that the disruption of the SsRSS1 gene,which encodes a salicylic acid(SA)sensing regulator,does not affect phenotypic traits such as the morphology,growth rate,and sexual mating ability of haploid basidiospores,but rather reduces the tolerance of basidiospores to SA stress by blocking the induction of SsSRG1,a gene encoding a SA response protein in ***1 deletion resulted in the attenuation of the virulence of the *** addition to a significant reduction in whip formation,a portion of plantlets(18.3%)inoculated with theΔSsRSS1 strains were found to be infected but failed to produce whips for up to 90 days ***,the development of hyphae and teliospore from theΔSsRSS1-infected plants that formed whips seemed indistinguishable from that in the wild-type-infected ***,our findings suggested that SsRss1 is required for maintaining fungal fitness in planta by counteracting SA stress.

关键词： Sporisorium scitamineum SsRSS1 pathogenicity salicylic acid response