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Genome-wide identification,characterization and functional prediction of the SRS gene family in sesame(Sesamum indicum L.)

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Oil Crop Science 2024年第2期9卷 69-80页

作者： Farjana Afroz Susmi Tasmina Islam Simi Md Nahid Hasan Md Abdur Rahim department of genetics and Plant breeding Sher-e-Bangla Agricultural UniversityDhaka1207Bangladesh

Sesame(Sesamum indicum L.)is an ancient oilseed crop of the Pedaliaceae family with high oil content and potential health *** RELATED SEQUENCE(SRS)proteins are the transcription factors(TFs)specific to plants that contain RING-like zinc finger domain and are associated with the regulation of several physiological and biochemical *** also play vital roles in plant growth and development such as root formation,leaf development,floral development,hormone biosynthesis,signal transduction,and biotic and abiotic stress ***,the SRS gene family was not reported in sesame *** this study,identification,molecular characterization,phylogenetic relationship,cis-acting regulatory elements,protein-protein interaction,syntenic relationship,duplication events and expression pattern of SRS genes were analyzed in *** identified total six SiSRS genes on seven different linkage groups in the *** genome by comparing with the other species,including the model plant Arabidopsis *** SiSRS genes showed variation in their structure like2–5 exons and 1–4 *** other species,SiSRS proteins also contained‘RING-like zinc finger'and‘LRP1'***,the SiSRS genes were clustered into subclasses via phylogenetic analysis with proteins of ***,***,and some other plant *** cis-acting regulatory elements analysis revealed that the promoter region of SiSRS4(SIN_1011561)showed the highest 13 and 16 elements for light-and phytohormone-responses whereas,SiSRS1(SIN_1015187)showed the highest 15 elements for *** ABREs,or ABA-responsive elements,were found in a maximum of 8 copies in the SiSRS3(SIN 1009100).Moreover,the available RNA-seq based expression of SiSRS genes revealed variation in expression patterns between stress-treated and non-treated samples,especially in drought and salinity conditions *** SiSRS genes like SiSRS1(SIN_1015187)and SiSRS5(SIN_1021065),also exhibited variabl

关键词： SiSRS gene family SHI Transcription factor Characterization Sesamum indicum

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ChMYB1-ChbHLH42-ChTTG1 module regulates abscisic acidinduced anthocyanin biosynthesis in Cerasus humilis

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Horticultural Plant Journal 2024年第1期10卷 51-65页

作者： Xiaolong Ji Zhe Li Mingyu Zhang Shaoyu Lang Xingshun Song State Key Laboratory of Tree genetics and breeding Northeast Forestry UniversityHarbinHeilongjiang 150040China department of genetics College of Life ScienceNortheast Forestry UniversityHarbinHeilongjiang 150040China

Cerasus humilis is a kind of economic fruit tree peculiar to China,which is widely used in the food,landscape,and pharmaceutical *** are a phenolic metabolite that plays an essential role in fruit ***,the regulatory network of *** in anthocyanin biosynthesis is still *** this study,the R2R3-MYB transcription factor ChMYB1 was isolated from the full genome of the *** one-hybrid,dual-luciferase assays,and GUS staining showed that ChMYB1 significantly increased anthocyanin contents in *** fruit by promoting the expression of ChCHS and ChUFGT by binding MBS(MYB-binding elements).ChMYB1 interacted with ChbHLH42and ChTTG1 to form the MBW complex and further enhanced the expression of *** addition,abscisic acid(ABA)treatment promoted the expression of ChMYB1 and anthocyanin accumulation in *** ***,ABA treatment enhanced the interaction between ChMYB1 and ***,ChABI5 inhibited the interaction between ChMYB1 and *** data elucidated the primary molecular mechanism of anthocyanin biosynthesis in *** fruit,deepening the understanding of the regulatory network affecting anthocyanin metabolism in edible fruit crops.

