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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 ***,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 *** 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 *** of the female population based on whole-genome resequencing yielded 2120695 high-quality SNPs,39 of which were suggestively associated with ovarian *** note,a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified,with cpne5a determined as the causal gene of the ***,single-marker and haplotype association analyses were performed on cpne5a,revealing four genetic markers(P0.9)significantly associated with the *** 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 *** 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 *** 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 *** strains exhibiting population-synchronous ovarian

关键词： Coilia nasus GWAS Transcriptome Ovarian development SNP

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Self-fertilization in a gonochoristic fish yellow catfish

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aquaculture and fisheries 2024年第2期9卷 234-244页

作者： Yue Yu Ziyi Lu Min Chen Ya Liu Yang Ding Chenhao Hu Zhigang Shen College of fisheries Key Lab of Freshwater Animal BreedingMinistry of Agriculture and Rural AffairsWuhan430070China Key Lab of Agricultural Animal Genetics Breeding and Reproduction of Ministry of EducationWuhan430070China engineering technology research center for fish breeding and Culture in hubei Province Wuhan430070China engineering research center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt of Ministry of Education Huazhong Agricultural UniversityWuhan430070China hubei Huangyouyuan fishery Development Limited Company Wuhan430070China

Sex control techniques are in great demand for aquaculture because of the huge benefits of mono-sex *** a previous study on yellow catfish(Tachysurus fulvidraco),intersex individuals were produced by administrating 17α-methyltestosterone(MT)or aromatase inhibitor letrozole(LZ).The ovarian and testicular portions of intersexual gonads developed well and were completely separated,arousing our interest in producing self-fertilizable fish and clone-like fish *** this study,yellow catfish fry were treated with a combination of MT and LZ at a low dose(5 mg kg^(-1)MT,300 mg kg^(-1)LZ)at a low water temperature(27.0℃,mixed sex-producing temperature,LL group)and a high temperature(33.5◦C,male-producing temperature,HL group),and with a high dose(10 mg kg^(-1) MT,600 mg kg^(-1) LZ)at a low water temperature(LH group),during 12-65 days post-hatching,the critical period of sex *** XX and XY intersex were produced with different percentages at the same time through co-treatment with MT and LZ,with or without the help of male-producing *** highest percentage of XY intersex(53%in XY,36%in XX and XY)and XX intersex(47%in XX,25%in XX and XY)was produced in LH and HL groups,*** of gonadal morphology,histology,and sperm dynamic analysis indicate that some XX and XY intersex individuals were capable of self-fertilization through artificial *** reproductive performance of these intersex individuals was then investigated by injecting spawning agents,dissecting gonads,and artificially fertilizing eggs with their own *** XX,XY,and YY genotypic individuals were produced by the self-fertilization of XY intersex *** present study successfully produced high percentages of XX and XY intersex and conducted self-fertilization by mating the eggs and sperm of a single intersex ***-fertilization in fish will show great potential in aquaculture genetics and breeding,for example,generating high

关键词： Sex differentiation Self-fertilization Sex reversal Mono-sex Clone

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Rice gene OsUGT75A regulates seedling emergence under deep-sowing conditions

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The Crop Journal 2024年第1期12卷 133-141页

作者： Jia Zhao Siyu Liu Xiaoqian Zhao Zhibo Huang Shan Sun Zixuan Zeng Yongqi He Zhoufei Wang The Laboratory of Seed Science and technology Guangdong Key Laboratory of Plant Molecular BreedingNational Engineering Research Center of Plant Space BreedingSouth China Agricultural UniversityGuangzhou 510642GuangdongChina

Poor seedling emergence is a challenge for direct seeding of rice under deep-sowing field *** we reveal that UDP-glucosyltransferase OsUGT75A promotes rice seedling emergence under deepsowing conditions by increasing shoot *** of OsUGT75A was higher in the middle regions of the shoot and in shoots under deep-sowing *** of free abscisic acid(ABA)and jasmonates(JA)were higher in shoots of OsUGT75A mutants than in those of wild-type plants,and OsUGT75A mutants were more sensitive to ABA and JA *** shoot length was attributed to higher ABA INSENSITIVE 3(OsABI3)expression and lower JASMONATE-ZIM domain protein(OsJAZ)expression in *** extension by OsUGT75A is achieved mainly by promotion of cell *** elite haplotype of OsUGT75A associated with increased shoot length was identified among indica rice ***75A acts to increase seedling emergence under deep-sowing conditions.

