The phoma-like dilemma
Hou, L.W. ; Groenewald, J.Z. ; Pfenning, L.H. ; Yarden, O. ; Crous, P.W. ; Cai, L. - \ 2020
Studies in Mycology 96 (2020). - ISSN 0166-0616 - p. 309 - 396.
Al. anatii L.W. Hou & O. Yarden - Allophoma alba L.W. Hou, Pfenning, L. Cai & Crous - Amphisphaeria vincetoxici De Not. - As. koolunga (J.A. Davidson et al.) L.W. Hou, L. Cai & Crous - Ascochyta astragalina (Rehm ex Sacc.) L.W. Hou, L. Cai & Crous - Ascochyta ferulae Pat. - Ascochyta nobilis Kabát & Bubák - Ascochyta pilosella L.W. Hou, L. Cai & Crous - Calophoma parvula L.W. Hou, L. Cai & Crous - Calophoma vincetoxici (De Not.) L.W. Hou, L. Cai & Crous - Chaetasbolisia argentina L.W. Hou, L. Cai & Crous - Chaetasbolisia eupatorii (Died.) L.W. Hou, L. Cai & Crous - Did. guttulata L.W. Hou, L. Cai & Crous - Did. indica L.W. Hou, L. Cai & Crous - Did. mitis L.W. Hou, L. Cai & Crous - Did. prolaticolla L.W. Hou, L. Cai & Crous - Did. prosopidis (Crous & A.R. Wood) L.W. Hou, L. Cai & Crous - Did. subglobispora L.W. Hou, L. Cai & Crous - Did. subrosea L.W. Hou, L. Cai & Crous - Did. variabilis L.W. Hou, L. Cai & Crous - Didymella aloeicola L.W. Hou, L. Cai & Crous - Didymella combreti (Crous) L.W. Hou, L. Cai & Crous - Dimorphoma L.W. Hou, L. Cai & Crous - Dimorphoma saxea (Aveskamp et al.) L.W. Hou, L. Cai & Crous - Ectodidymella L.W. Hou, L. Cai & Crous - Ectodidymella nigrificans (P. Karst.) L.W. Hou, L. Cai & Crous - Ectophoma insulana (Mont.) L.W. Hou, L. Cai & Crous - Ep. dickmanii L.W. Hou & O. Yarden - Ep. longiostiolatum L.W. Hou, L. Cai & Crous - Ep. multiceps L.W. Hou, L. Cai & Crous - Ep. oryzae Ito & Iwadare - Ep. polychromum L.W. Hou, L. Cai & Crous - Ep. purpurascens Ehrenb. - Ep. variabile L.W. Hou, L. Cai & Crous - Epicoccum brahmansense L.W. Hou, L. Cai & Crous - Epicoccum mezzettii Goid. - Epicoccum oryzae S. Ito & Iwadare - Epicoccum tobaicum (Szilv.) L.W. Hou, L. Cai & Crous - Heterophoma verbasci-densiflori L.W. Hou, L. Cai & Crous - Le. sisyrinchiicola L.W. Hou, L. Cai & Crous - Leptosphaerulina obtusispora L.W. Hou, L. Cai & Crous - Lo. vitalbae (Briard & Har.) L.W. Hou, L. Cai & Crous - Longididymella clematidis (Woudenb. et al.) L.W. Hou, L. Cai & Crous - Longididymella L.W. Hou, L. Cai & Crous - Ma. terrestris L.W. Hou, L. Cai & Crous - Macroascochyta grandis L.W. Hou, L. Cai & Crous - Macroascochyta L.W. Hou, L. Cai & Crous - Macroventuria angustispora L.W. Hou, L. Cai & Crous - Mi. taxicola L.W. Hou, L. Cai & Crous - Mi. viridis L.W. Hou, L. Cai & Crous - Microsphaeropsis fusca L.W. Hou, L. Cai & Crous - Multi-locus phylogeny - Neoa. humicola L.W. Hou, L. Cai & Crous - Neoa. longispora L.W. Hou, L. Cai & Crous - Neoa. mortariensis L.W. Hou, L. Cai & Crous - Neoascochyta fusiformis L.W. Hou, L. Cai & Crous - Neodidymelliopsis tiliae L.W. Hou, L. Cai & Crous - New taxa - No. eucalyptigena (Crous) L.W. Hou, L. Cai & Crous - No. prosopidis (Crous & A.R. Wood) L.W. Hou, L. Cai & Crous - Nothophoma acaciae (Crous) L.W. Hou, L. Cai & Crous - Nothophoma infuscata L.W. Hou, L. Cai & Crous - Nothophoma nullicana L.W. Hou, L. Cai & Crous - Paramicrosphaeropsis ellipsoidea L.W. Hou, L. Cai & Crous - Paramicrosphaeropsis L.W. Hou, L. Cai & Crous - Phoma - Phoma eupatorii Died - Phoma eupatorii Died. - Phoma laurina Thüm., Phoma nemophilae Neerg. - Phomatodes pilosa L.W. Hou, L. Cai & Crous - Phyllosticta acetosellae A.L. Sm. & Ramsb. - Phyllosticta arachidis-hypogaeae V.G. Rao - Phyllosticta insulana Mont - Phyllosticta verbascicola Ellis & Kellerm. - Pleosphaerulina briosiana Pollacci - Pseudopeyronellaea eucalypti (Crous & M.J. Wingf.) L.W. Hou, L. Cai & Crous - Pseudopeyronellaea L.W. Hou, L. Cai & Crous - R. humicola L.W. Hou, L. Cai & Crous - Remotididymella brunnea L.W. Hou, L. Cai & Crous - Remotididymella capsici (Bond.-Mont.) L.W. Hou, L. Cai & Crous - rpb2 - Sclerotiophoma L.W. Hou, L. Cai & Crous - Sclerotiophoma versabilis (Boerema et al.) L.W. Hou, L. Cai & Crous - St. sambucella L.W. Hou, L. Cai & Crous - Stagonosporopsis cucumeris L.W. Hou, L. Cai & Crous - Stagonosporopsis nemophilae (Neerg). L.W. Hou, L. Cai & Crous - Taxonomy - Toruloidea tobaica Szilv - Va. laurina (Thüm.) L.W. Hou, L. Cai & Crous - Vacuiphoma ferulae (Pat.) L.W. Hou, L. Cai & Crous - Xenodidymella glycyrrhizicola L.W. Hou, L. Cai & Crous
