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Functional analysis and development of a CRISPR/Cas9 allelic series for a CPR5 ortholog necessary for proper growth of soybean trichomes.

Campbell BW, Hoyle JW, Bucciarelli B, Stec AO, Samac DA, Parrott WA, Stupar RM.

Sci Rep. 2019 Oct 14;9(1):14757. doi: 10.1038/s41598-019-51240-7.


Genomic changes and biochemical alterations of seed protein and oil content in a subset of fast neutron induced soybean mutants.

Islam N, Stupar RM, Qijian S, Luthria DL, Garrett W, Stec AO, Roessler J, Natarajan SS.

BMC Plant Biol. 2019 Oct 12;19(1):420. doi: 10.1186/s12870-019-1981-x.


Construction and comparison of three reference-quality genome assemblies for soybean.

Valliyodan B, Cannon SB, Bayer PE, Shu S, Brown AV, Ren L, Jenkins J, Chung CY, Chan TF, Daum CG, Plott C, Hastie A, Baruch K, Barry KW, Huang W, Patil G, Varshney RK, Hu H, Batley J, Yuan Y, Song Q, Stupar RM, Goodstein DM, Stacey G, Lam HM, Jackson SA, Schmutz J, Grimwood J, Edwards D, Nguyen HT.

Plant J. 2019 Dec;100(5):1066-1082. doi: 10.1111/tpj.14500. Epub 2019 Oct 28.


Screening populations for copy number variation using genotyping-by-sequencing: a proof of concept using soybean fast neutron mutants.

Lemay MA, Torkamaneh D, Rigaill G, Boyle B, Stec AO, Stupar RM, Belzile F.

BMC Genomics. 2019 Aug 6;20(1):634. doi: 10.1186/s12864-019-5998-1.


Identification and characterization of a fast-neutron-induced mutant with elevated seed protein content in soybean.

Prenger EM, Ostezan A, Mian MAR, Stupar RM, Glenn T, Li Z.

Theor Appl Genet. 2019 Nov;132(11):2965-2983. doi: 10.1007/s00122-019-03399-w. Epub 2019 Jul 19.


Whole-genome re-sequencing reveals the impact of the interaction of copy number variants of the rhg1 and Rhg4 genes on broad-based resistance to soybean cyst nematode.

Patil GB, Lakhssassi N, Wan J, Song L, Zhou Z, Klepadlo M, Vuong TD, Stec AO, Kahil SS, Colantonio V, Valliyodan B, Rice JH, Piya S, Hewezi T, Stupar RM, Meksem K, Nguyen HT.

Plant Biotechnol J. 2019 Aug;17(8):1595-1611. doi: 10.1111/pbi.13086. Epub 2019 Feb 20.


Genome Editing in Soybean with CRISPR/Cas9.

Liu J, Gunapati S, Mihelich NT, Stec AO, Michno JM, Stupar RM.

Methods Mol Biol. 2019;1917:217-234. doi: 10.1007/978-1-4939-8991-1_16.


Neo-Domestication of an Interspecific Tetraploid Helianthus annuus × Helianthus tuberous Population That Segregates for Perennial Habit.

Kantar MB, Hüber S, Herman A, Bock DG, Baute G, Betts K, Ott M, Brandvain Y, Wyse D, Stupar RM, Rieseberg LH.

Genes (Basel). 2018 Aug 21;9(9). pii: E422. doi: 10.3390/genes9090422.


Genetic Architecture of Soybean Yield and Agronomic Traits.

Diers BW, Specht J, Rainey KM, Cregan P, Song Q, Ramasubramanian V, Graef G, Nelson R, Schapaugh W, Wang D, Shannon G, McHale L, Kantartzi SK, Xavier A, Mian R, Stupar RM, Michno JM, An YC, Goettel W, Ward R, Fox C, Lipka AE, Hyten D, Cary T, Beavis WD.

