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A Domestication-Associated Gene GmPRR3b Regulates the Circadian Clock and Flowering Time in Soybean

Molecular Plant 2020年第5期13卷 745-759页

作者： Cong Li Ying-hui Li Yanfei Li Hongfeng Lu Huilong Hong Yu Tian Hongyu Li Tao Zhao Xiaowei Zhou Jun Liu Xinan Zhou scott a.jackson Bin Liu Li-juan Qiu The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI) Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingP.R.China Novogene Bioinformatics Institute BeijingP.R.China Key Laboratory of Oil Crop Biology(MOA) Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhanChina Center for Applied Genetic Technologies University of GeorgiaAthensGAUSA

Improved soybean cultivars have been adapted to grow at a wide range of latitudes,enabling expansion of cultivation ***,the genetic basis of this broad adaptation is still not ***,we report the identification of GmPRR3b as a major flowering time regulatory gene that has been selected during domestication and genetic improvement for geographic *** a genome-wide association study of a diverse soybean landrace panel consisting of 279 accessions,we identified 16 candidate quantitative loci associated with flowering time and maturity *** strongest signal resides in the known flowering gene E2,verifying the effectiveness of our *** detected strong signals associated with both flowering and maturity time in a genomic region containing *** analysis revealed that GmPRR3bH6 is the major form of GmPRR3b that has been utilized during recent breeding of modern *** profiling analysis showed that GmPRR3bH6 displays rhythmic and photoperiod-dependent expression and is preferentially induced under long-day *** of GmPRR3bH6 increased main stem node number and yield,while knockout of GmPRR3bH6 using CRISPR/Cas9 technology delayed growth and the floral ***3bH6 appears to act as a transcriptional repressor of multiple predicted circadian clock genes,including GmCCAIa,which directly upregulates J/GmELF3a to modulate flowering *** causal SNP(Chr12:5520945)likely endows GmPRR3bH6 a moderate but appropriate level of activity,leading to early flowering and vigorous growth traits preferentially selected during broad adaptation of landraces and improvement of cultivars.

关键词： flowering time soybean landrace domestication genome-wide association study GmPRR3b circadian clock

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Evolutionary Dynamics of Transposable Elements in Soybean

Evolutionary Dynamics of Transposable Elements in Soybean

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第十二届全国植物基因组学大会

作者： Christian S.Hans Howard M.Laten Steven B.Cannon scott a.jackson Randy C.Shoemaker Department of Agronomy Purdue UniversityWest Lafayette 47906USA Department of Biology Loyola University ChicagoChicagoIl 60660USA

The availability of complete or nearly complete genome sequences from several plant species permits detailed discovery and cross-species comparison of transposable elements(TEs) at the whole genome level. We initially investigated 510 long terminal repeat-retrotransposon(LTR-RT) families comprising 32 370 elements in *** 87%of these elements were located in recombination suppressed pericentromeric *** analysis revealed a significant positive correlation between ratio of solo LTRs to intact elements and LTR sizes,indicating that larger LTRs facilitate solo LTR *** analysis

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Reactive oxygen species promote endurance exercise-induced adaptations in skeletal muscles

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Journal of Sport and Health Science 2024年第6期13卷 780-792页

作者： scott K.Powers Zsolt Radak Li Li Ji Malcolm jackson Department of Applied Physiology University of FloridaGainesvilleFL 32608USA Research Institute of Sport Science Hungarian University of Sport ScienceBudapest 1123Hungary Department of Kinesiology University of MinnesotaSt.PaulMN 55455USA Department of Musculoskeletal and Ageing Science Institute of Life Course and Medical SciencesUniversity of LiverpoolLiverpool L78TXUK

The discovery that contracting skeletal muscle generates reactive oxygen species(ROS)was first reported over 40 years *** prevailing view in the 1980s was that exercise-induced ROS production promotes oxidation of proteins and lipids resulting in muscle ***,a paradigm shift occurred in the 1990s as growing research revealed that ROS are signaling molecules,capable of activating transcriptional activators/coactivators and promoting exercise-induced muscle *** evidence supports the notion that reduction-oxidation(redox)signaling pathways play an important role in the muscle remodeling that occurs in response to endurance exercise *** review examines the specific role that redox signaling plays in this endurance exercise-induced skeletal muscle *** begin with a discussion of the primary sites of ROS production in contracting muscle fibers followed by a summary of the antioxidant enzymes involved in the regulation of ROS levels in the *** then discuss which redox-sensitive signaling pathways promote endurance exercise-induced muscle adaptation and debate the strength of the evidence supporting the notion that redox signaling plays an essential role in muscle adaptation to endurance exercise *** hopes of stimulating future research,we highlight several important unanswered questions in this field.

