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Xu B, Shen T, Chen H, Li H, Rehman SU, Lyu S, Hua L, Wang G, Zhang C, Li K, Li H, Lan C, Chen GY, Hao M, Chen S. Mapping and characterization of rust resistance genes Lr53 and Yr35 introgressed from Aegilops species. Theor Appl Genet 2024; 137:113. [PMID: 38678511 PMCID: PMC11056342 DOI: 10.1007/s00122-024-04616-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/04/2024] [Indexed: 05/01/2024]
Abstract
KEY MESSAGE The rust resistance genes Lr53 and Yr35 were introgressed into bread wheat from Aegilops longissima or Aegilops sharonensis or their S-genome containing species and mapped to the telomeric region of chromosome arm 6BS. Wheat leaf and stripe rusts are damaging fungal diseases of wheat worldwide. Breeding for resistance is a sustainable approach to control these two foliar diseases. In this study, we used SNP analysis, sequence comparisons, and cytogenetic assays to determine that the chromosomal segment carrying Lr53 and Yr35 was originated from Ae.longissima or Ae. sharonensis or their derived species. In seedling tests, Lr53 conferred strong resistance against all five Chinese Pt races tested, and Yr35 showed effectiveness against Pst race CYR34 but susceptibility to race CYR32. Using a large population (3892 recombinant gametes) derived from plants homozygous for the ph1b mutation obtained from the cross 98M71 × CSph1b, both Lr53 and Yr35 were successfully mapped to a 6.03-Mb telomeric region of chromosome arm 6BS in the Chinese Spring reference genome v1.1. Co-segregation between Lr53 and Yr35 was observed within this large mapping population. Within the candidate region, several nucleotide-binding leucine-rich repeat genes and protein kinases were identified as candidate genes. Marker pku6B3127 was completely linked to both genes and accurately predicted the absence or presence of alien segment harboring Lr53 and Yr35 in 87 tetraploid and 149 hexaploid wheat genotypes tested. We developed a line with a smaller alien segment (< 6.03 Mb) to reduce any potential linkage drag and demonstrated that it conferred resistance levels similar to those of the original donor parent 98M71. The newly developed introgression line and closely linked PCR markers will accelerate the deployment of Lr53 and Yr35 in wheat breeding programs.
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Affiliation(s)
- Binyang Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Tao Shen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100000, China
| | - Hong Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Shams Ur Rehman
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Shikai Lyu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Chaozhong Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kairong Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Hao Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guo-Yue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China.
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Zhou Z, Yang Y, Ai G, Zhao M, Han B, Zhao C, Chen Y, Zhang Y, Pan H, Lan C, He C, Li Q, Xu J, Yan W. Overcoming genotypic dependency and bypassing immature embryos in wheat transformation by using morphogenic regulators. Sci China Life Sci 2024:10.1007/s11427-023-2565-9. [PMID: 38647567 DOI: 10.1007/s11427-023-2565-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/08/2024] [Indexed: 04/25/2024]
Affiliation(s)
- Ziru Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yawen Yang
- WIMI Biotechnology Co., Ltd., Changzhou, 213025, China
| | - Guo Ai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Miaomiao Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baozhu Han
- WIMI Biotechnology Co., Ltd., Changzhou, 213025, China
| | - Chunjie Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yiqian Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Pan
- WIMI Biotechnology Co., Ltd., Changzhou, 213025, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jieting Xu
- WIMI Biotechnology Co., Ltd., Changzhou, 213025, China.
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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Ai G, He C, Bi S, Zhou Z, Liu A, Hu X, Liu Y, Jin L, Zhou J, Zhang H, Du D, Chen H, Gong X, Saeed S, Su H, Lan C, Chen W, Li Q, Mao H, Li L, Liu H, Chen D, Kaufmann K, Alazab KF, Yan W. Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat. Plant Commun 2024:100879. [PMID: 38486454 DOI: 10.1016/j.xplc.2024.100879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 04/30/2024]
Abstract
Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.
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Affiliation(s)
- Guo Ai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Siteng Bi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziru Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanyan Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liujie Jin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - JiaCheng Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Heping Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dengxiang Du
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Gong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sulaiman Saeed
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; 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 Sciences, Shenzhen 518120, China
| | - Hao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität Zu Berlin, 10115 Berlin, Germany
| | - Khaled F Alazab
- Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo 13759, Egypt
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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4
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Zhu A, Liu M, Tian Z, Liu W, Hu X, Ao M, Jia J, Shi T, Liu H, Li D, Mao H, Su H, Yan W, Li Q, Lan C, Fernie AR, Chen W. Chemical-tag-based semi-annotated metabolomics facilitates gene identification and specialized metabolic pathway elucidation in wheat. Plant Cell 2024; 36:540-558. [PMID: 37956052 PMCID: PMC10896294 DOI: 10.1093/plcell/koad286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023]
Abstract
The importance of metabolite modification and species-specific metabolic pathways has long been recognized. However, linking the chemical structure of metabolites to gene function in order to explore the genetic and biochemical basis of metabolism has not yet been reported in wheat (Triticum aestivum). Here, we profiled metabolic fragment enrichment in wheat leaves and consequently applied chemical-tag-based semi-annotated metabolomics in a genome-wide association study in accessions of wheat. The studies revealed that all 1,483 quantified metabolites have at least one known functional group whose modification is tailored in an enzyme-catalyzed manner and eventually allows efficient candidate gene mining. A Triticeae crop-specific flavonoid pathway and its underlying metabolic gene cluster were elucidated in further functional studies. Additionally, upon overexpressing the major effect gene of the cluster TraesCS2B01G460000 (TaOMT24), the pathway was reconstructed in rice (Oryza sativa), which lacks this pathway. The reported workflow represents an efficient and unbiased approach for gene mining using forward genetics in hexaploid wheat. The resultant candidate gene list contains vast molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets and will ultimately aid in achieving wheat crop improvement.
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Affiliation(s)
- Anting Zhu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Mengmeng Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Min Ao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingqi Jia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Taotao Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Department of Root Biology and Symbiosis, Potsdam-Golm 14476, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Jouenne A, Hamici K, Varlet I, Sourdon J, Daudé P, Lan C, Kober F, Landrier JF, Bernard M, Desrois M. Relationship of cardiac remodeling and perfusion alteration with hepatic lipid metabolism in a prediabetic high fat high sucrose diet female rat model. Biochem Biophys Res Commun 2023; 682:207-215. [PMID: 37826944 DOI: 10.1016/j.bbrc.2023.09.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/08/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND AND AIMS Cardiovascular disease (CVD) is known to be linked with metabolic associated fatty liver disease and type 2 diabetes, but few studies assessed this relationship in prediabetes, especially among women, who are at greater risk of CVD. We aimed to evaluate cardiac alterations and its relationship with hepatic lipid metabolism in prediabetic female rats submitted to high-fat-high-sucrose diet (HFS). METHODS AND RESULTS Wistar female rats were divided into 2 groups fed for 5 months with standard or HFS diet. We analyzed cardiac morphology, function, perfusion and fibrosis by Magnetic Resonance Imaging. Hepatic lipid contents along with inflammation and lipid metabolism gene expression were assessed. Five months of HFS diet induced glucose intolerance (p < 0.05), cardiac remodeling characterized by increased left-ventricular volume, wall thickness and mass (p < 0.05). No significant differences were found in left-ventricular ejection fraction and cardiac fibrosis but increased myocardial perfusion (p < 0.01) and reduced cardiac index (p < 0.05) were shown. HFS diet induced hepatic lipid accumulation with increased total lipid mass (p < 0.001) and triglyceride contents (p < 0.05), but also increased mitochondrial (CPT1a, MCAD; (p < 0.001; p < 0.05) and peroxisomal (ACO, LCAD; (p < 0.05; p < 0.001) β-oxidation gene expression. Myocardial wall thickness and perfusion were correlated with hepatic β-oxidation genes expression. Furthermore, myocardial perfusion was also correlated with hepatic lipid content and glucose intolerance. CONCLUSION This study brings new insights on the relationship between cardiac sub-clinical alterations and hepatic metabolism in female prediabetic rats. Further studies are warranted to explore its involvement in the higher CVD risk observed among prediabetic women.
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Affiliation(s)
- A Jouenne
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France.
| | - K Hamici
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France.
| | - I Varlet
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France.
| | - J Sourdon
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France.
| | - P Daudé
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France.
| | - C Lan
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France.
| | - F Kober
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France.
| | - J F Landrier
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Marseille, France.
| | - M Bernard
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France.
| | - M Desrois
- Aix-Marseille Univ, CNRS, CRMBM, Marseille, France.
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Mutreja I, Lan C, Li Q, Aparicio C. Chemoselective Coatings of GL13K Antimicrobial Peptides for Dental Implants. Pharmaceutics 2023; 15:2418. [PMID: 37896178 PMCID: PMC10609907 DOI: 10.3390/pharmaceutics15102418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Dental implant-associated infection is a clinical challenge which poses a significant healthcare and socio-economic burden. To overcome this issue, developing antimicrobial surfaces, including antimicrobial peptide coatings, has gained great attention. Different physical and chemical routes have been used to obtain these biofunctional coatings, which in turn might have a direct influence on their bioactivity and functionality. In this study, we present a silane-based, fast, and efficient chemoselective conjugation of antimicrobial peptides (Cys-GL13K) to coat titanium implant surfaces. Comprehensive surface analysis was performed to confirm the surface functionalization of as-prepared and mechanically challenged coatings. The antibacterial potency of the evaluated surfaces was confirmed against both Streptococcus gordonii and Streptococcus mutans, the primary colonizers and pathogens of dental surfaces, as demonstrated by reduced bacteria viability. Additionally, human dental pulp stem cells demonstrated long-term viability when cultured on Cys-GL13K-grafted titanium surfaces. Cell functionality and antimicrobial capability against multi-species need to be studied further; however, our results confirmed that the proposed chemistry for chemoselective peptide anchoring is a valid alternative to traditional site-unspecific anchoring methods and offers opportunities to modify varying biomaterial surfaces to form potent bioactive coatings with multiple functionalities to prevent infection.
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Affiliation(s)
- Isha Mutreja
- MDRCBB−Minnesota Dental Research Center for Biomaterials and Biomechanics, Minneapolis, MN 55455, USA; (I.M.); (Q.L.)
| | - Caixia Lan
- MDRCBB−Minnesota Dental Research Center for Biomaterials and Biomechanics, Minneapolis, MN 55455, USA; (I.M.); (Q.L.)
| | - Qishun Li
- MDRCBB−Minnesota Dental Research Center for Biomaterials and Biomechanics, Minneapolis, MN 55455, USA; (I.M.); (Q.L.)
- The Affiliated Stomatological Hospital of Nanchang University, Nanchang 330000, China
| | - Conrado Aparicio
- MDRCBB−Minnesota Dental Research Center for Biomaterials and Biomechanics, Minneapolis, MN 55455, USA; (I.M.); (Q.L.)
