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Article ; Online: Genetic Association between Blast Resistance and Yield Traits in Rice Detected Using a High-Density Bin Map

Lydia Kanyange / Ye-Yang Fan / Zhen-Hua Zhang / De-Run Huang / Ting-Xu Huang / Jie-Yun Zhuang / Yu-Jun Zhu

Agronomy, Vol 12, Iss 1173, p

2022 Volume 1173

Abstract: Avoiding linkage drag of the resistance genes will facilitate the use of gene resources for rice breeding. This study was conducted to confirm the avoidance of linkage drag due to Pi26 and Pi25 blast resistance genes, and to analyze the association of ... ...

Abstract	Avoiding linkage drag of the resistance genes will facilitate the use of gene resources for rice breeding. This study was conducted to confirm the avoidance of linkage drag due to Pi26 and Pi25 blast resistance genes, and to analyze the association of Pi26 , Pi25 , Pib and Pita with quantitative trait loci (QTL) for yield traits. A recombinant inbred line population was derived from an indica rice cross Dan 71/Zhonghui 161. A linkage map consisting of 1219 bin markers, 22 simple sequence repeats and five gene markers was constructed. A total of 75 QTL were identified, including 2 for leaf blast resistance and 73 for eight yield traits. The two QTL for blast resistance were closely linked and located in the Pi26 and Pi25 regions, explaining 69.06 and 12.73% of the phenotypic variance, respectively. In a region covering Pi26 and Pi25 , QTL were detected for grain yield and its key components. The alleles for enhancing blast resistance and grain yield were all from Dan 71. Not only was the linkage drag due to Pi26 and Pi25 avoided, but the results also indicate that these resistance genes may be used for simultaneously enhancing blast resistance and grain yield in rice. In the Pib and Pita regions, QTL was not detected for blast resistance, but was for yield traits. In each region, the allele for improving trait performance was derived from the parent carrying the resistance allele. In addition, four QTL clusters for grain weight and size, qGL4 / qGW4.1 , qGL11.2 / qRLW11 , qTGW11 / qGW11 and qGL12 / qGW12 / qRLW12 , were shown to be promising candidates for map-based cloning.
Keywords	favorable association ; blast resistance ; yield trait ; quantitative trait locus ; bin map ; rice ; Agriculture ; S
Subject code	630
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Improvement of soil fertility and rice yield after long-term application of cow manure combined with inorganic fertilizers

Peng GAO / Tuo ZHANG / Xing-yu LEI / Xin-wei CUI / Yao-xiong LU / Peng-fei FAN / Shi-ping LONG / Jing HUANG / Ju-sheng GAO / Zhen-hua ZHANG / Hui-min ZHANG

Journal of Integrative Agriculture, Vol 22, Iss 7, Pp 2221-

2023 Volume 2232

Abstract: Fertilization is an effective technique to improve soil fertility and increase crop yield. The long-term effects of different fertilizers on soil considerably vary. Over 38 consecutive years of different fertilization positioning experiments in a double ... ...

Abstract	Fertilization is an effective technique to improve soil fertility and increase crop yield. The long-term effects of different fertilizers on soil considerably vary. Over 38 consecutive years of different fertilization positioning experiments in a double cropping rice field of Qiyang Red Soil Experimental Station, seven different fertilization treatments including CK (no fertilization), NPK (nitrogen, phosphorus, and potassium fertilizer), M (cow manure), NPKM (nitrogen, phosphorus, and potassium with cow manure), NPM (nitrogen and phosphorus with cow manure), NKM (nitrogen and potassium with cow manure), and PKM (phosphorus and potassium with cow manure) were applied to study the effects on rice yield, soil fertility, and nutrient apparent balance in a paddy field. The results showed that the annual average yields of rice in NPKM, NPM, NKM, PKM, M, NPK and CK treatments ranged from 6 214 to 11 562 kg ha–1. Yields under long-term organic and inorganic treatments (NPKM, NPM, NKM and PKM) were 22.58, 15.35, 10.53 and 4.41%, respectively, greater than under the NPK treatment. Soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN) and available potassium (AK) concentration with long-term organic and inorganic treatment (NPKM, NPM, NKM and PKM) were significantly higher than in inorganic fertilizer (NPK) treatments. Soil total phosphorus (TP) and available phosphorus (AP) contentration with organic fertilizer combined with inorganic N and P fertilizer treatment (NPKM, NPM and PKM) were significantly higher than with inorganic fertilizer alone (NPK treatments). The average annual rice yield (11 562 kg ha–1), SOC (20.88 g kg–1), TN (2.30 g kg–1), TP (0.95 g kg–1), TK (22.50 g kg–1) and AP (38.94 mg kg–1) concentrations were the highest in the NPKM treatment. The soil AN concentration (152.40 mg kg–1) and AK contentration (151.00 mg kg–1) were the highest in the NKM treatment. N and P application led to a surplus of nitrogen and phosphorus in the soil, but NPKM treatment effectively reduced the surplus ...
Keywords	long-term fertilization ; rice yield ; soil fertility ; nutrient balance ; Agriculture (General) ; S1-972
Subject code	630
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Control of Thousand-Grain Weight by OsMADS56 in Rice

