@article{dong_hu_chen_shemyakina_chau_whipple_fletcher_chuck_2024, title={A regulatory network controlling developmental boundaries and meristem fates contributed to maize domestication}, volume={10}, ISSN={["1546-1718"]}, url={https://doi.org/10.1038/s41588-024-01943-z}, DOI={10.1038/s41588-024-01943-z}, journal={NATURE GENETICS}, author={Dong, Zhaobin and Hu, Gaoyuan and Chen, Qiuyue and Shemyakina, Elena A. and Chau, Geeyun and Whipple, Clinton J. and Fletcher, Jennifer C. and Chuck, George}, year={2024}, month={Oct} }
 @article{washburn_varela_xavier_chen_ertl_gage_holland_lima_romay_lopez-cruz_et al._2024, title={Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates}, url={https://doi.org/10.1101/2024.09.13.612969}, DOI={10.1101/2024.09.13.612969}, abstractNote={Abstract Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of the planet, and create other positive outcomes. In 2022 and 2023 the first open-to-the-public Genomes to Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using a large dataset including genomic variation, phenotype and weather measurements and field management notes, gathered by the project over nine years. The competition attracted registrants from around the world with representation from academic, government, industry, and non-profit institutions as well as unaffiliated. These participants came from diverse disciplines include plant science, animal science, breeding, statistics, computational biology and others. Some participants had no formal genetics or plant-related training, and some were just beginning their graduate education. The teams applied varied methods and strategies, providing a wealth of modeling knowledge based on a common dataset. The winner’s strategy involved two models combining machine learning and traditional breeding tools: one model emphasized environment using features extracted by Random Forest, Ridge Regression and Least-squares, and one focused on genetics. Other high-performing teams’ methods included quantitative genetics, classical machine learning/deep learning, mechanistic models, and model ensembles. The dataset factors used, such as genetics; weather; and management data, were also diverse, demonstrating that no single model or strategy is far superior to all others within the context of this competition.}, author={Washburn, Jacob D. and Varela, José Ignacio and Xavier, Alencar and Chen, Qiuyue and Ertl, David and Gage, Joseph L. and Holland, James B. and Lima, Dayane Cristina and Romay, Maria Cinta and Lopez-Cruz, Marco and et al.}, year={2024}, month={Sep} }
 @article{tian_wang_chen_qin_yang_zhao_xia_du_zhu_wu_et al._2024, title={Maize smart-canopy architecture enhances yield at high densities}, volume={6}, ISSN={["1476-4687"]}, DOI={10.1038/s41586-024-07669-6}, journal={NATURE}, author={Tian, Jinge and Wang, Chenglong and Chen, Fengyi and Qin, Wenchao and Yang, Hong and Zhao, Sihang and Xia, Jinliang and Du, Xian and Zhu, Yifan and Wu, Lishuan and et al.}, year={2024}, month={Jun} }
 @article{li_jia_li_huang_chen_yin_yang_chen_tian_zhang_et al._2023, title={Divergent selection of KNR6 maximizes grain production by balancing the flowering-time adaptation and ear size in maize}, volume={21}, ISSN={["1467-7652"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85152658026&partnerID=MN8TOARS}, DOI={10.1111/pbi.14050}, abstractNote={State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, China National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China Food Crops Institute, Hubei Academy of Agricultural Science, Hubei Hongshan Laboratory, Wuhan, China Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, USA}, number={7}, journal={PLANT BIOTECHNOLOGY JOURNAL}, author={Li, Weiya and Jia, Haitao and Li, Manfei and Huang, Yiqin and Chen, Wenkang and Yin, Pengfei and Yang, Zhixing and Chen, Qiuyue and Tian, Feng and Zhang, Zuxin and et al.}, year={2023}, month={Apr} }
 @article{lima_washburn_varela_chen_gage_romay_holland_ertl_lopez-cruz_aguate_et al._2023, title={Genomes to Fields 2022 Maize Genotype by Environment Prediction Competition}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85167628924&partnerID=MN8TOARS}, DOI={10.21203/rs.3.rs-2973451/v1}, abstractNote={Abstract Objectives: The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (G x E) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize G x E project field trials, leveraging the datasets previously generated by this project and other publicly available data. Data description: This resource used data from the Maize G x E project within the G2F Initiative [1]. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022. Also, soil, weather, environmental covariates data and metadata information for all environments (combination of year and location). Competitors also had access to ReadMe files which described all the files provided. The Maize G x E is a collaborative project and all the data generated becomes publicly available [2]. The dataset used in the 2022 Prediction Competition was curated and lightly filtered for quality and to ensure naming uniformity across years.}, journal={Research Square}, author={Lima, D.C. and Washburn, J.D. and Varela, J.I. and Chen, Q. and Gage, J.L. and Romay, M.C. and Holland, J. and Ertl, D. and Lopez-Cruz, M. and Aguate, F.M. and et al.}, year={2023} }
 @article{lima_washburn_varela_chen_gage_romay_holland_ertl_lopez-cruz_aguate_et al._2023, title={Genomes to Fields 2022 Maize genotype by Environment Prediction Competition}, volume={16}, ISSN={["1756-0500"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85165112390&partnerID=MN8TOARS}, DOI={10.1186/s13104-023-06421-z}, abstractNote={Abstract
                Objectives
                The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data.
              
                Data description
                This resource used data from the Maize GxE project within the G2F Initiative [1]. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022. Also, soil, weather, environmental covariates data and metadata information for all environments (combination of year and location). Competitors also had access to ReadMe files which described all the files provided. The Maize GxE is a collaborative project and all the data generated becomes publicly available [2]. The dataset used in the 2022 Prediction Competition was curated and lightly filtered for quality and to ensure naming uniformity across years.
