|
Aboul-Maaty N A F, Oraby H A S. 2019. Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method. Bulletin of the National Research Centre, 43, 25.
Alemu A, Suliman S, Hagras A, Thabet S, Al-Abdallat A, Abdelmula A A, Tadesse W. 2021. Multi-model genome-wide association and genomic prediction analysis of 16 agronomic, physiological and quality related traits in ICARDA spring wheat. Euphytica, 217, 205.
Alexander D H, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19, 1655–1664.
Aregbesola E, Ortega-Beltran A, Falade T, Jonathan G, Hearne S, Bandyopadhyay R. 2020. A detached leaf assay to rapidly screen for resistance of maize to Bipolaris maydis, the causal agent of southern corn leaf blight. European Journal of Plant Pathology, 156, 133–145.
Barrett J C, Fry B, Maller J, Daly M J. 2005. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263–265.
Beyene Y, Gowda M, Suresh L M, Mugo S, Olsen M, Oikeh S O, Juma C, Tarekegne A, Prasanna B M. 2017. Genetic analysis of tropical maize inbred lines for resistance to maize lethal necrosis disease. Euphytica, 213, 224.
Bhandari A, Bartholomé J, Cao-Hamadoun T V, Kumari N, Frouin J, Kumar A, Ahmadi N. 2019. Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice. PLoS ONE, 14, e0208871.
Cerrudo D, Cao S, Yuan Y, Martinez C, Suarez E A, Babu R, Zhang X, Trachsel S. 2018. Genomic selection outperforms marker assisted selection for grain yield and physiological traits in a maize doubled haploid population across water treatments. Frontiers in Plant Science, 9, 366.
Chen C, Zhao Y, Tabor G, Nian H, Phillips J, Wolters P, Yang Q, Balint-Kurti P. 2023. A leucine-rich repeat receptor kinase gene confers quantitative susceptibility to maize southern leaf blight. New Phytologist, 238, 1182–1197.
Chen G, Xiao Y, Dai S, Dai Z, Wang X, Li B, Jaqueth J S, Li W, Lai Z, Ding J, Yan J. 2023. Genetic basis of resistance to southern corn leaf blight in the maize multi-parent population and diversity panel. Plant Biotechnology Journal, 21, 506–520.
Chen Y L, Mao X W, Wang J X, Wu L Y, Zhou M G, Hou Y P. 2018. Activity of the dinitroaniline fungicide fluazinam against Bipolaris maydis. Pesticide Biochemistry and Physiology, 148, 8–15.
Cortes C, Vapnik V. 1995. Support-vector networks. Machine Learning, 20, 273–297.
Covarrubias-Pazaran G. 2016. Genome-assisted prediction of quantitative traits using the R package sommer. PLoS ONE, 11, e0156744.
Cuevas B D, Abell A N, Johnson G L. 2007. Role of mitogen-activated protein kinase kinase kinases in signal integration. Oncogene, 26, 3159–3171.
Dai Z, Yang Q, Chen D, Li B, Que J, Hu L, Zhang B, Zhang Z, Chen K, Zhang S, Lai Z. 2023. ZmAGO18b negatively regulates maize resistance against southern leaf blight. Theoretical and Applied Genetics, 136, 158.
Danecek P, Auton A, Abecasis G, Albers C A, Banks E, DePristo M A, Handsaker R E, Lunter G, Marth G T, Sherry S T, McVean G, Durbin R, 1000 Genomes Project Analysis Group. 2011. The variant call format and VCFtools. Bioinformatics, 27, 2156–2158.
Deng C, Leonard A, Cahill J, Lv M, Li Y, Thatcher S, Li X, Zhao X, Du W, Li Z, Li H, Llaca V, Fengler K, Marshall L, Harris C, Tabor G, Li Z, Tian Z, Yang Q, Chen Y, et al. 2022. The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize. Molecular Plant, 15, 904–912.
Eggen A. 2012. The development and application of genomic selection as a new breeding paradigm. Animal Frontiers, 2, 10–15.
Endelman J B. 2011. Ridge regression and other kernels for genomic selection with R package rrBLUP. The Plant Genome, 4, 250-255.