关键词： Abscisic acid Deep-sowing Jasmonic acid Rice Shoot length

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Identification and effective regulation of scarb1 gene involved in pigmentation change in autotetraploid Carassius auratus

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Zoological research 2024年第2期45卷 381-397页

作者： Xi-Dan Xu Yue Zhou Chong-Qing Wang Xu Huang Kun Zhang Xiao-Wei Xu Li-Wen He Xin-Yue Zhang Xin-Zhu Fu Ming Ma Qin-Bo Qin Shao-Jun Liu State Key Laboratory of Developmental Biology of Freshwater fish Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education MinistryCollege of Life SciencesHunan Normal UniversityChangshaHunan 410081China Nansha-South China Agricultural University fishery research Institute GuangzhouGuangdong 511458China Hunan Yuelu Mountain Science and technology Co.Ltd.for Aquatic breeding ChangshaHunan 410081China College of Chemistry and Chemical engineering Hunan Normal UniversityChangshaHunan 410081China

The autotetraploid Carassius auratus(4nRR,4n=200,RRRR)is derived from whole-genome duplication of Carassius auratus red var.(RCC,2n=100,RR).In the current study,we demonstrated that chromatophores and pigment changes directly caused the coloration and variation of 4nRR skin(red in RCC,brownish-yellow in4nRR).To further explore the molecular mechanisms underlying coloration formation and variation in 4nRR,we performed transcriptome profiling and molecular functional verification in RCC and *** revealed that scarb1,associated with carotenoid metabolism,underwent significant down-regulation in *** editing of this candidate pigment gene provided clear evidence of its significant role in RCC ***,we identified four divergent scarb1 homeologs in 4nRR:two original scarb1 homeologs from RCC and two duplicated ***,three of these homeologs possessed two highly conserved alleles,exhibiting biased and allelespecific expression in the ***,after precise editing of both the original and duplicated scarb1homeologs and/or alleles,4nRR individuals,whether singly or multiply mutated,displayed a transition from brownishyellow skin to a cyan-gray ***,the proportional areas of the cyan-gray regions displayed a gene-dose *** findings illustrate the subfunctionalization of duplicated scarb1,with all scarb1genes synergistically and equally contributing to the pigmentation of *** is the first report concerning the functional differentiation of duplicated homeologs in an autopolyploidfish,substantiallyenrichingour understanding of coloration formation and change within this group of organisms.

关键词： Autopolyploidization Coloration change scarb1 Functional differentiation Genetic changes

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Identification of Shell Color-Associated Genes Using Mantle Branch-Specific RNA Sequencing of Yellow-Colored Line of Pearl Oyster Pinctada fucata martensii

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Journal of Ocean University of China 2024年第4期23卷 1076-1086页

作者： PENG Haiming LIAO Yongshan YANG Chuangye MKUYE Robert DENG Yuewen YUE Chenyang fisheries College Guangdong Ocean UniversityZhanjiang 524088China Pearl research Institute Guangdong Ocean UniversityZhanjiang 524088China Guangdong Science and Innovation center for Pearl Culture Zhanjiang 524088China Pearl breeding and Processing engineering technology research center of Guangdong Province Zhanjiang 524088China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and healthy Culture Zhanjiang 524088China

The yellow-colored line of pearl oyster Pinctada fucata martensii displays a yellow prismatic layer and a white nacreous layer that can be used as an ideal model for research on shell color ***-Raman spectroscopy and transcriptome analyses were performed to explore the potential molecular mechanism underlying the phenotype *** micro-Raman spectroscopy results indicate that the prismatic layer exhibits distinct characteristic peaks of carotenoids,while these peaks are not prominent in the nacreous *** the transcriptome comparison of the central zone of mantle and mantle edge tissue,which function in nacreous and prismatic layer formation,respectively,935 significantly differentially expressed genes(DEGs)were identified,with 385 genes upregulated and 227 genes downregulated(|log_(2)(Fold change)|>1 and false discovery rate<0.05)in the mantle edge *** these genes,some were associated with melanoma/melanogenesis,such as tyrosinase,zinc metalloprotease,glutathione S-transferase,and ATP-binding cassette sub-family;some were associated with the carotenoid-related pathway,including scavenger receptors,cytochrome P450 and lipoprotein *** associated with porphyrin metabolism,including porphobilinogen deaminase,and copper/zinc superoxide dismutase,and genes associated with shell matrix protein,including amorphous calcium carbonate binding protein,shematrin,PIF,and collagen,also exhibited significantly different *** is speculated that the different colours between prismatic layer and nacreous layer in the yellow-colored line of *** might be resulted from melanin,carotenoids and porphyrin metabolism,while genes related to shell structure and biomineralization might also affect *** results provide new insights to understand the mechanism of shell color formation in mollusca.