              }, number={1}, journal={BMC RESEARCH NOTES}, author={Lima, Dayane Cristina and Washburn, Jacob D. and Varela, Jose Ignacio and Chen, Qiuyue and Gage, Joseph L. and Romay, Maria Cinta and Holland, James and Ertl, David and Lopez-Cruz, Marco and Aguate, Fernando M. and et al.}, year={2023}, month={Jul} }
 @article{chen_samayoa_yang_olukolu_york_jesus sanchez-gonzalez_xue_glaubitz_bradbury_romay_et al._2021, title={A conserved genetic architecture among populations of the maize progenitor, teosinte, was radically altered by domestication}, volume={118}, url={https://doi.org/10.1073/pnas.2112970118}, DOI={10.1073/pnas.2112970118}, abstractNote={Significance We investigated the genetic architecture of maize domestication using a quantitative genetics approach. With multiple populations of teosinte and maize, we also compared the genetic architecture among populations within maize and teosinte. We showed that genetic architecture among populations within teosinte or maize is generally conserved, in contrast to the radical differences between teosinte and maize. Our results suggest that while selection drove changes in essentially all traits between teosinte and maize, selection is far less important for explaining domestication trait differences among populations within teosinte or maize.}, number={43}, journal={Proceedings of the National Academy of Sciences}, author={Chen, Qiuyue and Samayoa, Luis Fernando and Yang, Chin Jian and Olukolu, Bode A. and York, Alessandra M. and Jesus Sanchez-Gonzalez, Jose and Xue, Wei and Glaubitz, Jeffrey C. and Bradbury, Peter J. and Romay, Maria Cinta and et al.}, year={2021}, month={Oct} }
 @article{samayoa_olukolu_yang_chen_stetter_york_jesus sanchez-gonzalez_glaubitz_bradbury_romay_et al._2021, title={Domestication reshaped the genetic basis of inbreeding depression in a Maize landrace compared to its wild relative, Teosinte}, volume={9}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85118270806&partnerID=MN8TOARS}, DOI={10.1101/2021.09.01.458502}, abstractNote={AbstractInbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to rare large-effect variation versus potentially more common variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load predicted from sequence data in the maize population. For many traits - and more commonly in maize - genetic variation among selffertilized families was less than expected based on additive and dominance variance estimated in outcrossed families, suggesting that a negative covariance between additive and homozygous dominance effects limits the variation available to selection under partial inbreeding. We identified quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, smalleffect recessive variation underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following to the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against large effect variants, but polygenic load is harder to purge and segregating mutational burden increased in maize compared to teosinte.}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory}, author={Samayoa, L.F. and Olukolu, B.A. and Yang, C.J. and Chen, Q. and Stetter, Markus G. and York, Alessandra M. and Jesus Sanchez-Gonzalez, Jose and Glaubitz, Jeffrey C. and Bradbury, Peter J. and Romay, Maria Cinta and et al.}, year={2021} }
 @article{samayoa_olukolu_yang_chen_stetter_york_sanchez-gonzalez_glaubitz_bradbury_romay_et al._2021, title={Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte}, volume={17}, ISSN={["1553-7404"]}, url={https://doi.org/10.1371/journal.pgen.1009797}, DOI={10.1371/journal.pgen.1009797}, abstractNote={Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte.}, number={12}, journal={PLOS GENETICS}, publisher={Public Library of Science (PLoS)}, author={Samayoa, Luis Fernando and Olukolu, Bode A. and Yang, Chin Jian and Chen, Qiuyue and Stetter, Markus G. and York, Alessandra M. and Sanchez-Gonzalez, Jose de Jesus and Glaubitz, Jeffrey C. and Bradbury, Peter J. and Romay, Maria Cinta and et al.}, editor={Walsh, BruceEditor}, year={2021}, month={Dec} }
 @article{chen_tian_2021, title={Towards knowledge-driven breeding}, volume={7}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85101193330&partnerID=MN8TOARS}, DOI={10.1038/s41477-021-00864-7}, number={3}, journal={Nature Plants}, author={Chen, Qiuyue and Tian, Feng}, year={2021}, pages={242–243} }
 @article{chen_li_tan_tian_2021, title={Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding}, volume={14}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85098645416&partnerID=MN8TOARS}, DOI={10.1016/j.molp.2020.12.006}, abstractNote={Crop domestication has fundamentally altered the course of human history, causing a shift from hunter-gatherer to agricultural societies and stimulating the rise of modern civilization. A greater understanding of crop domestication would provide a theoretical basis for how we could improve current crops and develop new crops to deal with environmental challenges in a sustainable manner. Here, we provide a comprehensive summary of the similarities and differences in the domestication processes of maize and rice, two major staple food crops that feed the world. We propose that maize and rice might have evolved distinct genetic solutions toward domestication. Maize and rice domestication appears to be associated with distinct regulatory and evolutionary mechanisms. Rice domestication tended to select de novo, loss-of-function, coding variation, while maize domestication more frequently favored standing, gain-of-function, regulatory variation. At the gene network level, distinct genetic paths were used to acquire convergent phenotypes in maize and rice domestication, during which different central genes were utilized, orthologous genes played different evolutionary roles, and unique genes or regulatory modules were acquired for establishing new traits. Finally, we discuss how the knowledge gained from past domestication processes, together with emerging technologies, could be exploited to improve modern crop breeding and domesticate new crops to meet increasing human demands.}, number={1}, journal={Molecular Plant}, author={Chen, Q and Li, W and Tan, L and Tian, F}, year={2021}, pages={9–26} }
 @article{chen_samayoa_yang_bradbury_olukolu_neumeyer_romay_sun_lorant_buckler_et al._2020, title={The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication}, volume={16}, ISSN={["1553-7404"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85085904066&partnerID=MN8TOARS}, DOI={10.1371/journal.pgen.1008791}, abstractNote={The genetics of domestication has been extensively studied ever since the rediscovery of Mendel’s law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is “missing” in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect.}, number={5}, journal={PLOS GENETICS}, publisher={Public Library of Science (PLoS)}, author={Chen, Qiuyue and Samayoa, Luis Fernando and Yang, Chin Jian and Bradbury, Peter J. and Olukolu, Bode A. and Neumeyer, Michael A. and Romay, Maria Cinta and Sun, Qi and Lorant, Anne and Buckler, Edward S. and et al.}, editor={Mauricio, RodneyEditor}, year={2020}, month={May} }
