Yufan Zhang

Zhejiang University

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i-10 index

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Co-Authors

Mark J. Guiltinan

Pennsylvania State University

Siela N. Maximova

Pennsylvania State University

Zi Shi

Hohai University

Rod A. Wing

King Abdullah University of Science and Technology

Manuel Ruíz

Électricité de France (France)

Melissa Kramer

Cold Spring Harbor Laboratory

Gaëtan Droc

Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Claire Lanaud

Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Jean‐Marc Aury

Commissariat à l'Énergie Atomique et aux Énergies Alternatives

Karina Peres Gramacho

Comissão Executiva do Plano da Lavoura Cacaueira

Cooperative Institutions

Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Centre National de la Recherche Scientifique

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Agropolis International

Genetic Improvement and Adaptation of Mediterranean and Tropical Plants

Sun Yat-sen University

Université de Montpellier

Pennsylvania State University

Institut Agro Montpellier

Chinese Academy of Sciences

Author Statistics

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A rapid and reliable method for analyzing millet and rice organic residues in archaeological samples

Microchemical Journal (2024)

Yufan Zhang Luo Li Shujuan Tian Bingjian Zhang Qiang Li

10.1016/j.microc.2024.112243

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Citations (0)

Deciphering the genome structure and paleohistory of Theobroma cacao

Nature Precedings (2010)

Cristian Chaparro Florent Murat John E. Carlson Valentin Guignon G.Mathias Tahi

Abstract We sequenced and assembled the genome of Theobroma cacao , an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for T. cacao disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions. The T. cacao genome can be considered as a simple living relic of higher plant evolution.

Theobroma

Genome size

Ancestor

Sterculiaceae

10.1038/npre.2010.4908.1

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Citations (3)

Characterization of a stearoyl-acyl carrier protein desaturase gene family from chocolate tree, Theobroma cacao L

Frontiers in Plant Science (2015)

Yufan Zhang Siela N. Maximova Mark J. Guiltinan

In plants, the conversion of stearoyl-ACP to oleoyol-ACP is catalyzed by a plastid-localized soluble stearoyl-acyl carrier protein (ACP) desaturase (SAD). The activity of SAD significantly impacts the ratio of saturated and unsaturated fatty acids, and is thus a major determinant of fatty acid composition. The cacao genome contains eight putative SAD isoforms with high amino acid sequence similarities and functional domain conservation with SAD genes from other species. Sequence variation in known functional domains between different SAD family members suggested that these eight SAD isoforms might have distinct functions in plant development, a hypothesis supported by their diverse expression patterns in various cacao tissues. Notably, TcSAD1 is universally expressed across all the tissues, and its expression pattern in seeds is highly correlated with the dramatic change in fatty acid composition during seed maturation. Interestingly, TcSAD3 and TcSAD4 appear to be exclusively and highly expressed in flowers, functions of which remain unknown. To test the function of TcSAD1 in vivo, transgenic complementation of the Arabidopsis ssi2 mutant was performed, demonstrating that TcSAD1 successfully rescued all AtSSI2 related phenotypes further supporting the functional orthology between these two genes. The identification of the major SAD gene responsible for cocoa butter biosynthesis provides new strategies for screening for novel genotypes with desirable fatty acid compositions, and for use in breeding programs to help pyramid genes for quality and other traits such as disease resistance.

Theobroma

Fatty acid synthesis

Stearoyl-CoA Desaturase

Functional divergence

Protein-fragment complementation assay

10.3389/fpls.2015.00239

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Citations (65)

An integrated transcriptome and physiological analysis of nitrogen use efficiency in rice (Oryza sativa L. ssp. indica) under drought stress

Frontiers in Genetics (2024)

Yu Wang Yufan Zhang Han Qiao Yutong Zheng Xin Hou

Nitrogen is a critical nutrient vital for crop growth. However, our current understanding of nitrogen use efficiency (NUE) under drought remains inadequate. To delve into the molecular mechanisms underlying NUE under drought, a transcriptome and physiological co-expression analysis was performed in rice, which is particularly sensitive to drought. We conducted a pot experiment using rice grown under normal irrigation, mild drought stress, and severe drought stress. Compared to the normal treatment, drought stress led to a significant reduction in NUE across growth stages, with decreases ranging from 2.18% to 31.67%. Totals of 4,424 and 2,452 genes were identified as NUE-related DEGs that showed differential expressions (DEGs) and significantly correlated with NUE (NUE-related) under drought in the vegetative and reproductive stages, respectively. Interestingly, five genes involved in nitrogen metabolism were found in the overlapped genes of these two sets. Furthermore, the two sets of NUE-related DEGs were enriched in glyoxylate and dicarboxylate metabolism, as well as carbon fixation in photosynthetic organisms. Several genes in these two pathways were identified as hub genes in the two sets of NUE-related DEGs. This study offers new insights into the molecular mechanism of rice NUE under drought in agricultural practices and provides potential genes for breeding drought-resistant crops with high NUE.

Drought stress

Drought Tolerance

Nitrogen Cycle

10.3389/fgene.2024.1483113

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Citations (0)

Evaluation of Net-free Erosion Control Blankets

Rabin Bhattarai Yufan Zhang Owen Yao

Erosion control blankets (ECBs) protect soil from being detached and transported by raindrops and subsequential overland runoff while assisting in vegetation growth. ECBs have several characteristics, for example, thickness, mass per unit area, tensile strength, elongation, water absorption, etc. However, the impact of these characteristics on the performance in mitigating erosion has yet to be well understood. To better understand the interactions of ECB properties with the detachment and transport of sediment, field tests were conducted at the Erosion Control Research and Training Center at the University of Illinois Urbana-Champaign. Various ECBs, including net-free ECBs and bionet ECBs, were tested on a 3H:1V hillslope under a 30-minute simulated rainfall event (2 in./hr). The soil used on the testing plot was silty clay loam. To investigate ECB effectiveness, total runoff volume, runoff start/end time, peak runoff rate, and sediment yield were monitored during each test. The results showed that water absorption played a big role in enhancing the performance of ECBs. The materials absorbed a large amount of water at the beginning and then acted as a wet film to cover the hillslope, reducing soil erosion by the overland flow when the soil was saturated. This wet film continued to reduce soil detachment, although it probably did not help with runoff reduction after saturation. Among the blankets tested, Profile F4 Netless was the most degradable and lightest one. North American Green DS75 had the most cost efficiency with $0.4 /sq. yd. There was no big difference in the installation method.

Erosion Control

WEPP

10.36501/0197-9191/23-026

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Citations (0)

Deciphering the genome structure and paleohistory of Theobroma cacao

Nature Precedings (2010)

Mark J. Guiltinan Cristian Chaparro Florent Murat John R. Carlson Valentin Guignon

We sequenced and assembled the genome of Theobroma cacao, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for T. cacao disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions. The T. cacao genome can be considered as a simple living relic of higher plant evolution.

Theobroma

Genome size

Sterculiaceae

Ancestor

10.1038/npre.2010.4908

Cite

Citations (0)

Functional Genomics Of Theobroma Cacao Fatty Acid Biosynthesis:convergence Of Fatty Acid Desaturation, Embryo Development, And Defense Signaling Responses

Yufan Zhang

Theobroma

Functional Genomics

Source