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Identifying loci with breeding potential across temperate and tropical adaptation via EigenGWAS and EnvGWAS.

Li J, Chen GB, Rasheed A, Li D, Sonder K, Zavala Espinosa C, Wang J, Costich DE, Schnable PS, Hearne SJ, Li H.

Mol Ecol. 2019 Jul 9. doi: 10.1111/mec.15169. [Epub ahead of print]


Identification of Loci Controlling Adaptation in Chinese Soybean Landraces via a Combination of Conventional and Bioclimatic GWAS.

Li YH, Li D, Jiao YQ, Schnable JC, Li YF, Li HH, Chen HZ, Hong HL, Zhang T, Liu B, Liu ZX, You QB, Tian Y, Guo Y, Guan RX, Zhang LJ, Chang RZ, Zhang Z, Reif J, Zhou XA, Schnable PS, Qiu LJ.

Plant Biotechnol J. 2019 Jul 6. doi: 10.1111/pbi.13206. [Epub ahead of print]


Optimizing Selection and Mating in Genomic Selection with a Look-Ahead Approach: An Operations Research Framework.

Moeinizade S, Hu G, Wang L, Schnable PS.

G3 (Bethesda). 2019 Jul 9;9(7):2123-2133. doi: 10.1534/g3.118.200842.


Maize glossy6 is involved in cuticular wax deposition and drought tolerance.

Li L, Du Y, He C, Dietrich CR, Li J, Ma X, Wang R, Liu Q, Liu S, Wang G, Schnable PS, Zheng J.

J Exp Bot. 2019 Jun 28;70(12):3089-3099. doi: 10.1093/jxb/erz131.


Development of Decreased-Gluten Wheat Enabled by Determination of the Genetic Basis of lys3a Barley.

Moehs CP, Austill WJ, Holm A, Large TAG, Loeffler D, Mullenberg J, Schnable PS, Skinner W, van Boxtel J, Wu L, McGuire C.

Plant Physiol. 2019 Apr;179(4):1692-1703. doi: 10.1104/pp.18.00771. Epub 2019 Jan 29.


The genome of broomcorn millet.

Zou C, Li L, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Jia W, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable PS, Chang Y, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu JK, Zhang H.

Nat Commun. 2019 Jan 25;10(1):436. doi: 10.1038/s41467-019-08409-5.


Semiautomated Feature Extraction from RGB Images for Sorghum Panicle Architecture GWAS.

Zhou Y, Srinivasan S, Mirnezami SV, Kusmec A, Fu Q, Attigala L, Salas Fernandez MG, Ganapathysubramanian B, Schnable PS.

Plant Physiol. 2019 Jan;179(1):24-37. doi: 10.1104/pp.18.00974. Epub 2018 Nov 2.


Co-expression analysis aids in the identification of genes in the cuticular wax pathway in maize.

Zheng J, He C, Qin Y, Lin G, Park WD, Sun M, Li J, Lu X, Zhang C, Yeh CT, Gunasekara CJ, Zeng E, Wei H, Schnable PS, Wang G, Liu S.

Plant J. 2019 Feb;97(3):530-542. doi: 10.1111/tpj.14140. Epub 2018 Dec 7.


ZmMADS69 functions as a flowering activator through the ZmRap2.7-ZCN8 regulatory module and contributes to maize flowering time adaptation.

Liang Y, Liu Q, Wang X, Huang C, Xu G, Hey S, Lin HY, Li C, Xu D, Wu L, Wang C, Wu W, Xia J, Han X, Lu S, Lai J, Song W, Schnable PS, Tian F.

New Phytol. 2019 Mar;221(4):2335-2347. doi: 10.1111/nph.15512. Epub 2018 Oct 30.


Harnessing Phenotypic Plasticity to Improve Maize Yields.

Kusmec A, de Leon N, Schnable PS.

Front Plant Sci. 2018 Sep 19;9:1377. doi: 10.3389/fpls.2018.01377. eCollection 2018.


FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana.

Guo H, Nolan TM, Song G, Liu S, Xie Z, Chen J, Schnable PS, Walley JW, Yin Y.

Curr Biol. 2018 Oct 22;28(20):3316-3324.e6. doi: 10.1016/j.cub.2018.07.078. Epub 2018 Sep 27.


Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize.

Yang J, Yeh CE, Ramamurthy RK, Qi X, Fernando RL, Dekkers JCM, Garrick DJ, Nettleton D, Schnable PS.

G3 (Bethesda). 2018 Nov 6;8(11):3567-3575. doi: 10.1534/g3.118.200636.


Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels.

Liu S, Schnable JC, Ott A, Yeh CE, Springer NM, Yu J, Muehlbauer G, Timmermans MCP, Scanlon MJ, Schnable PS.

