Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Belowground soil water response in the afforestation-cropland interface under semi-arid conditions
    Huang, Ze ; Yang, Wen Jin ; Liu, Yu ; Shen, Weibo ; López-Vicente, Manuel ; Wu, Gao Lin - \ 2020
    Catena 193 (2020). - ISSN 0341-8162
    Agroforestry system interface - Semi-arid area - Soil water deficit degree - Soil water storage

    Agroforestry is an effective measure to control soil erosion and maintain or increase productivity in semi-arid areas. However, the belowground soil water responses in the afforestation-cropland interface (ACI) is not well known. This study analyzed the variability of soil water storage (SWS) and deficit in three ACIs taking into account the distance between the forest and cropland. The variations of soil water content up to 4 m depth and at five distances from the interface (−5 m (in forest), 0 m (interface), 1 m, 3 m and 5 m (in cropland)) were estimated in three artificial forests (Salix matsudana, Sophora japonica, and Populus cathayana) and their adjacent croplands (maize). The results showed that soil water at the interfaces was significantly affected by forest. This effect was effective up to 160–170 cm of soil depth, and the ACI of S. matsudana had the greatest impact on the farmland soil water. There was no significant relative soil water deficit between 1 and 3 m length, and the ACI of P. cathayana showed the lowest changes in the lateral direction. The SWS of S. japonica in the ACI was clearly higher than the other two artificial forests (P < 0.05). Our findings indicated that S. japonica was the most suitable forest species for agriculture sustainability in the study area. The tree species and the distance between cropland and forest should be considered during the establishment of agroforestry systems. This study provided insights for water conservation and effective management of ACIs in semi-arid areas.

    Cumulative Burden of Colorectal Cancer–Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
    Archambault, Alexi N. ; Su, Yu Ru ; Jeon, Jihyoun ; Thomas, Minta ; Lin, Yi ; Conti, David V. ; Win, Aung Ko ; Sakoda, Lori C. ; Lansdorp-Vogelaar, Iris ; Peterse, Elisabeth F.P. ; Zauber, Ann G. ; Duggan, David ; Holowatyj, Andreana N. ; Huyghe, Jeroen R. ; Brenner, Hermann ; Cotterchio, Michelle ; Bézieau, Stéphane ; Schmit, Stephanie L. ; Edlund, Christopher K. ; Southey, Melissa C. ; MacInnis, Robert J. ; Campbell, Peter T. ; Chang-Claude, Jenny ; Slattery, Martha L. ; Chan, Andrew T. ; Joshi, Amit D. ; Song, Mingyang ; Cao, Yin ; Woods, Michael O. ; White, Emily ; Weinstein, Stephanie J. ; Ulrich, Cornelia M. ; Hoffmeister, Michael ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Hampe, Jochen ; Li, Christopher I. ; Schafmayer, Clemens ; Offit, Kenneth ; Pharoah, Paul D. ; Moreno, Victor ; Lindblom, Annika ; Wolk, Alicja ; Wu, Anna H. ; Li, Li ; Gunter, Marc J. ; Gsur, Andrea ; Keku, Temitope O. ; Pearlman, Rachel ; Bishop, D.T. ; Castellví-Bel, Sergi ; Moreira, Leticia ; Vodicka, Pavel ; Kampman, Ellen ; Giles, Graham G. ; Albanes, Demetrius ; Baron, John A. ; Berndt, Sonja I. ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Trichopoulou, Antonia ; Severi, Gianluca ; Chirlaque, María Dolores ; Sánchez, Maria José ; Palli, Domenico ; Kühn, Tilman ; Murphy, Neil ; Cross, Amanda J. ; Burnett-Hartman, Andrea N. ; Chanock, Stephen J. ; Chapelle, Albert de la; Easton, Douglas F. ; Elliott, Faye ; English, Dallas R. ; Feskens, Edith J.M. ; FitzGerald, Liesel M. ; Goodman, Phyllis J. ; Hopper, John L. ; Hudson, Thomas J. ; Hunter, David J. ; Jacobs, Eric J. ; Joshu, Corinne E. ; Küry, Sébastien ; Markowitz, Sanford D. ; Milne, Roger L. ; Platz, Elizabeth A. ; Rennert, Gad ; Rennert, Hedy S. ; Schumacher, Fredrick R. ; Sandler, Robert S. ; Seminara, Daniela ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Toland, Amanda E. ; Duijnhoven, Franzel J.B. van; Visvanathan, Kala ; Vodickova, Ludmila ; Potter, John D. ; Männistö, Satu ; Weigl, Korbinian ; Figueiredo, Jane ; Martín, Vicente ; Larsson, Susanna C. ; Parfrey, Patrick S. ; Huang, Wen Yi ; Lenz, Heinz Josef ; Castelao, Jose E. ; Gago-Dominguez, Manuela ; Muñoz-Garzón, Victor ; Mancao, Christoph ; Haiman, Christopher A. ; Wilkens, Lynne R. ; Siegel, Erin ; Barry, Elizabeth ; Younghusband, Ban ; Guelpen, Bethany Van; Harlid, Sophia ; Zeleniuch-Jacquotte, Anne ; Liang, Peter S. ; Du, Mengmeng ; Casey, Graham ; Lindor, Noralane M. ; Marchand, Loic Le; Gallinger, Steven J. ; Jenkins, Mark A. ; Newcomb, Polly A. ; Gruber, Stephen B. ; Schoen, Robert E. ; Hampel, Heather ; Corley, Douglas A. ; Hsu, Li ; Peters, Ulrike ; Hayes, Richard B. - \ 2020
    Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1274 - 1286.e12.
    Colon Cancer - EOCRC - Penetrance - SNP

