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The genetic structure of flax illustrates environmental and anthropogenic selections that gave rise to its eco-geographical adaptation.

Sertse D, You FM, Ravichandran S, Cloutier S.

Mol Phylogenet Evol. 2019 Aug;137:22-32. doi: 10.1016/j.ympev.2019.04.010. Epub 2019 Apr 9.


Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species.

Zhu T, Wang L, You FM, Rodriguez JC, Deal KR, Chen L, Li J, Chakraborty S, Balan B, Jiang CZ, Brown PJ, Leslie CA, Aradhya MK, Dandekar AM, McGuire PE, Kluepfel D, Dvorak J, Luo MC.

Hortic Res. 2019 Mar 25;6:55. doi: 10.1038/s41438-019-0139-1. eCollection 2019.


Genome-Wide Association Studies for Pasmo Resistance in Flax (Linum usitatissimum L.).

He L, Xiao J, Rashid KY, Yao Z, Li P, Jia G, Wang X, Cloutier S, You FM.

Front Plant Sci. 2019 Jan 14;9:1982. doi: 10.3389/fpls.2018.01982. eCollection 2018.


Evaluation of Genomic Prediction for Pasmo Resistance in Flax.

He L, Xiao J, Rashid KY, Jia G, Li P, Yao Z, Wang X, Cloutier S, You FM.

Int J Mol Sci. 2019 Jan 16;20(2). pii: E359. doi: 10.3390/ijms20020359.


Genome-wide regulatory gene-derived SSRs reveal genetic differentiation and population structure in fiber flax genotypes.

Saha D, Rana RS, Das S, Datta S, Mitra J, Cloutier SJ, You FM.

J Appl Genet. 2019 Feb;60(1):13-25. doi: 10.1007/s13353-018-0476-z. Epub 2018 Oct 27.


Genome-Wide Association Analysis of Mucilage and Hull Content in Flax (Linum usitatissimum L.) Seeds.

Soto-Cerda BJ, Cloutier S, Quian R, Gajardo HA, Olivos M, You FM.

Int J Mol Sci. 2018 Sep 21;19(10). pii: E2870. doi: 10.3390/ijms19102870.


Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax.

You FM, Xiao J, Li P, Yao Z, Jia G, He L, Kumar S, Soto-Cerda B, Duguid SD, Booker HM, Rashid KY, Cloutier S.

Int J Mol Sci. 2018 Aug 6;19(8). pii: E2303. doi: 10.3390/ijms19082303.


Rht23 (5Dq') likely encodes a Q homeologue with pleiotropic effects on plant height and spike compactness.

Zhao K, Xiao J, Liu Y, Chen S, Yuan C, Cao A, You FM, Yang D, An S, Wang H, Wang X.

Theor Appl Genet. 2018 Sep;131(9):1825-1834. doi: 10.1007/s00122-018-3115-5. Epub 2018 May 31.


Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size.

Dvorak J, Wang L, Zhu T, Jorgensen CM, Deal KR, Dai X, Dawson MW, Müller HG, Luo MC, Ramasamy RK, Dehghani H, Gu YQ, Gill BS, Distelfeld A, Devos KM, Qi P, You FM, Gulick PJ, McGuire PE.

Plant J. 2018 Aug;95(3):487-503. doi: 10.1111/tpj.13964. Epub 2018 Jun 17.


Chromosome-scale pseudomolecules refined by optical, physical and genetic maps in flax.

You FM, Xiao J, Li P, Yao Z, Jia G, He L, Zhu T, Luo MC, Wang X, Deyholos MK, Cloutier S.

Plant J. 2018 Jul;95(2):371-384. doi: 10.1111/tpj.13944. Epub 2018 May 21.


Genetic analysis and QTL mapping of the seed hardness trait in a black common bean (Phaseolus vulgaris) recombinant inbred line (RIL) population.

Sandhu KS, You FM, Conner RL, Balasubramanian PM, Hou A.

Mol Breed. 2018;38(3):34. doi: 10.1007/s11032-018-0789-y. Epub 2018 Feb 23.


Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J.

Nature. 2017 Nov 23;551(7681):498-502. doi: 10.1038/nature24486. Epub 2017 Nov 15.


Genetic Variability of 27 Traits in a Core Collection of Flax (Linum usitatissimum L.).

You FM, Jia G, Xiao J, Duguid SD, Rashid KY, Booker HM, Cloutier S.