Species of Didymellaceae have a cosmopolitan distribution and are geographically widespread, occurring in diverse ecosystems. The family includes several important plant pathogenic fungi associated with fruit, leaf, stem and root diseases on a wide variety of hosts, as well as endophytic, saprobic and clinically relevant species. The Didymellaceae was recently revised based on morphological and phylogenetic analyses of ex-type strains subjected to DNA sequencing of partial gene data of the LSU, ITS, rpb2 and tub2 loci. Several poly- and paraphyletic genera, including Ascochyta, Didymella and Phoma were redefined, along with the introduction of new genera. In the present study, a global collection of 1 124 Didymellaceae strains from 92 countries, 121 plant families and 55 other substrates, including air, coral, human tissues, house dust, fungi, insects, soil, and water were examined via multi-locus phylogenetic analyses and detailed morphological comparisons, representing the broadest sampling of Didymellaceae to date. Among these, 97 isolates representing seven new genera, 40 new species and 21 new combinations were newly introduced in Didymellaceae. In addition, six epitypes and six neotypes were designated to stabilise the taxonomy and use of older names. A robust, multi-locus reference phylogenetic tree of Didymellaceae was generated. In addition, rpb2 was revealed as the most effective locus for the identification of Didymellaceae at species level, and is proposed as a secondary DNA marker for the family.
Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach
Rawandoozi, Zena J. ; Hartmann, Timothy P. ; Carpenedo, Silvia ; Gasic, Ksenija ; Silva Linge, Cassia da; Cai, Lichun ; Weg, Eric van de; Byrne, David H. - \ 2020
BMC Genomics 21 (2020)1. - ISSN 1471-2164
Blush - FlexQTL - Haplotype - Peach QTL - Pedigree-based analysis - Soluble solids concentration - Titratable acidity
Background: Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves resources and time. Results: Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. One major QTL for fruit blush was found on linkage group 4 (LG4) at 40-46 cM that explained from 20 to 32% of the total phenotypic variance and showed three QTL alleles of different effects. For soluble solids concentration (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39% of the phenotypic variance. A major QTL for titratable acidity (TA) co-localized with the major locus for low-acid fruit (D-locus). It was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles. Conclusions: A multi-family-based QTL discovery approach enhanced the ability to discover a new TA QTL at the distal end of LG5 and validated other QTLs which were reported in previous studies. Haplotype characterization of the mapped QTLs distinguishes this work from the previous QTL studies. Identified predictive SNPs and their original sources will facilitate the selection of parents and/or seedlings that have desired QTL alleles. Our findings will help peach breeders develop new predictive, DNA-based molecular marker tests for routine use in marker-assisted breeding.
Protein A-mesoporous silica composites for chromatographic purification of immunoglobulin G
Huang, Si ; Cheng, Si Yuan ; Zhang, Shu Yuan ; Yan, Yi Lun ; Cai, Song Liang ; Li, Xin Le ; Zheng, Sheng Run ; Fan, Jun ; Zhang, Wei Guang - \ 2020
New Journal of Chemistry 44 (2020)19. - ISSN 1144-0546 - p. 7884 - 7890.
The development of a robust and efficient stationary phase for chromatographic biopharmaceutical purification is of prime importance but remains challenging. Herein, we have developed a series of protein A-mesoporous silica composites for the first time by covalently coupling protein A with the tagged carbonyl imidazole moieties in the column, which constitutes a facile and efficient route for the preparation of protein A immunoaffinity materials. The resultant composites are employed as the stationary phase for chromatographic purification of immunoglobulin G (IgG). The effect of silica's pore size and coupled protein A on the antibody purification is systematically investigated. When the pore size of silica increased from 100 to 1000 Å, the amount of coupled protein A decreased, and the surface coverage on the silica significantly improved, accompanied by an increase in the amount of purified rabbit IgG. With an increasing coupled protein A, the surface coverage increased at first and decreased subsequently, which shows a similar trend to the amount of purified IgG and specific activity. When practically implemented for purifying several immunoglobulins that are central for commercial ELISA Kits, the protein A-mesoporous silica composite exhibited superior performance compared to the GE-Mabselcetxtra rProtein A column, particularly in the purification of immunoglobulin M (IgM), which cannot be realized by the GE-Mabselcetxtra rProtein A column. This study sheds new light on the rational development of protein-affinity chromatography for biopharmaceutical purification.