Zi-Wei Zuo / Zhen-Hua Zhang / De-Run Huang / Ye-Yang Fan / Si-Bin Yu / Jie-Yun Zhuang / Yu-Jun Zhu

International Journal of Molecular Sciences, Vol 23, Iss 125, p

2022 Volume 125

Abstract: Grain weight and size are important traits determining grain yield and influencing grain quality in rice. In a previous study, a quantitative trait locus controlling thousand-grain weight (TGW) in rice, qTGW10-20.8 , was mapped in a 70.7 kb region on ... ...

Abstract	Grain weight and size are important traits determining grain yield and influencing grain quality in rice. In a previous study, a quantitative trait locus controlling thousand-grain weight (TGW) in rice, qTGW10-20.8 , was mapped in a 70.7 kb region on chromosome 10. Validation of the candidate gene for qTGW10-20.8 , OsMADS56 encoding a MADS-box transcription factor, was performed in this study. In a near-isogenic line (NIL) population segregated only at the OsMADS56 locus, NILs carrying the OsMADS56 allele of IRBB52 were 1.9% and 2.9% lower in TGW than NILs carrying the OsMADS56 allele of Teqing in 2018 and 2020, respectively. Using OsMADS56 knock-out mutants and overexpression transgenic plants, OsMADS56 was validated as the causal gene for qTGW10-20.8 . Compared with the recipients, the TGW of the knock-out mutants was reduced by 6.0–15.0%. In these populations, decreased grain weight and size were associated with a reduction in the expression of OsMADS56 . In transgenic populations of OsMADS56 driven by a strong constitutive promoter, grain weight and size of the positive plants were significantly higher than those of the negative plants. Haplotype analysis showed that the Teqing-type allele of OsMADS56 is the major type presented in cultivated rice and used in variety improvement. Cloning of OsMADS56 provides a new gene resource to improve grain weight and size through molecular design breeding.
Keywords	minor effect ; grain weight ; heading date ; quantitative trait locus ; rice ; MADS-box ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	669
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Integrated Transcriptional and Proteomic Profiling Reveals Potential Amino Acid Transporters Targeted by Nitrogen Limitation Adaptation

Qiong Liao / Tian-jiao Tang / Ting Zhou / Hai-xing Song / Ying-peng Hua / Zhen-hua Zhang

International Journal of Molecular Sciences, Vol 21, Iss 6, p

2020 Volume 2171

Abstract: Nitrogen (N) is essential for plant growth and crop productivity. Organic N is a major form of remobilized N in plants’ response to N limitation. It is necessary to understand the regulatory role of N limitation adaption (NLA) in organic N remobilization ...

Abstract	Nitrogen (N) is essential for plant growth and crop productivity. Organic N is a major form of remobilized N in plants’ response to N limitation. It is necessary to understand the regulatory role of N limitation adaption (NLA) in organic N remobilization for this adaptive response. Transcriptional and proteomic analyses were integrated to investigate differential responses of wild-type (WT) and nla mutant plants to N limitation and to identify the core organic N transporters targeted by NLA. Under N limitation, the nla mutant presented an early senescence with faster chlorophyll loss and less anthocyanin accumulation than the WT, and more N was transported out of the aging leaves in the form of amino acids. High-throughput transcriptomic and proteomic analyses revealed that N limitation repressed genes involved in photosynthesis and protein synthesis, and promoted proteolysis; these changes were higher in the nla mutant than in the WT. Both transcriptional and proteomic profiling demonstrated that LHT1, responsible for amino acid remobilization, were only significantly upregulated in the nla mutant under N limitation. These findings indicate that NLA might target LHT1 and regulate organic N remobilization, thereby improving our understanding of the regulatory role of NLA on N remobilization under N limitation.
Keywords	nla ; n limitation ; transcriptional profiling ; proteomic change ; n remobilization ; amino acid transporter ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	580
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome-Wide Differential DNA Methylation and miRNA Expression Profiling Reveals Epigenetic Regulatory Mechanisms Underlying Nitrogen-Limitation-Triggered Adaptation and Use Efficiency Enhancement in Allotetraploid Rapeseed