    Background & Aims: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. Methods: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. Results: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28–4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80–3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10–5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61–5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70–3.00). Sensitivity analyses were consistent with these findings. Conclusions: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.

    Circulating Levels of Insulin-like Growth Factor 1 and Insulin-like Growth Factor Binding Protein 3 Associate With Risk of Colorectal Cancer Based on Serologic and Mendelian Randomization Analyses
    Murphy, Neil ; Carreras-Torres, Robert ; Song, Mingyang ; Chan, Andrew T. ; Martin, Richard M. ; Papadimitriou, Nikos ; Dimou, Niki ; Tsilidis, Konstantinos K. ; Banbury, Barbara ; Bradbury, Kathryn E. ; Besevic, Jelena ; Rinaldi, Sabina ; Riboli, Elio ; Cross, Amanda J. ; Travis, Ruth C. ; Agnoli, Claudia ; Albanes, Demetrius ; Berndt, Sonja I. ; Bézieau, Stéphane ; Bishop, D.T. ; Brenner, Hermann ; Buchanan, Daniel D. ; Onland-Moret, N.C. ; Burnett-Hartman, Andrea ; Campbell, Peter T. ; Casey, Graham ; Castellví-Bel, Sergi ; Chang-Claude, Jenny ; Chirlaque, María Dolores ; Chapelle, Albert de la; English, Dallas ; Figueiredo, Jane C. ; Gallinger, Steven J. ; Giles, Graham G. ; Gruber, Stephen B. ; Gsur, Andrea ; Hampe, Jochen ; Hampel, Heather ; Harrison, Tabitha A. ; Hoffmeister, Michael ; Hsu, Li ; Huang, Wen Yi ; Huyghe, Jeroen R. ; Jenkins, Mark A. ; Keku, Temitope O. ; Kühn, Tilman ; Kweon, Sun Seog ; Marchand, Loic Le; Li, Christopher I. ; Li, Li ; Lindblom, Annika ; Martín, Vicente ; Milne, Roger L. ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Ogino, Shuji ; Ose, Jennifer ; Perduca, Vittorio ; Phipps, Amanda I. ; Platz, Elizabeth A. ; Potter, John D. ; Qu, Conghui ; Rennert, Gad ; Sakoda, Lori C. ; Schafmayer, Clemens ; Schoen, Robert E. ; Slattery, Martha L. ; Tangen, Catherine M. ; Ulrich, Cornelia M. ; Duijnhoven, Franzel J.B. van; Guelpen, Bethany Van; Visvanathan, Kala ; Vodicka, Pavel ; Vodickova, Ludmila ; Vymetalkova, Veronika ; Wang, Hansong ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Zheng, Wei ; Peters, Ulrike ; Gunter, Marc J. - \ 2020
    Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1300 - 1312.e20.
    CRC - GWAS - Risk Factors - Signal Transduction

    Background & Aims: Human studies examining associations between circulating levels of insulin-like growth factor 1 (IGF1) and insulin-like growth factor binding protein 3 (IGFBP3) and colorectal cancer risk have reported inconsistent results. We conducted complementary serologic and Mendelian randomization (MR) analyses to determine whether alterations in circulating levels of IGF1 or IGFBP3 are associated with colorectal cancer development. Methods: Serum levels of IGF1 were measured in blood samples collected from 397,380 participants from the UK Biobank, from 2006 through 2010. Incident cancer cases and cancer cases recorded first in death certificates were identified through linkage to national cancer and death registries. Complete follow-up was available through March 31, 2016. For the MR analyses, we identified genetic variants associated with circulating levels of IGF1 and IGFBP3. The association of these genetic variants with colorectal cancer was examined with 2-sample MR methods using genome-wide association study consortia data (52,865 cases with colorectal cancer and 46,287 individuals without [controls]) Results: After a median follow-up period of 7.1 years, 2665 cases of colorectal cancer were recorded. In a multivariable-adjusted model, circulating level of IGF1 associated with colorectal cancer risk (hazard ratio per 1 standard deviation increment of IGF1, 1.11; 95% confidence interval [CI] 1.05–1.17). Similar associations were found by sex, follow-up time, and tumor subsite. In the MR analyses, a 1 standard deviation increment in IGF1 level, predicted based on genetic factors, was associated with a higher risk of colorectal cancer risk (odds ratio 1.08; 95% CI 1.03–1.12; P = 3.3 × 10–4). Level of IGFBP3, predicted based on genetic factors, was associated with colorectal cancer risk (odds ratio per 1 standard deviation increment, 1.12; 95% CI 1.06–1.18; P = 4.2 × 10–5). Colorectal cancer risk was associated with only 1 variant in the IGFBP3 gene region (rs11977526), which also associated with anthropometric traits and circulating level of IGF2. Conclusions: In an analysis of blood samples from almost 400,000 participants in the UK Biobank, we found an association between circulating level of IGF1 and colorectal cancer. Using genetic data from 52,865 cases with colorectal cancer and 46,287 controls, a higher level of IGF1, determined by genetic factors, was associated with colorectal cancer. Further studies are needed to determine how this signaling pathway might contribute to colorectal carcinogenesis.