Identification of Novel Loci and New Risk Variant in Known Loci for Colorectal Cancer Risk in East Asians
Lu, Yingchang ; Kweon, Sun Seog ; Cai, Qiuyin ; Tanikawa, Chizu ; Shu, Xiao Ou ; Jia, Wei Hua ; Xiang, Yong Bing ; Huyghe, Jeroen R. ; Harrison, Tabitha A. ; Kim, Jeongseon ; Shin, Aesun ; Kim, Dong Hyun ; Matsuo, Keitaro ; Jee, Sun Ha ; Guo, Xingyi ; Wen, Wanqing ; Shi, Jiajun ; Li, Bingshan ; Wang, Nan ; Shin, Min Ho ; Li, Hong Lan ; Ren, Zefang ; Oh, Jae Hwan ; Oze, Isao ; Ahn, Yoon Ok ; Jung, Keum Ji ; Gao, Jing ; Gao, Yu Tang ; Pan, Zhi Zhong ; Kamatani, Yoichiro ; Chan, Andrew T. ; Gsur, Andrea ; Hampe, Jochen ; Marchand, Loic Le; Li, Li ; Lindblom, Annika ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharoah, Paul D.P. ; Duijnhoven, Franzel J.B. van; Guelpen, Bethany Van; Vodicka, Pavel ; Weinstein, Stephanie J. ; Wolk, Alicja ; Wu, Anna H. ; Hsu, Li ; Zeng, Yi Xin ; Long, Jirong ; Peters, Ulrike ; Matsuda, Koichi ; Zheng, Wei - \ 2020
Cancer Epidemiology Biomarkers & Prevention 29 (2020)2. - ISSN 1055-9965 - p. 477 - 486.
BACKGROUND: Risk variants identified so far for colorectal cancer explain only a small proportion of familial risk of this cancer, particularly in Asians. METHODS: We performed a genome-wide association study (GWAS) of colorectal cancer in East Asians, including 23,572 colorectal cancer cases and 48,700 controls. To identify novel risk loci, we selected 60 promising risk variants for replication using data from 58,131 colorectal cancer cases and 67,347 controls of European descent. To identify additional risk variants in known colorectal cancer loci, we performed conditional analyses in East Asians. RESULTS: An indel variant, rs67052019 at 1p13.3, was found to be associated with colorectal cancer risk at P = 3.9 × 10-8 in Asians (OR per allele deletion = 1.13, 95% confidence interval = 1.08-1.18). This association was replicated in European descendants using a variant (rs2938616) in complete linkage disequilibrium with rs67052019 (P = 7.7 × 10-3). Of the remaining 59 variants, 12 showed an association at P < 0.05 in the European-ancestry study, including rs11108175 and rs9634162 at P < 5 × 10-8 and two variants with an association near the genome-wide significance level (rs60911071, P = 5.8 × 10-8; rs62558833, P = 7.5 × 10-8) in the combined analyses of Asian- and European-ancestry data. In addition, using data from East Asians, we identified 13 new risk variants at 11 loci reported from previous GWAS. CONCLUSIONS: In this large GWAS, we identified three novel risk loci and two highly suggestive loci for colorectal cancer risk and provided evidence for potential roles of multiple genes and pathways in the etiology of colorectal cancer. In addition, we showed that additional risk variants exist in many colorectal cancer risk loci identified previously. IMPACT: Our study provides novel data to improve the understanding of the genetic basis for colorectal cancer risk.
Transdisciplinary innovation in irrigated smallholder agriculture in africa
Froebrich, Jochen ; Ludi, Eva ; Bouarfa, Sami ; Rollin, Dominique ; Jovanovic, Nebo ; Roble, Maria ; Ajmi, Tarek ; Albasha, Rami ; Bah, Sékou ; Bahri, Haithem ; Barberá, Gonzalo ; Beek, Christy van; Cheviron, Bruno ; Chishala, Benson ; Clercq, Willem de; Coulibaly, Yacouba ; Dicko, Mohammed ; Diawara, Bandiougou ; Dolinska, Aleksandra ; Ducrot, Raphaëlle ; Erkossa, Teklu ; Famba, Sebastiao ; Fissahaye, Degol ; Miguel Garcia, Angel De; Habtu, Solomon ; Hanafi, Salia ; Harper, Julia ; Heesmans, Hanneke ; Jamin, Jean Yves ; van't Klooster, Kees ; Mason, Nathaniel ; Mailhol, Jean Claude ; Marlet, Serge ; Mekki, Insaf ; Musvoto, Constansia ; Mosello, Beatrice ; Mweetwa, Alice ; Oates, Naomi ; Phiri, Elijah ; Pradeleix, Ludivine ; Querner, Erik ; Rozanov, Andrei ; Ker Rault, Philippe ; Rougier, Jean Emmanuel ; Shepande, Chizumba ; Sánchez Reparaz, Maite ; Tangara, Bréhima ; Vente, Joris De; Witt, Marlene de; Xueliang, Cai ; Zairi, Abdelaziz - \ 2020
Irrigation and Drainage 69 (2020)S1. - ISSN 1531-0353 - p. 6 - 22.