Ying-peng Hua / Ting Zhou / Jin-yong Huang / Cai-peng Yue / Hai-xing Song / Chun-yun Guan / Zhen-hua Zhang

International Journal of Molecular Sciences, Vol 21, Iss 8453, p

2020 Volume 8453

Abstract: Improving crop nitrogen (N) limitation adaptation (NLA) is a core approach to enhance N use efficiency (NUE) and reduce N fertilizer application. Rapeseed has a high demand for N nutrients for optimal plant growth and seed production, but it exhibits low ...

Abstract	Improving crop nitrogen (N) limitation adaptation (NLA) is a core approach to enhance N use efficiency (NUE) and reduce N fertilizer application. Rapeseed has a high demand for N nutrients for optimal plant growth and seed production, but it exhibits low NUE. Epigenetic modification, such as DNA methylation and modification from small RNAs, is key to plant adaptive responses to various stresses. However, epigenetic regulatory mechanisms underlying NLA and NUE remain elusive in allotetraploid B. napus . In this study, we identified overaccumulated carbohydrate, and improved primary and lateral roots in rapeseed plants under N limitation, which resulted in decreased plant nitrate concentrations, enhanced root-to-shoot N translocation, and increased NUE. Transcriptomics and RT-qPCR assays revealed that N limitation induced the expression of NRT1.1 , NRT1.5 , NRT1.7 , NRT2.1/NAR2.1 , and Gln1;1 , and repressed the transcriptional levels of CLCa , NRT1.8 , and NIA1 . High-resolution whole genome bisulfite sequencing characterized 5094 differentially methylated genes involving ubiquitin-mediated proteolysis, N recycling, and phytohormone metabolism under N limitation. Hypermethylation/hypomethylation in promoter regions or gene bodies of some key N-metabolism genes might be involved in their transcriptional regulation by N limitation. Genome-wide miRNA sequencing identified 224 N limitation-responsive differentially expressed miRNAs regulating leaf development, amino acid metabolism, and plant hormone signal transduction. Furthermore, degradome sequencing and RT-qPCR assays revealed the miR827-NLA pathway regulating limited N-induced leaf senescence as well as the miR171- SCL6 and miR160- ARF17 pathways regulating root growth under N deficiency. Our study provides a comprehensive insight into the epigenetic regulatory mechanisms underlying rapeseed NLA, and it will be helpful for genetic engineering of NUE in crop species through epigenetic modification of some N metabolism-associated genes.
Keywords	allotetraploid rapeseed ; DNA methylation ; microRNA ; nitrogen ; nitrogen limitation adaptation ; nitrogen use efficiency ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	570 ; 580
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Detection of inflammatory factor and protease content as well as oxidative stress level in gingival crevicular fluid after fiber post and metal post repair

Zhen-Hua Zhang / Xiao-Hui Zhang / Yue Zhang / Min Fang

Journal of Hainan Medical University, Vol 22, Iss 14, Pp 148-

2016 Volume 151

Abstract: Objective: To study inflammatory factor and protease content as well as oxidative stress level in gingival crevicular fluid after fiber post and metal post repair. Methods: 60 cases of patients with large tooth defect who received post-core restoration ... ...

Abstract	Objective: To study inflammatory factor and protease content as well as oxidative stress level in gingival crevicular fluid after fiber post and metal post repair. Methods: 60 cases of patients with large tooth defect who received post-core restoration in our hospital from May 2012 to August 2015 were selected for study and divided into fiber post group (n=28) and metal post repair group (n=32) according to different post-core restoration materials, and the content of inflammatory factors, proteases, oxidative stress molecules in gingival crevicular fluid were detected. Results: IL-12p35, IL-12p40, CXCL16, NFATc1, RANK, MMP-1, MMP-8, MMP- 13, P.g-TLP, EA, ROS, MDA, LPO and 8-OHdG content in gingival crevicular fluid of fiber post group were lower than those of metal post group; IL-4, IL-13, SOD, GP-x and CAT content in gingival crevicular fluid of fiber post group were higher than those of metal post group; serum IL-12p35, IL-12p40, CXCL16, NFATc1, RANK, IL-4 and IL-13 content of two groups were not different. Conclusion: Fiber post causes less trauma to periodontal tissue, and the content of pro-inflammatory factors, proteases and peroxidation products in gingival crevicular fluid were lower.
Keywords	Tooth defect ; Fiber post ; Metal post ; Inflammatory factors ; Protease ; Oxidative stress ; Medicine ; R
Language	English
Publishing date	2016-07-01T00:00:00Z
Publisher	Editorial Board of Journal of Hainan Medical University
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Electronic properties of phosphorene nanoribbons with nanoholes