- Faculty of Odontology, UIC Barcelona−International University of Catalonia, 08198 Sant Cugat del Vallès, Spain
- IBEC Institute for Bioengineering of Catalonia, 08170 Barcelona, Spain
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7
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Gao J, Hu X, Gao C, Chen G, Feng H, Jia Z, Zhao P, Yu H, Li H, Geng Z, Fu J, Zhang J, Cheng Y, Yang B, Pang Z, Xiang D, Jia J, Su H, Mao H, Lan C, Chen W, Yan W, Gao L, Yang W, Li Q. Deciphering genetic basis of developmental and agronomic traits by integrating high-throughput optical phenotyping and genome-wide association studies in wheat. Plant Biotechnol J 2023; 21:1966-1977. [PMID: 37392004 PMCID: PMC10502759 DOI: 10.1111/pbi.14104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/11/2023] [Accepted: 06/07/2023] [Indexed: 07/02/2023]
Abstract
Dissecting the genetic basis of complex traits such as dynamic growth and yield potential is a major challenge in crops. Monitoring the growth throughout growing season in a large wheat population to uncover the temporal genetic controls for plant growth and yield-related traits has so far not been explored. In this study, a diverse wheat panel composed of 288 lines was monitored by a non-invasive and high-throughput phenotyping platform to collect growth traits from seedling to grain filling stage and their relationship with yield-related traits was further explored. Whole genome re-sequencing of the panel provided 12.64 million markers for a high-resolution genome-wide association analysis using 190 image-based traits and 17 agronomic traits. A total of 8327 marker-trait associations were detected and clustered into 1605 quantitative trait loci (QTLs) including a number of known genes or QTLs. We identified 277 pleiotropic QTLs controlling multiple traits at different growth stages which revealed temporal dynamics of QTLs action on plant development and yield production in wheat. A candidate gene related to plant growth that was detected by image traits was further validated. Particularly, our study demonstrated that the yield-related traits are largely predictable using models developed based on i-traits and provide possibility for high-throughput early selection, thus to accelerate breeding process. Our study explored the genetic architecture of growth and yield-related traits by combining high-throughput phenotyping and genotyping, which further unravelled the complex and stage-specific contributions of genetic loci to optimize growth and yield in wheat.
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Affiliation(s)
- Jie Gao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xin Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Chunyan Gao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Guang Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Hui Feng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhen Jia
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Peimin Zhao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Haiyang Yu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Huaiwen Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zedong Geng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Jingbo Fu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Jun Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yikeng Cheng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Bo Yang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhanghan Pang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Daoquan Xiang
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSaskatchewanCanada
| | - Jizeng Jia
- Institute of Crop SciencesChinese Academy of Crop Sciences (CAAS)BeijingChina
| | - Handong Su
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Caixia Lan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Wei Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Lifeng Gao
- Institute of Crop SciencesChinese Academy of Crop Sciences (CAAS)BeijingChina
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Qiang Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- The Center of Crop NanobiotechnologyHuazhong Agricultural UniversityWuhanChina
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8
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Li H, Hua L, Zhao S, Hao M, Song R, Pang S, Liu Y, Chen H, Zhang W, Shen T, Gou JY, Mao H, Wang G, Hao X, Li J, Song B, Lan C, Li Z, Deng XW, Dubcovsky J, Wang X, Chen S. Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides. Nat Commun 2023; 14:6072. [PMID: 37770474 PMCID: PMC10539295 DOI: 10.1038/s41467-023-41833-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
Leaf rust, caused by Puccinia triticina Eriksson (Pt), is one of the most severe foliar diseases of wheat. Breeding for leaf rust resistance is a practical and sustainable method to control this devastating disease. Here, we report the identification of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides. Lr47 encodes a coiled-coil nucleotide-binding leucine-rich repeat protein that is both necessary and sufficient to confer Pt resistance, as demonstrated by loss-of-function mutations and transgenic complementation. Lr47 introgression lines with no or reduced linkage drag are generated using the Pairing homoeologous1 mutation, and a diagnostic molecular marker for Lr47 is developed. The coiled-coil domain of the Lr47 protein is unable to induce cell death, nor does it have self-protein interaction. The cloning of Lr47 expands the number of leaf rust resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.
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Affiliation(s)
- Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuqing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Rui Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuyong Pang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Yanna Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Hong Chen
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tao Shen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jin-Ying Gou
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100193, Beijing, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Xiaohua Hao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jian Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zaifeng Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China.
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9
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Yin Y, Yuan C, Zhang Y, Li S, Bai B, Wu L, Ren Y, Singh RP, Lan C. Genetic analysis of stripe rust resistance in the common wheat line Kfa/2*Kachu under a Chinese rust environment. Theor Appl Genet 2023; 136:185. [PMID: 37566234 DOI: 10.1007/s00122-023-04432-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023]
Abstract
KEY MESSAGE We mapped a new race-specific seedling stripe rust resistance gene on wheat chromosome 5BL and a new APR locus QYr.hazu-2BS from CIMMYT wheat line Kfa/2*Kachu. Breeding resistant wheat (Triticum aestivum) varieties is the most economical and efficient way to manage wheat stripe rust, but requires the prior identification of new resistance genes and development of associated molecular markers for marker-assisted selection. To map stripe rust resistance loci in wheat, we used a recombinant inbred line population generated by crossing the stripe rust-resistant parent 'Kfa/2*Kachu' and the susceptible parent 'Apav#1'. We employed genotyping-by-sequencing and bulked segregant RNA sequencing to map a new race-specific seedling stripe rust resistance gene, which we designated YrK, to wheat chromosome arm 5BL. TraesCS5B02G330700 encodes a receptor-like kinase and is a high-confidence candidate gene for YrK based on virus-induced gene silencing results and the significant induction of its expression 24 h after inoculation with wheat stripe rust. To assist breeding, we developed functional molecular markers based on the polymorphic single nucleotide polymorphisms in the coding sequence region of YrK. We also mapped four adult plant resistance (APR) loci to wheat chromosome arms 1BL, 2AS, 2BS and 4AL. Among these APR loci, we determined that QYr.hazu-1BL and QYr.hazu-2AS are allelic to the known pleiotropic resistance gene Lr46/Yr29/Pm39 and the race-specific gene Yr17, respectively. However, QYr.hazu-2BS is likely a new APR locus, for which we converted closely linked SNP polymorphisms into breeder-friendly Kompetitive allele-specific PCR (KASP) markers. In the present study, we provided new stripe rust resistance locus/gene and molecular markers for wheat breeder to develop rust-resistant wheat variety.
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Affiliation(s)
- Yuruo Yin
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan City, 430070, Hubei Province, China
| | - Chan Yuan
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan City, 430070, Hubei Province, China
| | - Yichen Zhang
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan City, 430070, Hubei Province, China
| | - Shunda Li
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan City, 430070, Hubei Province, China
| | - Bin Bai
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, People's Republic of China
| | - Ling Wu
- Crop Research Institute Sichuan Academy of Agricultural Sciences, Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory, Chengdu, 610066, Sichuan Province, China
| | - Yong Ren
- Mianyang Institute of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang, 621023, Sichuan, China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera, México-Veracruz, CP 56237, El Batán, Texcoco, E do. de México, Mexico
| | - Caixia Lan
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan City, 430070, Hubei Province, China.
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10
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Ma H, Ding W, Chen Y, Zhou J, Chen W, Lan C, Mao H, Li Q, Yan W, Su H. Centromere Plasticity With Evolutionary Conservation and Divergence Uncovered by Wheat 10+ Genomes. Mol Biol Evol 2023; 40:msad176. [PMID: 37541261 PMCID: PMC10422864 DOI: 10.1093/molbev/msad176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 08/06/2023] Open
Abstract
Centromeres (CEN) are the chromosomal regions that play a crucial role in maintaining genomic stability. The underlying highly repetitive DNA sequences can evolve quickly in most eukaryotes, and promote karyotype evolution. Despite their variability, it is not fully understood how these widely variable sequences ensure the homeostasis of centromere function. In this study, we investigated the genetics and epigenetics of CEN in a population of wheat lines from global breeding programs. We captured a high degree of sequences, positioning, and epigenetic variations in the large and complex wheat CEN. We found that most CENH3-associated repeats are Cereba element of retrotransposons and exhibit phylogenetic homogenization across different wheat lines, but the less-associated repeat sequences diverge on their own way in each wheat line, implying specific mechanisms for selecting certain repeat types as functional core CEN. Furthermore, we observed that CENH3 nucleosome structures display looser wrapping of DNA termini on complex centromeric repeats, including the repositioned CEN. We also found that strict CENH3 nucleosome positioning and intrinsic DNA features play a role in determining centromere identity among different lines. Specific non-B form DNAs were substantially associated with CENH3 nucleosomes for the repositioned centromeres. These findings suggest that multiple mechanisms were involved in the adaptation of CENH3 nucleosomes that can stabilize CEN. Ultimately, we proposed a remarkable epigenetic plasticity of centromere chromatin within the diverse genomic context, and the high robustness is crucial for maintaining centromere function and genome stability in wheat 10+ lines as a result of past breeding selections.
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Affiliation(s)
- Huan Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Wentao Ding
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Yiqian Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Jingwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- 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 Sciences, Shenzhen, China
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11
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Liu P, Zhang Z, Yin Y, Yan S, Ren Y, Sang W, Xu H, Han X, Cui F, Nie Y, Kong D, Li W, Lan C, Mu P. Quality traits analysis of 153 wheat lines derived from CIMMYT and China. Front Genet 2023; 14:1198835. [PMID: 37600662 PMCID: PMC10433775 DOI: 10.3389/fgene.2023.1198835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
In order to understand the difference of quality for Chinese and CIMMYT wheat varieties (lines), we selected 153 wheat germplasm from both China and CIMMYT to explore the contribution relationship of different allelic variation combinations to wheat quality through genotyping and phenotyping, including grain hardness, polyphenol oxidase (PPO) activity, lipoxygenase (LOX) activity, yellow pigment (YP) content and protein content. In terms of flour milling quality, Chinese wheat varieties were mainly carrying Pina-D1a/Pinb-D1b, accounting for 32.0% of the total tested varieties, while the CIMMYT wheat lines were mainly carrying Pina-D1b/Pinb-D1a with 45.8% of the total collection. The distribution frequencies of subunit 1/2* and 5 + 10 were 47.0% and 42.5%, respectively, in CIMMYT varieties, however they were only 31.4% and 13.7% respectively of the Chinese wheat tested varieties. In addition, the proportion of phytoene synthase (PSY) allele, PPO allele and LOX active allele were roughly the same between Chinese and CIMMYT varieties. Based on the present study, we found that Pina gene had a greater impact on grain hardness value than Pinb gene; The influence of PPO-A1 gene on polyphenol oxidase activity was more significant than PPO-D1 gene. The high protein content of varieties mostly containing hardness genes and 1/2*/5 + 10 subunit combinations. Based on the present study, we found that the quality gene distribution of Chinese and CIMMYT varieties was quite different, for instance, the high-quality HMW-GS subunits of Chinese varieties were lower than CIMMYT lines. It will be much useful for Chinese wheat breeders to develop good quality wheat variety by crossing with 3 good strong gluten CIMMYT wheat lines by molecular marker-assisted selection.