    Genome-wide detection of key genes and epigenetic markers for chicken fatty liver
    Tan, Xiaodong ; Liu, Ranran ; Xing, Siyuan ; Zhang, Yonghong ; Li, Qinghe ; Zheng, Maiqing ; Zhao, Guiping ; Wen, Jie - \ 2020
    International Journal of Molecular Sciences 21 (2020)5. - ISSN 1661-6596
    Chicken - DNA methylation - Epigenetics - Fatty liver - Lipid metabolism - Long noncoding RNA

    Chickens are one of the most important sources of meat worldwide, and the occurrence of fatty liver syndrome (FLS) is closely related to production efficiency. However, the potential mechanism of FLS remains poorly understood. An integrated analysis of data from whole-genome bisulfite sequencing and long noncoding RNA (lncRNA) sequencing was conducted. A total of 1177 differentially expressed genes (DEGs) and 1442 differentially methylated genes (DMGs) were found. There were 72% of 83 lipid-and glucose-related genes upregulated; 81% of 150 immune-related genes were downregulated in fatty livers. Part of those genes was within differentially methylated regions (DMRs). Besides, sixty-seven lncRNAs were identified differentially expressed and divided into 13 clusters based on their expression pattern. Some lipid-and glucose-related lncRNAs (e.g., LNC_006756, LNC_012355, and LNC_005024) and immune-related lncRNAs (e.g., LNC_010111, LNC_010862, and LNC_001272) were found through a co-expression network and functional annotation. From the expression and epigenetic profiles, 23 target genes (e.g., HAO1, ABCD3, and BLMH) were found to be hub genes that were regulated by both methylation and lncRNAs. We have provided comprehensive epigenetic and transcriptomic profiles on FLS in chicken, and the identification of key genes and epigenetic markers will expand our understanding of the molecular mechanism of chicken FLS.

    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.

    Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a
    Creutzburg, S.C.A. ; Wu, Wen ; Mohanraju, P. ; Swartjes, Thomas ; Alkan, F. ; Gorodkin, J. ; Staals, R.H.J. ; Oost, J. van der - \ 2020
    Nucleic acids research 48 (2020)6. - ISSN 1362-4962 - p. 3228 - 3243.
    Genome editing has recently made a revolutionary development with the introduction of the CRISPR–Cas technology. The programmable CRISPR-associated Cas9 and Cas12a nucleases generate specific dsDNA breaks in the genome, after which host DNA-repair mechanisms can be manipulated to implement the desired editing. Despite this spectacular progress, the efficiency of Cas9/Cas12a-based engineering can still be improved. Here, we address the variation in guide-dependent efficiency of Cas12a, and set out to reveal the molecular basis of this phenomenon. We established a sensitive and robust in vivo targeting assay based on loss of a target plasmid encoding the red fluorescent protein (mRFP). Our results suggest that folding of both the precursor guide (pre-crRNA) and the mature guide (crRNA) have a major influence on Cas12a activity. Especially, base pairing of the direct repeat, other than with itself, was found to be detrimental to the activity of Cas12a. Furthermore, we describe different approaches to minimize base-pairing interactions between the direct repeat and the variable part of the guide. We show that design of the 3′ end of the guide, which is not involved in target strand base pairing, may result in substantial improvement of the guide's targeting potential and hence of its genome editing efficiency.
    Effect of divergent selection for intramuscular fat content on muscle lipid metabolism in chickens
    Liu, Lu ; Cui, Huanxian ; Xing, Siyuan ; Zhao, Guiping ; Wen, Jie - \ 2020
    Animals 10 (2020)1. - ISSN 2076-2615
    Chicken - Differential lipid metabolism - Intramuscular fat - Selection - Signaling pathway

    Intramuscular fat (IMF)—an important factor affecting meat quality—can be appropriately increased by genetic selection. Chicken lines divergently selected for IMF content were used in this study to investigate the mechanisms behind differential IMF deposition. Sixty 15th generation chickens were genotyped using the IASCHICK 55K single nucleotide polymorphism (SNP) chip. After quality control, 59 chickens and 36,893 SNPs were available for subsequent analysis. Population structure assessment indicated that the lines were genetically differentiated. Based on the top 1% paired fixation index values, three pathways were significantly (p < 0.05) enriched, and nine genes were considered candidate genes for differential IMF deposition. Differences between the lines in the expressions of representative genes involved in the above pathways were detected in 16th generation chickens. This study suggests that genetic selection for increased IMF in the pectoralis major muscle may enhance fatty acid synthesis, transport, and esterification, and reduce triglyceride hydrolysis. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, glycerolipid metabolism, and fatty acid degradation pathway may have contributed to the differences in IMF deposition between the lines. These results contribute to the understanding of the genetic mechanisms behind IMF deposition, and the improvement of chicken meat quality.