Mol Biol Evol. 2018 Nov 1;35(11):2762-2772. doi: 10.1093/molbev/msy174.


Linked read technology for assembling large complex and polyploid genomes.

Ott A, Schnable JC, Yeh CT, Wu L, Liu C, Hu HC, Dalgard CL, Sarkar S, Schnable PS.

BMC Genomics. 2018 Sep 4;19(1):651. doi: 10.1186/s12864-018-5040-z.


Correction to: Genome-wide discovery and characterization of maize long non-coding RNAs.

Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MMS, Scanlon MJ, Yu J, Schnable PS, Timmermans MCP, Springer NM, Muehlbauer GJ.

Genome Biol. 2018 Aug 23;19(1):122. doi: 10.1186/s13059-018-1508-z.


Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes.

Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, Song W, Zhang M, Cui Y, Dong X, Liu H, Ma X, Jiao Y, Wang B, Wei X, Stein JC, Glaubitz JC, Lu F, Yu G, Liang C, Fengler K, Li B, Rafalski A, Schnable PS, Ware DH, Buckler ES, Lai J.

Nat Genet. 2018 Sep;50(9):1289-1295. doi: 10.1038/s41588-018-0182-0. Epub 2018 Jul 30.


Exploiting the Genomic Diversity of Rice (Oryza sativa L.): SNP-Typing in 11 Early-Backcross Introgression-Breeding Populations.

Ali J, Aslam UM, Tariq R, Murugaiyan V, Schnable PS, Li D, Marfori-Nazarea CM, Hernandez JE, Arif M, Xu J, Li Z.

Front Plant Sci. 2018 Jun 22;9:849. doi: 10.3389/fpls.2018.00849. eCollection 2018.


Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets.

AlKhalifah N, Campbell DA, Falcon CM, Gardiner JM, Miller ND, Romay MC, Walls R, Walton R, Yeh CT, Bohn M, Bubert J, Buckler ES, Ciampitti I, Flint-Garcia S, Gore MA, Graham C, Hirsch C, Holland JB, Hooker D, Kaeppler S, Knoll J, Lauter N, Lee EC, Lorenz A, Lynch JP, Moose SP, Murray SC, Nelson R, Rocheford T, Rodriguez O, Schnable JC, Scully B, Smith M, Springer N, Thomison P, Tuinstra M, Wisser RJ, Xu W, Ertl D, Schnable PS, De Leon N, Spalding EP, Edwards J, Lawrence-Dill CJ.

BMC Res Notes. 2018 Jul 9;11(1):452. doi: 10.1186/s13104-018-3508-1.


Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids.

Liang Z, Gupta SK, Yeh CT, Zhang Y, Ngu DW, Kumar R, Patil HT, Mungra KD, Yadav DV, Rathore A, Srivastava RK, Gupta R, Yang J, Varshney RK, Schnable PS, Schnable JC.

G3 (Bethesda). 2018 Jul 2;8(7):2513-2522. doi: 10.1534/g3.118.200242.


FarmCPUpp: Efficient large-scale genomewide association studies.

Kusmec A, Schnable PS.

Plant Direct. 2018 Apr 10;2(4):e00053. doi: 10.1002/pld3.53. eCollection 2018 Apr.


Correction: Mendelian and Non-Mendelian Regulation of Gene Expression in Maize.

Li L, Petsch K, Shimizu R, Liu S, Xu WW, Ying K, Yu J, Scanlon MJ, Schnable PS, Timmermans MCP, Springer NM, Muehlbauer GJ.

PLoS Genet. 2018 Feb 14;14(2):e1007234. doi: 10.1371/journal.pgen.1007234. eCollection 2018 Feb.


Genotype-by-environment interactions affecting heterosis in maize.

Li Z, Coffey L, Garfin J, Miller ND, White MR, Spalding EP, de Leon N, Kaeppler SM, Schnable PS, Springer NM, Hirsch CN.

PLoS One. 2018 Jan 17;13(1):e0191321. doi: 10.1371/journal.pone.0191321. eCollection 2018.


Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize.

Chen L, Zhang P, Fan Y, Lu Q, Li Q, Yan J, Muehlbauer GJ, Schnable PS, Dai M, Li L.

New Phytol. 2018 Feb;217(3):1292-1306. doi: 10.1111/nph.14901. Epub 2017 Nov 20.


Distinct genetic architectures for phenotype means and plasticities in Zea mays.

Kusmec A, Srinivasan S, Nettleton D, Schnable PS.

Nat Plants. 2017 Sep;3(9):715-723. doi: 10.1038/s41477-017-0007-7. Epub 2017 Sep 4.


The effect of artificial selection on phenotypic plasticity in maize.