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Affiliation(s)
- Pengpeng Liu
- Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, Xinjiang, China
| | - Zhe Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuruo Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shanshan Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yong Ren
- Mianyang Institute of Agricultural Science, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang City, Sichuan, China
| | - Wei Sang
- Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, Xinjiang, China
| | - Hongjun Xu
- Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, Xinjiang, China
| | - Xinnian Han
- Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, Xinjiang, China
| | - Fengjuan Cui
- Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, Xinjiang, China
| | - Yingbin Nie
- Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, Xinjiang, China
| | - Dezhen Kong
- Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, Xinjiang, China
| | - Wei Li
- Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, Xinjiang, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Peiyuan Mu
- Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, Xinjiang, China
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12
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Wang Y, Zeng Z, Li J, Zhao D, Zhao Y, Peng C, Lan C, Wang C. Identification and validation of new quantitative trait loci for spike-related traits in two RIL populations. Mol Breed 2023; 43:64. [PMID: 37533603 PMCID: PMC10390419 DOI: 10.1007/s11032-023-01401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/19/2023] [Indexed: 08/04/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important cereal crops for ensuring food security worldwide. Identification of major quantitative trait loci (QTL) for spike-related traits is important for improvement of yield potential in wheat breeding. In this study, by using the wheat 55K single nucleotide polymorphism (SNP) array and diversity array technology (DArT), two recombinant inbred line populations derived from crosses avocet/chilero and avocet/huites were used to map QTL for kernel number per spike (KNS), total spikelet number per spike (TSS), fertile spikelet number per spike (FSS), and spike compactness (SC). Forty-two QTLs were identified on chromosomes 2A (4), 2B (3), 3A (2), 3B (7), 5A (11), 6A (4), 6B, and 7A (10), explaining 3.13-21.80% of the phenotypic variances. Twelve QTLs were detected in multi-environments on chromosomes 2A, 3B (2), 5A (4), 6A (3), 6B, and 7A, while four QTL clusters were detected on chromosomes 3A, 3B, 5A, and 7A. Two stable and new QTL clusters, QKns/Tss/Fss/SC.haust-5A and QKns/Tss/Fss.haust-7A, were detected in the physical intervals of 547.49-590.46 Mb and 511.54-516.15 Mb, accounting for 7.53-14.78% and 7.01-20.66% of the phenotypic variances, respectively. High-confidence annotated genes for QKns/Tss/Fss/SC.haust-5A and QKns/Tss/Fss.haust-7A were more highly expressed in spike development. The results provide new QTL and molecular markers for marker-assisted breeding in wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01401-4.
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Affiliation(s)
- Yuying Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Zhankui Zeng
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Jiachuang Li
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Dehui Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Yue Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Chen Peng
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Caixia Lan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
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13
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Liu S, Liu D, Zhang C, Zhang W, Wang X, Mi Z, Gao X, Ren Y, Lan C, Liu X, Zhao Z, Liu J, Li H, Yuan F, Su B, Kang Z, Li C, Han D, Wang C, Cao X, Wu J. Slow stripe rusting in Chinese wheat Jimai 44 conferred by Yr29 in combination with a major QTL on chromosome arm 6AL. Theor Appl Genet 2023; 136:175. [PMID: 37498321 DOI: 10.1007/s00122-023-04420-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023]
Abstract
YrJ44, a more effective slow rusting gene than Yr29, was localized to a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479 on chromosome 6AL. "Slow rusting" (SR) is a type of adult plant resistance (APR) that can provide non-specific durable resistance to stripe rust in wheat. Chinese elite wheat cultivar Jimai 44 (JM44) has maintained SR to stripe rust in China since its release despite exposure to a changing and variable pathogen population. An F2:6 population comprising 295 recombinant inbred lines (RILs) derived from a cross between JM44 and susceptible cultivar Jimai 229 (JM229) was used in genetic analysis of the SR. The RILs and parental lines were evaluated for stripe rust response in five field environments and genotyped using the Affymetrix Wheat55K SNP array and 13 allele-specific quantitative PCR-based (AQP) markers. Two stable QTL on chromosome arms 1BL and 6AL were identified by inclusive composite interval mapping. The 1BL QTL was probably the pleiotropic gene Lr46/Yr29/Sr58. QYr.nwafu-6AL (hereafter named YrJ44), mapped in a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479, was more effective than Yr29 in reducing disease severity and relative area under the disease progress curve (rAUDPC). RILs harboring both YrJ44 and Yr29 displayed levels of SR equal to the resistant parent JM44. The AQP markers linked with YrJ44 were polymorphic and significantly correlated with stripe rust resistance in a panel of 1,019 wheat cultivars and breeding lines. These results suggested that adequate SR resistance can be obtained by combining YrJ44 and Yr29 and the AQP markers can be used in breeding for durable stripe rust resistance.
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Affiliation(s)
- Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chuanliang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Wenjing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zhiwen Mi
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture and Rural Affairs, Laboratory of Agricultural Information Perception and Intelligent Services, College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xin Gao
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Yong Ren
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Institute of Agricultural Science, Mianyang, 621023, Sichuan, China
| | - Caixia Lan
- College of Plant Science and Technology, Huazhong Agricultural University/Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiukun Liu
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Zhendong Zhao
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Jianjun Liu
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Haosheng Li
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Baofeng Su
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture and Rural Affairs, Laboratory of Agricultural Information Perception and Intelligent Services, College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chunlian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Changfa Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Xinyou Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China.
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Zhang L, He C, Lai Y, Wang Y, Kang L, Liu A, Lan C, Su H, Gao Y, Li Z, Yang F, Li Q, Mao H, Chen D, Chen W, Kaufmann K, Yan W. Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis. Genome Biol 2023; 24:65. [PMID: 37016448 PMCID: PMC10074895 DOI: 10.1186/s13059-023-02908-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/23/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types. RESULTS Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process. CONCLUSIONS Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.
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Affiliation(s)
- Lihua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuting Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yating Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Kang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuwen Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zeqing Li
- Wuhan Igenebook Biotechnology Co., Ltd, Wuhan, 430014, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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15
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Chen J, Zhang Y, Yin H, Liu W, Hu X, Li D, Lan C, Gao L, He Z, Cui F, Fernie AR, Chen W. The pathway of melatonin biosynthesis in common wheat (Triticum aestivum). J Pineal Res 2023; 74:e12841. [PMID: 36396897 PMCID: PMC10078269 DOI: 10.1111/jpi.12841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/25/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022]
Abstract
Melatonin (Mel) is a multifunctional biomolecule found in both animals and plants. In plants, the biosynthesis of Mel from tryptophan (Trp) has been delineated to comprise of four consecutive reactions. However, while the genes encoding these enzymes in rice are well characterized no systematic evaluation of the overall pathway has, as yet, been published for wheat. In the current study, the relative contents of six Mel-pathway-intermediates including Trp, tryptamine (Trm), serotonin (Ser), 5-methoxy tryptamine (5M-Trm), N-acetyl serotonin (NAS) and Mel, were determined in 24 independent tissues spanning the lifetime of wheat. These studies indicated that Trp was the most abundant among the six metabolites, followed by Trm and Ser. Next, the candidate genes expressing key enzymes involved in the Mel pathway were explored by means of metabolite-based genome-wide association study (mGWAS), wherein two TDC genes, a T5H gene and one SNAT gene were identified as being important for the accumulation of Mel pathway metabolites. Moreover, a 463-bp insertion within the T5H gene was discovered that may be responsible for variation in Ser content. Finally, a ASMT gene was found via sequence alignment against its rice homolog. Validations of these candidate genes were performed by in vitro enzymatic reactions using proteins purified following recombinant expression in Escherichia coli, transient gene expression in tobacco, and transgenic approaches in wheat. Our results thus provide the first comprehensive investigation into the Mel pathway metabolites, and a swift candidate gene identification via forward-genetics strategies, in common wheat.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yueqi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | | | - Lifeng Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fa Cui
- Wheat Molecular Breeding Innovation Research Group, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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16
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Zeng Z, Zhao D, Wang C, Yan X, Song J, Chen P, Lan C, Singh RP. QTL cluster analysis and marker development for kernel traits based on DArT markers in spring bread wheat ( Triticum aestivum L.). Front Plant Sci 2023; 14:1072233. [PMID: 36844075 PMCID: PMC9951491 DOI: 10.3389/fpls.2023.1072233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/17/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Genetic dissection of yield component traits including kernel characteristics is essential for the continuous improvement in wheat yield. In the present study, one recombinant inbred line (RIL) F6 population derived from a cross between Avocet and Chilero was used to evaluate the phenotypes of kernel traits of thousand-kernel weight (TKW), kernel length (KL), and kernel width (KW) in four environments at three experimental stations during the 2018-2020 wheat growing seasons. The high-density genetic linkage map was constructed with the diversity arrays technology (DArT) markers and the inclusive composite interval mapping (ICIM) method to identify the quantitative trait loci (QTLs) for TKW, KL, and KW. A total of 48 QTLs for three traits were identified in the RIL population on the 21 chromosomes besides 2A, 4D, and 5B, accounting for 3.00%-33.85% of the phenotypic variances. Based on the physical positions of each QTL, nine stable QTL clusters were identified in the RILs, and among these QTL clusters, TaTKW-1A was tightly linked to the DArT marker interval 3950546-1213099, explaining 10.31%-33.85% of the phenotypic variances. A total of 347 high-confidence genes were identified in a 34.74-Mb physical interval. TraesCS1A02G045300 and TraesCS1A02G058400 were among the putative candidate genes associated with kernel traits, and they were expressed during grain development. Moreover, we also developed high-throughput kompetitive allele-specific PCR (KASP) markers of TaTKW-1A, validated in a natural population of 114 wheat varieties. The study provides a basis for cloning the functional genes underlying the QTL for kernel traits and a practical and accurate marker for molecular breeding.
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Affiliation(s)
- Zhankui Zeng
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Dehui Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Xuefang Yan
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Junqiao Song
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Peng Chen
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Caixia Lan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ravi P. Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico
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17
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Ren P, Zhao D, Zeng Z, Yan X, Zhao Y, Lan C, Wang C. Pleiotropic effect analysis and marker development for grain zinc and iron concentrations in spring wheat. Mol Breed 2022; 42:49. [PMID: 37313424 PMCID: PMC10248664 DOI: 10.1007/s11032-022-01317-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the main food crops in the world and a primary source of zinc (Zn) and iron (Fe) in the human body. The genetic mechanisms underlying related traits have been clarified, thereby providing a molecular theoretical foundation for the development of germplasm resources. In this study, a total of 23,536 high-quality DArT markers was used to map quantitative trait loci (QTL) of grain Zn (GZn) and grain Fe (GFe) concentrations in recombinant inbred lines crossed by Avocet/Chilero. A total of 17 QTLs was located on chromosomes 1BL, 2BL, 3BL, 4AL, 4BS, 5AL, 5DL, 6AS, 6BS, 6DS, and 7AS accounting for 0.38-16.62% of the phenotypic variance. QGZn.haust-4AL, QGZn.haust-7AS.1, and QGFe.haust-6BS were detected on chromosomes 4AL, 6BS, and 7AS, accounting for 10.63-16.62% of the phenotypic variance. Four stable QTLs, QGZn.haust-4AL, QGFe.haust-1BL, QGFe.haust-4AL, and QGFe.haust-5DL, were located on chromosomes 1BL, 4AL, and 5DL. Three pleiotropic effects loci for GZn and GFe concentrations were located on chromosomes 1BL, 4AL, and 5DL. Two high-throughput Kompetitive Allele Specific PCR markers were developed by closely linking single-nucleotide polymorphisms on chromosomes 4AL and 5DL, which were validated by a germplasm panel. Therefore, it is the most important that quantitative trait loci and KASP marker for grain zinc and iron concentrations were developed for utilizing in marker-assisted breeding and biofortification of wheat grain in breeding programs.