G3 (Bethesda). 2018 Oct 3;8(10):3367-3375. doi: 10.1534/g3.118.200332.


Dissecting the Genetic Basis of Local Adaptation in Soybean.

Bandillo NB, Anderson JE, Kantar MB, Stupar RM, Specht JE, Graef GL, Lorenz AJ.

Sci Rep. 2017 Dec 8;7(1):17195. doi: 10.1038/s41598-017-17342-w.


CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula.

Curtin SJ, Xiong Y, Michno JM, Campbell BW, Stec AO, Čermák T, Starker C, Voytas DF, Eamens AL, Stupar RM.

Plant Biotechnol J. 2018 Jun;16(6):1125-1137. doi: 10.1111/pbi.12857. Epub 2017 Dec 4.


Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism.

Burghardt LT, Guhlin J, Chun CL, Liu J, Sadowsky MJ, Stupar RM, Young ND, Tiffin P.

Mol Ecol. 2017 Nov;26(21):6122-6135. doi: 10.1111/mec.14285. Epub 2017 Sep 5.


Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula.

Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J.

BMC Genomics. 2017 Aug 4;18(1):578. doi: 10.1186/s12864-017-3971-4.


Hybrid assembly with long and short reads improves discovery of gene family expansions.

Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT.

BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8.


Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes.

Zhou P, Silverstein KA, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND.

BMC Genomics. 2017 Mar 27;18(1):261. doi: 10.1186/s12864-017-3654-1.


An Induced Chromosomal Translocation in Soybean Disrupts a KASI Ortholog and Is Associated with a High-Sucrose and Low-Oil Seed Phenotype.

Dobbels AA, Michno JM, Campbell BW, Virdi KS, Stec AO, Muehlbauer GJ, Naeve SL, Stupar RM.

G3 (Bethesda). 2017 Apr 3;7(4):1215-1223. doi: 10.1534/g3.116.038596.


Validating Genome-Wide Association Candidates Controlling Quantitative Variation in Nodulation.

Curtin SJ, Tiffin P, Guhlin J, Trujillo DI, Burghart LT, Atkins P, Baltes NJ, Denny R, Voytas DF, Stupar RM, Young ND.

Plant Physiol. 2017 Feb;173(2):921-931. doi: 10.1104/pp.16.01923. Epub 2017 Jan 5.


The Role of Deleterious Substitutions in Crop Genomes.

Kono TJ, Fu F, Mohammadi M, Hoffman PJ, Liu C, Stupar RM, Smith KP, Tiffin P, Fay JC, Morrell PL.

Mol Biol Evol. 2016 Sep;33(9):2307-17. doi: 10.1093/molbev/msw102. Epub 2016 Jun 14.


Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes.

Campbell BW, Hofstad AN, Sreekanta S, Fu F, Kono TJ, O'Rourke JA, Vance CP, Muehlbauer GJ, Stupar RM.

Theor Appl Genet. 2016 Sep;129(9):1725-38. doi: 10.1007/s00122-016-2735-x. Epub 2016 Jun 9.


Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants.

Anderson JE, Michno JM, Kono TJ, Stec AO, Campbell BW, Curtin SJ, Stupar RM.

BMC Biotechnol. 2016 May 12;16(1):41. doi: 10.1186/s12896-016-0271-z.


Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects.

Campbell BW, Stupar RM.

Curr Protoc Plant Biol. 2016 Mar;1(2):307-327. doi: 10.1002/cppb.20015.


Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans.

Anderson JE, Kono TJ, Stupar RM, Kantar MB, Morrell PL.

G3 (Bethesda). 2016 Apr 7;6(4):835-43. doi: 10.1534/g3.116.026914.


Perennial Grain and Oilseed Crops.

Kantar MB, Tyl CE, Dorn KM, Zhang X, Jungers JM, Kaser JM, Schendel RR, Eckberg JO, Runck BC, Bunzel M, Jordan NR, Stupar RM, Marks MD, Anderson JA, Johnson GA, Sheaffer CC, Schoenfuss TC, Ismail B, Heimpel GE, Wyse DL.