Farooq M A, Ayyaz A, Zou H X, Zhou W, Hannan F, Yan X. 2024. Jasmonic acid mediates Ca2+ dependent signal transduction and plant immunity. Plant Science, 348, 112239.
Gao Y, Dhillon G S, Joshi P, Wheeler J, Kaur A, Chen J. 2025. Enhancing genomic predictive ability of yield and yield-related traits in spring wheat by integrating major plant adaptation genes as a fixed effect. Theoretical and Applied Genetics, 138, 290.
Guan H, Lu Y, Li X, Liu B, Li Y, Zhang D, Liu X, He G, Li Y, Wang H, Wang T, Li C. 2024. Development of a MaizeGerm50K array and application to maize genetic studies and breeding. The Crop Journal, 12, 1686–1696.
Gui S, Yang L, Li J, Luo J, Xu X, Yuan J, Chen L, Li W, Yang X, Wu S, Li S, Wang Y, Zhu Y, Gao Q, Yang N, Yan J. 2020. ZEAMAP, a comprehensive database adapted to the maize multi-omics era. iScience, 23, 101241.
Guo Z, Tucker D M, Lu J, Kishore V, Gay G. 2012. Evaluation of genome-wide selection efficiency in maize nested association mapping populations. Theoretical and Applied Genetics, 124, 261–275.
Hasan N, Choudhary S, Naaz N, Sharma N, Laskar R A. 2021. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. Journal of Genetic Engineering and Biotechnology, 19, 128.
Hooker A L. 1974. Cytoplasmic susceptibility in plant disease. Annual Review of Phytopathology, 12, 167–179.
Huang H, Zhao W, Li C, Qiao H, Song S, Yang R, Sun L, Ma J, Ma X, Wang S. 2022. SlVQ15 interacts with jasmonate-ZIM domain proteins and SlWRKY31 to regulate defense response in tomato. Plant Physiology, 190, 828–842.
Jacquin L, Cao T V, Ahmadi N. 2016. A unified and comprehensible view of parametric and kernel methods for genomic prediction with application to rice. Frontiers in Genetics, 7, 145.
Kang H M, Sul J H, Service S K, Zaitlen N A, Kong S, Freimer N B, Sabatti C, Eskin E. 2010. Variance component model to account for sample structure in genome-wide association studies. Nature Genetics, 42, 348–354.
Ke G, Meng Q, Finley T, Wang T, Chen W, Ma W, Ye Q, Liu T Y. 2017. LightGBM: A highly efficient gradient boosting decision tree. Neural Information Processing Systems, 30, 3146–3154.
Kraja A, Dudley J W, White D G. 2000. Identification of tropical and temperate maize populations having favorable alleles for disease resistance. Crop Science, 40, 948–954.
Kumar B, Choudhary M, Kumar K, Kumar P, Kumar Santosh, Bagaria P K, Sharma M, Lahkar C, Singh B K, Pradhan H, Jha A K, Kumar Sonu, Rakshit S. 2022. Maydis leaf blight of maize: Update on status, sustainable management and genetic architecture of its resistance. Physiological and Molecular Plant Pathology, 121, 101889.
Kump K L, Bradbury P J, Wisser R J, Buckler E S, Belcher A R, Oropeza-Rosas M A, Zwonitzer J C, Kresovich S, McMullen M D, Ware D, Balint-Kurti P J, Holland J B. 2011. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nature Genetics, 43, 163-168.
Letunic I, Bork P. 2021. Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Research, 49, W293–W296.
Li Y, Ruperao P, Batley J, Edwards D, Khan T, Colmer T D, Pang J, Siddique K H M, Sutton T. 2018. Investigating drought tolerance in chickpea using genome-wide association mapping and genomic selection based on whole-genome resequencing data. Frontiers in Plant Science, 9, 190.
Liu X, Huang M, Fan B, Buckler E S, Zhang Z. 2016. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genetics, 12, e1005767.
Ma D, Xie R, Yu X, Li S, Gao J. 2022. Historical trends in maize morphology from the 1950s to the 2010s in China. Journal of Integrative Agriculture, 21, 2159–2167.