Sun, Lin / Hao Wang / Mo Li / Zhen Hua Zhang

RSC advances. 2018 Feb. 15, v. 8, no. 14

2018

Abstract: Using first-principles calculation based on density-functional theory, the electronic properties of monolayer black phosphorus nanoribbons (PNRs) with and without punched nanoholes (PNRPNHs) and their mechanical stability are studied systematically. We ... ...

Abstract	Using first-principles calculation based on density-functional theory, the electronic properties of monolayer black phosphorus nanoribbons (PNRs) with and without punched nanoholes (PNRPNHs) and their mechanical stability are studied systematically. We show that while the perfect PNRs and the PNRPNHs have similar properties as semiconductors in both armchair-edge PNR and zigzag-edge PNR structures, the nanoholes can lead to changes in the electronic structure: the zigzag-edge PNRPNH undergoes a direct-to-indirect bandgap transition while the armchair-edge PNRPNH still retains a direct bandgap but with a significant increase in the bandgap as compared to the perfect PNRs. We found also that nanoholes have little influence on the structural stability of PNRs; but the applied external transverse electric field and strain can be more effective in modulating the bandgaps in the PNRPNHs. These new findings show that PNRs are a promising candidate for future nanoelectronic and optoelectronic applications.
Keywords	density functional theory ; electric field ; phosphorus ; semiconductors
Language	English
Dates of publication	2018-0215
Size	p. 7486-7493.
Publishing place	The Royal Society of Chemistry
Document type	Article
ISSN	2046-2069
DOI	10.1039/c7ra12351e
Database	NAL-Catalogue (AGRICOLA)

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Article: Increased rice yield in long-term crop rotation regimes through improved soil structure, rhizosphere microbial communities, and nutrient bioavailability in paddy soil

Lu, Sheng / Joe Eugene Lepo / Hai-Xing Song / Chun-Yun Guan / Zhen-Hua Zhang

Biology and fertility of soils. 2018 Nov., v. 54, no. 8

2018

Abstract: Soil in short-term crop rotation systems (STCR) is still in the initial development stage of farmland soil, whereas after long-term crop rotation treatment (LTCR), soil properties are significantly different. This study compares STCR (4 years) and LTCR ( ... ...

Abstract	Soil in short-term crop rotation systems (STCR) is still in the initial development stage of farmland soil, whereas after long-term crop rotation treatment (LTCR), soil properties are significantly different. This study compares STCR (4 years) and LTCR (30 years) rice-rice-fallow, rice-rice-rape rotation practices under the same soil type background and management system. To reveal ecosystem mechanisms within soils and their effects on rice yield following LTCR, we analyzed the physical, chemical, and microbiological properties of soils with different rotations and rotation times. Relative to STCR, LTCR significantly reduced soil water-stable aggregate (WSA) content in the < 0.053-mm range, while > 2 mm WSA content significantly increased. Soil organic matter increased in fields under LTCR, mainly in > 2 mm, 2–0.25 mm, and < 0.053 mm soil WSA in 0–10 cm soil layer. LTCR was associated with significantly increased total soil organic matter, at the same time being associated with increasing the amount of active organic matter in the 0–20 cm soil layer. The two crop rotation regimes significantly differed in soil aggregate composition as well as in soil N and P, microbial biomass, and community composition. Relative to STCR, LTCR field soils had significantly higher soil organic matter, active organic matter content, soil enzyme activities, and overall microbial biomass, while soil WSA and microbial community composition was significantly different. Our results demonstrate that LTCR could significantly improve soil quality and rice yield and suggest that length of rotation time and rice-rice-rape rotation are critical factors for the development of green agriculture.
Keywords	agricultural soils ; bioavailability ; community structure ; crop rotation ; ecosystems ; enzyme activity ; grain yield ; microbial biomass ; microbial communities ; paddy soils ; rhizosphere ; soil aggregates ; soil enzymes ; soil organic matter ; soil quality ; soil structure
Language	English
Dates of publication	2018-11
Size	p. 909-923.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	742137-0
ISSN	1432-0789 ; 0178-2762
ISSN (online)	1432-0789
ISSN	0178-2762
DOI	10.1007/s00374-018-1315-4
Database	NAL-Catalogue (AGRICOLA)