 @article{xu_cao_wang_chen_jin_li_tian_2019, title={Evolutionary metabolomics identifies substantial metabolic divergence between maize and its wild ancestor, teosinte}, volume={31}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85071784527&partnerID=MN8TOARS}, DOI={10.1105/TPC.19.00111}, abstractNote={Maize (Zea mays subsp mays) was domesticated from its wild ancestor, teosinte (Zea mays subsp parviglumis). Maize's distinct morphology and adaptation to diverse environments required coordinated changes in various metabolic pathways. However, how the metabolome was reshaped since domestication remains poorly understood. Here, we report a comprehensive assessment of divergence in the seedling metabolome between maize and teosinte. In total, 461 metabolites exhibited significant divergence due to selection. Interestingly, teosinte and tropical and temperate maize, representing major stages of maize evolution, targeted distinct sets of metabolites. Alkaloids, terpenoids, and lipids were specifically targeted in the divergence between teosinte and tropical maize, while benzoxazinoids were specifically targeted in the divergence between tropical and temperate maize. To identify genetic factors controlling metabolic divergence, we assayed the seedling metabolome of a large maize-by-teosinte cross population. We show that the recent metabolic divergence between tropical and temperate maize tended to have simpler genetic architecture than the divergence between teosinte and tropical maize. Through integrating transcriptome data, we identified candidate genes contributing to metabolic divergence, many of which were under selection at the nucleotide and transcript levels. Through overexpression or mutant analysis, we verified the roles of Flavanone 3-hydroxylase1, Purple aleurone1, and maize terpene synthase1 in the divergence of their related biosynthesis pathways. Our findings not only provide important insights into domestication-associated changes in the metabolism but also highlight the power of combining omics data for trait dissection.}, number={9}, journal={Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Xu, Guanghui and Cao, Jingjing and Wang, Xufeng and Chen, Qiuyue and Jin, Weiwei and Li, Zhen and Tian, Feng}, year={2019}, pages={1990–2009} }
 @article{fu_xu_chen_wang_chen_huang_li_xu_tian_wu_et al._2019, title={QTL mapping for leaf morphology traits in a large maize-teosinte population}, volume={39}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85068263980&partnerID=MN8TOARS}, DOI={10.1007/s11032-019-1012-5}, number={7}, journal={Molecular Breeding}, author={Fu, Y. and Xu, G. and Chen, H. and Wang, X. and Chen, Q. and Huang, C. and Li, D. and Xu, D. and Tian, J. and Wu, W. and et al.}, year={2019} }
 @article{chen_yang_york_xue_daskalska_devalk_krueger_lawton_spiegelberg_schnell_et al._2019, title={TeoNAM: A nested association mapping population for domestication and agronomic trait analysis in maize}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85095620344&partnerID=MN8TOARS}, DOI={10.1101/647461}, abstractNote={Abstract Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping population (TeoNAM), derived from crossing five teosinte inbreds to the maize inbred line W22. The resulting 1257 BC 1 S 4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTLs from JLM were identified with many of these mapping to known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1 , a rice domestication gene, is also a QTL associated with tillering in teosinte and maize. We detected multiple QTLs for flowering time and other traits for which the teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.}, journal={bioRxiv}, author={Chen, Q. and Yang, C.J. and York, A.M. and Xue, W. and Daskalska, L.L. and DeValk, C.A. and Krueger, K.W. and Lawton, S.B. and Spiegelberg, B.G. and Schnell, J.M. and et al.}, year={2019} }
 @article{chen_yang_york_xue_daskalska_devalk_krueger_lawton_spiegelberg_schnell_et al._2019, title={TeoNAM: A nested association mapping population for domestication and agronomic trait analysis in maize}, volume={213}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85074552508&partnerID=MN8TOARS}, DOI={10.1534/genetics.119.302594}, abstractNote={Abstract Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping (TeoNAM) population, derived from crossing five teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and a genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTL from JLM were identified, with many of these mapping near known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in teosinte and maize. We detected multiple QTL for flowering time and other traits for which the teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.}, number={3}, journal={Genetics}, author={Chen, Qiuyue and Yang, Chin Jian and York, Alessandra M. and Xue, Wei and Daskalska, Lora L. and DeValk, Craig A. and Krueger, Kyle W. and Lawton, Samuel B. and Spiegelberg, Bailey G. and Schnell, Jack M. and et al.}, year={2019}, pages={1065–1078} }
 @article{tian_wang_xia_wu_xu_wu_li_qin_han_chen_et al._2019, title={Teosinte ligule allele narrows plant architecture and enhances high-density maize yields}, volume={365}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85070682732&partnerID=MN8TOARS}, DOI={10.1126/science.aax5482}, abstractNote={Less space but greater maize yield To meet increasing demands for food, modern agriculture works with increasingly dense plantings. Tian et al. identified a gene in teosinte, the wild ancestor of maize, and used it to alter maize such that the plant has a narrower architecture that nonetheless allows leaves access to sunlight (see the Perspective by Hake and Richardson). The yield advantage only becomes evident with the high-density plantings characteristic of modern agriculture, perhaps explaining why this gene was not brought into the fold during the previous millennia of maize domestication. Science , this issue p. 658 ; see also p. 640}, number={6454}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Tian, Jinge and Wang, Chenglong and Xia, Jinliang and Wu, Lishuan and Xu, Guanghui and Wu, Weihao and Li, Dan and Qin, Wenchao and Han, Xu and Chen, Qiuyue and et al.}, year={2019}, pages={658–664} }
 @article{chen_han_liu_wang_sun_zhao_li_tian_liang_yan_et al._2018, title={Genome-wide association analyses reveal the importance of alternative splicing in diversifying gene function and regulating phenotypic variation in Maize}, volume={30}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85055533782&partnerID=MN8TOARS}, DOI={10.1105/tpc.18.00109}, abstractNote={Alternative splicing (AS) enhances transcriptome diversity and plays important roles in regulating plant processes. Although widespread natural variation in AS has been observed in plants, how AS is regulated and contribute to phenotypic variation is poorly understood. Here, we report a population-level transcriptome assembly and genome-wide association study to identify splicing quantitative trait loci (sQTLs) in developing maize (Zea mays) kernels from 368 inbred lines. We detected 19,554 unique sQTLs for 6570 genes. Most sQTLs showed small isoform usage changes without involving major isoform switching between genotypes. The sQTL-affected isoforms tend to display distinct protein functions. We demonstrate that nonsense-mediated mRNA decay, microRNA-mediated regulation, and small interfering peptide-mediated peptide interference are frequently involved in sQTL regulation. The natural variation in AS and overall mRNA level appears to be independently regulated with different cis-sequences preferentially used. We identified 214 putative trans-acting splicing regulators, among which ZmGRP1, encoding an hnRNP-like glycine-rich RNA binding protein, regulates the largest trans-cluster. Knockout of ZmGRP1 by CRISPR/Cas9 altered splicing of numerous downstream genes. We found that 739 sQTLs colocalized with previous marker-trait associations, most of which occurred without changes in overall mRNA level. Our findings uncover the importance of AS in diversifying gene function and regulating phenotypic variation.}, number={7}, journal={Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Chen, Qiuyue and Han, Yingjia and Liu, Haijun and Wang, Xufeng and Sun, Jiamin and Zhao, Binghao and Li, Weiya and Tian, Jinge and Liang, Yameng and Yan, Jianbing and et al.}, year={2018}, pages={1404–1423} }
