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Structural variation-driven FADS2P1 expression modulates hair trait diversity through unsaturated fatty acid metabolism in goats 认领 引用
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作者 Wenze Li Qi Lv +23 位作者 Yixin Su Can Liu Xianjin Jing Yujiang Wu Xin Wang Guobo Quan Di Han Chun Li Bouabid Badaoui Langda Suo Gao Gong Na Wang Oljibilig Chen Yixing Fan Jianning He Shaobin Li Peng Zhao Xiaochun Yan Ruijun Wang Yanjun Zhang Jinquan Li Zhiying Wang Yongbin Liu Rui Su 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2026年第8期1519-1534,共16页
Through natural and artificial selection,goats develop distinct hair phenotypes driven by genomic variations,such as structural variations(SVs).The fatty acid desaturase(FADS)family plays an important role in hair fol... Through natural and artificial selection,goats develop distinct hair phenotypes driven by genomic variations,such as structural variations(SVs).The fatty acid desaturase(FADS)family plays an important role in hair follicle(HF)growth,yet its molecular mechanisms remain unclear.In this study,we construct a goat graph-based pangenome containing 99,792 non-redundant presence-absence variations(PAVs)from 16goat breeds.Using this pangenome,we identify 15,866 allelic variants of PAVs with distinct dominant frequencies(dPAVs)from the resequencing data of 300 goats.Among them,1290 dPAVs regulate the expression of 772 corresponding genes in cashmere goats(CGs)with different hair types over 12 months.We identify an expanded FADS2P1 gene family with two intact copies and one truncated copy within segmental duplications.An intron deletion in the truncated FADS2P1 copy shows population-specific distribution patterns among goats with cashmere traits.All FADS2P1 copies are significantly upregulated in short-hair CGs,and their expression levels are negatively correlated with oleic acid(OA)levels.Functional validation in FADS2P1 knock-in mice indicates a slower hair growth rate and reduced HF numbers.These findings demonstrate that SV-driven FADS2P1 expression regulates HF development and growth through OA metabolism,providing insights into how PAVs influence complex phenotypes. 展开更多
关键词 Structural variations Fatty acid desaturase Unsaturated fatty acids Periodic growth Hair follicles Goat
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Complex plastome structural variation caused by intermolecular and intramolecular recombination accounts for leaf variegation in Heptapleurum ellipticum 认领 引用
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作者 Kainan Ma Shuaixi Zhou +1 位作者 Ying Liu Renchao Zhou 《Plant Diversity》 SCIE CAS CSCD 2026年第1期140-150,共11页
Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastom... Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastome structural variation,which is induced by one pair of small inverted repeats,can also result in leaf variegation.Here we show a complex plastome structural variation caused by intermolecular and intramolecular recombination across three pairs of small inverted repeats accounts for leaf variegation in a widely cultivated shrub Heptapleurum ellipticum(Araliaceae).This plastome structural variation contains two deletions and two duplications,resulting in dramatic expansion of IRs,substantial contraction of LSC and loss of 11 genes that essential for photosynthesis.Plastome heteroplasmy was detected in both green and albino sectors of variegated leaves.Relative to green sectors,albino sectors in the variegated leaves exhibit significantly reduced expression for the 11 genes lost in the mutated plastome as well as 26 other genes,but significantly increased expression for one gene related to translation apparatus.Optical and transmission electron microscopy observations showed that mesophyll cells of albino sectors possess plastids lacking grana lamellae,which likely carry the mutated plastome and contribute to albinism.In both sectors,the first layer of spongy mesophyll cells beneath the lower epidermis contains normal chloroplasts,suggesting periclinal division of the lower epidermis during development.Our study demonstrates that multiple small repeats can collectively mediate intra-and inter-molecular recombination in plastome and offers a new mechanism accounting for leaf variegation in plants. 展开更多
关键词 Heteroplasmy Recombination Plastome Structural variation Variegation Small repeats