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Article: Integrated genomic and transcriptomic insights into the two-component high-affinity nitrate transporters in allotetraploid rapeseed

Hua, Ying-peng / Chun-yun Guan / Hai-xing Song / Ting Zhou / Zhen-hua Zhang

Plant and soil. 2018 June, v. 427, no. 1-2

2018

Abstract: BACKGROUND AND AIMS: The two-component high-affinity nitrate (NO3−) transport system (THATS) proteins (NRT2/NAR2) play key roles in the efficient nitrogen (N) uptake and transport under N limitations. We aimed at uncovering the core THATS gene(s) ... ...

Abstract	BACKGROUND AND AIMS: The two-component high-affinity nitrate (NO3−) transport system (THATS) proteins (NRT2/NAR2) play key roles in the efficient nitrogen (N) uptake and transport under N limitations. We aimed at uncovering the core THATS gene(s) regulating N use efficiency (NUE) in allotetraploid rapeseed (Brassica napus L.). METHODS: Genomic information, high-throughput transcriptome sequencing and gene co-expression network were integrated to identify and characterize the core THATS genes. RESULTS: We identified 17 BnaNRT2 and eight BnaNAR2.1 homologs spanning across the rapeseed genome. Copy number and gene presence/absence variations of BnaNRT2s/BnaNAR2.1 s, undergoing strong purifying selection, occurred. The over-representation of Dof, MYB and WRKY cis-regulatory elements and the enrichment of CpG islands, and protein phosphorylation sites indicated the importance of transcriptional and epigenetic regulation in the BnaNRT2 activities, respectively. qRT-PCR assays and high-throughput RNA-seq revealed that both BnaNRT2s and BnaNAR2.1 s were expressed preferentially in the roots; and they showed significantly differential expression under different N forms or different levels of NO3− supply. A gene co-expression network identified BnaC8.NRT2.1a and BnaC2.NAR2.1 as the core THATS genes. CONCLUSIONS: The core THATS members can serve as elite gene resources for crop NUE improvement. The transcriptomics-assisted gene co-expression network analysis provides novel insights regarding the rapid identification of central members within large gene families of plant species with complex genomes.
Keywords	allotetraploidy ; Brassica napus ; epigenetics ; gene expression regulation ; genes ; genomic islands ; genomics ; high-throughput nucleotide sequencing ; nitrates ; nitrogen ; nutrient use efficiency ; protein phosphorylation ; quantitative polymerase chain reaction ; rapeseed ; regulatory sequences ; reverse transcriptase polymerase chain reaction ; roots ; transcription (genetics) ; transcriptomics ; transporters
Language	English
Dates of publication	2018-06
Size	p. 245-268.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	208908-7
ISSN	1573-5036 ; 0032-079X
ISSN (online)	1573-5036
ISSN	0032-079X
DOI	10.1007/s11104-018-3652-3
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Copper-catalyzed enantioselective Sonogashira-type oxidative cross-coupling of unactivated C(sp 3)−H bonds with alkynes

Zhen-Hua Zhang / Xiao-Yang Dong / Xuan-Yi Du / Qiang-Shuai Gu / Zhong-Liang Li / Xin-Yuan Liu

Nature Communications, Vol 10, Iss 1, Pp 1-

2019 Volume 10

Abstract: Enantioselective oxidative cross-coupling of unactivated C(sp 3)−H bonds and terminal alkynes is challenging. Here, the authors developed a copper/cinchona alkaloid catalyst for the asymmetric Sonogashira-type alkynylation of C(sp 3)-H bonds via radical ... ...

Abstract	Enantioselective oxidative cross-coupling of unactivated C(sp 3)−H bonds and terminal alkynes is challenging. Here, the authors developed a copper/cinchona alkaloid catalyst for the asymmetric Sonogashira-type alkynylation of C(sp 3)-H bonds via radical intermediates.
Keywords	Science ; Q
Language	English
Publishing date	2019-12-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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