关键词： Cerasus humilis Anthocyanin ChMYB1 Fruit ABA

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Hepatic steatosis is associated with dysregulated cholesterol metabolism and altered protein acetylation dynamics in chickens

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Journal of Animal Science and Biotechnology 2024年第1期15卷 53-67页

作者： Xiaoli Guo Qianqian Zhou Jiaming Jin Fangren Lan Chaoliang Wen Junying Li Ning Yang Congjiao Sun National Engineering Laboratory for Animal breeding and Key Laboratory of Animal genetics Breeding and ReproductionMinistry of Agriculture and Rural AffairsChina Agricultural UniversityBeijing 100193China

Background Hepatic steatosis is a prevalent manifestation of fatty liver, that has detrimental effect on the health and productivity of laying hens, resulting in economic losses to the poultry industry. Here, we aimed to systematically investigate the genetic regulatory mechanisms of hepatic steatosis in laying *** Ninety individuals with the most prominent characteristics were selected from 686 laying hens according to the accumulation of lipid droplets in the liver, and were graded into three groups, including the control, mild hepatic steatosis and severe hepatic steatosis groups. A combination of transcriptome, proteome, acetylome and lipidome analyses, along with bioinformatics analysis were used to screen the key biological processes, modifications and lipids associated with hepatic *** The rationality of the hepatic steatosis grouping was verified through liver biochemical assays and RNA-seq. Hepatic steatosis was characterized by increased lipid deposition and multiple metabolic abnormalities. Integration of proteome and acetylome revealed that differentially expressed proteins(DEPs) interacted with differentially acetylated proteins(DAPs) and were involved in maintaining the metabolic balance in the liver. Acetylation alterations mainly occurred in the progression from mild to severe hepatic steatosis, i.e., the enzymes in the fatty acid oxidation and bile acid synthesis pathways were significantly less acetylated in severe hepatic steatosis group than that in mild group(P < 0.05). Lipidomics detected a variety of sphingolipids(SPs) and glycerophospholipids(GPs) were negatively correlated with hepatic steatosis(r ≤-0.5, P < 0.05). Furthermore, the severity of hepatic steatosis was associated with a decrease in cholesterol and bile acid synthesis and an increase in exogenous cholesterol *** In addition to acquiring a global and thorough picture of hepatic steatosis in laying hens, we were able to reveal the role of ac

关键词： Acetylation Cholesterol metabolism Hepatic steatosis Laying hens Multiomics

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Hi-Tag:a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers

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Science China(Life Sciences) 2024年第5期67卷 1027-1034页

作者： Xiaolong Qi Lu Zhang Qiulin Zhao Peng Zhou Sai Xian Zhang Jingjin Li Zhuqing Zheng Yue Xiang Xueting Dai Zhe Jin Yaobang Jian Xinyun Li Liangliang Fu Shuhong Zhao Key Lab of Agricultural Animal genetics Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of AgricultureCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China The Cooperative Innovation Center for Sustainable Pig Production Wuhan 430070China Hubei Hongshan Laboratory Frontiers Science Center for Animal Breeding and Sustainable ProductionWuhan 430070China

Protein-mediated chromatin interactions can be revealed by coupling proximity-based ligation with chromatin ***,these techniques require complex experimental procedures and millions of cells per experiment,which limits their widespread application in life science ***,we develop a novel method,Hi-Tag,that identifies high-resolution,long-range chromatin interactions through transposase tagmentation and chromatin proximity ligation(with a phosphorothioate-modified linker).Hi-Tag can be implemented using as few as 100,000 cells,involving simple experimental procedures that can be completed within 1.5 ***,Hi-Tag is capable of using its own data to identify the binding sites of specific proteins,based on which,it can acquire accurate interaction *** results suggest that Hi-Tag has great potential for advancing chromatin interaction studies,particularly in the context of limited cell availability.

关键词： Hi-Tag chromatin interactions transposase tagmentation chromatin proximity ligation low cell numbers

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Identification and Transcriptional Regulation of CAMTA Genes in Liriodendron chinense

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Phyton-International Journal of Experimental Botany 2024年第3期93卷 413-425页

作者： Kaiyue Hong Yasmina Radani Teja Manda Jinhui Chen Liming Yang State Key Laboratory of Tree genetics and breeding College of Life SciencesNanjing Forestry UniversityNanjing210037China