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Erratum to"GenomeSyn:a bioinformatics tool for visualizing genome synteny and structural variations"[J.Genet.Genom.(2022)49,11741176] 认领 引用
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作者 Zu-Wen Zhou Zhi-Guang Yu +4 位作者 Xiao-Ming Huang Jin-Shen Liu Yi-Xiong Guo Ling-Ling Chen Jia-Ming Song 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2025年第8期1068-1069,共2页
Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural... Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural variations and other annotation information.B:The second type of visualization map was simple and only showed the synteny relationship between the chromosomes of two or three genomes.C:Multiplatform general GenomeSyn submission page,applicable to Windows,MAC and web platforms;other analysis files can be entered in the"other"option.The publisher would like to apologise for any inconvenience caused. 展开更多
关键词 two three genomes structural variations synteny relationship genomesyn visualizing genome synteny characterizing structural variationsa genome synteny synteny visualization map
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Exploring cattle structural variation in the era of long reads,pangenome graphs,and near-complete assemblies 认领 引用
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作者 George E.Liu 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2026年第2期583-590,共8页
Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph co... Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph construction,and near-complete genome assemblies now allow accurate SV detection and genotyping.These innovations overcome the limitations of single-reference genomes,enabling the discovery of complex SVs,including nested and overlapping variants,and providing access to previously inaccessible genomic regions such as centromeres and telomeres.This review highlights the current landscape of cattle SV research,with emphasis on integrating longread sequencing and pangenome frameworks to uncover breed-specific and population-level variation.While many SVs are linked to economically important traits such as feed efficiency and disease resistance,their broader regulatory impacts remain an active area of investigation.Emerging functional genomics approaches,including transcriptomics,epigenomics,and genome editing,will clarify how SVs influence gene regulation and phenotype.Looking forward,the integration of SV catalogs with multi-omics data,imputation resources,and artificial intelligence-driven models will be essential for translating discoveries into breeding and conservation applications.Integrating structural variants into breeding pipelines promises to revolutionize livestock genomics,enabling precision selection and sustainable agriculture despite challenges in cost,data sharing,and functional validation. 展开更多
关键词 Cattle Genome assembly Genomic prediction Long read sequencing Pangenome graph Structure variation
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Genome assembly of pomegranate highlights structural variations driving population differentiation and key loci underpinning cold adaption 认领 引用 被引量：1
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作者 Xiang Luo Zhenyang Shua +12 位作者 Diguang Zhao Beibei Liu Hua Luo Ying Chen Dong Meng Zhihua Song Qing Yang Zicheng Wang Dong Tang Xingguo Zhang Juan Zhang Kai Ma Wen Yao 《Horticulture Research》 SCIE CSCD 2025年第5期85-98,共14页
Cold damage poses a significant challenge to the cultivation of soft-seeded pomegranate varieties,hindering the growth of the pomegranate industry.The genetic basis of cold tolerance in pomegranates has remained elusi... Cold damage poses a significant challenge to the cultivation of soft-seeded pomegranate varieties,hindering the growth of the pomegranate industry.The genetic basis of cold tolerance in pomegranates has remained elusive,largely due to the lack of high-quality genome assemblies for cold-tolerant varieties and comprehensive population-scale genomic studies.In this study,we addressed these challenges by assembling a high-quality chromosome-level reference genome for’Sanbai’,a pomegranate variety renowned for its freezing resistance,achieving an impressive contig N50 of 15.93 Mb.This robust assembly,enhanced by long-read sequencing of 38 pomegranate accessions,facilitated the identification of 14239 polymorphic structural variants,revealing their critical roles in genomic diversity and population differentiation related