Front Plant Sci. 2017 Sep 21;8:1636. doi: 10.3389/fpls.2017.01636. eCollection 2017.


Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides.

Ren J, Chen L, Jin X, Zhang M, You FM, Wang J, Frenkel V, Yin X, Nevo E, Sun D, Luo MC, Peng J.

Front Plant Sci. 2017 Mar 14;8:258. doi: 10.3389/fpls.2017.00258. eCollection 2017.


Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16.

Kassa MT, You FM, Hiebert CW, Pozniak CJ, Fobert PR, Sharpe AG, Menzies JG, Humphreys DG, Rezac Harrison N, Fellers JP, McCallum BD, McCartney CA.

BMC Plant Biol. 2017 Feb 15;17(1):45. doi: 10.1186/s12870-017-0993-7.


UGT74S1 is the key player in controlling secoisolariciresinol diglucoside (SDG) formation in flax.

Fofana B, Ghose K, McCallum J, You FM, Cloutier S.

BMC Plant Biol. 2017 Feb 2;17(1):35. doi: 10.1186/s12870-017-0982-x.


Pseudogenes and Their Genome-Wide Prediction in Plants.

Xiao J, Sekhwal MK, Li P, Ragupathy R, Cloutier S, Wang X, You FM.

Int J Mol Sci. 2016 Nov 28;17(12). pii: E1991. Review.


RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants.

Li P, Quan X, Jia G, Xiao J, Cloutier S, You FM.

BMC Genomics. 2016 Nov 2;17(1):852.


Genetics and mapping of seedling resistance to Ug99 stem rust in winter wheat cultivar Triumph 64 and differentiation of SrTmp, SrCad, and Sr42.

Hiebert CW, Kassa MT, McCartney CA, You FM, Rouse MN, Fobert P, Fetch TG.

Theor Appl Genet. 2016 Nov;129(11):2171-2177. Epub 2016 Aug 9.


PIECE 2.0: an update for the plant gene structure comparison and evolution database.

Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D.

Nucleic Acids Res. 2017 Jan 4;45(D1):1015-1020. doi: 10.1093/nar/gkw935. Epub 2016 Oct 13.


A saturated SNP linkage map for the orange wheat blossom midge resistance gene Sm1.

Kassa MT, Haas S, Schliephake E, Lewis C, You FM, Pozniak CJ, Krämer I, Perovic D, Sharpe AG, Fobert PR, Koch M, Wise IL, Fenwick P, Berry S, Simmonds J, Hourcade D, Senellart P, Duchalais L, Robert O, Förster J, Thomas JB, Friedt W, Ordon F, Uauy C, McCartney CA.

Theor Appl Genet. 2016 Aug;129(8):1507-17. doi: 10.1007/s00122-016-2720-4. Epub 2016 May 9.


GSP: a web-based platform for designing genome-specific primers in polyploids.

Wang Y, Tiwari VK, Rawat N, Gill BS, Huo N, You FM, Coleman-Derr D, Gu YQ.

Bioinformatics. 2016 Aug 1;32(15):2382-3. doi: 10.1093/bioinformatics/btw134. Epub 2016 Mar 9.


Genetic mapping of SrCad and SNP marker development for marker-assisted selection of Ug99 stem rust resistance in wheat.

Kassa MT, You FM, Fetch TG, Fobert P, Sharpe A, Pozniak CJ, Menzies JG, Jordan MC, Humphreys G, Zhu T, Luo MC, McCartney CA, Hiebert CW.

Theor Appl Genet. 2016 Jul;129(7):1373-1382. doi: 10.1007/s00122-016-2709-z. Epub 2016 Apr 18.


Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials.

Luo MC, You FM, Li P, Wang JR, Zhu T, Dandekar AM, Leslie CA, Aradhya M, McGuire PE, Dvorak J.

BMC Genomics. 2015 Sep 17;16:707. doi: 10.1186/s12864-015-1906-5.


Disease Resistance Gene Analogs (RGAs) in Plants.

Sekhwal MK, Li P, Lam I, Wang X, Cloutier S, You FM.

Int J Mol Sci. 2015 Aug 14;16(8):19248-90. doi: 10.3390/ijms160819248. Review.


QTL for fatty acid composition and yield in linseed (Linum usitatissimum L.).

Kumar S, You FM, Duguid S, Booker H, Rowland G, Cloutier S.