participatory innovation - smallholder farming, irrigation - transdisciplinary approach
Boosting the productivity of smallholder farming systems continues to be a major need in Africa. Challenges relating to how to improve irrigation are multi-factor and multisectoral, and they involve a broad range of actors who must interact to reach decisions collectively. We provide a systematic reflection on findings from the research project EAU4Food, which adopted a transdisciplinary approach to irrigation for food security research in five case studies in Ethiopia, Mali, Mozambique, South Africa and Tunisia. The EAU4Food experiences emphasize that actual innovation at irrigated smallholder farm level remains limited without sufficient improvement of the enabling environment and taking note of the wider political economy environment. Most project partners felt at the end of the project that the transdisciplinary approach has indeed enriched the research process by providing different and multiple insights from actors outside the academic field. Local capacity to facilitate transdisciplinary research and engagement with practitioners was developed and could support the continuation and scaling up of the approach. Future projects may benefit from a longer time frame to allow for deeper exchange of lessons learned among different stakeholders and a dedicated effort to analyse possible improvements of the enabling environment from the beginning of the research process.
Modelling root water uptake under deficit irrigation and rewetting in Northwest China
Wang, Xiaowen ; Cai, Huanjie ; Zheng, Zhen ; Yu, Lianyu ; Wang, Zishen ; Li, Liang - \ 2020
Agronomy Journal 112 (2020)1. - ISSN 0002-1962 - p. 158 - 174.
The spatial and temporal distribution of root water uptake (RWU) under deficit irrigation are critical factors for crop growth. The SWAP (soil–water–atmosphere–plant) model was applied to analyze the pattern of RWU for winter wheat (Triticum aestivum L.) under three irrigation levels: no water deficit (100% evapotranspiration [ET]), moderate water deficit (80% ET) and severe water deficit (60% ET). The 2–yr experiments indicated that SWAP was highly accurate (mean relative error [MRE] <21.7%, root mean square error [RMSE] <0.07 cm3 cm−3) in simulating the soil water content (SWC). Root water uptake was significantly (P < 0.01) different in the 0- to 60-cm soil layer. The 0- to 60-cm soil layer was the main source of RWU, and the average value accounted for 89.4% of the total root zone. Water stress had the greatest adverse effect on heading to grain filling, reducing RWU by 0.0026 cm3 cm−3 d−1. The critical SWC was 67.9% of the field capacity, when the RWU dropped to 95% of the control treatment. After rewetting, compensation and hysteresis effects on RWU were observed. The ranking of RWU recovery ability after rewetting was: emergence to jointing > jointing to heading > grain filling to maturity > heading to grain filling. Recovery time of RWU was 2 to 11 d and gradually increased with growth stage. The simplified RWU model established using path analysis and regression performed well (R2 = 0.836; P < 0.01) for RWU. This provided a more convenient way to accurately estimate RWU with fewer variables.
The fertilization effect of global dimming on crop yields is not attributed to an improved light interception
Shao, Liping ; Li, Gang ; Zhao, Qiannan ; Li, Yabing ; Sun, Yutong ; Wang, Weinan ; Cai, Chuang ; Chen, Weiping ; Liu, Ronghua ; Luo, Weihong ; Yin, Xinyou ; Lee, Xuhui - \ 2020
Global Change Biology 26 (2020)3. - ISSN 1354-1013 - p. 1697 - 1713.
acclimation - diffuse radiation - fertilization effect - global dimming - radiation use efficiency - rice - wheat - yield
Global dimming, a decadal decrease in incident global radiation, is often accompanied with an increase in the diffuse radiation fraction, and, therefore, the impact of global dimming on crop production is hard to predict. A popular approach to quantify this impact is the statistical analysis of historical climate and crop data, or use of dynamic crop simulation modelling approach. Here, we show that statistical analysis of historical data did not provide plausible values for the effect of diffuse radiation versus direct radiation on rice or wheat yield. In contrast, our field experimental study of 3 years demonstrated a fertilization effect of increased diffuse radiation fraction, which partly offset yield losses caused by decreased global radiation, in both crops. The fertilization effect was not attributed to any improved canopy light interception but mainly to the increased radiation use efficiency (RUE). The increased RUE was explained not only by the saturating shape of photosynthetic light response curves but also by plant acclimation to dimming that gradually increased leaf nitrogen concentration. Crop harvest index slightly decreased under dimming, thereby discounting the fertilization effect on crop yields. These results challenge existing modelling paradigms, which assume that the fertilization effect on crop yields is mainly attributed to an improved light interception. Further studies on the physiological mechanism of plant acclimation are required to better quantify the global dimming impact on agroecosystem productivity under future climate change.
The acclimation of leaf photosynthesis of wheat and rice to seasonal temperature changes in T-FACE environments
Cai, Chuang ; Li, Gang ; Di, Lijun ; Ding, Yunjie ; Fu, Lin ; Guo, Xuanhe ; Struik, Paul C. ; Pan, Genxing ; Li, Haozheng ; Chen, Weiping ; Luo, Weihong ; Yin, Xinyou - \ 2020
Global Change Biology 26 (2020)2. - ISSN 1354-1013 - p. 539 - 556.
climate change - free-air CO enrichment - growth temperature - leaf nitrogen content - Oryza sativa L. - photosynthesis model - stomatal conductance - Triticum aestivum L.