to cold tolerance.Of particular significance was the discovery of a~5.4-Mb inversion on chromosome 1,which emerged as an important factor affecting cold tolerance in pomegranate.Moreover,through the integration of bulked segregant analysis,differential selection analysis,and genetic transformation techniques,we identified and validated the interaction between the PgNAC12 transcription factor and PgCBF1,disclosing their pivotal roles in response to cold stress.These findings mark a significant advancement in pomegranate genomics,offering novel insights into the genetic mechanisms of cold tolerance and providing valuable resources for the genetic improvement of soft-seeded pomegranate varieties. 展开更多
关键词 cold adaptation structural variations chromosome level reference genome polymorphic structural variants cold tolerance pomegranate population differentiation genetic basis
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Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity 认领 引用 被引量：1
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作者 Haolin Wu Wenjie Yang +3 位作者 Guanyong Dong Quanjun Hu Dawei Li Jianquan Liu 《Horticulture Research》 SCIE CSCD 2025年第6期203-218,共16页
Kiwifruits,belonging to the genus Actinidia,are acknowledged as one of the most successfully domesticated fruits in the twentieth century.Despite the rich wild resources and diverse phenotypes within this genus,insigh... Kiwifruits,belonging to the genus Actinidia,are acknowledged as one of the most successfully domesticated fruits in the twentieth century.Despite the rich wild resources and diverse phenotypes within this genus,insights into the genomic changes are still limited.Here,we conducted whole-genome sequencing on seven representative materials from highly diversified sections of Actinidia,leading to the assembly and annotation of 14 haplotype genomes with sizes spanning from 602.0 to 699.6 Mb.By compiling these haplotype genomes,we constructed a super pan-genome for the genus.We identified numerous structural variations(SVs,including variations in gene copy number)and highly diverged regions in these genomes.Notably,significant SV variability was observed within the intronic regions of the MED25 and TTG1 genes across different materials,suggesting their potential roles in influencing fruit size and trichome formation.Intriguingly,our findings indicated a high genetic divergence between two haplotype genomes,with one individual,tentatively named Actinidia x leiocacarpae,from sect.Leiocacarpae.This likely hybrid with a heterozygous genome exhibited notable genetic adaptations related to resistance against bacterial canker,particularly through the upregulation of the RPM1 gene,which contains a specific SV,after infection by Pseudomonas syringae pv.actinidiae.In addition,we also discussed the interlineage hybridizations and taxonomic treatments of the genus Actinidia.Overall,the comprehensive pan-genome constructed here,along with our findings,lays a foundation for examining genetic compositions and markers,particularly those related to SVs,to facilitate hybrid breeding aimed at developing desired phenotypes in kiwifruits. 展开更多
关键词 assembly annotation haplotype genomes structural variations super pan genome genomic changes phenotypic diversity med gene Actinidia haplotype genomes
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Structural variation-based and gene-based pangenome construction reveals untapped diversity of hexaploid wheat 认领 引用 被引量：1
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作者 Hong Cheng Lingpeng Kong +7 位作者 Kun Zhu Hang Zhao Xiuli Li Yanwen Zhang Weidong Ning Mei Jiang Bo Song Shifeng Cheng 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2025年第6期774-785,共12页
Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lac... Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat. 展开更多
关键词 Wheat Pangenome Structural variation Centromere plasticity Growth habit
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Genomic insights into demographic history,structural variation landscape,and complex traits from 514 Hu sheep genomes 认领 引用 被引量：1
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作者 Kaiyu Chen Yuelang Zhang +6 位作者 Yizhe Pan Xin Xiang Chen Peng Jiayi He Guiqing Huang Zhengguang Wang Pengju Zhao 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2025年第2期245-257,共13页