关键词： Pinctada fucata martensii shell coloration transcriptome

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Striking a growth–defense balance:Stress regulators that function in maize development

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Journal of Integrative Plant Biology 2024年第3期66卷 424-442页

作者： Shiyi Xie Hongbing Luo Wei Huang Weiwei Jin Zhaobin Dong Maize engineering and technology research center of Hunan Province College of AgronomyHunan Agricultural UniversityChangsha 410128China State Key Laboratory of Maize Bio-breeding National Maize Improvement CenterFrontiers Science Center for Molecular Design BreedingChina Agricultural UniversityBeijing 100193China Tianjin Key Laboratory of Intelligent breeding of Major Crops Fresh Corn Research Center of BTHCollege of Agronomy&Resources and EnvironmentTianjin Agricultural UniversityTianjin 300384China

Maize(Zea mays)cultivation is strongly affected by both abiotic and biotic stress,leading to reduced growth and *** has recently become clear that regulators of plant stress responses,including the phytohormones abscisic acid(ABA),ethylene(ET),and jasmonic acid(JA),together with reactive oxygen species(ROS),shape plant growth and *** their well established functions in stress responses,these molecules play crucial roles in balancing growth and defense,which must be finely tuned to achieve high yields in crops while maintaining some level of *** this review,we provide an in-depth analysis of recent research on the developmental functions of stress regulators,focusing specifically on *** unraveling the contributions of these regulators to maize development,we present new avenues for enhancing maize cultivation and growth while highlighting the potential risks associated with manipulating stress regulators to enhance grain yields in the face of environmental challenges.

关键词： stress regulators maize development ABA ET JA ROS

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Brain Transcriptome Analysis Reveals Metabolic Changes Adapting to Hyperhaline or Hypohaline Environments in Spotted Scat(Scatophagus argus)

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Journal of Ocean University of China 2024年第3期23卷 755-765页

作者： LIN Ting ZHAI Yi TIAN Changxu JIANG Dongneng SHI Hongjuan JIANG Mouyan LI Guangli DENG Siping fisheries College Guangdong Ocean UniversityZhanjiang 524088China Guangdong research center on Reproductive Control and breeding technology of Indigenous Valuable fish Species Zhanjiang 524088China Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals Zhanjiang 524088China

The fish brain is crucial for adjusting to environmental *** changes play a vital role in the adaptation to salinity change in aquatic ***,few studies have evaluated the responses of the fish brain to salinity *** evaluate the response to various salinities,spotted scat(Scatophagus argus)was cultured in water with salinity levels of 5(low salinity:LS),25(control group:Ctrl),and 35(high salinity group:HS)for 22 *** brain transcriptome was *** total,1698 differentially expressed genes(DEGs)were identified between the HS and Ctrl groups,and 841 DEGs were identified between the LS and Ctrl *** analysis showed that the DEGs in the HS *** comparison were involved in steroid biosynthesis,terpenoid backbone biosynthesis,fatty acid biosynthesis,ascorbate and aldarate metabolism,other types of O-glycan biosynthesis,and fatty acid *** and dicarboxylate metabolism,one carbon pool by folate,steroid biosynthesis,and cysteine and methionine metabolism were significantly enriched in the LS *** ***,the genes related to metabolism(acc,fas,hmgcr,hmgcs1,mvd,soat1,nsdhl,sqle,cel,fdft1,dnmt3a and mtr)were significantly up-regulated in the HS *** *** genes related to metabolism(lipa,sqle,acc,fas,bhmt,mpst,dnmt3a,mtr,hao2,LOC111225351 and hmgcs1)were significantly up-regulated,while hmgcr and soat1 were significantly down-regulated in the LS *** *** results suggest that salinity stress affects signaling pathways and genes’expressions involved in metabolic processes in the brain,and the differences in metabolism play an important role in adaptation to hyperhaline or hypohaline environments in spotted *** research provides a comprehensive overview of transcriptional changes in the brain under hyperhaline or hypohaline conditions,which is helpful to understand the mechanisms underlying salinity adaptation in euryhaline fishes.

关键词： Scatophagus argus brain salinity transcriptome analysis

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Transcriptome profiling and RXR gene family identification reveals the molecular mechanism of rapid aging after spawning of cuttlefish Sepiella japonica

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Journal of Oceanology and Limnology 2024年第3期42卷 865-880页

作者： Zhenyu DONG Jiemei ZHAO Feng GUO Shuangrui LIN Huai YANG Yingying YE Changfei CHI Hongfei LI Baoying GUO College of Marine Science and technology Zhejiang Ocean UniversityZhoushan 316022China National engineering research center for Marine aquaculture Zhejiang Ocean UniversityZhoushan 316022China Donghai Laboratory Zhoushan 316021China