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Affiliation(s)
- Pengxun Ren
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Dehui Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Zhankui Zeng
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Xuefang Yan
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
| | - Yue Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Caixia Lan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
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18
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Liu D, Yuan C, Singh RP, Randhawa MS, Bhavani S, Kumar U, Huerta-Espino J, Lagudah E, Lan C. Stripe rust and leaf rust resistance in CIMMYT wheat line "Mucuy" is conferred by combinations of race-specific and adult-plant resistance loci. Front Plant Sci 2022; 13:880138. [PMID: 36061764 PMCID: PMC9437451 DOI: 10.3389/fpls.2022.880138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Developing wheat varieties with durable resistance is a core objective of the International Maize and Wheat Improvement Center (CIMMYT) and many other breeding programs worldwide. The CIMMYT advanced wheat line "Mucuy" displayed high levels of resistance to stripe rust (YR) and leaf rust (LR) in field evaluations in Mexico and several other countries. To determine the genetic basis of YR and LR resistance, 138 F5 recombinant inbred lines (RILs) derived from the cross of Apav#1× Mucuy were phenotyped for YR responses from 2015 to 2020 at field sites in India, Kenya, and Mexico, and LR in Mexico. Seedling phenotyping for YR and LR responses was conducted in the greenhouse in Mexico using the same predominant races as in field trials. Using 12,681 polymorphic molecular markers from the DArT, SNP, and SSR genotyping platforms, we constructed genetic linkage maps and QTL analyses that detected seven YR and four LR resistance loci. Among these, a co-located YR/LR resistance loci was identified as Yr29/Lr46, and a seedling stripe rust resistance gene YrMu was mapped on the 2AS/2NS translocation. This fragment also conferred moderate adult plant resistance (APR) under all Mexican field environments and in one season in Kenya. Field trial phenotyping with Lr37-virulent Puccinia triticina races indicated the presence of an APR QTL accounting for 18.3-25.5% of the LR severity variation, in addition to a novel YR resistance QTL, QYr.cim-3DS, derived from Mucuy. We developed breeder-friendly KASP and indel molecular markers respectively for Yr29/Lr46 and YrMu. The current study validated the presence of known genes and identified new resistance loci, a QTL combination effect, and flanking markers to facilitate accelerated breeding for genetically complex, durable rust resistance.
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Affiliation(s)
- Demei Liu
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Innovation Academy for Seed Design Chinese Academy of Sciences (CAS), Xining, China
| | - Chan Yuan
- Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Julio Huerta-Espino
- Campo Experimental Valle de México, Instituto Nacional de Investigacion Forestales Agricolas y Pecuarias (INIFAP), Texcoco, Mexico
| | - Evans Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Canberra, ACT, Australia
| | - Caixia Lan
- Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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19
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Bai B, Li Z, Wang H, Du X, Wu L, Du J, Lan C. Genetic Analysis of Adult Plant Resistance to Stripe Rust in Common Wheat Cultivar "Pascal". Front Plant Sci 2022; 13:918437. [PMID: 35874020 PMCID: PMC9298664 DOI: 10.3389/fpls.2022.918437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Wheat stripe rust is an important foliar disease that affects the wheat yield globally. Breeding for resistant wheat varieties is one of the most economically and environmentally effective ways to control this disease. The common wheat (Triticum aestivum L.) cultivar "Pascal" exhibited susceptibility to stripe rust at the seedling stage but it showed high resistance to stripe rust at the adult plant stage over 20 years in Gansu, a hotspot of the disease in northwestern China. To understand the genetic mechanism of stripe rust resistance in this cultivar, a 55K SNP array was used to analyze the two parents and the 220 recombinant inbred lines (RILs) derived from the cross of "Huixianhong" × "Pascal." We detected three new stripe rust adult plant resistance (APR) quantitative trait locus (QTL) contributed by Pascal, viz. QYr.gaas-1AL, QYr.gaas-3DL, and QYr.gaas-5AS, using the inclusive composite interval mapping method. They were flanked by SNP markers AX-111218361-AX-110577861, AX-111460455-AX-108798599, and AX-111523523-AX-110028503, respectively, and explained the phenotypic variation ranging from 11.0 to 23.1%. Bulked segregant exome capture sequencing (BSE-Seq) was used for fine mapping of QYr.gaas-1AL and selection of candidate genes, TraesCS1A02G313700, TraesCS1A02G313800, and TraesCS1A02G314900 for QYr.gaas-1AL. KASP markers BSE-1A-12 and HXPA-3D for QYr.gaas-1AL and QYr.gaas-3DL were developed for breeders to develop durable stripe rust-resistant wheat varieties.
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Affiliation(s)
- Bin Bai
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Zimeng Li
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongmei Wang
- Institute of Biotechnology, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaolin Du
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ling Wu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jiuyuan Du
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Caixia Lan
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Zhang P, Lan C, Singh RP, Huerta-Espino J, Li Z, Lagudah E, Bhavani S. Identification and Characterization of Resistance Loci to Wheat Leaf Rust and Stripe Rust in Afghan Landrace "KU3067". Front Plant Sci 2022; 13:894528. [PMID: 35837449 PMCID: PMC9274257 DOI: 10.3389/fpls.2022.894528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Leaf rust and stripe rust are important wheat diseases worldwide causing significant losses where susceptible varieties are grown. Resistant cultivars offer long-term control and reduce the use of hazardous chemicals, which can be detrimental to both human health and the environment. Land races have been a valuable resource for mining new genes for various abiotic and biotic stresses including wheat rusts. Afghan wheat landrace "KU3067" displayed high seedling infection type (IT) for leaf rust and low IT for stripe rust; however, it displayed high levels of field resistance for both rusts when tested for multiple seasons against the Mexican rust isolates. This study focused on identifying loci-conferring seedling resistance to stripe rust, and also loci-conferring adult plant resistance (APR) against the Mexican races of leaf rust and stripe rust. A backcrossed inbred line (BIL) population advanced to the BC1F5 generation derived from the cross of KU3067 and Apav (triple rust susceptible line) was used for both, inheritance and QTL mapping studies. The population and parents were genotyped with Diversity Arrays Technology-genotyping-by-sequencing (DArT-Seq) and phenotyped for leaf rust and stripe rust response at both seedling and adult plant stages during multiple seasons in Mexico with relevant pathotypes. Mapping results identified an all-stage resistance gene for stripe rust, temporarily designated as YrKU, on chromosome 7BL. In total, six QTL-conferring APR to leaf rust on 1AS, 2AL, 4DL, 6BL, 7AL, and 7BL, and four QTL for stripe rust resistance on 1BS, 2AL, 4DL, and 7BL were detected in the analyses. Among these, pleiotropic gene Lr67/Yr46 on 4DL with a significantly large effect is the first report in an Afghan landrace-conferring resistance to both leaf and stripe rusts. QLr.cim-7BL/YrKU showed pleiotropic resistance to both rusts and explained 7.5-17.2 and 12.6-19.3% of the phenotypic variance for leaf and stripe rusts, respectively. QYr.cim-1BS and QYr.cim-2AL detected in all stripe environments with phenotypic variance explained (PVE) 12.9-20.5 and 5.4-12.5%, and QLr.cim-6BL are likely to be new. These QTL and their closely linked markers will be useful for fine mapping and marker-assisted selection (MAS) in breeding for durable resistance to multiple rust diseases.
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Affiliation(s)
- Peipei Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Caixia Lan
- Hubei Hongshan Laboratory, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México the National Institute of Forestry, Agricultural and Livestock Research (INIFAP), Texcoco, Mexico
| | - Zaifeng Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Evans Lagudah
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, ACT, Australia
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Zang Y, Gong Q, Xu Y, Liu H, Bai H, Li N, Du L, Ye X, Lan C, Wang K. Production of Conjoined Transgenic and Edited Barley and Wheat Plants for Nud Genes Using the CRISPR/SpCas9 System. Front Genet 2022; 13:873850. [PMID: 35601488 PMCID: PMC9117629 DOI: 10.3389/fgene.2022.873850] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The Nudum (Nud) gene controls the caryopsis type of cereal crops by regulating lipid biosynthetic pathways. Based on the HvNud sequence and its homologous gene sequences in wheat, a conserved sgRNA was designed to obtain the mutants from the barley variety “Vlamingh” and the wheat variety “Fielder” via Agrobacterium-mediated transformation. A total of 19 and 118 transgenic plants were obtained, and 11 and 61 mutant plants were identified in T0 transgenic plants in barley and wheat after PCR-RE detection, and the editing efficiencies of the targeted gene were 57.9 and 51.7% in barley and wheat, respectively. The grain shape of the barley mutants was naked. Five different combinations of mutations for wheat TaNud genes were identified in the T0 generation, and their homozygous-edited plants were obtained in the T1 generation. Interestingly, the conjoined plants in which one plant has different genotypes were first identified. The different tillers in an individual T0 plant showed independent transgenic or mutant events in both barley and wheat, and the different genotypes can stably inherit into T1 generation, indicating that the T0 transgenic plants were the conjoined type. In addition, we did not find any off-target mutations in both barley and wheat. A candidate method for detecting putative-edited wheat plants was suggested to avoid losing mutations in this investigation. This study provides not only materials for studying the function of the Nud gene in barley and wheat but also a system for detecting the mutants in wheat.
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Affiliation(s)
- Yiming Zang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Huiyun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hao Bai
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Na Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lipu Du
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Caixia Lan
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Caixia Lan, ; Ke Wang,
| | - Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Caixia Lan, ; Ke Wang,
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Wang JZ, Zheng CL, Zheng H, Liu XG, Lan C. [Effects on extravascular lung water of lung protective ventilation strategy applied on piglets with acute respiratory distress syndrome induced by paraquat]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2022; 40:7-11. [PMID: 35255554 DOI: 10.3760/cma.j.cn121094-20201224-00715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To study the effects on extravascular lung water of lung protective ventilation strategy applying on piglets with acute respiratory distress syndrome (ARDS) induced by paraquat (PQ) under pulse indicating continuous cardiac output (PiCCO) monitoring. Methods: The piglets models with ARDS induced by PQ were established in June 2020 and all of them were received mechanical ventilation and divided into three groups according to tidal volume (V(T)) : small V(T) group (6 ml/kg) , middle V(T) group (10 ml/kg) and large V(T) group (15 ml/kg) , there were 5 piglets in each group. The positive end expiratory pressure (PEEP) were all setup on 10 cmH(2)O. The indexes such as arterial blood gas analysis, oxygenation index (OI) , extravascular lung water index (ELWI) and pulmonary vascular permeability index (PVPI) were monitored at time of before the model was established (baseline) , time of the model was established (t(0)) and 2 h (t(2)) , 4 h (t(4)) , 6 h (t(6)) after mechanical ventilation. Lung tissue were punctured at time of baseline, t(0) and t(6) to be stained by Hematoxylin-eosin (HE) staining and pulmonary pathology were observed under light microscopy. Results: The heart rate (HR) , mean arterial pressure (MAP) and partial pressure of carbon dioxide (PaCO(2)) of all groups were higher than the base value while the pH values, partial pressure of oxygen (PaO(2)) and OI were lower than the base value when the models were established (P<0.05) . After mechanical ventilation, the HR and MAP values of all groups at t(2), t(4) and t(6) were lower than t(0) while the PaCO(2) of t(4) and t(6) were all higher than t(0), the differences were statistically significant (P<0.05) . The PaO(2) and OI of all groups showed a trend of rising at first and then decreasing after mechanical ventilation. The MAP, PaO(2), PaCO(2) and OI of the middle V(T) group and large V(T) group were apparently lower than that of the small V(T) group at t(2), t(4) and t(6) (P<0.05) . The ELWI and PVPI at t(0) of all groups were higher than that of baseline (P<0.05) . The ELWI of the small V(T) group at t(6) were lower than t(0) of the same group and t(6) of the middle V(T) group and large V(T) group (P<0.05) . HE staining showed congestion and edema of alveolar tissue, swelling of capillaries, exudation of red blood cells and widening of alveolar septum in piglets after successful modeling. And further widening of alveolar septum and rupture of alveolar septum could be seen in the lung tissues of each group at t(6), and the injury was the slightest in the small V(T) group. Conclusion: The lung protective ventilation strategy can alleviate the extravascular lung water and ARDS induced by PQ and improve oxygenation.