Hu sheep is an indigenous breed from the Taihu Lake Plain in China,known for its high fertility.Although Hu sheep belong to the Mongolian group,their demographic history and genetic architecture remain inconclusive.He... Hu sheep is an indigenous breed from the Taihu Lake Plain in China,known for its high fertility.Although Hu sheep belong to the Mongolian group,their demographic history and genetic architecture remain inconclusive.Here,we analyze 697 sheep genomes from representatives of Mongolian sheep breeds.Our study suggests that the ancestral Hu sheep first separated from the Mongolian group approximately 3000 years ago.As Hu sheep migrated from the north and flourished in the Taihu Lake Plain around 1000 years ago,they developed a unique genetic foundation and phenotypic characteristics,which are evident in the genomic footprints of selective sweeps and structural variation landscape.Genes associated with reproductive traits(BMPR1B and TDRD10)and horn phenotype(RXFP2)exhibit notable selective sweeps in the genome of Hu sheep.A genome-wide association analysis reveals that structural variations at LOC101110773,MAST2,and ZNF385B may significantly impact polledness,teat number,and early growth in Hu sheep,respectively.Our study offers insights into the evolutionary history of Hu sheep and may serve as a valuable genetic resource to enhance the understanding of complex traits in Hu sheep. 展开更多
关键词 Hu sheep Population sequencing Demographic history Structural variation Genome-wide association study
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Structural variation in Heinong 531 soybean genome underlies yield and resistance traits 认领 引用
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作者 Yu Tian Jia You +8 位作者 Zihao Zheng Hao Zhang Shiyu Guo Xueqing Wang Jinrong Li Lichun Huang Jiajun Wang Ying-hui Li Li-juan Qiu 《The Crop Journal》 SCIE CAS CSCD 2025年第5期1574-1584,共11页
Soybean(Glycine max)is a globally important crop that serves as a primary source of edible oil and protein for both humans and animals.Cultivated soybean varieties exhibit considerable genetic diversity depending on t... Soybean(Glycine max)is a globally important crop that serves as a primary source of edible oil and protein for both humans and animals.Cultivated soybean varieties exhibit considerable genetic diversity depending on their geographical origin.Heinong 531(HN531)is an elite cultivar that was released in China in June 2021 with 22.34%seed oil,high resistance to soybean cyst nematode(SCN)race 3,and enhanced yield.However,the genetic basis for these desirable agronomic traits is unclear.In this study,we generated a high-quality genome assembly for HN531 and used it to systematically analyze genes related to agronomic traits such as resistance to SCN.The assembled genome spans 981.20 Mb,featuring a contig N50 of 19.47 Mb,and contains 58,151 predicted gene models.Pan-genomic comparison with 27 previously reported soybean genomes revealed 95,071 structural variants(SVs)of>50 bp,of which 602 were HN531-specific.Furthermore,we identified a copy number variation at rhg1 that underlies resistance to SCN,and we found elite alleles of functional genes underlying important agronomic traits such as seed oil content,adaptability,and yield.This high-quality HN531 genome can be used to explore the genetic basis for the excellent agronomic traits of this cultivar,and is a valuable resource for breeders aiming to improve HN531 and related cultivars. 展开更多
关键词 Soybean Genome assembly Structural variation R genes SCN
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Transposable elements shape the landscape of heterozygous structural variation in a bird genome 认领 引用
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作者 Bo-Ping Li Na Kang +7 位作者 Zao-Xu Xu Hao-Ran Luo Shi-Yu Fan Xiao-Han Ao Xing Li Ya-Peng Han Xiao-Bin Ou Luo-Hao Xu 《Zoological Research》 SCIE CAS CSCD 2025年第1期75-86,共12页
