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Azam M, Zhang S, Huai Y, Abdelghany AM, Shaibu AS, Qi J, Feng Y, Liu Y, Li J, Qiu L, Li B, Sun J. Identification of genes for seed isoflavones based on bulk segregant analysis sequencing in soybean natural population. Theor Appl Genet 2023; 136:13. [PMID: 36662254 DOI: 10.1007/s00122-023-04258-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
We identified four hub genes for isoflavone biosynthesis based on BSA-seq and WGCNA methods and validated that GmIE3-1 positively contribute to isoflavone accumulation in soybean. Soybean isoflavones are secondary metabolites of great interest owing to their beneficial impact on human health. Herein, we profiled the seed isoflavone content by HPLC in 1551 soybean accessions grown in two locations for two years and constructed two extreme pools with high (4065.1 µg g-1) and low (1427.23 µg g-1) isoflavone contents to identify candidate genes involved in isoflavone biosynthesis pathways using bulk segregant analysis sequencing (BSA-seq) approach. The results showed that the average sequencing depths were 50.3× and 65.7× in high and low pools, respectively. A total of 23,626 polymorphic SNPs and 5299 InDels were detected between both pools and 1492 genes with different variations were identified. Based on differential genes in BSA-seq and weighted gene co-expression network analysis (WGCNA), four hub genes, Glyma.06G290400 (designated as GmIE3-1), Glyma.01G239200, Glyma.01G241500, Glyma.13G256100 were identified, encoding E3 ubiquitin-protein ligase, arm repeat protein interacting with ABF2, zinc metallopeptidase EGY3, and dynamin-related protein 3A, respectively. The allelic variation in GmIE3-1 showed a significant influence on isoflavone accumulation. The virus-induced gene silencing (VIGS) and RNAi hairy root transformation of GmIE3-1 revealed partial suppression of this gene could cause a significant decrease (P < 0.0001) of total isoflavone content, suggesting GmIE3-1 is a positive regulator for isoflavones. The present study demonstrated that the BSA-seq approach combined with WGCNA, VIGS and hairy root transformation can efficiently identify isoflavone candidate genes in soybean natural population.
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Affiliation(s)
- Muhammad Azam
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Shengrui Zhang
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuanyuan Huai
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Ahmed M Abdelghany
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
- Crop Science Department, Faculty of Agriculture, Damanhour University, Damanhour, 22516, Egypt
| | - Abdulwahab S Shaibu
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
- Department of Agronomy, Bayero University, Kano, Nigeria
| | - Jie Qi
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yue Feng
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yitian Liu
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Jing Li
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lijuan Qiu
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Bin Li
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China.
| | - Junming Sun
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China.
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Shaibu AS, Zhang S, Ma J, Feng Y, Huai Y, Qi J, Li J, Abdelghany AM, Azam M, Htway HTP, Sun J, Li B. The GmSNAP11 Contributes to Resistance to Soybean Cyst Nematode Race 4 in Glycine max. Front Plant Sci 2022; 13:939763. [PMID: 35860531 PMCID: PMC9289622 DOI: 10.3389/fpls.2022.939763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Soybean cyst nematode (SCN) has devastating effects on soybean production, making it crucial to identify genes conferring SCN resistance. Here we employed next-generation sequencing-based bulked segregant analysis (BSA) to discover genomic regions, candidate genes, and diagnostic markers for resistance to SCN race 4 (SCN4) in soybean. Phenotypic analysis revealed highly significant differences among the reactions of 145 recombinant inbred lines (RILs) to SCN4. In combination with euclidean distance (ED) and Δsingle-nucleotide polymorphism (SNP)-index analyses, we identified a genomic region on Gm11 (designated as rhg1-paralog) associated with SCN4 resistance. Overexpression and RNA interference analyzes of the two candidate genes identified in this region (GmPLAC8 and GmSNAP11) revealed that only GmSNAP11 significantly contributes to SCN4 resistance. We developed a diagnostic marker for GmSNAP11. Using this marker, together with previously developed markers for SCN-resistant loci, rhg1 and Rhg4, we evaluated the relationship between genotypes and SCN4 resistance in 145 RILs and 30 soybean accessions. The results showed that all the SCN4-resistant lines harbored all the three loci, however, some lines harboring the three loci were still susceptible to SCN4. This suggests that these three loci are necessary for the resistance to SCN4, but they alone cannot confer full resistance. The GmSNAP11 and the diagnostic markers developed could be used in genomic-assisted breeding to develop soybean varieties with increased resistance to SCN4.