Crops show considerable capacity to adjust their photosynthetic characteristics to seasonal changes in temperature. However, how photosynthesis acclimates to changes in seasonal temperature under future climate conditions has not been revealed. We measured leaf photosynthesis (An) of wheat (Triticum aestivum L.) and rice (Oryza sativa L.) grown under four combinations of two levels of CO2 (ambient and enriched up to 500 µmol/mol) and two levels of canopy temperature (ambient and increased by 1.5–2.0°C) in temperature by free-air CO2 enrichment (T-FACE) systems. Parameters of a biochemical C3-photosynthesis model and of a stomatal conductance (gs) model were estimated for the four conditions and for several crop stages. Some biochemical parameters related to electron transport and most gs parameters showed acclimation to seasonal growth temperature in both crops. The acclimation response did not differ much between wheat and rice, nor among the four treatments of the T-FACE systems, when the difference in the seasonal growth temperature was accounted for. The relationships between biochemical parameters and leaf nitrogen content were consistent across leaf ranks, developmental stages, and treatment conditions. The acclimation had a strong impact on gs model parameters: when parameter values of a particular stage were used, the model failed to correctly estimate gs values of other stages. Further analysis using the coupled gs–biochemical photosynthesis model showed that ignoring the acclimation effect did not result in critical errors in estimating leaf photosynthesis under future climate, as long as parameter values were measured or derived from data obtained before flowering.
Integrating Participatory Data Acquisition and Modelling of Irrigation Strategies to Enhance Water Productivity in a Small-Scale Irrigation Scheme in Tigray, Ethiopia
Habtu, Solomon ; Erkossa, Teklu ; Froebrich, Jochen ; Tquabo, Filmon ; Fissehaye, Degol ; Kidanemariam, Tesfay ; Xueliang, Cai - \ 2020
Irrigation and Drainage 69 (2020)S1. - ISSN 1531-0353 - p. 23 - 37.
Application d'eau sur le terrain - AquaCrop model - Bilan hydrique - Crop yield - Field water application - Modèle AquaCrop - Modélisation participative - Participatory modelling - Rendement des cultures - Water balance
Application of participatory modelling to water-saving strategies in smallholder farming is rare. Farmer-preferred and efficient strategies were identified through participatory modelling. The farmers' basin irrigation and scheduling (I), farmers' scheduling with furrow strategy (II), farmers' scheduling with alternate furrow strategy (III) and scheduling at 55% maximum allowable depletion (MAD) (IV) were evaluated for maize (Zea mais) and barley (Hordeum vulgare) using the FAO AquaCrop model. The results showed that I resulted in over-irrigation for maize and under-irrigation for barley, while IV resulted in maximum yield (8.6 t ha-1 for maize and 2 t ha-1 for barley) with maximum (1.8 kg m-3) and minimum (0.8 kg m-3) water productivity of maize under IV and I, respectively. A shift from I to IV (most preferred strategy by farmers) can save 8440 mm of water, which can possibly bring back 18.5 ha of land into irrigation. It is essential to interact with farmers on a basis of mutual comprehension to increase their trust and to lay a base for discussion, awareness raising and decision making. The transdisciplinary approach, Community of Practice (CoP) and Learning Practice Alliance (LPA) were appropriate platforms for participation. The increased crop yield and water productivity may contribute to ecological and economical sustainability and social equity.
Changing the game: Resolving systematic issues in key Fusarium species complexes
Lombard, L. ; Sandoval-Denis, M. ; Cai, L. ; Crous, P.W. - \ 2019
Persoonia 43 (2019). - ISSN 0031-5850 - p. i - ii.
Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage (Brassica rapa)
Sun, Xiao Xue ; Basnet, Ram Kumar ; Yan, Zhichun ; Bucher, Johan ; Cai, Chengcheng ; Zhao, Jianjun ; Bonnema, Guusje - \ 2019
Horticulture Research 6 (2019)1. - ISSN 2052-7276
Chinese cabbage plants go through seedling and rosette stages before forming their leafy head. Chinese cabbage plants resemble pak-choi plants at their seedling stage, but in their rosette stage the leaves of Chinese cabbage differentiate, as they increase in size with shorter petioles. In order to understand the molecular pathways that play a role in leafy head formation, transcript abundance of young emerging leaves was profiled during development of two Chinese cabbage genotypes and a single pak-choi genotype. The two Chinese cabbages differed in many aspects, among others earliness, leaf size and shape, leaf numbers, and leafy head shape. Genome-wide transcriptome analysis clearly separated the seedling stages of all three genotypes together with the later stages from pak-choi, from the later developmental stages of both Chinese cabbages (rosette, folding, and heading). Weighted correlation network analysis and hierarchical clustering using Euclidean distances resulted in gene clusters with transcript abundance patterns distinguishing the two Chinese cabbages from pak-choi. Three clusters included genes with transcript abundance affected by both genotype and developmental stage, whereas two clusters showed only genotype effects. This included a genotype by developmental stage cluster highly enriched with the MapMan category photosynthesis, with high expression during rosette and folding in Chinese cabbages and low expression in the heading inner leaves that are not exposed to light. The other clusters contained many genes in the MapMan categories Cell, showing again differences between pak-choi and both Chinese cabbages. We discuss how this relates to the differences in leaf blade growth between Chinese cabbage and pak-choi, especially at the rosette stage. Overall, comparison of the transcriptome between leaves of two very different Chinese cabbages with pak-choi during plant development allowed the identification of specific gene categories associated with leafy head formation.