 @article{guo_wang_zhao_huang_li_li_yang_york_xue_xu_et al._2018, title={Stepwise cis-Regulatory Changes in ZCN8 Contribute to Maize Flowering-Time Adaptation}, volume={28}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85053503203&partnerID=MN8TOARS}, DOI={10.1016/j.cub.2018.07.029}, abstractNote={Maize (Zea mays ssp. mays) was domesticated in southwestern Mexico ∼9,000 years ago from its wild ancestor, teosinte (Zea mays ssp. parviglumis) [1]. From its center of origin, maize experienced a rapid range expansion and spread over 90° of latitude in the Americas [2-4], which required a novel flowering-time adaptation. ZEA CENTRORADIALIS 8 (ZCN8) is the maize florigen gene and has a central role in mediating flowering [5, 6]. Here, we show that ZCN8 underlies a major quantitative trait locus (QTL) (qDTA8) for flowering time that was consistently detected in multiple maize-teosinte experimental populations. Through association analysis in a large diverse panel of maize inbred lines, we identified a SNP (SNP-1245) in the ZCN8 promoter that showed the strongest association with flowering time. SNP-1245 co-segregated with qDTA8 in maize-teosinte mapping populations. We demonstrate that SNP-1245 is associated with differential binding by the flowering activator ZmMADS1. SNP-1245 was a target of selection during early domestication, which drove the pre-existing early flowering allele to near fixation in maize. Interestingly, we detected an independent association block upstream of SNP-1245, wherein the early flowering allele that most likely originated from Zea mays ssp. mexicana introgressed into the early flowering haplotype of SNP-1245 and contributed to maize adaptation to northern high latitudes. Our study demonstrates how independent cis-regulatory variants at a gene can be selected at different evolutionary times for local adaptation, highlighting how complex cis-regulatory control mechanisms evolve. Finally, we propose a polygenic map for the pre-Columbian spread of maize throughout the Americas.}, number={18}, journal={Current Biology}, author={Guo, L. and Wang, X. and Zhao, M. and Huang, C. and Li, C. and Li, D. and Yang, C.J. and York, A.M. and Xue, W. and Xu, G. and et al.}, year={2018}, pages={3005–3015.e4} }
 @article{xu_wang_huang_xu_li_tian_chen_wang_liang_wu_et al._2017, title={Complex genetic architecture underlies maize tassel domestication}, volume={214}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85015785301&partnerID=MN8TOARS}, DOI={10.1111/nph.14400}, abstractNote={Summary Maize ( Zea mays ) tassels underwent profound morphological changes during maize domestication and improvement. Although a number of genes affecting maize inflorescence development have been identified, the genetic basis of the morphological changes in maize tassels since domestication is not well understood. Here, using a large population of 866 maize‐teosinte BC 2 S 3 recombinant inbred lines genotyped using 19 838 single nucleotide polymorphism ( SNP ) markers, we performed high‐resolution quantitative trait locus ( QTL ) mapping for five tassel morphological traits. We showed that the five tassel traits were associated with different genetic architecture features. Known genes for maize inflorescence development identified by mutagenesis were significantly enriched in the tassel trait QTL s, and many of these genes, including ramosa1 ( ra1 ), barren inflorescence2 ( bif2 ), unbranched2 ( ub2 ), zea floricaula leafy2 ( zfl2 ) and barren stalk fastigiate1 ( baf1 ), showed evidence of selection. An in‐depth nucleotide diversity analysis at the bif2 locus identified strong selection signatures in the 5′‐regulatory region. We also found that several known flowering time genes co‐localized with tassel trait QTL s. A further association analysis indicated that the maize photoperiod gene Zm CCT was significantly associated with tassel size variation. Using near‐isogenic lines, we narrowed down a major‐effect QTL for tassel length, qTL 9‐1 , to a 513‐kb physical region. These results provide important insights into the genetic architecture that controls maize tassel evolution.}, number={2}, journal={New Phytologist}, author={Xu, G. and Wang, X. and Huang, C. and Xu, D. and Li, D. and Tian, J. and Chen, Q. and Wang, C. and Liang, Y. and Wu, Y. and et al.}, year={2017}, pages={852–864} }
 @article{wang_chen_wu_lemmon_xu_huang_liang_xu_li_doebley_et al._2018, title={Genome-wide Analysis of Transcriptional Variability in a Large Maize-Teosinte Population}, volume={11}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85042157570&partnerID=MN8TOARS}, DOI={10.1016/j.molp.2017.12.011}, abstractNote={<h2>Abstract</h2> Gene expression regulation plays an important role in controlling plant phenotypes and adaptation. Here, we report a comprehensive assessment of gene expression variation through the transcriptome analyses of a large maize-teosinte experimental population. Genome-wide mapping identified 25 660 expression quantitative trait loci (eQTL) for 17 311 genes, capturing an unprecedented range of expression variation. We found that local eQTL were more frequently mapped to adjacent genes, displaying a mode of expression piggybacking, which consequently created co-regulated gene clusters. Genes within the co-regulated gene clusters tend to have relevant functions and shared chromatin modifications. Distant eQTL formed 125 significant distant eQTL hotspots with their targets significantly enriched in specific functional categories. By integrating different sources of information, we identified putative <i>trans</i>- regulators for a variety of metabolic pathways. We demonstrated that the bHLH transcription factor <i>R1</i> and hexokinase HEX9 might act as crucial regulators for flavonoid biosynthesis and glycolysis, respectively. Moreover, we showed that domestication or improvement has significantly affected global gene expression, with many genes targeted by selection. Of particular interest, the <i>Bx</i> genes for benzoxazinoid biosynthesis may have undergone coordinated <i>cis</i>-regulatory divergence between maize and teosinte, and a transposon insertion that inactivates <i>Bx12</i> was under strong selection as maize spread into temperate environments with a distinct herbivore community.}, number={3}, journal={Molecular Plant}, author={Wang, X. and Chen, Q. and Wu, Y. and Lemmon, Z.H. and Xu, G. and Huang, C. and Liang, Y. and Xu, D. and Li, D. and Doebley, J.F. and et al.}, year={2018}, pages={443–459} }