关键词： Antioxidants Mitochondrial biogenesis Radicals Redox signaling

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Genome-wide signatures of the geographic expansion and breeding of soybean

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Science China(Life Sciences) 2023年第2期66卷 350-365页

作者： Ying-Hui Li Chao Qin Li Wang Chengzhi Jiao Huilong Hong Yu Tian Yanfei Li Guangnan Xing Jun Wang Yongzhe Gu Xingpeng Gao Delin Li Hongyu Li Zhangxiong Liu Xin Jing Beibei Feng Tao Zhao Rongxia Guan Yong Guo Jun Liu Zhe Yan Lijuan Zhang Tianli Ge Xiangkong Li Xiaobo Wang Hongmei Qiu Wanhai Zhang Xiaoyan Luan Yingpeng Han Dezhi Han Ruzhen Chang Yalong Guo Jochen C.Reif scott a.jackson Bin Liu Shilin Tian Li-juan Qiu The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA) Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture/Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen 518000China Novogene Bioinformatics Institute Beijing 100098China State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute Nanjing Agricultural UniversityNanjing 210095China Soybean Research Institute/MOA National Center for Soybean Improvement/MOA Key Laboratory for Biology and Genetic Improvement of Soybean(General)/State Key Laboratory for Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095China College of Agriculture Yangtze UniversityJingzhou 451199China School of Agronomy Anhui Agricultural UniversityHefei 230036China Jilin Academy of Agricultural Sciences Changchun 130119China Hulun Buir Institution of Agricultural Sciences Hulun Buir 021008China Soybean Research Institute Heilongjiang Academy of Agricultural SciencesHarbin 150086China Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry) Northeast Agricultural UniversityHarbin 150030China Heihe Branch of Heilongjiang Academy of Agricultural Sciences Harbin 150086China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China Department of Breeding Research Leibniz Institute of Plant Genetics and Crop Plant Research(IPK)Gatersleben DE D-06466Germany Center for Applied Genetic Technologies University of GeorgiaAthens 30602USA Department of Ecology/Tibetan Centre for Ecology and Conservation at WHU-TU/Hubei Key

Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean(Glycine soja Sieb. & Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces(G. max(L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.

关键词： soybean adaptation introgression flowering time breeding

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Tumor necrosis factor alpha inhibits in vitro bovine embryo development through a prostaglandin mediated mechanism

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Journal of Animal Science and Biotechnology 2012年第1期3卷 21-24页

作者： Lauren R jackson Char E Farin scott Whisnant Department of Animal Science North Carolina State University PO Box 7621 Raleigh NC 27695-7621 USA

Mastitis or other infectious diseases have been related to reduced fertility in cattle. Inflammatory cytokines such as tumor necrosis factor α （TNFα are released in response to infection and may have negative effects on embryo development, in the current study the effect of exposure to TNFα on the development of in vitro fertilized bovine embryos was examined. Indomethacin, a prostaglandin synthesis inhibitor, was used to determine if blockade of prostaglandin synthesis would alter the effects of TNFα Ovaries were obtained from a local abattoir and immature COC were isolated from 2-10 mm follicles, in vitro matured and fertilized. After fertilization, groups of presumptive zygotes were randomly placed into either control development medium, medium containing 25 ng/mL TNFα or medium containing 25 ng/mL TNFα plus 1 μg/mL indomethacin. The proportion of blastocysts formed was assessed at day 7 of culture. Fewer embryos exposed to TNFα alone reached the blastocyst stage （17.5 ± 2.4%, P 〈 0.01） compared with controls （30.5 ± 2.4%） or embryos developed in TNFα plus indomethacin （25.8 ± 2.8%）. There was no difference between control embryos and embryos developed in TNFα plus indomethacin. These results indicate that TNFα is inhibitory to the in vitro development of bovine embryos and that this inhibition may be mediated by prostaglandins because it can be blocked by indomethacin.