Hydrogen bond guidance and aromatic stacking drive liquid-liquid phase separation of intrinsically disordered histidine-rich peptides
Gabryelczyk, Bartosz ; Cai, Hao ; Shi, Xiangyan ; Sun, Yue ; Swinkels, Piet J.M. ; Salentinig, Stefan ; Pervushin, Konstantin ; Miserez, Ali - \ 2019
Nature Communications 10 (2019)1. - ISSN 2041-1723
Liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) is involved in both intracellular membraneless organelles and extracellular tissues. Despite growing understanding of LLPS, molecular-level mechanisms behind this process are still not fully established. Here, we use histidine-rich squid beak proteins (HBPs) as model IDPs to shed light on molecular interactions governing LLPS. We show that LLPS of HBPs is mediated though specific modular repeats. The morphology of separated phases (liquid-like versus hydrogels) correlates with the repeats’ hydrophobicity. Solution-state NMR indicates that LLPS is a multistep process initiated by deprotonation of histidine residues, followed by transient hydrogen bonding with tyrosine, and eventually by hydrophobic interactions. The microdroplets are stabilized by aromatic clustering of tyrosine residues exhibiting restricted molecular mobility in the nano-to-microsecond timescale according to solid-state NMR experiments. Our findings provide guidelines to rationally design pH-responsive peptides with LLPS ability for various applications, including bioinspired protocells and smart drug-delivery systems.
Joint toxicity of binary complexes of cartap, spirotetramat, copper, and cadmium to Vibrio fischeri
Yin, Hong Yang ; Zhao, Yuan ; Zheng, Yi ; Bao, Cong ; Huang, Xin Xin ; Ding, Ying Jie ; Cai, Qiang - \ 2019
Journal of Agro-Environment Science 38 (2019)9. - ISSN 1672-2043 - p. 2080 - 2085.
Acute toxicity - Heavy metals - Joint toxicity evaluation - Pesticide - Vibrio fischeri
In view of the widespread use of cartap, spirotetramat, and common heavy metal pollutants, such as copper and cadmium in agri? cultural activities, the joint toxicity of their complexes on Vibrio fischeri was studied. The EC50(median effective concentration)was calcu? lated with the acute toxic effects of binary complex contamination on Vibrio fischeri employing different exposure times. The Mixtures Toxic? ity Index method was employed to evaluate the joint toxicity. The acute toxicity experiments showed that the EC50 of copper, cadmium, car? tap, and spirotetramat on Vibrio fischeri at 15 mins was 0.53, 0.74, 79.06 mg·L-1, and 116.67 mg·L-1, respectively. The joint toxicity of car? tap and heavy metals on Vibrio fischeri was mainly additive. When the spirotetramat accounted for a low proportion in the binary mixtures, the joint toxicity was partially additive. The presence of cartap and spirotetramat may slow down the rate of metal ions entering the cell. Therefore, the study of exposure time for joint toxicity on Vibrio fischeri should be extended to 45 mins.
Narrow-wide-row planting pattern increases the radiation use efficiency and seed yield of intercrop species in relay-intercropping system
Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Cai, Gao Ren ; Khalid, Muhammad Hayder Bin ; Iqbal, Nasir ; Hassan, Muhammad Jawad ; Meraj, Tehseen Ahmad ; Naeem, Muhammd ; Khan, Imran ; Ur Rehman, Sana ; Ansar, Muhammad ; Ahmed, Mukhtar ; Yang, Feng ; Yang, Wenyu - \ 2019
Food and Energy Security 8 (2019)3. - ISSN 2048-3694
competition - intercropping - land equivalent ratio - radiation use efficiency
Planting arrangements affect radiation use efficiency (RUE) and competitiveness of intercrop species in intercropping systems. Here, we reveal that narrow-wide-row planting arrangement in maize-soybean relay-intercropping system increases the dry matter and competitiveness of soybean, increased the RUE of maize and soybean, and compensates the yield loss of maize by substantially increasing the yield of soybean. In this field study, maize was planted with soybean in different planting arrangements (P1, 20:180, P2, 40:160; P3, 60:140, and P4, 80:120) of relay intercropping, all the relay-intercropping treatments were compared with sole crops of maize (SM) and soybean (SS). Results showed that P1 improved the total RUE 3.26 g/MJ (maize RUE + soybean RUE) of maize and soybean in relay-intercropping system. Compared to P4, treatment P1 increased the soybean competition ratio (CR) values (by 55%) but reduced the maize CR values (by 29%), which in turn significantly improved the yield of soybean by maintaining the maize yield. Generally, in P1, soybean produced 82% of SS yield, and maize produced 88% of SM yield, and it achieved the land equivalent ratio of 1.7. These results suggest that by maintaining the appropriate planting distances between maize and soybean we can improve the competitiveness and yield of intercrop species in relay-intercropping system.