Avian genomes exhibit compact organization and remarkable chromosomal stability.However,the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorl... Avian genomes exhibit compact organization and remarkable chromosomal stability.However,the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorly explored.This study generated a diploid genome assembly for the golden pheasant(Chrysolophus pictus),a species distinguished by the vibrant plumage of males.Each haploid genome assembly included complete chromosomalmodels,incorporatingall microchromosomes.Analysis revealed extensive tandem amplification of immune-related genes across the smallest microchromosomes(dot chromosomes),with an average copy number of 54.Structural variation between the haploid genomes was primarily shaped by large insertions and deletions(indels),with minimal contributions from inversions or duplications.Approximately 28%of these large indels were associated with recent insertions of transposable elements,despite their typically low activity in bird genomes.Evidence for significant effects of transposable elements on gene expression was minimal.Evolutionary strata on the sex chromosomes were identified,along with a drastic rearrangement of the W chromosome.These analyses of the high-quality diploid genome of the golden pheasant provide valuable insights into the evolutionary patterns of structural variation in avian genomes. 展开更多
关键词 Golden pheasant Structural variation Transposable elements Chromosome evolution
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The nature of complex structural variations in tomatoes 认领 引用
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作者 Xue Cui Yuxin Liu +18 位作者 Miao Sun Qiyue Zhao Yicheng Huang Jianwei Zhang Qiulin Yao Hang Yin Huixin Zhang Fulei Mo Hongbin Zhong Yang Liu Xiuling Chen Yao Zhang Jiayin Liu Youwen Qiu Mingfang Feng Xu Chen Hossein Ghanizadeh Yao Zhou Aoxue Wang 《Horticulture Research》 SCIE CSCD 2025年第7期258-268,共11页
Structural variations(SVs)in repetitive sequences could only be detected within a broad region due to imprecise breakpoints,leading to classification errors and inaccurate trait analysis.Through manual inspection at 4... Structural variations(SVs)in repetitive sequences could only be detected within a broad region due to imprecise breakpoints,leading to classification errors and inaccurate trait analysis.Through manual inspection at 4532 variant regions identified by integrating 14 detection pipelines between two tomato genomes,we generated an SV benchmark at base-pair resolution.Evaluation of all pipelines yielded F1-scores below 53.77%with this benchmark,underscoring the urgent need for advanced detection algorithms in plant genomics.Analyzing the alignment features of the repetitive sequences in each region,we summarized four patterns of SV breakpoints and revealed that deviations in breakpoint identification were primarily due to copy misalignment.According to the similarities among copies,we identified 1635 bona fide SVs with precise breakpoints,including substitutions(223),which should be taken as a fundamental SV type,alongside insertions(780),deletions(619),and inversions(13),all showing preferences for SV occurrence within AT-repeat regions of regulatory loci.This precise resolution of complex SVs will foster genome analysis and crop improvement. 展开更多
关键词 trait analysisthrough classification errors advanced detection algorithms integrating detection pipelines tomato genomeswe sv benchmark manual inspection structural variations svs
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High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers 认领 引用 被引量：6
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作者 Joung-Ho Lee Jelli Venkatesh +18 位作者 Jinkwan Jo Siyoung Jang Geon Woo Kim Jung-Min Kim Koeun Han Nayoung Ro Hea-Young Lee Jin-Kyung Kwon Yong-Min Kim Tae-Ho Lee Doil Choi Allen Van Deynze Theresa Hill Nir Kfir Aviad Freiman Nelson HDavila Olivas Yonatan Elkind Ilan Paran Byoung-Cheorl Kang 《Horticulture Research》 SCIE CSCD 2022年第1期3795-3807,共13页
Pepper(Capsicum annuum)is an important vegetable crop that has been subjected to intensive breeding,resulting in limited genetic diversity,especially for sweet peppers.Previous studies have reported pepper draft genom... Pepper(Capsicum annuum)is an important vegetable crop that has been subjected to intensive breeding,resulting in limited genetic diversity,especially for sweet peppers.Previous studies have reported pepper draft genome assemblies using short read sequencing,but their capture of the extent of large structural variants(SVs),such as presence-absence variants(PAVs),inversions,and copy-number variants(CNVs)in the complex pepper genome falls short.In this study,we sequenced the genomes of representative sweet and hot pepper accessions by long-read and/or linked-read methods and advanced scaffolding technologies.First,we developed a high-quality reference genome for the sweet pepper cultivar‘Dempsey’and then used the reference genome to identify SVs in 11 other pepper accessions and constructed a graph-based pan-genome for pepper.We