Man J, Gallagher J P, Bartlett M. 2020. Structural evolution drives diversification of the large LRR-RLK gene family. New Phytologist, 226, 1492-1505.
Mangal V, Verma L K, Singh S K, Saxena K, Roy A, Karn A, Rohit R, Kashyap S, Bhatt A, Sood S. 2024. Triumphs of genomic-assisted breeding in crop improvement. Heliyon, 10, e35513.
Meuwissen T H E, Hayes B J, Goddard M E. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157, 1819–1829.
Mir Z A, Chandra T, Saharan A, Budhlakoti N, Mishra D C, Saharan M S, Mir R R, Singh A K, Sharma S, Vikas V K, Kumar S. 2023. Recent advances on genome-wide association studies (GWAS) and genomic selection (GS); prospects for Fusarium head blight research in Durum wheat. Molecular Biology Reports, 50, 3885–3901.
Mou S, Shi L, Lin W, Liu Y, Shen L, Guan D, He S. 2015. Over-expression of rice CBS domain containing protein, OsCBSX3, confers rice resistance to Magnaporthe oryzae inoculation. International Journal of Molecular Sciences, 16, 15903–15917.
Paire L, McCabe C, McCabe T. 2024. Multi-model genome-wide association study on key organic naked barley agronomic, phenological, diseases, and grain quality traits. Euphytica, 220, 118.
Pickrell J K, Pritchard J K. 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics, 8, e1002967.
Piepho H P, Möhring J. 2007. Computing heritability and selection response from unbalanced plant breeding trials. Genetics, 177, 1881–1888.
Price M N, Dehal P S, Arkin A P. 2010. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE, 5, e9490.
Qiu D, Xiao J, Xie W, Cheng H, Li X, Wang S. 2009. Exploring transcriptional signaling mediated by OsWRKY13, a potential regulator of multiple physiological processes in rice. BMC Plant Biology, 9, 74.
Rashid Z, Sofi M, Harlapur S I, Kachapur R M, Dar Z A, Singh P K, Zaidi P H, Vivek B S, Nair S K. 2020. Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to northern corn leaf blight. Scientific Reports, 10, 21949.
Ravelombola W, Qin J, Shi A, Song Q, Yuan J, Wang F, Chen P, Yan L, Feng Y, Zhao T, Meng Y, Guan K, Yang C, Zhang M. 2021. Genome-wide association study and genomic selection for yield and related traits in soybean. PLoS ONE, 16, e0255761.
Sachdeva S, Singh R, Maurya A, Singh V K, Singh U M, Kumar A, Singh G P. 2024. Multi-model genome-wide association studies for appearance quality in rice. Frontiers in Plant Science, 14, 1304388.
Sarinelli J M, Murphy J P, Tyagi P, Holland J B, Johnson J W, Mergoum M, Mason R E, Babar A, Harrison S, Sutton R, Griffey C A, Brown-Guedira G. 2019. Training population selection and use of fixed effects to optimize genomic predictions in a historical USA winter wheat panel. Theoretical and Applied Genetics, 132, 1247–1261.
Sehgal D, Rosyara U, Mondal S, Singh R, Poland J, Dreisigacker S. 2020. Incorporating genome-wide association mapping results into genomic prediction models for grain yield and yield stability in CIMMYT spring bread wheat. Frontiers in Plant Science, 11, 197.
Sood S, Bhardwaj V, Bairwa A, Dalamu, Sharma S, Sharma A K, Kumar A, Lal M, Kumar V. 2023. Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.). Frontiers in Plant Science, 14, 1211472.
Spindel J E, Begum H, Akdemir D, Collard B, Redoña E, Jannink J L, McCouch S. 2016. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement. Heredity, 116, 395–408.
Sun J, Yang B, Xia L, Yang R, Ding C, Sun Y, Chen X, Gu C, Yang X, Chen Y. 2025. Amino acid substitutions in succinate dehydrogenase complex conferring resistance to the SDHI fungicide pydiflumetofen in Cochliobolus heterostrophus causing southern corn leaf blight. Journal of Integrative Agriculture, 24, 2670–2685.
VanRaden P M. 2008. Efficient methods to compute genomic predictions. Journal of Dairy Science, 91, 4414–4423.