Linking Probabilistic Exposure and Pharmacokinetic Modeling to Assess the Cumulative Risk from the Bisphenols BPA, BPS, BPF, and BPAF for Europeans
Karrer, Cecile ; Boer, Waldo De; Delmaar, Christiaan ; Cai, Yaping ; Crépet, Amélie ; Hungerbühler, Konrad ; Goetz, Natalie Von - \ 2019
Environmental Science and Technology 53 (2019)15. - ISSN 0013-936X - p. 9181 - 9191.
The bisphenols S, F, and AF (BPS, BPF, and BPAF) are used to replace the endocrine disrupting chemical bisphenol A (BPA) while exerting estrogenic effects of comparable potency. We assessed the cumulative risk for the aforementioned BPs in Europe and compared the risk before and after the year 2011, which was when the first BPA restrictions became effective. For this, we probabilistically modeled external exposures from food, personal care products (PCPs), thermal paper, and dust (using the tools MCRA and PACEM for exposures from food and PCPs, respectively). We calculated internal concentrations of unconjugated BPs with substance-specific PBPK models and cumulated these concentrations normalized by estrogenic potency. The resulting mean internal cumulative exposures to unconjugated BPs were 3.8 and 2.1 ng/kg bw/day before and after restrictions, respectively. This decline was mainly caused by the replacement of BPA by BPS in thermal paper and the lower dermal uptake of BPS compared to BPA. However, the decline was not significant: the selected uncertainty intervals overlapped (P2.5-P97.5 uncertainty intervals of 2.7-4.9 and 1.3-6.3 ng/kg bw/day before and after restrictions, respectively). The upper uncertainty bounds for cumulative exposure were higher after restrictions, which reflects the larger uncertainty around exposures to substitutes compared to BPA.
High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow
Vanderzande, Stijn ; Howard, Nicholas P. ; Cai, Lichun ; Silva Linge, Cassia Da; Antanaviciute, Laima ; Bink, Marco C.A.M. ; Kruisselbrink, Johannes W. ; Bassil, Nahla ; Gasic, Ksenija ; Iezzoni, Amy ; Weg, Eric Van de; Peace, Cameron - \ 2019
PLoS ONE 14 (2019)6. - ISSN 1932-6203
High-quality genotypic data is a requirement for many genetic analyses. For any crop, errors in genotype calls, phasing of markers, linkage maps, pedigree records, and unnoticed variation in ploidy levels can lead to spurious marker-locus-trait associations and incorrect origin assignment of alleles to individuals. High-throughput genotyping requires automated scoring, as manual inspection of thousands of scored loci is too time-consuming. However, automated SNP scoring can result in errors that should be corrected to ensure recorded genotypic data are accurate and thereby ensure confidence in downstream genetic analyses. To enable quick identification of errors in a large genotypic data set, we have developed a comprehensive workflow. This multiple-step workflow is based on inheritance principles and on removal of markers and individuals that do not follow these principles, as demonstrated here for apple, peach, and sweet cherry. Genotypic data was obtained on pedigreed germplasm using 6-9K SNP arrays for each crop and a subset of well-performing SNPs was created using ASSIsT. Use of correct (and corrected) pedigree records readily identified violations of simple inheritance principles in the genotypic data, streamlined with FlexQTL software. Retained SNPs were grouped into haploblocks to increase the information content of single alleles and reduce computational power needed in downstream genetic analyses. Haploblock borders were defined by recombination locations detected in ancestral generations of cultivars and selections. Another round of inheritance-checking was conducted, for haploblock alleles (i.e., haplotypes). High-quality genotypic data sets were created using this workflow for pedigreed collections representing the U.S. breeding germplasm of apple, peach, and sweet cherry evaluated within the RosBREED project. These data sets contain 3855, 4005, and 1617 SNPs spread over 932, 103, and 196 haploblocks in apple, peach, and sweet cherry, respectively. The highly curated phased SNP and haplotype data sets, as well as the raw iScan data, of germplasm in the apple, peach, and sweet cherry Crop Reference Sets is available through the Genome Database for Rosaceae.
Genera of phytopathogenic fungi: GOPHY 3
Marin-Felix, Y. ; Hernández-Restrepo, M. ; Iturrieta-González, I. ; García, D. ; Gené, J. ; Groenewald, J.Z. ; Cai, L. ; Chen, Q. ; Quaedvlieg, W. ; Schumacher, R.K. ; Taylor, P.W.J. ; Ambers, C. ; Bonthond, G. ; Edwards, J. ; Krueger-Hadfield, S.A. ; Luangsa-ard, J.J. ; Morton, L. ; Moslemi, A. ; Sandoval-Denis, M. ; Tan, Y.P. ; Thangavel, R. ; Vaghefi, N. ; Cheewangkoon, R. ; Crous, P.W. - \ 2019
Studies in Mycology 94 (2019). - ISSN 0166-0616 - p. 1 - 124.
DNA barcodes - Fungal systematics - New taxa
This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names.
Black spot partial resistance in diploid roses : QTL discovery and linkage map creation
Yan, M. ; Byrne, D.H. ; Klein, P.E. ; Weg, W.E. van de; Yang, J. ; Cai, L. - \ 2019
Acta Horticulturae 1232 (2019). - ISSN 0567-7572 - p. 135 - 141.