annotated an average of 42972 gene families in each pepper accession,defining a set of 19662 core and 23115 non-core gene families.The new pepper pan-genome includes informative variants,222159 PAVs,12322 CNVs,and 16032 inversions.Pan-genome analysis revealed PAVs associated with important agricultural traits,including potyvirus resistance,fruit color,pungency,and pepper fruit orientation.Comparatively,a large number of genes are affected by PAVs,which is positively correlated with the high frequency of transposable elements(TEs),indicating TEs play a key role in shaping the genomic landscape of peppers.The datasets presented herein provide a powerful new genomic resource for genetic analysis and genome-assisted breeding for pepper improvement. 展开更多
关键词 short read sequencingbut structural variations chromosome scale genomes large structural variants svs such sequenced genomes copy number variants inversions draft genome assemblies
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Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs 认领 引用 被引量：4
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作者 Wencheng Zong Jinbu Wang +8 位作者 Runze Zhao Naiqi Niu Yanfang Su Ziping Hu Xin Liu Xinhua Hou Ligang Wang Lixian Wang Longchao Zhang 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2024年第1期68-87,共20页
Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability ... Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds. 展开更多
关键词 Body size GWAS Pig Skeleton Structural variations
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The occurrence,inheritance,and segregation of complex genomic structural variation in synthetic Brassica napus 认领 引用 被引量：4
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作者 Dandan Hu Jin Lu +12 位作者 Wenwen Li Yinghui Yang Junxiong Xu Han Qin Hao Wang Yan Niu Huaiqi Zhang Qingqing Liu Xiangxiang He Annaliese S.Mason JChris Pires Zhiyong Xiong Jun Zou 《The Crop Journal》 SCIE CSCD 2024年第2期515-528,共14页
"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic s... "Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation. 展开更多
关键词 Allopolyploid Large Genome structural variation Linkage mapping Synthetic polyploids Inheritance and segregation
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Structural Variation Analysis of Mutated Nannochloropsis oceanica Caused by Zeocin Through Genome Re-Sequencing 认领 引用 被引量：3
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作者 LIN Genmei ZHANG Zhongyi +2 位作者 GUO Li DING Haiyan YANG Guanpin 《Journal of Ocean University of China》 SCIE CAS CSCD 2018年第5期1225-1230,共6页
Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such fu... Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such function of Zeocin, The results showed that Zeocin can mutate the N. oceanica genome and cause the structural variation. Zeocin either swept away or selected the alleles of genes functioning in ubiquitin-mediated proteolysis, alpha-linolenic acid metabolism, ascorbate and aldarate metabolism, ribosome biogenesis, and circadian rhythm, indicating that N. oceanica may have adjusted its metabolic performances for protein, carbohydrate, and lipid, and changed its ribosome biosynthesis and living rhythm to survive in Zeocin containing medium. In addition, Zeocin caused mutation may have influenced the expression of a set of tanscription factors. It was concluded that Zeocin effectively caused the structural variation of the genome of N. oceanica, and forced the microalgae to select out the alleles of a set of genes around these variations in order to adapt to Zeocin containing medium. Further studies on the genetic basis of the phenotypic adaptation of this haploid and asexual microalga and the application of Zeocin to its genetic improvement are very important. 展开更多
关键词 Nannochloropsis oceanica Zeocin mutation genome re-sequencing structural variation
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Snapshot of Structural Variations in the Tibetan Wild Boar Genome at Single-Nucleotide Resolution 认领 引用 被引量：1
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作者 Lei Chen Long Jin +9 位作者 Mingzhou Li Shilin Tian Tiandong Che Qianzi Tang Jing Lan Zhi Jiang Ruiqiang Li Yiren Gu Xuewei Li Jinyong Wang 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2014年第12期653-657,共5页