This study explores CAMTA genes in the rare and endangered Chinese plant species,Liriodendron *** the completion of whole-genome sequencing,the roles of CAMTA genes in calcium regulation and stress responses in this species remain largely *** the *** genome,we identiﬁed two CAMTA genes,Lchi09764 and Lchi222536,characterized by four functional domains:CG-1,TIG,ANK repeats,and IQ *** analyses,including phylogenetic investigations,cis-regulatory element analyses,and chromosomal location studies,aim to elucidate the deﬁning features of CAMTA genes in *** Weighted Gene Co-Expression Network Analysis(WGCNA),we explored the impact of CAMTA genes on different organs and their regulation under abiotic stress *** identiﬁcation of signiﬁcant gene modules and the prediction of promoter binding sites revealed co-expressed genes associated with CAMTA transcription *** summary,this study provides initial insights into CAMTA genes in ***,laying the groundwork for future research on their evolution and biological *** knowledge enhancement contributes to a better understanding of plant responses to environmental stress—an essential aspect of plant biology.

关键词： Liriodendron chinense CAMTA genes abiotic stress WGCNA different organs

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Rice Heat Tolerance breeding: A Comprehensive Review and Forward Gaze

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Rice science 2024年第4期31卷 375-400,I0022页

作者： Ravindran Lalithambika VISAKH Sreekumar ANAND Sukumaran Nair ARYA Behera SASMITA Uday Chand JHA Rameswar Prasad SAH Radha BEENA department of genetics and Plant breeding College of AgricultureVellayaniKerala Agricultural UniversityThiruvananthapuramKerala 695522India Crop Improvement Division Indian Council of Agricultural Research-National Rice Research InstituteCuttackOdisha 7530006India department of Plant breeding and genetics Indian Institute of Pulse ResearchKanpur 208024India department of Plant Physiology College of AgricultureVellayaniKerala Agricultural UniversityThiruvananthapuramKerala 695522India

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

关键词： genetic mechanism high-temperature stress molecular breeding genomics selection

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Single‑cell sequencing reveals the reproductive variations between primiparous and multiparous Hu ewes

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Journal of Animal Science and Biotechnology 2024年第2期15卷 614-631页

作者： Ting Ge Yifan Wen Bo Li Xiaoyu Huang Shaohua Jiang Enping Zhang Key Laboratory of Animal genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China

Background In the modern sheep production systems,the reproductive performance of ewes determines the economic profitability of *** the genetic mechanisms underlying differences in the litter size is important for the selection and breeding of highly prolific *** sheep,a high-quality Chinese sheep breed,is known for its high fecundity and is often used as a model to study prolificacy *** the current study,animals were divided into two groups according to their delivery rates in three consecutive lambing seasons(namely,the high and low reproductive groups with≥3 lambs and one lamb per season,n=3,respectively).The ewes were slaughtered within 12 h of estrus,and unilateral ovarian tissues were collected and analyzed by 10×Genomics single-cell RNA *** A total of 5 types of somatic cells were identified and corresponding expression profiles were mapped in the ovaries of each ***,the differences in the ovary somatic cell expression profiles between the high and low reproductive groups were mainly clustered in the granulosa ***,four granulosa cell subtypes were *** analysis revealed that the abundance of JPH1 expression and the reduction of LOC101112291 expression could lead to different evolutionary directions of the granulosa ***,the expression levels of FTH1 and FTL in mural granulosa cells of the highly reproductive group were significantly *** genes inhibit necroptosis and ferroptosis of mural granulosa cells,which helps prevent follicular *** This study provides insights into the molecular mechanisms underlying the high fecundity of Hu *** differences in gene expression profiles,particularly in the granulosa cells,suggest that these cells play a critical role in female *** findings also highlight the importance of genes such as JPH1,LOC101112291,FTH1,and FTL in regulating granulosa cell function and follicular development.