 @article{xu_wang_huang_xu_liang_chen_wang_li_tian_wu_et al._2017, title={Glossy15 Plays an Important Role in the Divergence of the Vegetative Transition between Maize and Its Progenitor, Teosinte}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85038104900&partnerID=MN8TOARS}, DOI={10.1016/j.molp.2017.09.016}, abstractNote={The timing of developmental transitions is important for plant growth and environmental adaptation. All plants undergo a series of developmental transitions during their life cycles, and each of these phases is characterized by unique morphological and physiological attributes (Bäurle and Dean, 2006Bäurle I. Dean C. The timing of developmental transitions in plants.Cell. 2006; 125: 655-664Abstract Full Text Full Text PDF PubMed Scopus (480) Google Scholar). In maize, the vegetative transition from juvenile-to-adult vegetative development occurs in a coordinated manner and is marked by the production of leaves that differ in a suite of morphological and physiological traits, many of which contribute to fitness and crop productivity (Moose and Sisco, 1994Moose S.P. Sisco P.H. Glossy15 controls the epidermal juvenile-to-adult phase transition in maize.Plant Cell. 1994; 6: 1343-1355Crossref PubMed Scopus (109) Google Scholar). Significant advances have been made in understanding the molecular mechanisms regulating the juvenile-to-adult vegetative transition. Glossy15 (Gl15), an APETALA2 (AP2)-like transcription factor, plays a key role in promoting juvenile leaf identity traits and suppressing adult leaf identity traits (Moose and Sisco, 1996Moose S.P. Sisco P.H. Glossy15, an APETALA2-like gene from maize that regulates leaf epidermal cell identity.Genes Dev. 1996; 10: 3018-3027Crossref PubMed Scopus (193) Google Scholar). microRNA172 (miR172) is a negative regulator that antagonizes the activity of Gl15 by mediating Gl15 mRNA degradation (Lauter et al., 2005Lauter N. Kampani A. Carlson S. Goebel M. Moose S.P. microRNA172 down-regulates glossy15 to promote vegetative phase change in maize.Proc. Natl. Acad. Sci. USA. 2005; 102: 9412-9417Crossref PubMed Scopus (363) Google Scholar). The dominant Corngrass1 (Cg1) mutant initiates more juvenile leaves than wild-type plants do, and this phenotype was found to be caused by the ectopic overexpression of two tandem microRNA156 (miR156) genes (Chuck et al., 2007Chuck G. Cigan A.M. Saeteurn K. Hake S. The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA.Nat. Genet. 2007; 39: 544-549Crossref PubMed Scopus (483) Google Scholar). In Cg1 mutants, overexpression of miR156 causes a decrease of miR172, which then leads to an increase in expression of Gl15 (Chuck et al., 2007Chuck G. Cigan A.M. Saeteurn K. Hake S. The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA.Nat. Genet. 2007; 39: 544-549Crossref PubMed Scopus (483) Google Scholar). This regulatory circuit of miR172, miR156, and AP2 transcription factor appears to be a general mechanism for regulating vegetative phase changes in higher plants. After the vegetative transition, plants switch to reproductive growth. The correct timing of the transition to flowering is of the utmost importance, as it ensures the reproductive success of plants in changing environments and therefore has an important impact on plant fitness. Maize (Zea mays ssp. mays) was domesticated from the wild ancestor teosinte (Zea mays ssp. parviglumis), an endemic species in southern and western Mexico (Matsuoka et al., 2002Matsuoka Y. Vigouroux Y. Goodman M.M. Sanchez G.J. Buckler E. Doebley J. A single domestication for maize shown by multilocus microsatellite genotyping.Proc. Natl. Acad. Sci. USA. 2002; 99: 6080-6084Crossref PubMed Scopus (888) Google Scholar). From its Meso-American tropical origin, maize has adapted to geographically widespread environments, accompanied by dramatic changes in its flowering time (Hung et al., 2012Hung H.Y. Shannon L.M. Tian F. Bradbury P.J. Chen C. Flint-Garcia S.A. McMullen M.D. Ware D. Buckler E.S. Doebley J.F. et al.ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize.Proc. Natl. Acad. Sci. USA. 2012; 109: E1913-E1921Crossref PubMed Scopus (225) Google Scholar). Several studies have been conducted to identify the genetic factors that control the difference in flowering time between maize and teosinte, and a few key genes have been cloned (Hung et al., 2012Hung H.Y. Shannon L.M. Tian F. Bradbury P.J. Chen C. Flint-Garcia S.A. McMullen M.D. Ware D. Buckler E.S. Doebley J.F. et al.ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize.Proc. Natl. Acad. Sci. USA. 2012; 109: E1913-E1921Crossref PubMed Scopus (225) Google Scholar, Yang et al., 2013Yang Q. Li Z. Li W. Ku L. Wang C. Ye J. Li K. Yang N. Li Y. Zhong T. et al.CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize.Proc. Natl. Acad. Sci. USA. 2013; 110: 16969-16974Crossref PubMed Scopus (241) Google Scholar). In contrast to the significant advances in understanding the reproductive transition, much less is known about the changes in the vegetative transition that occurred during maize domestication. It remains unclear whether the early developmental timing observed in maize also underwent significant divergence during its domestication and how these changes were regulated and associated with local adaptation. To examine the differences in the vegetative transition between maize and teosinte, we grew a panel of 50 diverse maize inbreds and 13 teosintes (Supplemental Table 1) in a winter nursery and investigated their variation regarding the timing of the juvenile-to-adult vegetative transition. The most visually obvious phenotypic marker that distinguishes juvenile from adult development is the production of leaf epicuticular wax (Moose and Sisco, 1994Moose S.P. Sisco P.H. Glossy15 controls the epidermal juvenile-to-adult phase transition in maize.Plant Cell. 1994; 6: 1343-1355Crossref PubMed Scopus (109) Google Scholar). Juvenile maize leaves are coated with epicuticular wax and lack epidermal hairs, whereas adult maize leaves are pubescent and glossy. Following a previous method (Foerster et al., 2015Foerster J.M. Beissinger T. de Leon N. Kaeppler S. Large effect QTL explain natural phenotypic variation for the developmental timing of vegetative phase change in maize (Zea mays L.).Theor. Appl. Genet. 2015; 128: 529-538Crossref PubMed Scopus (11) Google Scholar), we scored the last leaf with epicuticular wax (LLEW) as an indicator trait for measuring the timing of the juvenile-to-adult transition in the maize and teosinte lines. As shown in Figure 1A, the maize lines exhibited an average of 6.2 leaves with juvenile epicuticular wax, which was 2.5 leaves fewer than in the teosinte plants (P < 0.01), indicating that the juvenile identity ends much earlier in maize than that in teosinte. This result suggests that maize may have evolved an early juvenile-to-adult vegetative phase change from its wild ancestor, teosinte. To identify the genetic factors controlling the divergence of the vegetative transition between maize and teosinte, we conducted quantitative trait locus (QTL) mapping for the timing of the juvenile-to-adult vegetative phase change using a large maize-teosinte experimental population, including 866 BC2S3 recombinant inbred lines (RILs) that were previously genotyped based on 19 838 SNPs (Hung et al., 2012Hung H.Y. Shannon L.M. Tian F. Bradbury P.J. Chen C. Flint-Garcia S.A. McMullen M.D. Ware D. Buckler E.S. Doebley J.F. et al.ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize.Proc. Natl. Acad. Sci. USA. 2012; 109: E1913-E1921Crossref PubMed Scopus (225) Google Scholar). LLEW was scored in this maize-teosinte BC2S3 population. A total of 12 QTLs for LLEW were mapped, which collectively explained 43% of the total phenotypic variation (Figure 1B and Supplemental Table 2). Notably, a large-effect QTL explaining 13.7% of the observed phenotypic variation was detected on chromosome 9 (qVT9-1) (Figure 1B and Supplemental Table 2). None of the other QTLs could explain more than 6% of the phenotypic variation (Supplemental Table 2). These results suggest that the vegetative transition is controlled by a single large-effect QTL and many QTLs with small effects, which is a typical characteristic of genetic architecture observed for classical domestication traits. We further found that among the 12 QTLs for LLEW, 10 loci (83.3%) acted in the same direction with the maize allele promoting the juvenile-to-adult vegetative phase change (Figure 1C and Supplemental Table 2). This consistent direction of the allelic effect across the majority of mapped QTLs provides a genetic explanation for the directional divergence of the early juvenile-to-adult vegetative phase change during maize domestication. Given the predominant role of qVT9-1 in controlling the difference in the vegetative transition between maize and teosinte, we performed fine mapping to identify the candidate gene underlying qVT9-1 using near-isogenic lines (NILs) developed from a heterogeneous inbred family (HIF) that segregates only for the qVT9-1 region. A total of 35 recombinants were identified from an F2 population containing 1500 plants using markers M1 and M5. Additional markers were developed to further resolve the breakpoints of the recombinants (Supplemental Table 5), and the 35 recombinants can be classified into six genotype groups according to their genotypes across markers. For each genotype group, one recombinant family with enough F3 seeds was planted for progeny phenotypic testing. Following the previously described fine mapping strategy (Hung et al., 2012Hung H.Y. Shannon L.M. Tian F. Bradbury P.J. Chen C. Flint-Garcia S.A. McMullen M.D. Ware D. Buckler E.S. Doebley J.F. et al.ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize.Proc. Natl. Acad. Sci. USA. 2012; 109: E1913-E1921Crossref PubMed Scopus (225) Google Scholar), homozygous recombinant and homozygous nonrecombinant plants within each F3 family were identified and compared for the difference in LLEW. qVT9-1 was finally delimited to a 263-kb region between markers M3 and M4 that included one intact gene, GRMZM2G160730, and 600 bp of GRMZM2G145104 (Figure 1D). The GRMZM2G160730 gene corresponds to the AP2-like transcription factor Gl15, which has been identified as a qualitative mutation and found to play a primary role in the maintenance of the juvenile phase (Moose and Sisco, 1996Moose S.P. Sisco P.H. Glossy15, an APETALA2-like gene from maize that regulates leaf epidermal cell identity.Genes Dev. 1996; 10: 3018-3027Crossref PubMed Scopus (193) Google Scholar, Lauter et al., 2005Lauter N. Kampani A. Carlson S. Goebel M. Moose S.P. microRNA172 down-regulates glossy15 to promote vegetative phase change in maize.Proc. Natl. Acad. Sci. USA. 2005; 102: 9412-9417Crossref PubMed Scopus (363) Google Scholar). It was clear that Gl15 was most likely the underlying gene of qVT9-1. To examine how qVT9-1 affects the vegetative phase change, we developed NILs that were homozygous for the maize allele or the teosinte allele across the qVT9-1 region (designated NILmaize and NILteosinte, respectively) and compared the differences in the production of macrohairs across leaf stages in these plants. As shown in Figure 1E, NILmaize initiated the production of epidermal hairs in leaf 5, whereas NILteosinte initiated the production of epidermal hairs in leaf 6, showing a one-leaf delay in the onset of adult vegetative development. Despite the significant difference in the vegetative transition, NILmaize and NILteosinte exhibited the same number of leaves at maturity and flowered a similar number of days after sowing, indicating that qVT9-1 has no effect on the onset of reproductive development (Supplemental Figure 1). We next measured Gl15 mRNA expression in the shoot apices of NILmaize and NILteosinte during early shoot development. At 8 days after sowing (DAS), Gl15 was expressed at similarly high levels in NILmaize and NILteosinte (Figure 1F). After 8 DAS, Gl15 expression declined in both NILteosinte and NILmaize, but the Gl15 mRNA level decreased more rapidly in NILmaize than in NILteosinte. At 13 DAS, the Gl15 mRNA level in NILteosinte remained significantly higher than in NILmaize (P < 0.05) (Figure 1F). This significant expression difference extended until 16 DAS. At 21 DAS, the Gl15 mRNA level declined to a minimum level in both NILmaize and NILteosinte, with no significant difference in Gl15 expression being detected between these lines (Figure 1F). The differential Gl15 expression pattern during early shoot development correlated well with the early vegetative phase change in NILmaize and the late phase change in NILteosinte, supporting that Gl15 was most likely the candidate gene for qVT9-1. To identify potential functional variants in the Gl15 region, we conducted an association analysis by sequencing Gl15 and its upstream and downstream regions in a panel of 517 diverse maize lines scored for LLEW. A total of 286 variants (SNPs and InDels) with MAF ≥0.05 were identified across the 6-kb sequenced region around Gl15 (Figure 1G). Using a model that corrects for familiar population structure, we tested the sequence variants for associations with LLEW in the maize association panel. A total of 32 sequence variants showed significant associations with LLEW (0.01/286 = 3.5 × 10−5, Bonferroni multiple test correction) (Figure 1G and Supplemental Table 3). None of these associated variants were located in the conserved AP2 domain or miR172 target region. The maize and teosinte parents of the BC2S3 population showed allelic polymorphism at 24 of the associated variants (Supplemental Table 3). One of the most significant variants was SNP2154 (G/A) (P = 8.1 × 10−8), which corresponded to a stop codon polymorphism (TGG versus TGA), at which the B73 reference exhibited the G nucleotide (Figure 1H and Supplemental Table 3). The maize parent of the BC2S3 population carried a G nucleotide, which promotes the vegetative transition, while the teosinte parent carried an A nucleotide, which delays the vegetative transition (Figure 1H). The A nucleotide at SNP2154 corresponds to a stop codon, while the G nucleotide encodes tryptophan, causing a downstream stop codon (position 2175) 21 bp from SNP2154 to be used (Figure 1H). Thus, relative to the maize parent of the BC2S3 population, in which the stop codon is located at position 2175 (B73 reference allele), the teosinte parent exhibits a stop codon at position 2154. Interestingly, a recent genome-wide association study for LLEW in maize nested association mapping (NAM) population also revealed significant associations in the Gl15 region (Foerster et al., 2015Foerster J.M. Beissinger T. de Leon N. Kaeppler S. Large effect QTL explain natural phenotypic variation for the developmental timing of vegetative phase change in maize (Zea mays L.).Theor. Appl. Genet. 