Annu Rev Plant Biol. 2016 Apr 29;67:703-29. doi: 10.1146/annurev-arplant-043015-112311. Epub 2016 Jan 18. Review.


MicroRNA Maturation and MicroRNA Target Gene Expression Regulation Are Severely Disrupted in Soybean dicer-like1 Double Mutants.

Curtin SJ, Michno JM, Campbell BW, Gil-Humanes J, Mathioni SM, Hammond R, Gutierrez-Gonzalez JJ, Donohue RC, Kantar MB, Eamens AL, Meyers BC, Voytas DF, Stupar RM.

G3 (Bethesda). 2015 Dec 17;6(2):423-33. doi: 10.1534/g3.115.022137. Erratum in: G3 (Bethesda). 2020 Feb 6;10(2):875.


CRISPR/Cas mutagenesis of soybean and Medicago truncatula using a new web-tool and a modified Cas9 enzyme.

Michno JM, Wang X, Liu J, Curtin SJ, Kono TJ, Stupar RM.

GM Crops Food. 2015;6(4):243-52. doi: 10.1080/21645698.2015.1106063.


Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants.

Campbell BW, Mani D, Curtin SJ, Slattery RA, Michno JM, Ort DR, Schaus PJ, Palmer RG, Orf JH, Stupar RM.

G3 (Bethesda). 2014 Dec 1;5(1):123-31. doi: 10.1534/g3.114.015255.


Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean.

Bolon YT, Stec AO, Michno JM, Roessler J, Bhaskar PB, Ries L, Dobbels AA, Campbell BW, Young NP, Anderson JE, Grant DM, Orf JH, Naeve SL, Muehlbauer GJ, Vance CP, Stupar RM.

Genetics. 2014 Nov;198(3):967-81. doi: 10.1534/genetics.114.170340. Epub 2014 Sep 10.


To the reference and beyond: understanding variation in plant genomes.

Stupar RM.

Brief Funct Genomics. 2014 Jul;13(4):255-6. doi: 10.1093/bfgp/elu019. No abstract available.


A roadmap for functional structural variants in the soybean genome.

Anderson JE, Kantar MB, Kono TY, Fu F, Stec AO, Song Q, Cregan PB, Specht JE, Diers BW, Cannon SB, McHale LK, Stupar RM.

G3 (Bethesda). 2014 May 22;4(7):1307-18. doi: 10.1534/g3.114.011551.


Targeted mutagenesis for functional analysis of gene duplication in legumes.

Curtin SJ, Anderson JE, Starker CG, Baltes NJ, Mani D, Voytas DF, Stupar RM.

Methods Mol Biol. 2013;1069:25-42. doi: 10.1007/978-1-62703-613-9_3.


A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar.

O'Rourke JA, Iniguez LP, Bucciarelli B, Roessler J, Schmutz J, McClean PE, Jackson SA, Hernandez G, Graham MA, Stupar RM, Vance CP.

Front Plant Sci. 2013 Jun 25;4:210. doi: 10.3389/fpls.2013.00210. eCollection 2013.


Genomic heterogeneity and structural variation in soybean near isogenic lines.

Stec AO, Bhaskar PB, Bolon YT, Nolan R, Shoemaker RC, Vance CP, Stupar RM.

Front Plant Sci. 2013 Apr 24;4:104. doi: 10.3389/fpls.2013.00104. eCollection 2013.


Structural variants in the soybean genome localize to clusters of biotic stress-response genes.

McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM.

Plant Physiol. 2012 Aug;159(4):1295-308. doi: 10.1104/pp.112.194605. Epub 2012 Jun 13.


Co-expression of soybean Dicer-like genes in response to stress and development.

Curtin SJ, Kantar MB, Yoon HW, Whaley AM, Schlueter JA, Stupar RM.