    Dynamic process-based modelling of crop growth and competitive water extraction in relay strip intercropping: Model development and application to wheat-maize intercropping
    Tan, Meixiu ; Gou, Fang ; Stomph, Tjeerd Jan ; Wang, Jing ; Yin, Wen ; Zhang, Lizhen ; Chai, Qiang ; Werf, Wopke van der - \ 2020
    Field Crops Research 246 (2020). - ISSN 0378-4290
    AquaCrop - LER - Water use efficiency - WER

    Strip intercropping increases land use efficiency but the effect on water use efficiency is less well-known. Here we develop a modelling method to simulate the growth of an intercrop taking into account the acquisition of light and water by the component species in order to calculate the efficacy of light and water acquisition in an intercropping system as compared to sole crops. The model is parameterized, calibrated and validated using data on wheat-maize intercropping in Gansu province, Northwest China. Observed above-ground biomass was 1630 g m−2 for sole wheat and 1334 g m−2 for intercropped wheat while it was 3023 g m−2 for sole maize and 2259 g m−2 for intercropped maize. The average water use was 405 mm in sole wheat, 595 mm in sole maize and 711 mm in wheat-maize intercropping. Based on observed yields, the land equivalent ratio (LER) was 1.59 and the water equivalent ratio (WER) was 1.14, where LER and WER express the relative amounts of land and water needed to achieve the yields obtained in a unit area of intercrop using sole crops. These results indicate that relay strip intercropping of wheat and maize achieves an increase of land use efficiency of 59% and of water use efficiency of 14%. Overall the intercrop model gave satisfactory predictions, with coefficients of efficiency (CE) in validation of 0.86–0.97, 0.90–0.95, 0.85–0.91 and 0.98 for biomass of sole wheat, sole maize, intercropped wheat, and intercropped maize, respectively. Overall CE of water use was 0.95. Simulated LER and WER were similar to observed LER and WER. The results show that intercropping could be used to obtain more yield on less land with less water. Policies that limit water use per unit land and prohibit the use of intercropping on the basis of its high water use per unit area may therefore be counter-productive. The model for intercrop growth and development under water limitation may be used for exploring production possibilities under land and water constraints.

    A new chicken 55K SNP genotyping array
    Liu, Ranran ; Xing, Siyuan ; Wang, Jie ; Zheng, Maiqing ; Cui, Huanxian ; Crooijmans, Richard ; Li, Qinghe ; Zhao, Guiping ; Wen, Jie - \ 2019
    Wageningen University and Research
    Chicken - Commercial line - Genotyping array - SNP
    China has the richest local chicken breeding resources in the world and is the world’s second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chickens and breeding of meat-type chickens taking utility of those resources is urgently needed for conventional farms, breeding industry, and research areas. Results Eight representative local breeds or commercial broiler lines with 3 pools of 48 individuals within each breed/line were sequenced and supplied the major SNPs resource. There were 7.09 million - 9.41 million SNPs detected in each breed/line. After filtering using multiple criteria such as preferred incorporation of trait-related SNPs and uniformity of distribution across the genome, 52.18 K SNPs were selected in the final array. It consists of: (i) 19.22 K SNPs from the genomes of yellow-feathered, cyan-shank partridge and white-feathered chickens; (ii) 5.98 K SNPs related to economic traits from the Illumina 60 K SNP Bead Chip, which were found as significant associated SNPs with 15 traits in a Beijing-You crossed Cobb F2 resource population by genome-wide association study analysis; (iii) 7.63 K SNPs from 861 candidate genes of economic traits; (iv) the 0.94 K SNPs related to residual feed intake; and (v) 18.41 K from chicken SNPdb. The polymorphisms of 9 extra local breeds and 3 commercial lines were examined with this array, and 40 K - 47 K SNPs were polymorphic (with minor allele frequency > 0.05) in those breeds. The MDS result showed that those breeds can be clearly distinguished by this newly developed genotyping array. Conclusions We successfully developed a 55K genotyping array by using SNPs segregated from typical local breeds and commercial lines. Compared to the existing Affy 600 K and Illumina 60 K arrays, there were 21,41 K new SNPs included on our Affy 55K array. The results of the 55K genotyping data can therefore be imputed to high-density SNPs genotyping data. The array offers a wide range of potential applications such as genomic selection breeding, GWAS of interested traits, and investigation of diversity of different chicken breeds.
    Longitudinal RNA-seq Analysis of Tissue Development Reveals the Hub genes that Influencing the Chicken Intramuscular Fat and Abdominal Fat Deposition
    Xing, Siyuan ; Liu, Ranran ; Crooijmans, Richard ; Liu, Lu ; Madsen, Ole ; Zhou, Wu ; Cui, Huanxian ; Li, Qinghe ; Zheng, Maiqing ; Zhao, Guiping ; Groenen, Martien ; Wen, Jie - \ 2019
    Powerpoint presentation
    Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
    Zhao, Zhi Bo ; He, Ji Zheng ; Geisen, Stefan ; Han, Li Li ; Wang, Jun Tao ; Shen, Ju Pei ; Wei, Wen Xue ; Fang, Yun Ting ; Li, Pei Pei ; Zhang, Li Mei - \ 2019
    Microbiome 7 (2019)1. - ISSN 2049-2618
    High-throughput sequencing - Microbiome - Nitrogen fertilizers - Soil protists - Soil type