关键词： Granulosa cells Hu sheep Lambing number Ovarian somatic cells Single-cell RNA sequencing

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A 48-bp deletion upstream of LIGULELESS 1 alters rice panicle architecture

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The Crop Journal 2024年第2期12卷 354-363页

作者： Linhua Wu Min Hu Shuwei Lyu Wenfeng Chen Hang Yu Qing Liu Wei He Chen Li Zuofeng Zhu Rice Research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina National Center for Evaluation of Agricultural Wild Plants(Rice) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China State Key Laboratory for Rice Biology and breeding China National Rice Research InstituteHangzhou 310006ZhejiangChina Key Laboratory of genetics and breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province) Ministry of Agriculture and Rural AffairsGuangzhou 510640GuangdongChina Guangdong Key Laboratory of New Technology in Rice breeding Guangzhou 510640GuangdongChina Guangdong Rice Engineering Laboratory Guangzhou 510640GuangdongChina

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop *** investigate its molecular mechanisms in rice,we performed map-based cloning and characterization of OPEN PANICLE 1(OP1),a gain-of-function allele of LIGULELESS 1(LG1),controlling the spread-panicle *** allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary *** OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1(sp1).Knocking out BRASSINOSTEROID UPREGULATED1(BU1)gene in the background of OP1 complementary plants resulted in compact panicles,suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling *** regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

关键词： Upstream region Panicle architecture Gene expression BR Rice

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Synthesis of betanin by expression of the core betalain biosynthetic pathway in carrot

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Horticultural Plant Journal 2024年第3期10卷 732-742页

作者： Bo Wang Yahui Wang Yuanjie Deng Quanhong Yao Aisheng Xiong State Key Laboratory of Crop genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjingJiangsu 210095China Shanghai Key Laboratory of Agricultural genetics and breeding Biotechnology Research Institute of Shanghai Academy of Agricultural ScienceShanghai 201106China

Betalain has received increased attention because of its high nutritional value and crucial physiological *** on the elucidation of its core biosynthetic pathway,betalain can be produced in additional plants by metabolic *** of betalain in carrot(Daucus carota L.)can improve its nutritional quality and economic value by extracting betalain from the fleshy root,non-edible part,and processing residue of *** this study,two different constructs,namely,pYB:mCD(AomelOS,BvCYP76AD1S,and BvDODA1S)and p YB:CDD(BvCYP76AD1S,BvDODA1S,and MjcDOPA5GTS),were introduced into carrot for betanin synthesis by Agrobacterium-mediated *** can be synthetized in both transgenic calli,and p YB:m CD-transgenic callus can be used to produce betacyanin by suspension ***,pYB:mCD-transgenic seedlings can synthetize betanin only by tyrosine *** p YB:CDD-transgenic lines can synthetize betanin in whole *** betanin content in fleshy root of pYB:CDD-transgenic carrot was(63.4±9)μg·g^(-1)fresh weight according to quantitative *** betanin-producing carrot plant materials can be used to synthesize betanin for industrial application or consumption as dietary sources.

关键词： Daucus carota L. Betanin Biosynthesis Metabolic engineering Biofortification

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miR-24-3p promotes proliferation and inhibits apoptosis of porcine granulosa cells by targeting P27

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Journal of Integrative Agriculture 2024年第4期23卷 1315-1328页

作者： Shengjie Shi Lutong Zhang Liguang Wang Huan Yuan Haowei Sun Mielie Madaniyati Chuanjiang Cai Weijun Pang Lei Gao Guiyan Chu College of Animal Science and Technology Northwest A&F UniversityYangling 712100China Key Laboratory of Animal genetics Breeding and Reproduction of Shaanxi ProvinceYangling 712100China

Ovarian follicle development is associated with the physiological functions of granulosa cells(GCs),including proliferation and *** level of miR-24-3p in ovarian tissue of high-yielding Yorkshire×Landrace sows was significantly higher than that of low-yielding ***,the functions of miR-24-3p on GCs are *** this study,using flow cytometry,5-ethynyl-2′-de-oxyuridine(EdU)staining,and cell count,we showed that miR-24-3p promoted the proliferation of GCs increasing the proportion of cells in the S phase and upregulating the expression of cell cycle genes,moreover,miR-24-3p inhibited GC ***,on-line prediction,bioinformatics analysis,a luciferase reporter assay,RT-qPCR,and Western blot results showed that the target gene of miR-24-3p in proliferation and apoptosis is cyclin-dependent kinase inhibitor 1B(P27/CDKN1B).Furthermore,the effect of miR-24-3p on GC proliferation and apoptosis was attenuated by P27 *** findings suggest that miR-24-3p regulates the physiological functions of GCs.

关键词： miR-24-3p granulosa cells proliferation apoptosis

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