Funct Integr Genomics. 2012 Nov;12(4):671-82. doi: 10.1007/s10142-012-0278-z. Epub 2012 Apr 15.


Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases.

Curtin SJ, Zhang F, Sander JD, Haun WJ, Starker C, Baltes NJ, Reyon D, Dahlborg EJ, Goodwin MJ, Coffman AP, Dobbs D, Joung JK, Voytas DF, Stupar RM.

Plant Physiol. 2011 Jun;156(2):466-73. doi: 10.1104/pp.111.172981. Epub 2011 Apr 4.


Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean.

Bolon YT, Haun WJ, Xu WW, Grant D, Stacey MG, Nelson RT, Gerhardt DJ, Jeddeloh JA, Stacey G, Muehlbauer GJ, Orf JH, Naeve SL, Stupar RM, Vance CP.

Plant Physiol. 2011 May;156(1):240-53. doi: 10.1104/pp.110.170811. Epub 2011 Feb 14.


Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA).

Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JR, Joung JK.

Nat Methods. 2011 Jan;8(1):67-9. doi: 10.1038/nmeth.1542. Epub 2010 Dec 12.


Into the wild: The soybean genome meets its undomesticated relative.

Stupar RM.

Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):21947-8. doi: 10.1073/pnas.1016809108. Epub 2010 Dec 13. No abstract available.


The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82.

Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, Stupar RM.

Plant Physiol. 2011 Feb;155(2):645-55. doi: 10.1104/pp.110.166736. Epub 2010 Nov 29.


Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris.

Lin JY, Stupar RM, Hans C, Hyten DL, Jackson SA.

Plant Cell. 2010 Aug;22(8):2545-61. doi: 10.1105/tpc.110.074229. Epub 2010 Aug 20.


An integrative approach to genomic introgression mapping.

Severin AJ, Peiffer GA, Xu WW, Hyten DL, Bucciarelli B, O'Rourke JA, Bolon YT, Grant D, Farmer AD, May GD, Vance CP, Shoemaker RC, Stupar RM.

Plant Physiol. 2010 Sep;154(1):3-12. doi: 10.1104/pp.110.158949. Epub 2010 Jul 23.


Transcriptome analysis of the barley-deoxynivalenol interaction: evidence for a role of glutathione in deoxynivalenol detoxification.

Gardiner SA, Boddu J, Berthiller F, Hametner C, Stupar RM, Adam G, Muehlbauer GJ.

Mol Plant Microbe Interact. 2010 Jul;23(7):962-76. doi: 10.1094/MPMI-23-7-0962.


Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (gossypium).

Chaudhary B, Flagel L, Stupar RM, Udall JA, Verma N, Springer NM, Wendel JF.

Genetics. 2009 Jun;182(2):503-17. doi: 10.1534/genetics.109.102608. Epub 2009 Apr 10.


Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis.

Stupar RM, Gardiner JM, Oldre AG, Haun WJ, Chandler VL, Springer NM.

BMC Plant Biol. 2008 Apr 10;8:33. doi: 10.1186/1471-2229-8-33.


Natural variation for alleles under epigenetic control by the maize chromomethylase zmet2.

Makarevitch I, Stupar RM, Iniguez AL, Haun WJ, Barbazuk WB, Kaeppler SM, Springer NM.

Genetics. 2007 Oct;177(2):749-60. Epub 2007 Jul 29.


Phenotypic and transcriptomic changes associated with potato autopolyploidization.

Stupar RM, Bhaskar PB, Yandell BS, Rensink WA, Hart AL, Ouyang S, Veilleux RE, Busse JS, Erhardt RJ, Buell CR, Jiang J.

Genetics. 2007 Aug;176(4):2055-67. Epub 2007 Jun 11.


Allelic variation and heterosis in maize: how do two halves make more than a whole?

Springer NM, Stupar RM.

Genome Res. 2007 Mar;17(3):264-75. Epub 2007 Jan 25. Review.

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