    Background: Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons. Results: We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions. Conclusions: Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.

    The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development
    Xiang, Daoquan ; Quilichini, Teagen D. ; Liu, Ziying ; Gao, Peng ; Pan, Youlian ; Li, Qiang ; Nilsen, Kirby T. ; Venglat, Prakash ; Esteban, Eddi ; Pasha, Asher ; Wang, Yejun ; Wen, Rui ; Zhang, Zhongjuan ; Hao, Zhaodong ; Wang, Edwin ; Wei, Yangdou ; Cuthbert, Richard ; Kochian, Leon V. ; Sharpe, Andrew ; Provart, Nicholas ; Weijers, Dolf ; Gillmor, Stewart C. ; Pozniak, Curtis ; Datla, Raju - \ 2019
    The Plant Cell 31 (2019)12. - ISSN 1040-4651 - p. 2888 - 2911.

    Modern wheat production comes from two polyploid species, Triticum aestivum and Triticumturgidum (var durum), which putatively arose from diploid ancestors Triticumurartu, Aegilops speltoides, and Aegilopstauschii How gene expression during embryogenesis and grain development in wheats has been shaped by the differing contributions of diploid genomes through hybridization, polyploidization, and breeding selection is not well understood. This study describes the global landscape of gene activities during wheat embryogenesis and grain development. Using comprehensive transcriptomic analyses of two wheat cultivars and three diploid grasses, we investigated gene expression at seven stages of embryo development, two endosperm stages, and one pericarp stage. We identified transcriptional signatures and developmental similarities and differences among the five species, revealing the evolutionary divergence of gene expression programs and the contributions of A, B, and D subgenomes to grain development in polyploid wheats. The characterization of embryonic transcriptional programming in hexaploid wheat, tetraploid wheat, and diploid grass species provides insight into the landscape of gene expression in modern wheat and its ancestral species. This study presents a framework for understanding the evolution of domesticated wheat and the selective pressures placed on grain production, with important implications for future performance and yield improvements.plantcell;31/12/2888/FX1F1fx1.

    NODULE INCEPTION Recruits the Lateral Root Developmental Program for Symbiotic Nodule Organogenesis in Medicago truncatula
    Schiessl, Katharina ; Lilley, Jodi L.S. ; Lee, Tak ; Tamvakis, Ioannis ; Kohlen, Wouter ; Bailey, Paul C. ; Thomas, Aaron ; Luptak, Jakub ; Ramakrishnan, Karunakaran ; Carpenter, Matthew D. ; Mysore, Kirankumar S. ; Wen, Jiangqi ; Ahnert, Sebastian ; Grieneisen, Veronica A. ; Oldroyd, Giles E.D. - \ 2019
    Current Biology 29 (2019)21. - ISSN 0960-9822 - p. 3657 - 3668.e5.
    auxin - CYTOKININ RESPONSE FACTOR - endosymbiosis - LATERAL ORGAN BOUNDARIES DOMAIN - lateral root/nodule organogenesis - Medicago truncatula - nitrogen - NODULE INCEPTION - rhizobia - YUCCA

    To overcome nitrogen deficiencies in the soil, legumes enter symbioses with rhizobial bacteria that convert atmospheric nitrogen into ammonium. Rhizobia are accommodated as endosymbionts within lateral root organs called nodules that initiate from the inner layers of Medicago truncatula roots in response to rhizobial perception. In contrast, lateral roots emerge from predefined founder cells as an adaptive response to environmental stimuli, including water and nutrient availability. CYTOKININ RESPONSE 1 (CRE1)-mediated signaling in the pericycle and in the cortex is necessary and sufficient for nodulation, whereas cytokinin is antagonistic to lateral root development, with cre1 showing increased lateral root emergence and decreased nodulation. To better understand the relatedness between nodule and lateral root development, we undertook a comparative analysis of these two root developmental programs. Here, we demonstrate that despite differential induction, lateral roots and nodules share overlapping developmental programs, with mutants in LOB-DOMAIN PROTEIN 16 (LBD16) showing equivalent defects in nodule and lateral root initiation. The cytokinin-inducible transcription factor NODULE INCEPTION (NIN) allows induction of this program during nodulation through activation of LBD16 that promotes auxin biosynthesis via transcriptional induction of STYLISH (STY) and YUCCAs (YUC). We conclude that cytokinin facilitates local auxin accumulation through NIN promotion of LBD16, which activates a nodule developmental program overlapping with that induced during lateral root initiation.