Genomic structural variations （SVs）, particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contributio... Genomic structural variations （SVs）, particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contribution to biological diversity and phenotypic variation （Alkan et al., 2011; Bickhart and Liu, 2014）. With the rapid development of the next-generation sequencing technologies and the new assembly methodolo- gies, the multiple de novo assemblies of genomes within a species allow researchers to explore more detailed SV maps （Li et al., 2011）. Compared with the traditional read depth algorithm using the whole-genome resequencing approach and array-based technologies （Baker, 2012; Wang et al., 2012; 展开更多
关键词 gene Snapshot of Structural Variations in the Tibetan Wild Boar Genome at Single-Nucleotide Resolution
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Structural variations in oil crops:Types,and roles on domestication and breeding 认领 引用
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作者 Xiaobo Cui Miao Yao +4 位作者 Meili Xie Ming Hu Shengyi Liu Lijiang Liu Chaobo Tong 《Oil Crop Science》 CSCD 2024年第4期240-246,共7页
Structural variations(SVs),a newly discovered genetic variation,have gained increasing recognition for their importance,yet much about them remains unknown.With the completion of whole-genome sequencing projects in oi... Structural variations(SVs),a newly discovered genetic variation,have gained increasing recognition for their importance,yet much about them remains unknown.With the completion of whole-genome sequencing projects in oil crops,more SVs have been identified,revealing their types,genomic distribution,and characteristics.These findings have demonstrated the crucial roles of SVs in regulating gene expression,driving trait innovation,facilitating domestication,making this an opportune time for a systematic review.We summarized the progress of SV-related studies in oil crops,focusing on the types of SVs and their mechanisms of occurrence,the strategies and methods for SV detection,and the SVs identified in oil crops such as rapeseed,soybean,peanut,and sesame.The various types of SVs,such as presence-absence variations(PAVs),copy number variations(CNVs),and homeologous exchanges(HEs),have been shown.Along with their genomic characterization,their roles in crop domestication and breeding,and regulatory impact on gene expression and agronomic traits have also been demonstrated.This review will provide an overview of the SV research process in oil crops,enabling researchers to quickly understand key information and apply this knowledge in future studies and crop breeding. 展开更多
关键词 Structural variations Oil crops Copy number variations Presence or absence variations Homologous exchanges
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Leaf variegation caused by plastome structural variation:an example from Dianella tasmanica 认领 引用 被引量：2
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作者 Shuaixi Zhou Kainan Ma +2 位作者 Jeffrey P.Mower Ying Liu Renchao Zhou 《Horticulture Research》 SCIE CSCD 2024年第3期58-69,共12页
Variegated plants often exhibit plastomic heteroplasmy due to single-nucleotide mutations or small insertions/deletions in their albino sectors.Here,however,we identified a plastome structural variation in albino sect... Variegated plants often exhibit plastomic heteroplasmy due to single-nucleotide mutations or small insertions/deletions in their albino sectors.Here,however,we identified a plastome structural variation in albino sectors of the variegated plant Dianella tasmanica(Asphodelaceae),a perennial herbaceous plant widely cultivated as an ornamental in tropical Asia.This structural variation,caused by intermolecular recombination mediated by an 11-bp inverted repeat flanking a 92-bp segment in the large single-copy region(LSC),generates a giant plastome(228878 bp)with the largest inverted repeat of 105226 bp and the smallest LSC of 92 bp known in land plants.It also generates an ~7-kb deletion on the boundary of the LSC,which eliminates three protein coding genes(psbA,matK,and rps16)and one tRNA gene(trnK).Albino sectors exhibit dramatic changes in expression of many plastid genes,including negligible expression of psbA,matK,and rps16,reduced expression of photosynthesis-related genes,and increased expression of genes related to the translational apparatus.Microscopic and ultrastructure observations showed that albino tissues were present in both green and albino sectors of the variegated individuals,and chloroplasts were poorly developed in the mesophyll cells of the albino tissues of the variegated individuals.These poorly developed chloroplasts likely carry the large and rearranged plastome,which is likely responsible for the loss of photosynthesis and albinism in the leaf margins.Considering that short repeats are relatively common in plant plastomes and that photosynthesis is not necessary for albino sectors,structural variation of this kind may not be rare in the plastomes of variegated plants. 展开更多