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Affiliation(s)
- Abdulwahab S. Shaibu
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Agronomy, Bayero University Kano, Kano, Nigeria
| | - Shengrui Zhang
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junkui Ma
- Institute of Industrial Crop Research, Shanxi Academy of Agricultural Sciences, Fenyang, China
| | - Yue Feng
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanyuan Huai
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Qi
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Li
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ahmed M. Abdelghany
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Azam
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honey Thet Paing Htway
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junming Sun
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Li
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Ghosh S, Zhang S, Azam M, Qi J, Abdelghany AM, Shaibu AS, Gebregziabher BS, Feng Y, Huai Y, Htway HTP, Agyenim-Boateng KG, Liu Y, Feng H, Li J, Song W, Li B, Sun J. Seed tocopherol assessment and geographical distribution of 1151 Chinese soybean accessions from diverse ecoregions. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Azam M, Zhang S, Qi J, Abdelghany AM, Shaibu AS, Ghosh S, Feng Y, Huai Y, Gebregziabher BS, Li J, Li B, Sun J. Profiling and associations of seed nutritional characteristics in Chinese and USA soybean cultivars. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Penthorn NE, Hao X, Wang Z, Huai Y, Jiang HW. Experimental Observation of Single Skyrmion Signatures in a Magnetic Tunnel Junction. Phys Rev Lett 2019; 122:257201. [PMID: 31347909 DOI: 10.1103/physrevlett.122.257201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 06/10/2023]
Abstract
We have deterministically created a stable topological spin texture in magnetic tunnel junctions (MTJ) by using pulsed or microwave currents. The spin texture is characterized by a field-dependent intermediate resistance state and a new magnetic resonance. Micromagnetic simulations show that the observations are consistent with the nucleation of a single skyrmion, facilitated by a spatially nonuniform stray field. The unique resonance spectrum is identified as the skyrmion breathing mode and a skyrmion diameter of 75 nm is estimated. This work shows the possibility to create skyrmions in MTJs without the Dzyaloshinskii-Moriya interaction and could lead to noninvasive, on-chip skyrmion measurement.
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Affiliation(s)
- N E Penthorn
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
| | - X Hao
- Avalanche Technology, Fremont, California 95438, USA
| | - Z Wang
- Avalanche Technology, Fremont, California 95438, USA
| | - Y Huai
- Avalanche Technology, Fremont, California 95438, USA
| | - H W Jiang
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
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Gopman DB, Dennis CL, McMichael RD, Hao X, Wang Z, Wang X, Gan H, Zhou Y, Zhang J, Huai Y. Enhanced ferromagnetic resonance linewidth of the free layer in perpendicular magnetic tunnel junctions. AIP Adv 2017; 7:055932. [PMID: 28690916 PMCID: PMC5497521 DOI: 10.1063/1.4977969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/28/2016] [Indexed: 06/07/2023]
Abstract
We report the frequency dependence of the ferromagnetic resonance linewidth of the free layer in magnetic tunnel junctions with all perpendicular-to-the-plane magnetized layers. While the magnetic-field-swept linewidth nominally shows a linear growth with frequency in agreement with Gilbert damping, an additional frequency-dependent linewidth broadening occurs that shows a strong asymmetry between the absorption spectra for increasing- and decreasing external magnetic field. Inhomogeneous magnetic fields produced during reversal of the reference and pinned layer complex is demonstrated to be at the origin of the symmetry breaking and the linewidth enhancement. Consequentially, this linewidth enhancement provides indirect information on the magnetic coercivity of the reference and pinned layers. These results have important implications for the characterization of perpendicular magnetized magnetic random access memory bit cells.