    Earthworms Coordinate Soil Biota to Improve Multiple Ecosystem Functions
    Liu, Ting ; Chen, Xiaoyun ; Gong, Xin ; Lubbers, Ingrid M. ; Jiang, Yangyang ; Feng, Wen ; Li, Xianping ; Whalen, Joann K. ; Bonkowski, Michael ; Griffiths, Bryan S. ; Hu, Feng ; Liu, Manqiang - \ 2019
    Current Biology 29 (2019)20. - ISSN 0960-9822 - p. 3420 - 3429.
    bacterial-dominated channel - earthworm - ecosystem engineer - ecosystem service - soil fauna - soil microbe - sustainable agriculture

    Liu et al. study a 13-year-old field experiment to show that earthworms are beneficial to agroecosystems from a multifunctional perspective. This work incorporates the concerns of negative effects of earthworms in recently published syntheses and highlights the potential pathways in which earthworms contribute to sustainable agriculture.

    A new chicken 55K SNP genotyping array
    Liu, Ranran ; Xing, Siyuan ; Wang, Jie ; Zheng, Maiqing ; Cui, Huanxian ; Crooijmans, Richard P.M.A. ; Li, Qinghe ; Zhao, Guiping ; Wen, Jie - \ 2019
    BMC Genomics 20 (2019)1. - ISSN 1471-2164 - 1 p.
    Chicken - Commercial line - Genotyping array - SNP

    BACKGROUND: China has the richest local chicken breeding resources in the world and is the world's second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chickens and breeding of meat-type chickens taking utility of those resources is urgently needed for conventional farms, breeding industry, and research areas. RESULTS: Eight representative local breeds or commercial broiler lines with 3 pools of 48 individuals within each breed/line were sequenced and supplied the major SNPs resource. There were 7.09 million - 9.41 million SNPs detected in each breed/line. After filtering using multiple criteria such as preferred incorporation of trait-related SNPs and uniformity of distribution across the genome, 52.18 K SNPs were selected in the final array. It consists of: (i) 19.22 K SNPs from the genomes of yellow-feathered, cyan-shank partridge and white-feathered chickens; (ii) 5.98 K SNPs related to economic traits from the Illumina 60 K SNP Bead Chip, which were found as significant associated SNPs with 15 traits in a Beijing-You crossed Cobb F2 resource population by genome-wide association study analysis; (iii) 7.63 K SNPs from 861 candidate genes of economic traits; (iv) the 0.94 K SNPs related to residual feed intake; and (v) 18.41 K from chicken SNPdb. The polymorphisms of 9 extra local breeds and 3 commercial lines were examined with this array, and 40 K - 47 K SNPs were polymorphic (with minor allele frequency > 0.05) in those breeds. The MDS result showed that those breeds can be clearly distinguished by this newly developed genotyping array. CONCLUSIONS: We successfully developed a 55K genotyping array by using SNPs segregated from typical local breeds and commercial lines. Compared to the existing Affy 600 K and Illumina 60 K arrays, there were 21,41 K new SNPs included on our Affy 55K array. The results of the 55K genotyping data can therefore be imputed to high-density SNPs genotyping data. The array offers a wide range of potential applications such as genomic selection breeding, GWAS of interested traits, and investigation of diversity of different chicken breeds.

    Disentangling the genetics of lean mass
    Karasik, David ; Zillikens, M.C. ; Hsu, Yi Hsiang ; Aghdassi, Ali ; Akesson, Kristina ; Amin, Najaf ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Bochud, Murielle ; Borecki, Ingrid B. ; Broer, Linda ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos-Obando, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Chambers, John C. ; Chen, Zhao ; Cho, Nam H. ; Choi, Hyung Jin ; Chou, Wen Chi ; Cummings, Steven R. ; Groot, Lisette C.P.G.M. De; Jager, Phillip L. De; Demuth, Ilja ; Diatchenko, Luda ; Econs, Michael J. ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Eriksson, Joel ; Eriksson, Johan G. ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Gieger, Christian ; Grallert, Harald ; Gudnason, Vilmundur ; Lenore, Launer J. ; Hayward, Caroline ; Hofman, Albert ; Homuth, Georg ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Johnson, Toby ; Biffar, Reiner ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koller, Daniel L. ; Kooner, Jaspal S. ; Kraus, William E. ; Kritchevsky, Stephen ; Kutalik, Zoltán ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Lerch, Markus M. ; Lewis, Joshua R. ; Lill, Christina ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Livshits, Gregory ; Ljunggren, Östen ; Loos, Ruth J.F. ; Lorentzon, Mattias ; Luan, Jian An ; Luben, Robert N. ; Malkin, Ida ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Nethander, Maria ; Newman, Anne B. ; Oconnell, Jeffery R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Prince, Richard L. ; Psaty, Bruce M. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Rivadeneira, Fernando ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schipf, Sabine ; Shin, Chan Soo ; Smith, Albert V. ; Smith, Shad B. ; Soranzo, Nicole ; Spector, Timothy D. ; StanÄ Áková, Alena ; Stefansson, Kari ; Steinhagen-Thiessen, Elisabeth ; Stolk, Lisette ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorleifsson, Gudmar ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Uitterlinden, André G. ; Duijn, Cornelia M. Van; Schoor, Natasja M. Van; Vandenput, Liesbeth ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; J Wareham, Nicholas ; Waterworth, Dawn ; Weedon, Michael N. ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Yerges-Armstrong, Laura M. ; Yu, Lei ; Zhang, Weihua ; Zhao, Jing Hua ; Zhou, Yanhua ; Nielson, Carrie M. ; Harris, Tamara B. ; Demissie, Serkalem ; Kiel, Douglas P. ; Ohlsson, Claes - \ 2019
    American Journal of Clinical Nutrition 109 (2019)2. - ISSN 0002-9165 - p. 276 - 278.
    body composition - body fat - meta-Analysis of genome-wide association studies - metabolic profile - skeletal muscle