Wang H, Hou J, Ye P, Hu L, Huang J, Dai Z, Zhang B, Dai S, Que J, Min H, Chen G, Wang Y, Jiang M, Liang Y, Li L, Zhang X, Lai Z. 2021. A teosinte-derived allele of a MYB transcription repressor confers multiple disease resistance in maize. Molecular Plant, 14, 1846–1863.
Wang J, Liu X, Zhang A, Ren Y, Wu F, Wang G, Xu Y, Lei C, Zhu S, Pan T, Wang Y F, Zhang H, Wang F, Tan Y Q, Wang Y P, Jin X, Luo S, Zhou C, Zhang X, Liu J, et al. 2019. A cyclic nucleotide-gated channel mediates cytoplasmic calcium elevation and disease resistance in rice. Cell Research, 29, 820–831.
Wang J, Tang Y, Zhang Z. 2022. Performing genome-wide association studies with multiple models using GAPIT. Methods in Molecular Biology, 2481, 199-217.
Wang J, Zhang Z. 2021. GAPIT version 3: Boosting power and accuracy for genomic Association and prediction. Genomics Proteomics & Bioinformatics, 19, 629–640.
Wang X, Xu Y, Hu Z, Xu C. 2018. Genomic selection methods for crop improvement: Current status and prospects. The Crop Journal, 6, 330–340.
Welz H G, Geiger H H. 2000. Genes for resistance to northern corn leaf blight in diverse maize populations. Plant Breeding, 119, 1–14.
Woodhouse M R, Cannon E K, Portwood J L, Harper L C, Gardiner J M, Schaeffer M L, Andorf C M. 2021. A pan-genomic approach to genome databases using maize as a model system. BMC Plant Biology, 21, 385.
Xu X, Wang H, Liu J, Han S, Lin M, Guo Z, Chen X. 2022. OsWRKY62 and OsWRKY76 interact with importin α1s for negative regulation of defensive responses in rice nucleus. Rice, 15, 12. Yang Q, He Y, Kabahuma M, Chaya T, Kelly A, Borrego E, Bian Y, El Kasmi F, Yang L, Teixeira P, Kolkman J, Nelson R, Kolomiets M, Dangl J L, Wisser R, Caplan J, Li X, Lauter N, Balint-Kurti P. 2017. A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens. Nature Genetics, 49, 1364-1372.
Yuan M, Jiang Z, Bi G, Nomura K, Liu M, Wang Y, Cai B, Zhou J M, He S Y, Xin X F. 2021. Pattern-recognition receptors are required for NLR-mediated plant immunity. Nature, 592, 105–109.
Zhang C, Dong S S, Xu J Y, He W M, Yang T L. 2019. PopLDdecay: A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics, 35, 1786–1788.
Zhang J, Jia X, Wang G F, Ma S, Wang S, Yang Q, Chen X, Zhang Y, Lyu Y, Wang X, Shi J, Zhao Y, Chen Y, Wu L. 2022. Ascorbate peroxidase 1 confers resistance to southern corn leaf blight in maize. Journal of Integrative Plant Biology, 64, 1196–1211.
Zhang Y, Zhang M, Ye J, Xu Q, Feng Y, Xu S, Hu D, Wei X, Hu P, Yang Y. 2023. Integrating genome-wide association study into genomic selection for the prediction of agronomic traits in rice (Oryza sativa L.). Molecular Breeding, 43, 81.
Zhao Y, Mette M F, Reif J C. 2015. Genomic selection in hybrid breeding. Plant Breeding, 134, 1–10.
Zhou X, Stephens M. 2012. Genome-wide efficient mixed-model analysis for association studies. Nature Genetics, 44, 821–824.
Zila C T, Samayoa L F, Santiago R, Butrón A, Holland J B. 2013. A genome-wide association study reveals genes associated with fusarium ear rot resistance in a maize core diversity panel. G3: Genes, Genomes, Genetics, 3, 2095–2104.
Zou H, Hastie T. 2005. Regularization and variable selection via the elastic net. Journal of the Royal Statistical Society Series B (Statistical Methodology), 67, 301–320.
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