2015; 128: 529-538Crossref PubMed Scopus (11) Google Scholar). This previous study found that an SNP located in the 9th exon of Gl15 showed the most significant association with LLEW in the NAM population. This SNP corresponds to SNP2017 in our study and is in strong linkage disequilibrium (LD) with SNP2154 (r2 = 0.53). Due to the stop codon variant SNP2154, the maize and teosinte parents of the BC2S3 population exhibited seven amino acids difference at the C-terminus of Gl15 protein. To determine whether this difference has led to functional alteration of Gl15 protein, we performed transcriptional activation assay in yeast for the maize and teosinte Gl15 protein and further analyzed their subcellular localization in epidermal cells of Nicotiana benthamiana leaves. The results showed that the maize and teosinte Gl15 protein exhibited similar transcriptional activation activity (Supplemental Figure 2) and were both localized in the nucleus (Supplemental Figure 3), indicating that SNP2154 might not alter the protein function of Gl15. Although we cannot completely exclude the possibility that the altered C-terminal length might affect the interaction ability of Gl15 protein with other protein factors, our current findings suggest that SNP2154 more likely causes the differences in Gl15 expression level that have been observed between NILmaize and NILteosinte (Figure 1F). To further verify our hypothesis, we performed a dual-luciferase transient expression assay in maize protoplasts. The miR172 precursor (pre-miR172) driven by the CaMV 35S promoter was used as an effector, and luciferase (LUC) gene fused with the Gl15-3′UTR sequence containing the miR172 target site from the maize or the teosinte parent was used as the reporter (Figure 1I). Overexpression of miR172 significantly repressed the LUC activity in the construct containing the Gl15-3′UTR sequence from the maize or the teosinte parent (P < 0.05) (Figure 1I), which was consistent with the negative regulatory role of miR172 on Gl15 (Lauter et al., 2005Lauter N. Kampani A. Carlson S. Goebel M. Moose S.P. microRNA172 down-regulates glossy15 to promote vegetative phase change in maize.Proc. Natl. Acad. Sci. USA. 2005; 102: 9412-9417Crossref PubMed Scopus (363) Google Scholar). More importantly, LUC fused with Gl15-3′UTR from the maize parent exhibited significantly lower luciferase activity than LUC fused with Gl15-3′UTR from the teosinte parent when co-transfecting with the miR172 effector (Figure 1I). This result was consistent with the lower expression of Gl15 in NILmaize than in NILteosinte during early shoot development described above. Based on these findings, we speculate that SNP2154 most likely acts as a regulatory variant of Gl15 to control the natural variation in maize vegetative transition. To examine how Gl15 contributed to the divergence of the vegetative transition during maize domestication, we analyzed the nucleotide diversity of the region flanking SNP2154 in diverse teosinte and maize lines. Interestingly, SNP2154 was found to be a standing genetic variation in teosinte, with the G allele occurring as a minor allele (Figure 1J). In contrast, in the maize lines, the frequency of the G allele increased to 65%, and became a dominant allele (Figure 1J). Given the effect of the SNP2154-G allele in promoting the juvenile-to-adult vegetative transition, the significant increase in its frequency in maize might have resulted from strong selection for an earlier vegetative phase change during maize domestication, which is expected to leave a footprint of selection at the nucleotide level. To address this question, we compared the nucleotide diversity of the maize and teosinte lines in the region flanking SNP2154 (Supplemental Table 4). Overall, we did not find evidence of a selective sweep in this region, as the maize lines retained 56% of the nucleotide diversity of teosinte, in line with the average genomic reduction of nucleotide diversity due to the bottleneck effect of domestication. However, the maize lines carrying the SNP2154-G allele retained only 23% of the nucleotide diversity found in teosinte (Figure 1K and Supplemental Table 4), in contrast to the 49% of retained nucleotide diversity in the maize lines carrying the SNP2154-A allele. A coalescent simulation incorporating the maize domestication bottleneck (Eyre-Walker et al., 1998Eyre-Walker A. Gaut R.L. Hilton H. Feldman D.L. Gaut B.S. Investigation of the bottleneck leading to the domestication of maize.Proc. Natl. Acad. Sci. USA. 1998; 95: 4441-4446Crossref PubMed Scopus (278) Google Scholar) showed that the severe loss of genetic diversity in the maize lines carrying the SNP2154-G allele could not be explained by the maize domestication bottleneck alone, indicating strong past selection for the SNP2154-G allele. In conclusion, cultivated maize has evolved an early vegetative phase transition from its ancestor, teosinte. We provided genetic evidence showing that Gl15, a known AP2-like transcription factor, might play a critical role in regulating this divergence of the vegetative transition during maize domestication. Association analysis within diverse maize lines detected a stop codon polymorphism SNP2154, which showes the most significant association with the vegetative transition. Further analyses indicate that SNP2154 most likely functions through altering the expression level of Gl15. Population genetic analyses revealed that SNP2154 was the target of a partial selective sweep that drove a pre-existing low-frequency allele in teosinte to sweep throughout the maize population during domestication. Similar selective sweep from standing genetic variation has also been observed for the tb1 and gt1 genes, which were critical for the morphological domestication of maize (Studer et al., 2011Studer A. Zhao Q. Ross-Ibarra J. Doebley J. Identification of a functional transposon insertion in the maize domestication gene tb1.Nat. Genet. 2011; 43: 1160-1163Crossref PubMed Scopus (481) Google Scholar, Wills et al., 2013Wills D.M. Whipple C.J. Takuno S. Kursel L.E. Shannon L.M. Ross-Ibarra J. Doebley J.F. From many, one: genetic control of prolificacy during maize domestication.PLoS Genet. 2013; 9: e1003604Crossref PubMed Scopus (86) Google Scholar). These results suggest that selection from standing genetic variation might be pervasive and have played important roles in plant evolution. This research was supported by the National Key Research and Development Program of China (2016YFD0100303 and 2016YFD0100404), the Recruitment Program of Global Experts and the Fundamental Research Funds for the Central Universities.}, number={12}, journal={Molecular Plant}, author={Xu, D. and Wang, X. and Huang, C. and Xu, G. and Liang, Y. and Chen, Q. and Wang, C. and Li, D. and Tian, J. and Wu, L. and et al.}, year={2017}, pages={1579–1583} }