    Background Lean body mass (LM) plays an important role in mobility and metabolic function. We previously identified five loci associated with LM adjusted for fat mass in kilograms. Such an adjustment may reduce the power to identify genetic signals having an association with both lean mass and fat mass. Objectives To determine the impact of different fat mass adjustments on genetic architecture of LM and identify additional LM loci. Methods We performed genome-wide association analyses for whole-body LM (20 cohorts of European ancestry with n = 38,292) measured using dual-energy X-ray absorptiometry) or bioelectrical impedance analysis, adjusted for sex, age, age 2, and height with or without fat mass adjustments (Model 1 no fat adjustment; Model 2 adjustment for fat mass as a percentage of body mass; Model 3 adjustment for fat mass in kilograms). Results Seven single-nucleotide polymorphisms (SNPs) in separate loci, including one novel LM locus (TNRC6B), were successfully replicated in an additional 47,227 individuals from 29 cohorts. Based on the strengths of the associations in Model 1 vs Model 3, we divided the LM loci into those with an effect on both lean mass and fat mass in the same direction and refer to those as "sumo wrestler" loci (FTO and MC4R). In contrast, loci with an impact specifically on LM were termed "body builder" loci (VCAN and ADAMTSL3). Using existing available genome-wide association study databases, LM increasing alleles of SNPs in sumo wrestler loci were associated with an adverse metabolic profile, whereas LM increasing alleles of SNPs in "body builder" loci were associated with metabolic protection. Conclusions In conclusion, we identified one novel LM locus (TNRC6B). Our results suggest that a genetically determined increase in lean mass might exert either harmful or protective effects on metabolic traits, depending on its relation to fat mass.

    Effects of DEM resolution on the accuracy of gully maps in loess hilly areas
    Dai, Wen ; Yang, Xin ; Na, Jiaming ; Li, Jingwei ; Brus, Dick ; Xiong, Liyang ; Tang, Guoan ; Huang, Xiaoli - \ 2019
    Catena 177 (2019). - ISSN 0341-8162 - p. 114 - 125.
    Accuracy assessment - DEM resolution - Gully mapping - The Loess Plateau of China - Uncertainty

    Gully maps are important prerequisites for the study of gully erosion and land degradation. Many digital elevation model (DEM)-based methods have been proposed to enable automated gully mapping. However, the accuracy of a gully map derived from a DEM is inevitably affected by the DEM resolution. This study investigates the effects of DEM resolution on the accuracy of gully maps. A series of DEMs with resolutions of 0.1–10 m is employed to map gully areas. The effects of DEM resolution on the error in the mapped gully area and on the position error are described by regression models. The results from two catchments in hilly areas of the Loess Plateau in China are as follows. DEMs with resolutions of 0.5–2 m are the most suitable for gully mapping. Very high-resolution DEMs increase local position errors and over-predict the extents of gullies, whereas DEMs with coarser resolutions cause the downward migration of mapped gully boundaries, resulting in the under-prediction of gully areas. However, the effects of DEM resolution on gully maps are not constant but vary in space. The spatial disparities of the resolution effects are related to the gully morphology. The resolution effects on the gully maps in V-shaped gullies are stronger than those in U-shaped gullies. The findings of this study can be used to select a suitable DEM resolution for gully mapping in loess hilly areas and contribute to understanding the characterization of gullies by using DEMs.

    Correction to: In Vitro Seeding Activity of Glycoform-Deficient Prions from Variably Protease-Sensitive Prionopathy and Familial CJD Associated with PrPV180I Mutation
    Wang, Zerui ; Yuan, Jue ; Shen, Pingping ; Abskharon, Romany ; Lang, Yue ; Dang, Johnny ; Adornato, Alise ; Xu, Ling ; Chen, Jiafeng ; Feng, Jiachun ; Moudjou, Mohammed ; Kitamoto, Tetsuyuki ; Langeveld, Jan ; Appleby, Brian ; Ma, Jiyan ; Kong, Qingzhong ; Petersen, Robert B. ; Zou, Wen Quan ; Cui, Li - \ 2019
    Molecular Neurobiology 56 (2019)8. - ISSN 0893-7648 - p. 5470 - 5470.