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Affiliation(s)
- J Z Wang
- Department of Intensive Care Unit, High Tech Zone, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
| | - C L Zheng
- Department of Intensive Care Unit, High Tech Zone, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
| | - H Zheng
- Department of Intensive Care Unit, High Tech Zone, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
| | - X G Liu
- Department of Intensive Care Unit, High Tech Zone, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
| | - C Lan
- Department of Emergency Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450002, China
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Zhou J, Singh RP, Ren Y, Bai B, Li Z, Yuan C, Li S, Huerta-Espino J, Liu D, Lan C. Identification of Two New Loci for Adult Plant Resistance to Leaf Rust and Stripe Rust in the Chinese Wheat Variety 'Neimai 836'. Plant Dis 2021; 105:3705-3714. [PMID: 33779256 DOI: 10.1094/pdis-12-20-2654-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The characterization of leaf rust (caused by Puccinia triticina) and stripe rust (caused by Puccinia striiformis f. sp. tritici) resistance genes is the basis for breeding resistant wheat varieties and managing epidemics of these diseases in wheat. A cross between the susceptible wheat variety 'Apav#1' and resistant variety 'Neimai 836' was used to develop a mapping population containing 148 F5 recombinant inbred lines (RILs). Leaf rust phenotyping was done in field trials at Ciudad Obregón, Mexico, in 2017 and 2018, and stripe rust data were generated at Toluca, Mexico, in 2017 and in Mianyang, Ezhou, and Gansu, China, in 2019. Inclusive complete interval mapping (ICIM) was used to create a genetic map and identify significant resistance quantitative trait loci (QTL) with 2,350 polymorphic markers from a 15K wheat single-nucleotide polymorphism (SNP) array and simple-sequence repeats (SSRs). The pleiotropic multipathogen resistance gene Lr46/Yr29 and four QTL were identified, including two new loci, QLr.hzau-3BL and QYr.hzau-5AL, which explained 3 to 16% of the phenotypic variation in resistance to leaf rust and 7 to 14% of that to stripe rust. The flanking SNP markers for the two loci were converted to Kompetitive Allele-Specific PCR (KASP) markers and used to genotype a collection of 153 wheat lines, indicating the Chinese origin of the loci. Our results suggest that Neimai 836, which has been used as a parent for many wheat varieties in China, could be a useful source of high-level resistance to both leaf rust and stripe rust.
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Affiliation(s)
- Jingwei Zhou
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico D.F., Mexico
| | - Yong Ren
- Mianyang Academy of Agricultural Science/Mianyang Branch of National Wheat Improvement Center, Mianyang 621023, Sichuan, P.R. China
| | - Bin Bai
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, No. 1 Nongkeyuanxincun, Lanzhou 730070, Gansu Province, P.R. China
| | - Zhikang Li
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Chan Yuan
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Shunda Li
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
| | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico Instituto Nacional de Investigaciones Forestales Agricolas y Pecuarias (INIFAP), 56230 Chapingo, Edo. de Mexico, Mexico
| | - Demei Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Crop Molecular Breeding and China and Qinghai Provincial Key Laboratory of Crop Molecular Breeding Northwest Institute of Plateau Biology, Innovation Academy for Seed Design, Xining 810008, P.R. China
| | - Caixia Lan
- Huazhong Agricultural University, College of Plant Science & Technology, No. 1, Hongshan District, Wuhan 430070, Hubei Province, P.R. China
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Xu N, Liu C, Feng Y, Li F, Meng X, Lv Q, Lan C. Influence of the Internet of Things management system on hand hygiene compliance in an emergency intensive care unit. J Hosp Infect 2020; 109:101-106. [PMID: 33346043 DOI: 10.1016/j.jhin.2020.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/01/2020] [Accepted: 12/10/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Hand hygiene is a critical strategy for infection prevention in all healthcare settings. Automated electronic monitoring systems are expected to improve hand hygiene performance. AIM To investigate the impact of the Internet of Things (IoT) management system on hand hygiene compliance among medical staff in an emergency intensive care unit (EICU). METHODS This retrospective observational study was conducted between July 1st, 2017 and February 28th, 2018 in a 19-bed EICU. The changes in hand hygiene compliance among 54 members of medical staff and the incidence of hospital infections were compared, counted, and analysed before and after implementing the IoT management system in the EICU that was initiated on November 1st, 2017. FINDINGS After the application of the IoT management system, the hand hygiene compliance rates among the members of the medical staff before (29.5% (3347/11,338) vs 57.9% (4690/8094), P < 0.001) and after (59.9% (9915/16,556) vs 73.8% (17,194/23 286), P < 0.001) the contact with patients and surrounding environment significantly improved. However, hand hygiene compliance among three cleaning staff did not significantly improve after the application. Moreover, there was no significant difference in healthcare-acquired infection rates (2.535% (9/355) vs 2.047% (7/342), P = 0.667) nor in the detection rates of the four major multidrug-resistant bacteria in the EICU before and after the application of the IoT management system (P > 0.05). CONCLUSION The IoT management system significantly improved hand hygiene compliance among medical staff, except cleaners, in the EICU of one provincial hospital; however, the rates of nosocomial infection did not significantly decrease. The quality of hand hygiene implementation needs to be improved.
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Affiliation(s)
- N Xu
- Emergency Intensive Care Unit, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - C Liu
- Department of Infection Management, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Y Feng
- Department of Infection Management, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - F Li
- Department of Infection Management, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - X Meng
- Emergency Intensive Care Unit, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Q Lv
- Emergency Intensive Care Unit, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - C Lan
- Emergency Intensive Care Unit, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, PR China.
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Liao C, Hu L, Lan C. Hashimoto's thyroiditis associated with an extra-thyroidal triad of pretibial myxedema, ophthalmopathy, and acropachy. J BIOL REG HOMEOS AG 2020; 34:1085-1090. [PMID: 32683842 DOI: 10.23812/19-494-l-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- C Liao
- Department of Dermatology, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan, China
| | - L Hu
- DDepartment of Dermatology, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan, China
| | - C Lan
- DDepartment of Dermatology, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan, China
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Fourny N, Guilbert L, Lan C, Jouenne A, Bernard M, Desrois M. Greater impairment of energy metabolism and coronary flow in type 2 diabetic female rats than in male during myocardial ischemia-reperfusion injury. Archives of Cardiovascular Diseases Supplements 2020. [DOI: 10.1016/j.acvdsp.2020.03.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Lan C, Huang S, Lai S. 620 UVB radiation with high photon density induces dendritic cell maturation and contributes to cutaneous immune suppression via Treg cell expansion. J Invest Dermatol 2020. [DOI: 10.1016/j.jid.2020.03.631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Yuan C, Singh RP, Liu D, Randhawa MS, Huerta-Espino J, Lan C. Genome-Wide Mapping of Adult Plant Resistance to Leaf Rust and Stripe Rust in CIMMYT Wheat Line Arableu#1. Plant Dis 2020; 104:1455-1464. [PMID: 32196419 DOI: 10.1094/pdis-10-19-2198-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Leaf (brown) rust (LR) and stripe (yellow) rust (YR), caused by Puccinia triticina and P. striiformis f. sp. tritici, respectively, significantly reduce wheat production worldwide. Disease-resistant wheat varieties offer farmers one of the most effective ways to manage these diseases. The common wheat (Triticum aestivum L.) Arableu#1, developed by the International Maize and Wheat Improvement Center and released as Deka in Ethiopia, shows susceptibility to both LR and YR at the seedling stage but a high level of adult plant resistance (APR) to the diseases in the field. We used 142 F5 recombinant inbred lines (RILs) derived from Apav#1 × Arableu#1 to identify quantitative trait loci (QTLs) for APR to LR and YR. A total of 4,298 genotyping-by-sequencing markers were used to construct a genetic linkage map. The study identified four LR resistance QTLs and six YR resistance QTLs in the population. Among these, QLr.cim-1BL.1/QYr.cim-1BL.1 was located in the same location as Lr46/Yr29, a known pleiotropic resistance gene. QLr.cim-1BL.2 and QYr.cim-1BL.2 were also located on wheat chromosome 1BL at 37 cM from Lr46/Yr29 and may represent a new segment for pleiotropic resistance to both rusts. QLr.cim-7BL is likely Lr68 given its association with the tightly linked molecular marker cs7BLNLRR. In addition, QLr.cim-3DS, QYr.cim-2AL, QYr.cim-4BL, QYr.cim-5AL, and QYr.cim-7DS are probably new resistance loci based on comparisons with published QTLs for resistance to LR and YR. Our results showed the diversity of minor resistance QTLs in Arableu#1 and their role in conferring near-immune levels of APR to both LR and YR, when combined with the pleiotropic APR gene Lr46/Yr29.
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Affiliation(s)
- Chan Yuan
- Huazhong Agricultural University, College of Plant Science & Technology, Hongshan District, Wuhan, Hubei Province 430070, People's Republic of China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico D.F., Mexico
| | - Demei Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, People's Republic of China
| | - Mandeep S Randhawa
- International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico D.F., Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico INIFAP, 56230 Chapingo, Edo. de Mexico, Mexico
| | - Caixia Lan
- Huazhong Agricultural University, College of Plant Science & Technology, Hongshan District, Wuhan, Hubei Province 430070, People's Republic of China
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Li Z, Yuan C, Herrera-Foessel SA, Randhawa MS, Huerta-Espino J, Liu D, Dreisigacker S, Singh RP, Lan C. Four Consistent Loci Confer Adult Plant Resistance to Leaf Rust in the Durum Wheat Lines Heller#1 and Dunkler. Phytopathology 2020; 110:892-899. [PMID: 31850832 DOI: 10.1094/phyto-09-19-0348-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The durum wheat lines Heller#1 and Dunkler from the International Maize and Wheat Improvement Center Global Wheat Program showed moderate and stable adult plant resistance to leaf rust under high disease pressure over field environments in northwestern Mexico. Leaf rust phenotyping was performed on two recombinant inbred line (RIL) populations derived from crosses of Heller#1 and Dunkler with the susceptible parent Atred#2, conducted under artificially induced Puccinia triticina epidemics in 2013, 2014, 2015, and 2016. The Atred#2 × Heller#1 and Atred#2 × Dunkler populations were genotyped by single nucleotide polymorphism (SNP) platforms and diversity arrays technology markers, respectively. Four leaf rust resistance quantitative trait loci were detected simultaneously in the two RIL populations: Lr46, QLr.cim-2BC, QLr.cim-5BL, and QLr.cim-6BL based on phenotypic data across all four crop seasons. They explained 11.7 to 46.8%, 7.2 to 26.1%, 8.4 to 24.1%, and 12.4 to 28.5%, respectively, of the phenotypic variation for leaf rust resistance in Atred#2 × Heller#1 and 16.3 to 56.6%, 6.7 to 15.7%, 4.1 to 10.1%, and 5.1 to 20.2% of the variation in the Atred#2 × Dunkler population. Only the resistance allele of QLr.cim-2BC was from the susceptible parent Atred#2, and resistance alleles at other loci came from the resistant parents Heller#1 and Dunkler. The SNP markers closely linked to Lr46 and QLr.cim-2BC were converted to kompetitive allele specific PCR markers for use in marker-assisted selection to improve leaf rust resistance through crosses with Heller#1 and Dunkler sources.