 @article{huang_sun_xu_chen_liang_wang_xu_tian_wang_li_et al._2017, title={ZmCCT9 enhances maize adaptation to higher latitudes}, volume={115}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85040231570&partnerID=MN8TOARS}, DOI={10.1073/pnas.1718058115}, abstractNote={Significance Flowering time is a critical determinant of crop adaptation to local environments. As a result of natural and artificial selection, maize has evolved a reduced photoperiod sensitivity to adapt to regions over 90° of latitude in the Americas. Here we show that a distant Harbinger-like transposon acts as a cis -regulatory element to repress ZmCCT9 expression to promote flowering under the long days of higher latitudes. The transposon at ZmCCT9 and another functional transposon at a second flowering-time gene, ZmCCT10 , arose sequentially following domestication and were targeted by selection as maize spread from the tropics to higher latitudes. Our results demonstrate that new functional variation created by transposon insertions helped maize to spread over a broad range of latitudes rapidly.}, number={2}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Huang, C. and Sun, H. and Xu, D. and Chen, Q. and Liang, Y. and Wang, X. and Xu, G. and Tian, J. and Wang, C. and Li, D. and et al.}, year={2017}, pages={E334–E341} }
 @article{huang_chen_xu_xu_tian_tian_2016, title={Identification and fine mapping of quantitative trait loci for the number of vascular bundle in maize stem}, volume={58}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84953635778&partnerID=MN8TOARS}, DOI={10.1111/jipb.12358}, abstractNote={Abstract Studies that investigated the genetic basis of source and sink related traits have been widely conducted. However, the vascular system that links source and sink received much less attention. When maize was domesticated from its wild ancestor, teosinte, the external morphology has changed dramatically; however, less is known for the internal anatomy changes. In this study, using a large maize‐teosinte experimental population, we performed a high‐resolution quantitative trait locus (QTL) mapping for the number of vascular bundle in the uppermost internode of maize stem. The results showed that vascular bundle number is dominated by a large number of small‐effect QTLs, in which a total of 16 QTLs that jointly accounts for 52.2% of phenotypic variation were detected, with no single QTL explaining more than 6% of variation. Different from QTLs for typical domestication traits, QTLs for vascular bundle number might not be under directional selection following domestication. Using Near Isogenic Lines (NILs) developed from heterogeneous inbred family (HIF), we further validated the effect of one QTL qVb9‐2 on chromosome 9 and fine mapped the QTL to a 1.8‐Mb physical region. This study provides important insights for the genetic architecture of vascular bundle number in maize stem and sets basis for cloning of qVb9‐2 .}, number={1}, journal={Journal of Integrative Plant Biology}, author={Huang, C. and Chen, Q. and Xu, G. and Xu, D. and Tian, J. and Tian, F.}, year={2016}, pages={81–90} }
 @article{li_wang_zhang_chen_xu_xu_wang_liang_wu_huang_et al._2016, title={The genetic architecture of leaf number and its genetic relationship to flowering time in maize}, volume={210}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84959151298&partnerID=MN8TOARS}, DOI={10.1111/nph.13765}, abstractNote={Summary The number of leaves and their distributions on plants are critical factors determining plant architecture in maize ( Zea mays ), and leaf number is frequently used as a measure of flowering time, a trait that is key to local environmental adaptation. Here, using a large set of 866 maize‐teosinte BC 2 S 3 recombinant inbred lines genotyped by using 19 838 single nucleotide polymorphism markers, we conducted a comprehensive genetic dissection to assess the genetic architecture of leaf number and its genetic relationship to flowering time. We demonstrated that the two components of total leaf number, the number of leaves above ( LA ) and below ( LB ) the primary ear, were under relatively independent genetic control and might be subject to differential directional selection during maize domestication and improvement. Furthermore, we revealed that flowering time and leaf number are commonly regulated at a moderate level. The pleiotropy of the genes ZCN 8 , dlf1 and Zm CCT on leaf number and flowering time were validated by near‐isogenic line analysis. Through fine mapping, qLA 1‐1 , a major‐effect locus that specifically affects LA , was delimited to a region with severe recombination suppression derived from teosinte. This study provides important insights into the genetic basis of traits affecting plant architecture and adaptation. The genetic independence of LA from LB enables the optimization of leaf number for ideal plant architecture breeding in maize.}, number={1}, journal={New Phytologist}, author={Li, D. and Wang, X. and Zhang, X. and Chen, Q. and Xu, G. and Xu, D. and Wang, C. and Liang, Y. and Wu, L. and Huang, C. and et al.}, year={2016}, pages={256–268} }
 @article{chen_liu_wang_wang_lai_tian_2015, title={Transcriptome sequencing reveals the roles of transcription factors in modulating genotype by nitrogen interaction in maize}, volume={34}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84941875568&partnerID=MN8TOARS}, DOI={10.1007/s00299-015-1822-9}, abstractNote={Global transcriptome analysis in maize revealed differential nitrogen response between genotypes and implicate a crucial role of transcription factors in driving genotype by nitrogen interactions at gene expression level. Developing nitrogen-efficient cultivars are essential for sustainable and productive agriculture. Nitrogen use efficiency of plants is highly dependent on the interaction of environmental and genetic variation and results in adaptive phenotypes. This study used transcriptome sequencing to perform a comprehensive genotype by nitrogen (G × N) interaction analysis for two elite Chinese maize inbreds grown at normal and low nitrogen levels in field conditions. We demonstrated that the two maize inbreds showed contrasting agronomic and transcriptomic responses to changes in nitrogen availability. A total of 96 genes with a significant G × N interaction were detected. After characterizing the expression patterns of G × N interaction genes, we found that the G × N interaction genes tended to show condition-specific differential expression. The functional annotations of G × N interaction genes revealed that many different kinds of genes were involved in G × N interactions, but a significant enrichment for transcription factors was detected, particularly the AP2/EREBP and WRKY family, suggesting that transcription factors might play important roles in driving G × N interaction at gene expression level for nitrogen response in maize. Taken together, these results not only provide novel insights into the mechanism of nitrogen response in maize and set important basis for further characterization but also have important implications for other genotype by stress interaction.}, number={10}, journal={Plant Cell Reports}, author={Chen, Q. and Liu, Z. and Wang, B. and Wang, X. and Lai, J. and Tian, F.}, year={2015}, pages={1761–1771} }