    The original version of this article unfortunately contained a mistake. The email address Dr. Wen-Quan Zou, one of the corresponding authors should be written as “wxz6@case.edu” instead of “wxz@case.edu”.

    In Vitro Seeding Activity of Glycoform-Deficient Prions from Variably Protease-Sensitive Prionopathy and Familial CJD Associated with PrPV180I Mutation
    Wang, Zerui ; Yuan, Jue ; Shen, Pingping ; Abskharon, Romany ; Lang, Yue ; Dang, Johnny ; Adornato, Alise ; Xu, Ling ; Chen, Jiafeng ; Feng, Jiachun ; Moudjou, Mohammed ; Kitamoto, Tetsuyuki ; Langeveld, Jan ; Appleby, Brian ; Ma, Jiyan ; Kong, Qingzhong ; Petersen, Robert B. ; Zou, Wen Quan ; Cui, Li - \ 2019
    Molecular Neurobiology 56 (2019)8. - ISSN 0893-7648 - p. 5456 - 5469.
    Humanized transgenic mice - Polymorphism - Prion - Prion disease - Real-time quaking-induced conversion (RT-QuIC) - Serial protein misfolding cyclic amplification (sPMCA) - Variably protease-sensitive prionopathy (VPSPr)

    Both sporadic variably protease-sensitive prionopathy (VPSPr) and familial Creutzfeldt-Jakob disease linked to the prion protein (PrP) V180I mutation (fCJDV180I) have been found to share a unique pathological prion protein (PrPSc) that lacks the protease-resistant PrPSc glycosylated at residue 181 because two of four PrP glycoforms are apparently not converted into the PrPSc from their cellular PrP (PrPC). To investigate the seeding activity of these unique PrPSc molecules, we conducted in vitro prion conversion experiments using serial protein misfolding cyclic amplification (sPMCA) and real-time quaking-induced conversion (RT-QuIC) assays with different PrPC substrates. We observed that the seeding of PrPSc from VPSPr or fCJDV180I in the sPMCA reaction containing normal human or humanized transgenic (Tg) mouse brain homogenates generated PrPSc molecules that unexpectedly exhibited a dominant diglycosylated PrP isoform along with PrP monoglycosylated at residue 181. The efficiency of PrPSc amplification was significantly higher in non-CJDMM than in non-CJDVV human brain homogenate, whereas it was higher in normal TgVV than in TgMM mouse brain homogenate. PrPC from the mixture of normal TgMM and Tg mouse brain expressing PrPV180I mutation (Tg180) but not TgV180I alone was converted into PrPSc by seeding with the VPSPr or fCJDV180I. The RT-QuIC seeding activity of PrPSc from VPSPr and fCJDV180I was significantly lower than that of sCJD. Our results suggest that the formation of glycoform-selective prions may be associated with an unidentified factor in the affected brain and the glycoform-deficiency of PrPSc does not affect the glycoforms of in vitro newly amplified PrPSc.

    Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar
    Clifton-Brown, John ; Harfouche, Antoine ; Casler, Michael D. ; Dylan Jones, Huw ; Macalpine, William J. ; Murphy-Bokern, Donal ; Smart, Lawrence B. ; Adler, Anneli ; Ashman, Chris ; Awty-Carroll, Danny ; Bastien, Catherine ; Bopper, Sebastian ; Botnari, Vasile ; Brancourt-Hulmel, Maryse ; Chen, Zhiyong ; Clark, Lindsay V. ; Cosentino, Salvatore ; Dalton, Sue ; Davey, Chris ; Dolstra, Oene ; Donnison, Iain ; Flavell, Richard ; Greef, Joerg ; Hanley, Steve ; Hastings, Astley ; Hertzberg, Magnus ; Hsu, Tsai Wen ; Huang, Lin S. ; Iurato, Antonella ; Jensen, Elaine ; Jin, Xiaoli ; Jørgensen, Uffe ; Kiesel, Andreas ; Kim, Do Soon ; Liu, Jianxiu ; McCalmont, Jon P. ; McMahon, Bernard G. ; Mos, Michal ; Robson, Paul ; Sacks, Erik J. ; Sandu, Anatolii ; Scalici, Giovanni ; Schwarz, Kai ; Scordia, Danilo ; Shafiei, Reza ; Shield, Ian ; Slavov, Gancho ; Stanton, Brian J. ; Swaminathan, Kankshita ; Trindade, Luisa M. - \ 2019
    Global change biology Bioenergy 11 (2019)1. - ISSN 1757-1693 - p. 118 - 151.
    bioenergy - feedstocks - lignocellulose - M. sacchariflorus - M. sinensis - Miscanthus - Panicum virgatum - perennial biomass crop - Populus spp. - Salix spp.

    Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.

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