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Affiliation(s)
- D. B. Gopman
- Materials Science and Engineering Division, NIST, Gaithersburg, MD 20899, USA
| | - C. L. Dennis
- Materials Science and Engineering Division, NIST, Gaithersburg, MD 20899, USA
| | - R. D. McMichael
- Center for Nanoscale Science and Technology, NIST, Gaithersburg, MD 20899, USA
| | - X. Hao
- Avalanche Technology, Fremont, CA 95438, USA
| | - Z. Wang
- Avalanche Technology, Fremont, CA 95438, USA
| | - X. Wang
- Avalanche Technology, Fremont, CA 95438, USA
| | - H. Gan
- Avalanche Technology, Fremont, CA 95438, USA
| | - Y. Zhou
- Avalanche Technology, Fremont, CA 95438, USA
| | - J. Zhang
- Avalanche Technology, Fremont, CA 95438, USA
| | - Y. Huai
- Avalanche Technology, Fremont, CA 95438, USA
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Bedford A, Li Z, Li M, Ji S, Liu W, Huai Y, de Lange CFM, Li J. Epidermal growth factor-expressing Lactococcus lactis enhances growth performance of early-weaned pigs fed diets devoid of blood plasma. J Anim Sci 2012; 90 Suppl 4:4-6. [DOI: 10.2527/jas.53973] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- A. Bedford
- Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario N1G 2W1
| | - Z. Li
- Premix INVE Nutrition, Shenzhen, Guangdong, China, 518103
| | - M. Li
- Premix INVE Nutrition, Shenzhen, Guangdong, China, 518103
| | - S. Ji
- Premix INVE Nutrition, Shenzhen, Guangdong, China, 518103
| | - W. Liu
- College of Life Science, Foshan University, Foshan, Guangdong, China, 528000
| | - Y. Huai
- College of Life Science, Foshan University, Foshan, Guangdong, China, 528000
| | - C. F. M. de Lange
- Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario N1G 2W1
| | - J. Li
- Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario N1G 2W1
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Huai Y, Broughton JN, Gat E, Chaker M, Borges CFM, Beaudoin Y, PÉpin H, Moisan M. Pulsed-Laser Deposition and Characterization of Amorphous Diamondlike Carbon Films. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-349-471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
ABSTRACTUnhydrogenated amorphous carbon films were deposited by KrF pulsed laser ablation of graphite under a laser power density of 8×108 W/cm2. The films were characterized using x-ray reflectivity, optical transmittance, spectroscopic ellipsometry and Raman spectroscopy. The physical, optical and bonding properties of the films have been investigated in detail as functions of substrate temperatures Ts (22-300°C) and post-annealing temperatures. Films deposited at Ts, <200°C possessed diamond-like properties with mass densities p=2.8-3.1 g/cm3 and optical bandgaps Eg,=1.5-2.2 eV. Above Ts,=200°C, the films showed typical graphite characteristics. The diamond-like films annealed at temperatures up to 750°C show excellent thermal stability.
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Huang Y, Zhang E, Li Z, Wang J, Huai Y, Ma L, Chen F, Lan X, Lei C, Wang J, Fang X, Chen H. Six novel coding SNPs of the nucleophosmin 1 (<i>NPM1</i>) gene and their associations with growth traits in bovine (Brief Report). Arch Anim Breed 2010. [DOI: 10.5194/aab-53-368-2010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The Nucleophosmin 1 (NPM1) gene encodes a multifunctional nucleolar phosphoprotein that has crucial roles in the control of different aspects of cell growth and homeostasis, such as ribosome biogenesis, centrosome duplication, cell cycle progression, apoptosis and cell differentiation (GRISENDI et al. 2006, NAOE et al. 2006). As mutants of NPM1 gene impact protein synthesis, NPM1 is an essential protein in mouse development and cell growth (MAGGI et al. 2008). The bovine NPM1 gene contains one exon and locates at chromosome 9. In previous work, the 12-bp deletion was detected in bovine NPM1 gene coding region. (HUANG et al. 2010). In this study, the coding region of bovine NPM1 gene has been scanned by PCR-SSCP, DNA sequencing and forced PCR-RFLP methods for SNPs in 1 032 individuals belonging to four Chinese cattle breeds. Association of six mutations of NPM1 gene with growth traits was analyzed.
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Li Z, Zhang S, Diao Z, Ding Y, Tang X, Apalkov DM, Yang Z, Kawabata K, Huai Y. Perpendicular spin torques in magnetic tunnel junctions. Phys Rev Lett 2008; 100:246602. [PMID: 18643606 DOI: 10.1103/physrevlett.100.246602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Indexed: 05/26/2023]
Abstract
We quantitatively determine a perpendicular spin torque in magnetic tunnel junctions by measuring the room-temperature critical switching current at various magnetic fields and current pulse widths. We find that the magnitude of the torque is proportional to the product of the current density and the bias voltage, and the direction of the torque reverses as the polarity of the voltage changes. By taking into account the energy-dependent inelastic scattering of tunnel electrons, we formulate the bias dependence of the perpendicular spin torque which is in qualitative agreement with the experimental results.
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Affiliation(s)
- Z Li
- Grandis Inc., 1123 Cadillac Court, Milpitas, California 95035, USA
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