Gage JL, Jarquin D, Romay C, Lorenz A, Buckler ES, Kaeppler S, Alkhalifah N, Bohn M, Campbell DA, Edwards J, Ertl D, Flint-Garcia S, Gardiner J, Good B, Hirsch CN, Holland J, Hooker DC, Knoll J, Kolkman J, Kruger G, Lauter N, Lawrence-Dill CJ, Lee E, Lynch J, Murray SC, Nelson R, Petzoldt J, Rocheford T, Schnable J, Schnable PS, Scully B, Smith M, Springer NM, Srinivasan S, Walton R, Weldekidan T, Wisser RJ, Xu W, Yu J, de Leon N.

Nat Commun. 2017 Nov 7;8(1):1348. doi: 10.1038/s41467-017-01450-2.


Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS.

Lin HY, Liu Q, Li X, Yang J, Liu S, Huang Y, Scanlon MJ, Nettleton D, Schnable PS.

Genome Biol. 2017 Oct 17;18(1):192. doi: 10.1186/s13059-017-1328-6.


tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci.

Ott A, Liu S, Schnable JC, Yeh C', Wang KS, Schnable PS.

Nucleic Acids Res. 2017 Dec 1;45(21):e178. doi: 10.1093/nar/gkx853.


A High-Throughput, Field-Based Phenotyping Technology for Tall Biomass Crops.

Salas Fernandez MG, Bao Y, Tang L, Schnable PS.

Plant Physiol. 2017 Aug;174(4):2008-2022. doi: 10.1104/pp.17.00707. Epub 2017 Jun 15.


A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize.

Mei W, Liu S, Schnable JC, Yeh CT, Springer NM, Schnable PS, Barbazuk WB.

Front Plant Sci. 2017 May 10;8:694. doi: 10.3389/fpls.2017.00694. eCollection 2017.


Improving Response in Genomic Selection with a Population-Based Selection Strategy: Optimal Population Value Selection.

Goiffon M, Kusmec A, Wang L, Hu G, Schnable PS.

Genetics. 2017 Jul;206(3):1675-1682. doi: 10.1534/genetics.116.197103. Epub 2017 May 19.


RD26 mediates crosstalk between drought and brassinosteroid signalling pathways.

Ye H, Liu S, Tang B, Chen J, Xie Z, Nolan TM, Jiang H, Guo H, Lin HY, Li L, Wang Y, Tong H, Zhang M, Chu C, Li Z, Aluru M, Aluru S, Schnable PS, Yin Y.

Nat Commun. 2017 Feb 24;8:14573. doi: 10.1038/ncomms14573.


Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias.

Li L, Briskine R, Schaefer R, Schnable PS, Myers CL, Flagel LE, Springer NM, Muehlbauer GJ.

BMC Genomics. 2016 Nov 4;17(1):875.


Characterization of maize roothairless6 which encodes a D-type cellulose synthase and controls the switch from bulge formation to tip growth.

Li L, Hey S, Liu S, Liu Q, McNinch C, Hu HC, Wen TJ, Marcon C, Paschold A, Bruce W, Schnable PS, Hochholdinger F.

Sci Rep. 2016 Oct 6;6:34395. doi: 10.1038/srep34395.


Genomic prediction contributing to a promising global strategy to turbocharge gene banks.

Yu X, Li X, Guo T, Zhu C, Wu Y, Mitchell SE, Roozeboom KL, Wang D, Wang ML, Pederson GA, Tesso TT, Schnable PS, Bernardo R, Yu J.

Nat Plants. 2016 Oct 3;2:16150. doi: 10.1038/nplants.2016.150.


Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations.

Yáñez JM, Naswa S, López ME, Bassini L, Correa K, Gilbey J, Bernatchez L, Norris A, Neira R, Lhorente JP, Schnable PS, Newman S, Mileham A, Deeb N, Di Genova A, Maass A.

Mol Ecol Resour. 2016 Jul;16(4):1002-11. doi: 10.1111/1755-0998.12503. Epub 2016 Mar 1.


Genetic control of morphometric diversity in the maize shoot apical meristem.

Leiboff S, Li X, Hu HC, Todt N, Yang J, Li X, Yu X, Muehlbauer GJ, Timmermans MC, Yu J, Schnable PS, Scanlon MJ.

Nat Commun. 2015 Nov 20;6:8974. doi: 10.1038/ncomms9974.


Laser Microdissection-Mediated Isolation and In Vitro Transcriptional Amplification of Plant RNA.

Chandran D, Scanlon MJ, Ohtsu K, Timmermans MC, Schnable PS, Wildermuth MC.

Curr Protoc Mol Biol. 2015 Oct 1;112:25A.3.1-23. doi: 10.1002/0471142727.mb25a03s112.


Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel.

Yang J, Jiang H, Yeh CT, Yu J, Jeddeloh JA, Nettleton D, Schnable PS.

Plant J. 2015 Nov;84(3):587-96. doi: 10.1111/tpj.13029.


The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots.

Zhang Y, Paschold A, Marcon C, Liu S, Tai H, Nestler J, Yeh CT, Opitz N, Lanz C, Schnable PS, Hochholdinger F.

J Exp Bot. 2015 Sep;66(19):6081. doi: 10.1093/jxb/erv354. Epub 2015 Jul 23. No abstract available.


ALLMAPS: robust scaffold ordering based on multiple maps.

Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu J.

Genome Biol. 2015 Jan 13;16:3. doi: 10.1186/s13059-014-0573-1.


The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase.

Li L, Hill-Skinner S, Liu S, Beuchle D, Tang HM, Yeh CT, Nettleton D, Schnable PS.

Plant J. 2015 Feb;81(3):493-504. doi: 10.1111/tpj.12745. Epub 2015 Jan 9. Erratum in: Plant J. 2017 Mar;89(5):1076.


Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids.

Paschold A, Larson NB, Marcon C, Schnable JC, Yeh CT, Lanz C, Nettleton D, Piepho HP, Schnable PS, Hochholdinger F.

Plant Cell. 2014 Oct;26(10):3939-48. doi: 10.1105/tpc.114.130948. Epub 2014 Oct 14.


The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots.

Zhang Y, Paschold A, Marcon C, Liu S, Tai H, Nestler J, Yeh CT, Opitz N, Lanz C, Schnable PS, Hochholdinger F.

J Exp Bot. 2014 Sep;65(17):4919-30. doi: 10.1093/jxb/eru249. Epub 2014 Jun 13. Erratum in: J Exp Bot. 2015 Sep;66(19):6081.


Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase.

Nestler J, Liu S, Wen TJ, Paschold A, Marcon C, Tang HM, Li D, Li L, Meeley RB, Sakai H, Bruce W, Schnable PS, Hochholdinger F.

Plant J. 2014 Sep;79(5):729-40. doi: 10.1111/tpj.12578. Epub 2014 Jul 15.


Genetic control of maize shoot apical meristem architecture.

Thompson AM, Crants J, Schnable PS, Yu J, Timmermans MC, Springer NM, Scanlon MJ, Muehlbauer GJ.

G3 (Bethesda). 2014 May 22;4(7):1327-37. doi: 10.1534/g3.114.011940.


Histone lysine methyltransferase SDG8 is involved in brassinosteroid-regulated gene expression in Arabidopsis thaliana.

Wang X, Chen J, Xie Z, Liu S, Nolan T, Ye H, Zhang M, Guo H, Schnable PS, Li Z, Yin Y.

Mol Plant. 2014 Aug;7(8):1303-1315. doi: 10.1093/mp/ssu056. Epub 2014 May 16.


Genome-wide analysis of regulation of gene expression and H3K9me2 distribution by JIL-1 kinase mediated histone H3S10 phosphorylation in Drosophila.

Cai W, Wang C, Li Y, Yao C, Shen L, Liu S, Bao X, Schnable PS, Girton J, Johansen J, Johansen KM.

Nucleic Acids Res. 2014 May;42(9):5456-67. doi: 10.1093/nar/gku173. Epub 2014 Mar 5.


Genome-wide discovery and characterization of maize long non-coding RNAs.

Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MM, Scanlon MJ, Yu J, Schnable PS, Timmermans MC, Springer NM, Muehlbauer GJ.

Genome Biol. 2014 Feb 27;15(2):R40. doi: 10.1186/gb-2014-15-2-r40. Erratum in: Genome Biol. 2018 Aug 23;19(1):122.


The maize glossy13 gene, cloned via BSR-Seq and Seq-walking encodes a putative ABC transporter required for the normal accumulation of epicuticular waxes.

Li L, Li D, Liu S, Ma X, Dietrich CR, Hu HC, Zhang G, Liu Z, Zheng J, Wang G, Schnable PS.

PLoS One. 2013 Dec 6;8(12):e82333. doi: 10.1371/journal.pone.0082333. eCollection 2013. Erratum in: PLoS One. 2014;9(5):e99563.


The maize brown midrib2 (bm2) gene encodes a methylenetetrahydrofolate reductase that contributes to lignin accumulation.

Tang HM, Liu S, Hill-Skinner S, Wu W, Reed D, Yeh CT, Nettleton D, Schnable PS.

Plant J. 2014 Feb;77(3):380-92. doi: 10.1111/tpj.12394. Epub 2014 Jan 10.

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