关键词 dianella tasmanica asphodelaceae variegated plants herbaceous plant intermolecular recombination plastome structural variation plastomic heteroplasmy
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Effect of CO_2 on the structural variation of Na_2WO_4/Mn/SiO_2 catalyst for oxidative coupling of methane to ethylene 认领 引用 被引量：3
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作者 Jia Shi Lu Yao Changwei Hu 《Journal of Energy Chemistry》 SCIE EI CAS CSCD 2015年第4期394-400,共7页
In this work,the influence of CO2 on the structural variation and catalytic performance of Na2WO4/Mn/Si O2 for oxidative coupling of methane to ethylene was investigated. The catalyst was prepared by impregnation meth... In this work,the influence of CO2 on the structural variation and catalytic performance of Na2WO4/Mn/Si O2 for oxidative coupling of methane to ethylene was investigated. The catalyst was prepared by impregnation method and characterized by XRD,Raman and XPS techniques. Appropriate amount of CO2 in the reactant gases enhanced the formation of surface tetrahedral Na2WO4 species and promoted the migration of O in MOx,Na,W from the catalyst bulk to surface,which were favorable for oxidative coupling of methane. When the molar ratio of CH4/O2/CO2 was 3/1/2,enriched surface tetrahedral Na2WO4 species and high surface concentration of O in MOx,Na,W were detected,and then high CH4 conversion of 33.1% and high C2H4 selectivity of 56.2% were obtained. With further increase of CO2 in the reagent gases,the content of active surface tetrahedral Na2WO4 species and surface concentration of O in MOx,Na,W decreased,while that of inactive species（Mn WO4 and Mn2O3） increased dramatically,leading to low CH4 conversion and low C2H4 selectivity. It could be speculated that Na2WO4 crystal was transformed into Mn WO4 crystal with excessive CO2 added under the reaction conditions. Pretreatment of Na2WO4/Mn/Si O2 catalyst by moderate amount of CO2 before OCM also promoted the formation of Na2WO4 species. 展开更多
关键词 Oxidative coupling of methane CO2 C2H4 Na2WO4/Mn/SiO2catalyst Structural variation
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Structural variation drives rhizome innovation and adaptive divergence in sister Medicago species 认领 引用
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作者 Hongyin Hu Shuang Wu +12 位作者 Yudan Zheng† Ao Li Zhaoming Wang Kunjing Qu Ying Yang Na Wang Xue Yang Yingzhuo Wan Chenxiang Jiang Zhipeng Liu Jianquan Liu Haiqing Wang Guangpeng Ren 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2026年第2期406-424,共19页
Wild perennial sister species Medicago archiducisnicolai(rhizomatous/alpine)and M.ruthenica(nonrhizomatous/xeric)constitute vital genetic resources for forage improvement.To decode the genomic basis of their contrasti... Wild perennial sister species Medicago archiducisnicolai(rhizomatous/alpine)and M.ruthenica(nonrhizomatous/xeric)constitute vital genetic resources for forage improvement.To decode the genomic basis of their contrasting trait and habitat adaptation,we generated chromosome-scale genome assemblies,resequenced 128 individuals,profiled transcriptomes under cold/heat stress,and functionally validated causal alleles.We demonstrate that structural variations(SVs)—particularly gene duplications—are primary drivers of rhizome formation and alpine/xeric adaptation.Further,pervasive presence-absence SVs(PAVs)in noncoding regulatory regions underpin divergent allele-specific expression governing rhizome development and stress responses.Crucially,these regulatory PAVs induce contrasting expression patterns during trait development and stress adaptation.Our findings reveal a dual mechanism whereby coding and regulatory SVs convergently orchestrate phenotypic innovation and ecological specialization in sister species,offering valuable genomic resources for legume evolution studies and alfalfa breeding. 展开更多
关键词 adaptive divergence comparative genomics gene duplication rhizome development sister species structure variations
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