Sepiella japonica is a worldwide marine cuttlefish species of high economic *** routinely modifying behaviors in reproductive life,such as rapid aging until death after spawning,has been recognized in artificial ***,reproductive behavior at the level of genes is rarely reported,thus,the research on the genetic basis of behavior,reproduction,and artificial breeding was *** applied RNA-seq in different stages of reproduction to investigate the reason of rapid aging after spawning,pre-maturity,pre-spawning after maturity,and *** retinoid X receptor(RXR)gene family in *** was identified,and 1343–1452 differentially expressed genes(DEGs)in all 3 stages of reproductive life were identified from pairwise m RNA ***,through the GO term and KEGG analysis,*** could handle neuronal development and network formation before maturity and have a functional degradation of neural communication,signal transduction,vision,and gene expression after *** Sj RXRαs have been identified and they played different roles in growth development or ***,the regulation of several channels and receptors is the intrinsic molecular mechanism of rapid aging after spawning in *** study revealed the survival strategy and provided fundamental data on the level of genes for understanding the reproductive behavior and the reproduction of ***.

关键词： Sepiella japonica RAN-seq retinoid X receptor(RXR)gene family rapid aging intrinsic molecular mechanism

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New perspectives on the genetic structure of dotted gizzard shad(Konosirus punctatus)based on RAD-seq

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Marine Life Science & technology 2024年第1期6卷 50-67页

作者： Ying Peng Yifan Liu Jiasheng Li Kun Zhang Xun Jin Sixu Zheng Yunpeng Wang Zhenming Lu Liqin Liu Li Gong Bingjian Liu National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization Zhejiang Ocean UniversityZhoushan 316022China National engineering research center for Facilitated Marine aquaculture Marine Science and Technology CollegeZhejiang Ocean UniversityZhoushan 316022China

To maintain,develop and rationally utilize marine organisms,understanding their genetic structure and habitat adaptation pattern is *** punctatus,which is a commercial fish species inhabiting the Indo-west Pacific Ocean,has shown an obvious annual global capture and aquaculture production decline due to climate changes and human *** the present study,restriction-site associated DNA sequencing(RAD-seq)was used to describe its genome-wide single nucleotide polymorphisms panel(SNPs).Among 146 individuals collected at nine locations scattered in China,Korea and Japan,a set of 632,090 SNPs were *** genetic analysis showed that *** individuals were divided into two significant genetic ***,potential genetic differentiation between northern and southern population of *** was *** results indicated that gene flow existed among sampling locations of ***,especially from southern Japan to ***,candidate genes associated with habitat adaptations of *** were identified,which are involved in diverse physiological processes of *** including growth and development(e.g.,KIDINS220,PAN3),substance metabolism(e.g.,PGM5)and immune response(e.g.,VAV3,CCT7,HSPA12B).Our findings may aid in understanding the possible mechanisms for the population genetic structure and local adaptation of ***,which is beneficial to establish the management and conservation units of ***,guiding the rational use of resources,with reference significance for a profound understanding of the adaptative mechanisms of other marine organisms to the environment.

关键词： Population structure Konosirus punctatus SNP RAD-seq Local adaptation

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Differences in leaf cuticular wax induced by whole-genome duplication in autotetraploid sour jujube

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Horticultural Plant Journal 2024年第1期10卷 66-76页

作者： Meng Li Chenxing Zhang Lu Hou Xinru Liu Hanqing Zhao Xiaoming Pang Wenhao Bo Yingyue Li National engineering research center of Tree breeding and Ecological Restoration College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China Key Laboratory of Genetics and breeding in Forest Trees and Ornamental Plants Ministry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China The Tree and Ornamental Plant breeding and Biotechnology Laboratory of National Forestry and Grassland Administration Beijing Forestry UniversityBeijing 100083China

Drought-resistant plants exhibit strong water retention *** this regard,the autotetraploid sour jujube leaves exhibit better water retention than diploid *** comparisons and physiological comparisons of diploid and autotetraploid leaves showed that the autotetraploid leaves had thicker leaf cuticles and more leaf wax accumulation than the diploid leaves,which could reduce cuticle permeability and improve the drought tolerance of *** this study,the cuticular wax crystalloids on the adaxial and abaxial sides of young and mature jujube leaves were observed in the two ploidy types,and unique cuticular wax crystalloids covering a large area of the cuticle on autotetraploid sour jujube leaves may provide an advantage in reducing leaf non-stomata transpiration and improving plant drought *** on the transcriptome,115 differentially expressed genes between diploids and autotetraploids were further analyzed and found to be involved in the accumulation of cuticular wax components,including terpenoids,fatty acids,and lipids,as well as ABC transporter and wax biosynthetic ***,14 genes differentially expressed between glossy autotetraploid leaves and nonglossy diploid leaves,such as LOC107414787,LOC107411574 and LOC107413721,were screened as candidate genes by qRT-PCR *** findings provided insights into how polyploidization improved drought tolerance.

关键词： Autotetraploid Jujube Drought tolerance Cuticular wax RNA-seq

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