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Affiliation(s)
- Zhikang Li
- Huazhong Agricultural University, College of Plant Science & Technology, Wuhan City, Hubei Province 430070, People's Republic of China
| | - Chan Yuan
- Huazhong Agricultural University, College of Plant Science & Technology, Wuhan City, Hubei Province 430070, People's Republic of China
| | | | - Mandeep S Randhawa
- International Maize and Wheat Improvement Center, Mexico City 06600, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, Chapingo, State of Mexico, Mexico
| | - Demei Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, People's Republic of China
- China and Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, People's Republic of China
| | | | - Ravi P Singh
- International Maize and Wheat Improvement Center, Mexico City 06600, Mexico
| | - Caixia Lan
- Huazhong Agricultural University, College of Plant Science & Technology, Wuhan City, Hubei Province 430070, People's Republic of China
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Zhang P, Lan C, Asad MA, Gebrewahid TW, Xia X, He Z, Li Z, Liu D. QTL mapping of adult-plant resistance to leaf rust in the Chinese landraces Pingyuan 50/Mingxian 169 using the wheat 55K SNP array. Mol Breeding 2019. [PMID: 0 DOI: 10.1007/s11032-019-1004-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
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Huang J, Li H, Lan C, Lin Q, Weng H. RETROSPECTIVE ANALYSIS OF 17 CHINESE PATIENTS WITH SEVERE PULMONARY TB CHARACTERIZED BY ACUTE RESPIRATORY FAILURE AND DIFFUSE LUNG DISEASE. Chest 2019. [DOI: 10.1016/j.chest.2019.02.355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Huang J, Li H, Lan C, Zou S, Weng H. CONCOMITANT SEVERE INFLUENZA AND CRYPTOCOCCAL INFECTION: A CASE REPORT AND LITERATURE REVIEW. Chest 2019. [DOI: 10.1016/j.chest.2019.02.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Li C, Lan C, Zhang X, Yin L, Hao X, Tian J, Lin L, Sun H, Yao Z, Feng X, Jia J, Yang Y. Evaluation of Diffusional Kurtosis Imaging in Sub-acute Ischemic Stroke: Comparison with Rehabilitation Treatment Effect. Cell Transplant 2019; 28:1053-1061. [PMID: 30907127 PMCID: PMC6728709 DOI: 10.1177/0963689719837919] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Stroke is a serious worldwide medical condition that causes neurological function disability. Diffusional kurtosis imaging, which measures the non-Gaussianity of water diffusion, has been demonstrated to be a sensitive biomarker in many neuro-pathologies. This study explores the relationship between neural function recovery and transformation of the ischemic lesion and/or corticospinal tract during the sub-acute phase after stroke by using diffusional kurtosis imaging. We performed a prospective study of function recovery and K metrics of 43 patients with sub-acute ischemic stroke in the middle cerebral artery territory. The effect of rehabilitation treatment was evaluated using both the Fugl-Meyer motor function score and modified Barthel index score at post-treatment compared with admission, and patients were allocated to two groups: good and poor rehabilitation effect (GRE and PRE). Metrics of diffusional kurtosis imaging within ischemic lesion and along the corticospinal tract were acquired, respectively. All three relative axial diffusional kurtoses (rKas) along the corticospinal tract in the GRE group ( n = 21) were significantly larger than those of the PRE group ( n = 22), including rKa in the posterior limb of internal capsule, rKa in the cerebral peduncle, and rKa in the basal part of the pons ( p = 0.014, 0.005, and 0.021, respectively). This multi-parametric magnetic resonance imaging study showed that diffusional kurtosis imaging has the potential to complement existing stroke imaging techniques and revealed its own advantages in elucidating the possible biophysical mechanism of functional restoration underlying ischemic stroke.
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Affiliation(s)
- C. Li
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - C. Lan
- Department of Rehabilitation, Huashan Hospital, Fudan University, Shanghai, China
- Department of Rehabilitation, Shanxi Dayi Hospital, Taiyuan, China
| | - X. Zhang
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
- Department of Radiotherapy, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - L. Yin
- Department of Radiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, China
| | - X. Hao
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - J. Tian
- Department of Radiology, Renji Hospital, Shanghai Jiao Tong University, China
| | - L. Lin
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - H. Sun
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Z. Yao
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - X. Feng
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - J. Jia
- Department of Rehabilitation, Huashan Hospital, Fudan University, Shanghai, China
- Both the authors contributed equally to this article
| | - Y. Yang
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
- Both the authors contributed equally to this article
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Lan C, Li J, Huang X, Heindl A, Wang Y, Yan S, Yuan Y. Stromal cell ratio based on automated image analysis as a predictor for platinum-resistant recurrent ovarian cancer. BMC Cancer 2019; 19:159. [PMID: 30777045 PMCID: PMC6380057 DOI: 10.1186/s12885-019-5343-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 02/01/2019] [Indexed: 02/03/2023] Open
Abstract
Background Identifying high-risk patients for platinum resistance is critical for improving clinical management of ovarian cancer. We aimed to use automated image analysis of hematoxylin & eosin (H&E) stained sections to identify the association between microenvironmental composition and platinum-resistant recurrent ovarian cancer. Methods Ninety-one patients with ovarian cancer containing the data of automated image analysis for H&E histological sections were initially reviewed. Results Seventy-one patients with recurrent disease were finally identified. Among 30 patients with high stromal cell ratio, 60% of the patients had platinum-resistant recurrence, which was significantly higher than the rate in patients with low stromal cell ratio (9.80%, P < 0.001). Multivariate logistic regression analysis revealed elevated CA125 level after 3 cycles of chemotherapy (P < 0.001) and high stromal cell ratio (P = 0.002) were the negative predictors of platinum-resistant relapse. The area under the curve (AUC) of receiver operating characteristic (ROC) curves of the models for predicting platinum-resistant recurrence with stromal cell ratio, normalization of CA125 level, and the combination of two parameters were 0.78, 0.79, and 0.89 respectively. Conclusions Our results demonstrated stromal cell ratio based on automated image analysis may be a potential predictor for ovarian cancer patients at high risk of platinum-resistant recurrence, and it could improve the predictive value of model when combined with normalization of CA125 level after 3 cycles of chemotherapy.
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Affiliation(s)
- C Lan
- Department of Gynecologic Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou, China
| | - J Li
- Department of Gynecologic Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou, China
| | - X Huang
- Department of Gynecologic Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou, China
| | - A Heindl
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,Centre for Molecular Pathology, The Royal Marsden Hospital, London, UK.,Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Y Wang
- Department of Gynecologic Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou, China
| | - S Yan
- Department of Pathology, Sun Yat-sen University Cancer Centre, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou, China
| | - Y Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK. .,Centre for Molecular Pathology, The Royal Marsden Hospital, London, UK. .,Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
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Zhang R, Singh RP, Lillemo M, He X, Randhawa MS, Huerta-Espino J, Singh PK, Li Z, Lan C. Two Main Stripe Rust Resistance Genes Identified in Synthetic-Derived Wheat Line Soru#1. Phytopathology 2019; 109:120-126. [PMID: 30070970 DOI: 10.1094/phyto-04-18-0141-r] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Stripe rust is a major disease constraint of wheat production worldwide. Resistance to stripe rust was analyzed using 131 F6 recombinant inbred lines (RILs) derived from a cross between synthetic derived wheat line Soru#1 and wheat cultivar Naxos. The phenotype was evaluated in Mexico and Norway at both seedling and adult plant stages. Linkage groups were constructed based on 90K single-nucleotide polymorphism (SNP), sequence-tagged site, and simple sequence repeat markers. Two major resistance loci conferred by Soru#1 were detected and located on chromosomes 1BL and 4DS. The 1BL quantitative trait loci explained 15.8 to 40.2 and 51.1% of the phenotypic variation at adult plant and seedling stages, respectively. This locus was identified as Yr24/Yr26 based on the flanking markers and infection types. Locus 4DS was flanked by molecular markers D_GB5Y7FA02JMPQ0_238 and BS00108770_51. It explained 8.4 to 27.8 and 5.5% of stripe rust variation at the adult plant and seedling stages, respectively. The 4DS locus may correspond to known resistance gene Yr28 based on the resistance source. All RILs that combine Yr24/Yr26 and Yr28 showed significantly reduced stripe rust severity in all four environments compared with the lines with only one of the genes. SNP marker BS00108770_51 was converted into a breeder-friendly kompetitive allele-specific polymerase chain reaction marker that will be useful to accelerate Yr28 deployment in wheat breeding programs.
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Affiliation(s)
- Ruiqi Zhang
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Ravi P Singh
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Morten Lillemo
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Xinyao He
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Mandeep S Randhawa
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Julio Huerta-Espino
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Pawan K Singh
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Zhikang Li
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
| | - Caixia Lan
- First author: College of Agronomy/JCIC-MCP, Nanjing Agricultural University, Nanjing, P. R. China 210095; second, fourth, fifth, and seventh authors: International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México 06600; third author: Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway NO-1432; fourth author: Campo Experimental Valle de México INIFAP, Apdo. Postal 10, Chapingo, Edo. de México, México 56230; and eighth and ninth authors: College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P. R. China 430070
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Kong L, Song X, Xiao J, Sun H, Dai K, Lan C, Singh P, Yuan C, Zhang S, Singh R, Wang H, Wang X. Development and characterization of a complete set of Triticum aestivum-Roegneria ciliaris disomic addition lines. Theor Appl Genet 2018; 131:1793-1806. [PMID: 29855671 DOI: 10.1007/s00122-018-3114-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/14/2018] [Indexed: 05/14/2023]
Abstract
A complete set wheat-R. ciliaris disomic addition lines (DALs) were characterized and the homoeologous groups and genome affinities of R. ciliaris chromosomes were determined. Wild relatives are rich gene resources for cultivated wheat. The development of alien addition chromosome lines not only greatly broadens the genetic diversity, but also provides genetic stocks for comparative genomics studies. Roegneria ciliaris (genome ScScYcYc), a tetraploid wild relative of wheat, is tolerant or resistant to many abiotic and biotic stresses. To develop a complete set of wheat-R. ciliaris disomic addition lines (DALs), we undertook a euplasmic backcrossing program to overcome allocytoplasmic effects and preferential chromosome transmission. To improve the efficiency of identifying chromosomes from Sc and Yc, we established techniques including sequential genomic in situ hybridization/fluorescence in situ hybridization (FISH) and molecular marker analysis. Fourteen DALs of wheat, each containing one pair of R. ciliaris chromosomes pairs, were characterized by FISH using four repetitive sequences [pTa794, pTa71, RcAfa and (GAA)10] as probes. One hundred and sixty-two R. ciliaris-specific markers were developed. FISH and marker analysis enabled us to assign the homoeologous groups and genome affinities of R. ciliaris chromosomes. FHB resistance evaluation in successive five growth seasons showed that the amphiploid, DA2Yc, DA5Yc and DA6Sc had improved FHB resistance, indicating their potential value in wheat improvement. The 14 DALs are likely new gene resources and will be phenotyped for more agronomic performances traits.
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Affiliation(s)
- Lingna Kong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Xinying Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Haojie Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Keli Dai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Caixia Lan
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, D.F., Mexico
| | - Pawan Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, D.F., Mexico
| | - Chunxia Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Shouzhong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Ravi Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, D.F., Mexico
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, D.F., Mexico.
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, D.F., Mexico.
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Randhawa MS, Lan C, Basnet BR, Bhavani S, Huerta-Espino J, Forrest KL, Hayden MJ, Singh RP. Interactions among genes Sr2/Yr30, Lr34/Yr18/Sr57 and Lr68 confer enhanced adult plant resistance to rust diseases in common wheat (Triticum aestivum L.) line ‘Arula’. ACTA ACUST UNITED AC 2018. [DOI: 10.21475/ajcs.18.12.06.pne1305] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Leaf rust, stripe rust, and stem rust pose a significant threat to global wheat production. Growing rust resistant cultivars is the most efficient and environment friendly method to reduce yield losses. Genetic analysis is undertaken to identify genes and study their roles in conferring rust resistance in a given wheat background. This chapter summarizes the protocol for genetic analysis of rust resistance at both seedling and adult plant stages. Additionally, it examines statistical analysis and related software to characterize quantitative trait loci (QTL) linked with rust resistance.