Theor Appl Genet. 2015 May;128(5):965-84. doi: 10.1007/s00122-015-2483-3. Epub 2015 Mar 8.


Identification of candidate genes, regions and markers for pre-harvest sprouting resistance in wheat (Triticum aestivum L.).

Cabral AL, Jordan MC, McCartney CA, You FM, Humphreys DG, MacLachlan R, Pozniak CJ.

BMC Plant Biol. 2014 Nov 29;14:340. doi: 10.1186/s12870-014-0340-1.


Cassava genome from a wild ancestor to cultivated varieties.

Wang W, Feng B, Xiao J, Xia Z, Zhou X, Li P, Zhang W, Wang Y, Møller BL, Zhang P, Luo MC, Xiao G, Liu J, Yang J, Chen S, Rabinowicz PD, Chen X, Zhang HB, Ceballos H, Lou Q, Zou M, Carvalho LJ, Zeng C, Xia J, Sun S, Fu Y, Wang H, Lu C, Ruan M, Zhou S, Wu Z, Liu H, Kannangara RM, Jørgensen K, Neale RL, Bonde M, Heinz N, Zhu W, Wang S, Zhang Y, Pan K, Wen M, Ma PA, Li Z, Hu M, Liao W, Hu W, Zhang S, Pei J, Guo A, Guo J, Zhang J, Zhang Z, Ye J, Ou W, Ma Y, Liu X, Tallon LJ, Galens K, Ott S, Huang J, Xue J, An F, Yao Q, Lu X, Fregene M, López-Lavalle LA, Wu J, You FM, Chen M, Hu S, Wu G, Zhong S, Ling P, Chen Y, Wang Q, Liu G, Liu B, Li K, Peng M.

Nat Commun. 2014 Oct 10;5:5110. doi: 10.1038/ncomms6110.


Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.).

Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O, Luo MC.

Funct Integr Genomics. 2014 Mar;14(1):59-73. doi: 10.1007/s10142-014-0363-6. Epub 2014 Mar 8.


SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors.

Ren J, Chen L, Sun D, You FM, Wang J, Peng Y, Nevo E, Beiles A, Sun D, Luo MC, Peng J.

BMC Evol Biol. 2013 Aug 13;13:169. doi: 10.1186/1471-2148-13-169.


Genetic variation of six desaturase genes in flax and their impact on fatty acid composition.

Thambugala D, Duguid S, Loewen E, Rowland G, Booker H, You FM, Cloutier S.

Theor Appl Genet. 2013 Oct;126(10):2627-41. doi: 10.1007/s00122-013-2161-2. Epub 2013 Aug 9.


Arguments for standardizing transposable element annotation in plant genomes.

Ragupathy R, You FM, Cloutier S.

Trends Plant Sci. 2013 Jul;18(7):367-76. doi: 10.1016/j.tplants.2013.03.005. Epub 2013 Apr 23. Review.


A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.

Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen CM, Zhang Y, McGuire PE, Pasternak S, Stein JC, Ware D, Kramer M, McCombie WR, Kianian SF, Martis MM, Mayer KF, Sehgal SK, Li W, Gill BS, Bevan MW, Simková H, Dolezel J, Weining S, Lazo GR, Anderson OD, Dvorak J.

Proc Natl Acad Sci U S A. 2013 May 7;110(19):7940-5. doi: 10.1073/pnas.1219082110. Epub 2013 Apr 22.


Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat.

Ren J, Sun D, Chen L, You FM, Wang J, Peng Y, Nevo E, Sun D, Luo MC, Peng J.

Int J Mol Sci. 2013 Mar 28;14(4):7061-88. doi: 10.3390/ijms14047061.


Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat.

Wang J, Luo MC, Chen Z, You FM, Wei Y, Zheng Y, Dvorak J.

New Phytol. 2013 May;198(3):925-37. doi: 10.1111/nph.12164. Epub 2013 Feb 4.


Insular organization of gene space in grass genomes.

Gottlieb A, Müller HG, Massa AN, Wanjugi H, Deal KR, You FM, Xu X, Gu YQ, Luo MC, Anderson OD, Chan AP, Rabinowicz P, Devos KM, Dvorak J.

PLoS One. 2013;8(1):e54101. doi: 10.1371/journal.pone.0054101. Epub 2013 Jan 11.


Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries.

Kumar S, You FM, Cloutier S.