关键词： tumor necrosis factor o bovine embryo indomethacin

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Differential Diagnosis for the Dermatologist 2008

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2008年

作者： scott jackson Lee T. Nesbitt

Critical care medicine;Dermatology;Family medicine;Internal medicine;Pediatrics;Medicine & Public Health;Dermatology;General Practice / Family Medicine;Intensive / Critical Care Medicine;Internal Medicine;Pediatrics

ISBN: (数字)9783540758877

ISBN: (纸本)9783540758860

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Genic C-Methylation in Soybean Is Associated with Gene Paralogs Relocated to Transposable Element-Rich Pericentromeres

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Molecular Plant 2018年第3期11卷 485-495页

作者： Moaine El Baidouri Kyung Do Kim Brian Abernathy Ying-Hui Li Li-Juan Qiu scott A. jackson Center for Applied Genetic Technologies University of Georgia 111 Riverbend Road Athens GA 30602 USA Corporate R&D LG Chem LG Science Park 30 Magokjungang 10-ro Gangseo-gu Seoul 07796 Republic of Korea The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Institute of Crop Science Chinese Academy of Agricultural SciencesBeijing China These authors contributed equally to this article.

Most plants are polyploid due to whole-genome duplications （WGD） and can thus have duplicated genes. Following a WGD, paralogs are often fractionated （lost） and few duplicate pairs remain. Little attention has been paid to the role of DNA methylation in the functional divergence of paralogous genes. Using high- resolution methylation maps of accessions of domesticated and wild soybean, we show that in soybean, a recent paleopolyploid with many paralogs, DNA methylation likely contributed to the elimination of ge- netic redundancy of polyploidy-derived gene paralogs. Transcriptionally silenced paralogs exhibit partic- ular genomic features as they are often associated with proximal transposable elements （TEs） and are pref- erentially located in pericentromeres, likely due to gene movement during evolution. Additionally, we provide evidence that gene methylation associated with proximal TEs is implicated in the divergence of expression profiles between orthologous genes of wild and domesticated soybean, and within populations.

关键词： soybean paralog gene methylation proximal transposable element methylation spreading

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Analysis of simple sequence repeats in rice bean(Vigna umbellata) using an SSR-enriched library

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The Crop Journal 2016年第1期4卷 40-47页

作者： Lixia Wang Kyung Do Kim Dongying Gao Honglin Chen Suhua Wang Suk Ha Lee scott A. jackson Xuzhen Cheng Institute of Crop Science Chinese Academy of Agricultural Sciences Center for Applied Genetic Technologies University of Georgia Plant Genomics and Breeding Institute Seoul National University

Rice bean(Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important *** we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR *** 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides(17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT(14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that58 of 220 new primers can be used in rice bean and 53 can be transferred to mung ***, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in rice b

关键词： Vigna umbellata SSR Distribution and frequency Mapping Primer design

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Single Nucleotide Polymorphism Identification in Polyploids： A Review, Example, and Recommendations

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Molecular Plant 2015年第6期8卷 831-846页

作者： Josh Clevenger Carolina Chavarro Stephanie A. Pearl Peggy Ozias-Akins scott A. jackson Center for AppLied Genetic Technologies University of Georgia Athens GA 30602 USA Institute of Plant Breeding Genetics & Genomics University of Georgia Tifton GA 31793 USA These authors contributed equally to this article.

Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms （SNPs） have become popular tools for genetic mapping, discovery and appli- cation of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs （BWA-mem and Bowtie 2） and variant callers （SAMtools, GATK, and Freebayes）. Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.

关键词： genomics homeolog next-generation sequencing (NGS) peanut polyptoid single nucleotide poly-morphism (SNP)

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Longitudinal monitoring for the emergence of epidermal growth factor C797S resistance mutations in non-small cell lung cancer using blood-based droplet digital PCR

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Cancer Drug Resistance 2019年第3期2卷 912-916页

作者： Mark Bowling Hyder Arastu Victoria Edwards Leisa.jackson scott Thurston Jordan Reese Hestia Mellert Gary Pestano Paul Walker East Carolina University Mail Stop 628Internal Medicine-Hematology/OncologyGreenvilleNC 27834USA Biodesix Inc.2970 Wilderness PlaceBoulderCO 80301USA.

Validation of assays for the C797S mutation as a biomarker for osimertinib resistance is promising in guiding treatment decision-making for multidrug resistant non-small cell lung cancer. A newly developed droplet digital PCR (ddPCR) assay was used to retrospectively evaluate the emergence of the C797S mutation in six remnant plasma samples in this case report. It was found that the detected emergence of C797S clearly correlated with clinical signs of treatment resistance. Had these data been available to aid treatment selection in real time, there would have been hope for recaptured disease response and control instead of treatment cessation. The results of this study show that highly sensitive ddPCR methods can be used for the monitoring of emergent epidermal growth factor somatic variant mutations in circulation.

关键词： Epidermal growth factor non-small cell lung cancer C797S drug resistance

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