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Affiliation(s)
- Caixia Lan
- CIMMYT, Km. 45 Carretera Mex-Veracruz, El Batan, Texcoco, Mexico DF, Mexico.
| | | | - Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, Apdo., Postal 10, 56230, Chapingo, Edo. de México, Mexico
| | - Ravi P Singh
- CIMMYT, Km. 45 Carretera Mex-Veracruz, El Batan, Texcoco, Mexico DF, Mexico
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Lan C, Huang S, Wu C. 1403 High-glucose environment induces M1 macrophage polarization that impairs keratinocyte migration via TNF-α: A novel therapeutic approach promoting diabetic wound healing. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.1421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mathieu C, Tran T, Desrois M, Kober F, Lan C, Fourny N, Iche-Torres M, Lê T, Singer M, Mege J, Lalevée N, Bernard M, Leone M. Sex-mediated response to landiolol, a ß1 selectif adrenergic blocker, in myocardial dysfunction during sepsis. Archives of Cardiovascular Diseases Supplements 2018. [DOI: 10.1016/j.acvdsp.2018.02.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Fourny N, Lan C, Kober F, Bernard M, Desrois M. Tolerance to ischemia-reperfusion injury in a metabolic syndrome model: Effect of gender? Archives of Cardiovascular Diseases Supplements 2018. [DOI: 10.1016/j.acvdsp.2018.02.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Lan C, Song JL, Yan LN, Yang JY, Wen TF, Li B, Xu MQ. Pediatric Donor to Adult Recipients in Donation After Cardiac Death Liver Transplantation: A Single-Center Experience. Transplant Proc 2018; 49:1383-1387. [PMID: 28736011 DOI: 10.1016/j.transproceed.2017.01.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/11/2017] [Accepted: 01/24/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND The impact of using liver allografts from donors who are younger than 14 years at the time of donation after cardiac death (DCD) liver transplantation in terms of early allograft dysfunction (EAD) and graft survival is undefined. To determine if adults undergoing DCD liver transplantation who receive a graft from a donor age younger than or equal to 13 years have similar outcomes to recipients of organs from older than 18-year-old donors. METHODS Records from adult patients undergoing DCD liver transplantation between March 2012 and December 2015 who received whole grafts from donors after cardiac death were reviewed. Patients with donors younger than or equal to 13 years (group 1) and older than 18 years (group 2) were compared for EAD rates, hepatic artery thrombosis (HAT), and graft survival. RESULTS Records of 60 DCD liver transplantation patients were analyzed. The 90-day and 1-year graft survival rate of both groups was 90% versus 96% (P = .427) and 80% versus 84% (P = .668), respectively. The EAD rates of groups 1 and 2 were 30% versus 34% (P = .806). The incidence of HAT was 20% in group 1 compared with 12% in group 2 (P = .610). Also, 0.7% < graft to recipient weight ratio (GRWR) <0.8% was also usable for pediatric donor to adult recipients. CONCLUSIONS Whole liver grafts from donors younger than or equal to 13 years can potentially be used in selected size-matched (GRWR >0.7%) DCD adult recipients.
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Affiliation(s)
- C Lan
- Institute of Hepatobiliary, Pancreatic and Intestinal Diseases, North Sichuan Medical College, Nanchong, Sichuan, China; Department of Hepatobiliary Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - J L Song
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - L N Yan
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - J Y Yang
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - T F Wen
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - B Li
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - M Q Xu
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China.
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Martin K, Iyengar S, Kalyan A, Lan C, Simon AL, Stosic M, Kobara K, Ravi H, Truong T, Ryan A, Demko ZP, Benn P. Clinical experience with a single-nucleotide polymorphism-based non-invasive prenatal test for five clinically significant microdeletions. Clin Genet 2017; 93:293-300. [PMID: 28696552 DOI: 10.1111/cge.13098] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/30/2017] [Indexed: 01/06/2023]
Abstract
Single-nucleotide polymorphism (SNP)-based non-invasive prenatal testing (NIPT) can currently predict a subset of submicroscopic abnormalities associated with severe clinical manifestations. We retrospectively analyzed the performance of SNP-based NIPT in 80 449 referrals for 22q11.2 deletion syndrome and 42 326 referrals for 1p36, cri-du-chat, Prader-Willi, and Angelman microdeletion syndromes over a 1-year period, and compared the original screening protocol with a revision that reflexively sequenced high-risk calls at a higher depth of read. The prevalence of these microdeletion syndromes was also estimated in the referral population. The positive predictive value of the original test was 15.7% for 22q11.2 deletion syndrome, and 5.2% for the other 4 disorders combined. With the revised protocol, these values increased to 44.2% for 22q11.2 and 31.7% for the others. The 0.33% false-positive rate (FPR) for 22q11.2 deletion syndrome decreased to 0.07% with the revised protocol. Similarly, the FPR for the other 4 disorders combined decreased from 0.56% to 0.07%. Minimal prevalences were estimated to be 1 in 1255 for 22q11.2 deletion syndrome and 1 in 1464 for 1p36, cri-du-chat, and Angelman syndromes combined. Our results show that these microdeletions are relatively common in the referral population, and that the performance of SNP-based NIPT is improved with high-depth resequencing.
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Affiliation(s)
- K Martin
- Natera, Inc., San Carlos, California
| | - S Iyengar
- Natera, Inc., San Carlos, California
| | - A Kalyan
- Natera, Inc., San Carlos, California
| | - C Lan
- Natera, Inc., San Carlos, California
| | - A L Simon
- Natera, Inc., San Carlos, California
| | - M Stosic
- Natera, Inc., San Carlos, California
| | - K Kobara
- Natera, Inc., San Carlos, California
| | - H Ravi
- Natera, Inc., San Carlos, California
| | - T Truong
- Natera, Inc., San Carlos, California
| | - A Ryan
- Natera, Inc., San Carlos, California
| | - Z P Demko
- Natera, Inc., San Carlos, California
| | - P Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut
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Lan C, Hale IL, Herrera-Foessel SA, Basnet BR, Randhawa MS, Huerta-Espino J, Dubcovsky J, Singh RP. Characterization and Mapping of Leaf Rust and Stripe Rust Resistance Loci in Hexaploid Wheat Lines UC1110 and PI610750 under Mexican Environments. Front Plant Sci 2017; 8:1450. [PMID: 28878791 PMCID: PMC5573434 DOI: 10.3389/fpls.2017.01450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/04/2017] [Indexed: 05/18/2023]
Abstract
Growing resistant wheat varieties is a key method of minimizing the extent of yield losses caused by the globally important wheat leaf rust (LR) and stripe rust (YR) diseases. In this study, a population of 186 F8 recombinant inbred lines (RILs) derived from a cross between a synthetic wheat derivative (PI610750) and an adapted common wheat line (cv. "UC1110") were phenotyped for LR and YR response at both seedling and adult plant stages over multiple seasons. Using a genetic linkage map consisting of single sequence repeats and diversity arrays technology markers, in combination with inclusive composite interval mapping analysis, we detected a new LR adult plant resistance (APR) locus, QLr.cim-2DS, contributed by UC1110. One co-located resistance locus to both rusts, QLr.cim-3DC/QYr.cim-3DC, and the known seedling resistance gene Lr26 were also mapped. QLr.cim-2DS and QLr.cim-3DC showed a marginally significant interaction for LR resistance in the adult plant stage. In addition, two previously reported YR APR loci, QYr.ucw-3BS and Yr48, were found to exhibit stable performances in rust environments in both Mexico and the United States and showed a highly significant interaction in the field. Yr48 was also observed to confer intermediate seedling resistance against Mexican YR races, thus suggesting it should be re-classified as an all-stage resistance gene. We also identified 5 and 2 RILs that possessed all detected YR and LR resistance loci, respectively. With the closely linked molecular markers reported here, these RILs could be used as donors for multiple resistance loci to both rusts in wheat breeding programs.
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Affiliation(s)
- Caixia Lan
- International Maize and Wheat Improvement CenterMexico City, Mexico
| | - Iago L. Hale
- Department of Biological Sciences, University of New Hampshire, DurhamNH, United States
| | | | - Bhoja R. Basnet
- International Maize and Wheat Improvement CenterMexico City, Mexico
| | | | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico, Instituto Nacional de Investigaciones Forestales, Agrícolas y PecuariasChapingo, Mexico
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, DavisCA, United States
| | - Ravi P. Singh
- International Maize and Wheat Improvement CenterMexico City, Mexico
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Ren Y, Hou W, Lan C, Basnet BR, Singh RP, Zhu W, Cheng X, Cui D, Chen F. QTL Analysis and Nested Association Mapping for Adult Plant Resistance to Powdery Mildew in Two Bread Wheat Populations. Front Plant Sci 2017; 8:1212. [PMID: 28798752 PMCID: PMC5529384 DOI: 10.3389/fpls.2017.01212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/27/2017] [Indexed: 05/20/2023]
Abstract
CIMMYT wheat (Triticum aestivum L.) lines Francolin#1 and Quaiu#3 displayed effective and stable adult plant resistance (APR) to Chinese Blumeria graminis f. sp. tritici isolates in the field. To elucidate their genetic basis of resistance, two recombinant inbred line (RIL) populations of their crosses with Avocet, the susceptible parent, were phenotyped in Zhengzhou and Shangqiu in the 2014-2015 and 2015-2016 cropping seasons. These populations were also genotyped with SSR (simple sequence repeat markers) and DArT (diversity arrays technology) markers. Two common significant quantitative trait loci (QTL) on wheat chromosomes 1BL and 4BL were detected in both populations by joint and individual inclusive composite interval mapping, explaining 20.3-28.7% and 9.6-15.9% of the phenotypic variance in Avocet × Francolin#1 and 4.8-11.5% and 10.8-18.9% in Avocet × Quaiu#3, respectively. Additional QTL were mapped on chromosomes 1DL and 5BL in Avocet × Francolin#1 and on 2DL and 6BS in Avocet × Quaiu#3. Among these, QPm.heau-1DL is probably a novel APR gene contributing 6.1-8.5% of total phenotypic variance. The QTL on 1BL corresponds to the pleiotropic multi-pathogen resistance gene Yr29/Lr46/Pm39, whereas the QTL on 2DL maps to a similar region where stripe rust resistance gene Yr54 is located. The QTL identified can potentially be used for the improvement of powdery mildew and rust resistance in wheat breeding.