BMC Genomics. 2012 Dec 6;13:684. doi: 10.1186/1471-2164-13-684.


PIECE: a database for plant gene structure comparison and evolution.

Wang Y, You FM, Lazo GR, Luo MC, Thilmony R, Gordon S, Kianian SF, Gu YQ.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1159-66. doi: 10.1093/nar/gks1109. Epub 2012 Nov 24.


Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms.

You FM, Deal KR, Wang J, Britton MT, Fass JN, Lin D, Dandekar AM, Leslie CA, Aradhya M, Luo MC, Dvorak J.

BMC Genomics. 2012 Jul 31;13:354. doi: 10.1186/1471-2164-13-354.


The origin of spelt and free-threshing hexaploid wheat.

Dvorak J, Deal KR, Luo MC, You FM, von Borstel K, Dehghani H.

J Hered. 2012 May-Jun;103(3):426-41. doi: 10.1093/jhered/esr152. Epub 2012 Feb 29.


Characterizing the walnut genome through analyses of BAC end sequences.

Wu J, Gu YQ, Hu Y, You FM, Dandekar AM, Leslie CA, Aradhya M, Dvorak J, Luo MC.

Plant Mol Biol. 2012 Jan;78(1-2):95-107. doi: 10.1007/s11103-011-9849-y. Epub 2011 Nov 19.


A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes.

Palti Y, Genet C, Gao G, Hu Y, You FM, Boussaha M, Rexroad CE 3rd, Luo MC.

Mar Biotechnol (NY). 2012 Jun;14(3):343-57. doi: 10.1007/s10126-011-9418-z. Epub 2011 Nov 19.


Mapping and validation of quantitative trait loci associated with wheat yellow mosaic bymovirus resistance in bread wheat.

Zhu X, Wang H, Guo J, Wu Z, Cao A, Bie T, Nie M, You FM, Cheng Z, Xiao J, Liu Y, Cheng S, Chen P, Wang X.

Theor Appl Genet. 2012 Jan;124(1):177-88. doi: 10.1007/s00122-011-1696-3. Epub 2011 Sep 30.


Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon.

Huo N, Garvin DF, You FM, McMahon S, Luo MC, Gu YQ, Lazo GR, Vogel JP.

Theor Appl Genet. 2011 Aug;123(3):455-64. doi: 10.1007/s00122-011-1598-4. Epub 2011 May 20.


Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes.

Massa AN, Wanjugi H, Deal KR, O'Brien K, You FM, Maiti R, Chan AP, Gu YQ, Luo MC, Anderson OD, Rabinowicz PD, Dvorak J, Devos KM.

Mol Biol Evol. 2011 Sep;28(9):2537-47. doi: 10.1093/molbev/msr080. Epub 2011 Apr 6.


Collinearity-based marker mining for the fine mapping of Pm6, a powdery mildew resistance gene in wheat.

Qin B, Cao A, Wang H, Chen T, You FM, Liu Y, Ji J, Liu D, Chen P, Wang XE.

Theor Appl Genet. 2011 Jul;123(2):207-18. doi: 10.1007/s00122-011-1577-9. Epub 2011 Apr 6.


BAC libraries from wheat chromosome 7D: efficient tool for positional cloning of aphid resistance genes.

Simková H, Safář J, Kubaláková M, Suchánková P, Cíhalíková J, Robert-Quatre H, Azhaguvel P, Weng Y, Peng J, Lapitan NL, Ma Y, You FM, Luo MC, Bartoš J, Doležel J.

J Biomed Biotechnol. 2011;2011:302543. doi: 10.1155/2011/302543. Epub 2010 Dec 23.


Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence.

You FM, Huo N, Deal KR, Gu YQ, Luo MC, McGuire PE, Dvorak J, Anderson OD.

BMC Genomics. 2011 Jan 25;12:59. doi: 10.1186/1471-2164-12-59.


Transferability of microsatellite markers from Brachypodium distachyon to Miscanthus sinensis, a potential biomass crop.

Zhao H, Yu J, You FM, Luo M, Peng J.

J Integr Plant Biol. 2011 Mar;53(3):232-45. doi: 10.1111/j.1744-7909.2010.01026.x.


Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes.

Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Deal KR, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo H, Huo N, Lazo GR, Luo MC, Ma YQ, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J.

BMC Genomics. 2010 Dec 14;11:702. doi: 10.1186/1471-2164-11-702.

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