Consensus map - Genotyping-by-sequencing - Phenotyping - QTL - SNP
Black spot disease (Diplocarpon rosae) is the most important leaf disease of garden roses in warm humid areas. Although partial resistance to black spot has been shown to be moderately heritable, the responsible quantitative trait loci (QTL) remain unidentified. Because of the interspecific nature and high heterozygosity in commercial roses, as well as the relatively small research input compared to row crops, the genomic resources available for rose are limited. To effectively identify markers associated with QTL controlling black spot resistance, abundant markers across the genome and careful phenotyping are required. Fifteen inter-related diploid rose populations with black spot resistant cultivar R. wichuraiana ‘Basye’s Thornless’ in the genetic background were assessed based on the percent of total foliage covered with lesions in June, October and November of 2016 in College Station. Broad sense heritability was estimated at 0.51 which indicates black spot partial resistance is a moderately heritable trait. Genotyping-by-sequencing technology was used to generate SNP markers for linkage map construction. Previous anchor SSR markers were used to designate the linkage group number. The final consensus map used for black spot QTL detection contained 791 SNP covering 430 cM with the biggest gap being 6.6 cM on LG4. One major black spot QTL was discovered on LG3 explaining ~13% of the total phenotypic variance (equaling approximately 26% of the genetic variation) using pedigree-based analysis among all fifteen populations.
Sporocadaceae, a family of coelomycetous fungi with appendage-bearing conidia
Liu, F. ; Bonthond, G. ; Groenewald, J.Z. ; Cai, L. ; Crous, P.W. - \ 2019
Studies in Mycology 92 (2019). - ISSN 0166-0616 - p. 287 - 415.
Multi-locus phylogeny - New taxa - Seimatosporium - Sporocadus - Taxonomy
Species of Sporocadaceae are endophytic, plant pathogenic or saprobic, and associated with a wide range of host plants. Recent molecular studies that have attempted to address familial and generic boundaries of fungi belonging to Sporocadaceae were based on a limited number of samples and DNA loci. The taxonomy of this group of fungi is therefore still not fully resolved. The aim of the present study is to provide a natural classification for the Sporocadaceae based on multi-locus phylogenetic analyses, using LSU, ITS, tef-1α tub2 and rpb2 loci, in combination with morphological data. A total of 30 well-supported monophyletic clades in Sporocadaceae are recognised, representing 23 known and seven new genera. Typifications are proposed for the type species of five genera (Diploceras, Discosia, Monochaetia, Sporocadus and Truncatella) to stabilise the application of these names. Furthermore, Neotruncatella and Dyrithiopsis are synonymised under Hymenopleella, and the generic circumscriptions of Diploceras, Disaeta, Hymenopleella, Monochaetia, Morinia, Pseudopestalotiopsis, Sarcostroma, Seimatosporium, Synnemapestaloides and Truncatella are emended. A total of 51 new species, one nomina nova and 15 combinations are introduced.
Plastic film cover during the fallow season preceding sowing increases yield and water use efficiency of rain-fed spring maize in a semi-arid climate
Zhang, Zhe ; Zhang, Yanqing ; Sun, Zhanxiang ; Zheng, Jiaming ; Liu, Enke ; Feng, Liangshan ; Feng, Chen ; Si, Pengfei ; Bai, Wei ; Cai, Qian ; Yang, Ning ; Werf, Wopke van der; Zhang, Lizhen - \ 2019
Agricultural Water Management 212 (2019). - ISSN 0378-3774 - p. 203 - 210.
Film cover - Soil temperature - Water availability - Yield components
Plastic film mulch increases crop yields in rain-fed agriculture in cool semi-arid climates by warming the soil and reducing evaporative water losses. The semi-arid Khorchin area in Northeast China is an important production area for rain-fed maize. Drought stress occurs frequently, even if plastic film mulch is applied at sowing. We hypothesized that the yield and water capture of maize could be increased by reducing evaporative loss of water by use of plastic film cover during the autumn and winter preceding sowing. In this study, we compared maize growth, water uptake and yield in three film cover treatments: (1) film cover from the autumn before maize sowing until maize harvest (autumn mulching: AM), (2) film cover from maize sowing till harvest (conventional practice) (spring mulching: SM), (3) no film cover (no mulch: NM). Field experiments were conducted in Fuxin city, Khorchin region, Liaoning province, China in 2013/2014 and 2014/2015. Autumn mulching increased grain yield on average by 18% when compared to spring mulching and by 36% when compared to no mulching. The 1000-kernel weight in AM was 7% higher than in SM, and 12% higher than in NM. Soil water content in the root zone before sowing was 35 mm greater in AM than in SM and NM. Water uptake during the growing season was 34 mm greater in AM than in SM and NM. Water use efficiency for grain yield (yield per unit water uptake) in AM was on average 2.5% higher than in conventional mulching (SM) and 27% higher than in NM. Autumn mulching advanced development, with an advance of 5 days in tasseling time as compared to SM and 10 days when compared to NM. These results show that film cover during the fallow period before maize sowing can increase crop yield and water use efficiency, and reduce climate risks in rain-fed agriculture under semi-arid conditions.