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Affiliation(s)
- Yan Ren
- Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural UniversityZhengzhou, China
| | - Weixiu Hou
- Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural UniversityZhengzhou, China
| | - Caixia Lan
- International Maize and Wheat Improvement Center (CIMMYT)Mexico, Mexico
| | - Bhoja R. Basnet
- International Maize and Wheat Improvement Center (CIMMYT)Mexico, Mexico
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT)Mexico, Mexico
| | - Wei Zhu
- Shangqiu Academy of Agricultural and Forestry SciencesShangqiu, China
| | - Xiyong Cheng
- Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural UniversityZhengzhou, China
| | - Dangqun Cui
- Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural UniversityZhengzhou, China
| | - Feng Chen
- Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural UniversityZhengzhou, China
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Juliana P, Singh RP, Singh PK, Crossa J, Huerta-Espino J, Lan C, Bhavani S, Rutkoski JE, Poland JA, Bergstrom GC, Sorrells ME. Genomic and pedigree-based prediction for leaf, stem, and stripe rust resistance in wheat. Theor Appl Genet 2017; 130:1415-1430. [PMID: 28393303 PMCID: PMC5487692 DOI: 10.1007/s00122-017-2897-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/19/2017] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Genomic prediction for seedling and adult plant resistance to wheat rusts was compared to prediction using few markers as fixed effects in a least-squares approach and pedigree-based prediction. The unceasing plant-pathogen arms race and ephemeral nature of some rust resistance genes have been challenging for wheat (Triticum aestivum L.) breeding programs and farmers. Hence, it is important to devise strategies for effective evaluation and exploitation of quantitative rust resistance. One promising approach that could accelerate gain from selection for rust resistance is 'genomic selection' which utilizes dense genome-wide markers to estimate the breeding values (BVs) for quantitative traits. Our objective was to compare three genomic prediction models including genomic best linear unbiased prediction (GBLUP), GBLUP A that was GBLUP with selected loci as fixed effects and reproducing kernel Hilbert spaces-markers (RKHS-M) with least-squares (LS) approach, RKHS-pedigree (RKHS-P), and RKHS markers and pedigree (RKHS-MP) to determine the BVs for seedling and/or adult plant resistance (APR) to leaf rust (LR), stem rust (SR), and stripe rust (YR). The 333 lines in the 45th IBWSN and the 313 lines in the 46th IBWSN were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. The mean prediction accuracies ranged from 0.31-0.74 for LR seedling, 0.12-0.56 for LR APR, 0.31-0.65 for SR APR, 0.70-0.78 for YR seedling, and 0.34-0.71 for YR APR. For most datasets, the RKHS-MP model gave the highest accuracies, while LS gave the lowest. GBLUP, GBLUP A, RKHS-M, and RKHS-P models gave similar accuracies. Using genome-wide marker-based models resulted in an average of 42% increase in accuracy over LS. We conclude that GS is a promising approach for improvement of quantitative rust resistance and can be implemented in the breeding pipeline.
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Affiliation(s)
- Philomin Juliana
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico
| | - Pawan K Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, 56230, Chapingo, Edo, de México, Mexico
| | - Caixia Lan
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico
| | - Sridhar Bhavani
- CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market, Nairobi, 00621, Kenya
| | - Jessica E Rutkoski
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico
| | - Jesse A Poland
- Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Gary C Bergstrom
- Plant Pathology and Plant-microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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Wang X, Lang M, Zhao T, Feng X, Zheng C, Huang C, Hao J, Dong J, Luo L, Li X, Lan C, Yu W, Yu M, Yang S, Ren H. Cancer-FOXP3 directly activated CCL5 to recruit FOXP3 +Treg cells in pancreatic ductal adenocarcinoma. Oncogene 2017; 36:3048-3058. [PMID: 27991933 PMCID: PMC5454319 DOI: 10.1038/onc.2016.458] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/18/2016] [Accepted: 10/31/2016] [Indexed: 12/15/2022]
Abstract
Forkheadbox protein 3 (FOXP3), initially identified as a key transcription factor for regulatory T cells (Treg cells), was also expressed in many tumors including pancreatic ductal adenocarcinoma (PDAC). However, its role in PDAC progression remains elusive. In this study, we utilized 120 PDAC tissues after radical resection to detect cancer-FOXP3 and Treg cells by immunohistochemistry and evaluated clinical and pathological features of these patients. Cancer-FOXP3 was positively correlated with Treg cells accumulation in tumor tissues derived from PDAC patients. In addition, high cancer-FOXP3 expression was associated with increased tumor volumes and poor prognosis in PDAC especially combined with high levels of Treg cells. Overexpression of cancer-FOXP3 promoted the tumor growth in immunocompetent syngeneic mice but not in immunocompromised or Treg cell-depleted mice. Furthermore, CCL5 was directly trans-activated by cancer-FOXP3 and promoted the recruitment of Treg cells from peripheral blood to the tumor site in vitro and in vivo. This finding has been further reinforced by the evidence that Treg cells recruitment by cancer-FOXP3 was impaired by neutralization of CCL5, thereby inhibiting the growth of PDAC. In conclusion, cancer-FOXP3 serves as a prognostic biomarker and a crucial determinant of immunosuppressive microenvironment via recruiting Treg cells by directly trans-activating CCL5. Therefore, cancer-FOXP3 could be used to select patients with better response to CCL5/CCR5 blockade immunotherapy.
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MESH Headings
- Adult
- Aged
- Animals
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/immunology
- Carcinoma, Pancreatic Ductal/metabolism
- Carcinoma, Pancreatic Ductal/pathology
- Cells, Cultured
- Chemokine CCL5/metabolism
- Chemokine CCL5/pharmacology
- Chemotaxis, Leukocyte/drug effects
- Chemotaxis, Leukocyte/genetics
- Female
- Forkhead Transcription Factors/genetics
- Forkhead Transcription Factors/physiology
- Humans
- Lymphocyte Activation/drug effects
- Lymphocyte Activation/genetics
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Nude
- Mice, SCID
- Middle Aged
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/immunology
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/pathology
- T-Lymphocytes, Regulatory/drug effects
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Tumor Microenvironment/genetics
- Pancreatic Neoplasms
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Affiliation(s)
- X Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Department of Pancreatic Cancer, Tianjin, China
| | - M Lang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Department of Pancreatic Cancer, Tianjin, China
| | - T Zhao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Department of Pancreatic Cancer, Tianjin, China
| | - X Feng
- The State Key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - C Zheng
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Department of Pancreatic Cancer, Tianjin, China
| | - C Huang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Department of Pancreatic Cancer, Tianjin, China
| | - J Hao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Department of Pancreatic Cancer, Tianjin, China
| | - J Dong
- Department of Nutrition and Food Hygiene, School of Public Health, Tianjin Medical University, Tianjin, China
| | - L Luo
- Department of Gynaecology, Hepingqu Gynaecology and Obsterics Hospital, Tianjin, China
| | - X Li
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Department of Pancreatic Cancer, Tianjin, China
| | - C Lan
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Department of Pancreatic Cancer, Tianjin, China
| | - W Yu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Department of Pancreatic Cancer, Tianjin, China
| | - M Yu
- Department of Nutrition and Food Hygiene, School of Public Health, Tianjin Medical University, Tianjin, China
| | - S Yang
- Penn State College of Medicine, Hershey, PA, USA
| | - H Ren
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Department of Pancreatic Cancer, Tianjin, China
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48
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Fourny N, Lan C, Kober F, Bernard M, Desrois M. Intolerance to glucose and abdominal obesity in a diet-induced metabolic syndrome model were associated with modification of cardiac morphology and impaired myocardial function. Archives of Cardiovascular Diseases Supplements 2017. [DOI: 10.1016/s1878-6480(17)30469-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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49
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Lan C, Basnet BR, Singh RP, Huerta-Espino J, Herrera-Foessel SA, Ren Y, Randhawa MS. Genetic analysis and mapping of adult plant resistance loci to leaf rust in durum wheat cultivar Bairds. Theor Appl Genet 2017; 130:609-619. [PMID: 28004134 DOI: 10.1007/s00122-016-2839-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/01/2016] [Indexed: 05/02/2023]
Abstract
New leaf rust adult plant resistance (APR) QTL QLr.cim - 6BL was mapped and confirmed the known pleotropic APR gene Lr46 effect on leaf rust in durum wheat line Bairds. CIMMYT-derived durum wheat line Bairds displays an adequate level of adult plant resistance (APR) to leaf rust in Mexican field environments. A recombinant inbred line (RIL) population developed from a cross of Bairds with susceptible parent Atred#1 was phenotyped for leaf rust response at Ciudad Obregon, Mexico, during 2013, 2014, 2015 and 2016 under artificially created epidemics of Puccinia triticina (Pt) race BBG/BP. The RIL population and its parents were genotyped with the 50 K diversity arrays technology (DArT) sequence system and simple sequence repeat (SSR) markers. A genetic map comprising 1150 markers was used to map the resistance loci. Four significant quantitative trait loci (QTLs) were detected on chromosomes 1BL, 2BC (centromere region), 5BL and 6BL. These QTLs, named Lr46, QLr.cim-2BC, QLr.cim-5BL and QLr.cim-6BL, respectively, explained 13.5-60.8%, 9.0-14.3%, 2.8-13.9%, and 11.6-29.4%, respectively, of leaf rust severity variation by the inclusive composite interval mapping method. All of these resistance loci were contributed by the resistant parent Bairds, except for QLr.cim-2BC, which came from susceptible parent Atred#1. Among these, the QTL on chromosome 1BL was the known pleiotropic APR gene Lr46, whereas QLr.cim-6BL, a consistently detected locus, should be a new leaf rust resistance locus in durum wheat. The mean leaf rust severity of RILs carrying all four QTLs ranged from 8.0 to 17.5%, whereas it ranged from 10.9 to 38.5% for three QTLs (Lr46 + 5BL + 6BL) derived from the resistant parent Bairds. Two RILs with four QTLs combinations can be used as sources of complex APR in durum wheat breeding.
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Affiliation(s)
- Caixia Lan
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Texcoco, México D.F., Mexico.
| | - Bhoja R Basnet
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Texcoco, México D.F., Mexico
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Texcoco, México D.F., Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230, Chapingo, Texcoco, Edo. de México, Mexico
| | - Sybil A Herrera-Foessel
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Texcoco, México D.F., Mexico
| | - Yong Ren
- Mianyang Institute of Agricultural Science/Mianyang Branch of National Wheat Improvement Center, 8 Songjiang Road, Mianyang, 621023, Sichuan, People's Republic of China
| | - Mandeep S Randhawa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Texcoco, México D.F., Mexico
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50
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Manickavelu A, Joukhadar R, Jighly A, Lan C, Huerta-Espino J, Stanikzai AS, Kilian A, Singh RP, Ban T. Genome wide association mapping of stripe rust resistance in Afghan wheat landraces. Plant Sci 2016; 252:222-229. [PMID: 27717458 DOI: 10.1016/j.plantsci.2016.07.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/28/2016] [Accepted: 07/30/2016] [Indexed: 05/16/2023]
Abstract
Mining of new genetic resources is of paramount importance to combat the alarming spread of stripe rust disease and breakdown of major resistance genes in wheat. We conducted a genome wide association study on 352 un-utilized Afghan wheat landraces against stripe rust resistance in eight locations. High level of disease variation was observed among locations and a core-set of germplasm showed consistence performance. Linkage disequilibrium (LD) decayed rapidly (R2≈0.16 at 0cM) due to germplasm peerless diversity. The mixed linear model resulted in ten marker-trait associations (MTAs) across all environments representing five QTL. The extensively short LD blocks required us to repeat the analysis with less diverse subset of 220 landraces in which R2 decayed below 0.2 at 0.3cM. The subset GWAS resulted in 36 MTAs clustered in nine QTL. The subset analysis validated three QTL previously detected in the full list analysis. Overall, the study revealed that stripe rust epidemics in the geographical origin of this germplasm through time have permitted for selecting novel resistance loci.
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Affiliation(s)
- Alagu Manickavelu
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 2440813, Japan; Present address: Department of Genome Science, School of Biological Science, Central University of Kerala, Kasaragod, 671314, Kerala, India.
| | - Reem Joukhadar
- AgriBio, Centre for Agribioscience, DEDJTR, 5 Ring Road, Bundoora, Vic. 3083, Australia; Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic. 3083, Australia
| | - Abdulqader Jighly
- AgriBio, Centre for Agribioscience, DEDJTR, 5 Ring Road, Bundoora, Vic. 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Vic. 3083, Australia; The International Center for Agricultural Research in the Dry Areas (ICARDA), Aleppo, Syria
| | - Caixia Lan
- CIMMYT, Apdo. Postal 6-641, 06600, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México, INIFAP, Chapingo, Estado de México, Mexico
| | - Ahmad Shah Stanikzai
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 2440813, Japan; Ministry of Agriculture, Irrigation and Livestock, Afghanistan
| | | | | | - Tomohiro Ban
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 2440813, Japan
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