HapMap Publications
  • Bonhomme M, André O, Badis Y, Ronfort J, Burgarella C, Chantret N, Prosperi J-M, Briskine R, Mudge J, Debéllé F, Navier H, Miteul H, Hajri A, Baranger A, Tiffin P, Dumas B, Pilet-Navel M-L, Young ND, Jacquet C 2014 High density genome-wide association mapping implicates an F-box encoding gene in Medicago truncatula resistance Aphanomyces euteiches New Phytologist 201(4):1328-1342: doi: 10.1111/nph.12611 View Online
  • Bonhomme M, Boitart S, San Clemente H, Dumas B, Young ND, Jacquet C 2015 Genomic signature of selective sweeps reveals adaptation of Medicago truncatula to root-associated microorganisms Molecular Biology and Evolution 32(8): 2097-2110. doi: 10.1093/molbev/msv092 View Online
  • Branca A, Paape TD, Zhou P, Briskine R, Farmer AD, Mudge J, Bharti A, Woodward J, May G, Gentzbittel L, Ben C, Denny R, Sadowsky M, Ronfort J, Bataillon T, Young N, Tiffin P 2010 Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc. Natl. Acad. Sci 108(42):E864 -E870 View Online
  • Burgarella C, Chantret N, Gay L, Prosperi J-M., Bonhomme M, Tiffin P, Young, ND, Ronfort, J. 2016 Adaptation to climate variation through flowering phenology: a case study in Medicago truncatula Molecular Ecology doi: 10.1111/mec.13683. View Online
  • Burghardt LT, Epstein B, Guhlin J, Nelson MS, Taylor MR, Young ND, Sadowsky MJ, Tiffin P 2018 Select and re-sequence reveals relative fitness of bacterial strains in symbiotic and free-living environments Proc. Natl. Acad. Sci. USA doi/10.1073/pnas.1714246115 View Online
  • Burghardt LT, Guhlin J, Chun C, Liu J, Sadowsky MJ, Stupar RM, Young ND, Tiffin P 2017 Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism Molecular Ecology doi: 10.1111/mec.14285. View Online
  • Burghardt, LT, Young ND, Tiffin P 2017 A guide to genome-wide association mapping in plants Current Protocols in Plant Biology 2:22-38. doi: 10.1002/cppb.20041 View Online
  • Curtin SJ, Tiffin P, Guhlin J, Trujillo D, Burghardt LT, Atkins P, Baltes NJ, Denny R, Voytas DF, Stupar RM, Young ND 2017 Validating GWAS candidates by characterizing genes that control quantitative variation in nodulation Plant Physiology 173(2):921-931. doi: 10.1104/pp.16.01923 View Online
  • Epstein B, Branca A, Mudge J, Bharti AK, Briskine R, Farmer A, Sugawara M, Young ND, Sadowsky MJ, Tiffin P 2012 Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae. PLoS Genetics 8(8): e1002868 View Online
  • Gentzbittel L, Andersen SU, Ben C, Rickauer M, Stougaard J, Young ND 2015 Naturally occuring diversity helps to reveal genes of adaptive importance in legumes Frontiers in Plant Science 6: 269. doi: 10.3389/fpls.2015.00269 View Online
  • Guhlin J, Silverstein KAT, Zhou P, Tiffin P, Young ND 2017 ODG: Omics database generator – a tool for generating, querying, and analyzing multi-omics databases to facilitate biological understanding BMC Bioinformatics 18: 367. doi 10.1186/s12859-017-1777-7 View Online
  • Kang Y, Sakuroglu M, Krom N, Stanton-Geddes J, Wang M, Lee Y-C, Young ND, Udvardi M 2015 Genome-wide assocation of drought-related and biomass traits with HapMap SNPs in Medicago truncatula Plant Cell and Environment 38: 1997-2011. doi: 10.1111/pce.12520. View Online
  • Le Signor C, Aimé D, Bordat A, Belghazi M, Labas V, Gouzy J, Tiffin P, Young ND, Prosperi J-M, Leprince O, Thompson RD, Buitink J, Burstin J, Gallardo K 2017 Genome-wide association studies with proteomics data reveal genes important for synthesis, transport and packaging of globulins in legume seeds. New Phytologist doi: 10.1111/nph.14500 View Online
  • Martinez-Vaz B, Denny R, Young ND, Sadowsky M 2015 An alternative approach to “Identification of Unknowns”: Designing a protocol to verify the identities of nitrogen fixing bacteria Journal Microbiology and Biology Education 16(2):247-253. doi: 10.1128/jmbe.v16i2.973 View Online
  • Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu Junqi, Stupar R, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT 2017 Hybrid assembly with long and short reads improves discovery of gene family expansions BMC Genomics 18:541. doi: 10.1186/s12864-017-3927-8 View Online
  • Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J 2017 Strategies for utilizing bionano and dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula BMC Genomics 18:587 doi: 10.1186/s12864-017-3971-4 View Online
  • Nallu S, Silverstein KAT, Zhou P, Young, ND, VandenBosch KA 2014 Patterns of divergence of a large family of nodule cysteine-rich genes in accessions of Medicago truncatula The Plant Journal 78(4): 697-705. doi:10.1111/tpj.12506 View Online
  • Paape T, Bataillon T, Zhou P, Kono T, Briskine R, Young ND, Tiffin P 2013 Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula. Molecular Ecology 22: 3525-3538 doi: 10.1111/mec.12329 View Online
  • Paape T, Bataillon T, Zhou P, Kono T, Briskine R, Young ND, Tiffin P 2013 Selection, genome wide fitness effects, and evolutionary rates in the model legume Medicago truncatula. Molecular Ecology 22(13): 3525-3538. doi: 10.1111/mec.12329. View Online
  • Paape T, Zhou P, Branca A, Briskine R, Young N, Tiffin P 2012 Fine-Scale Population Recombination Rates, Hotspots, and Correlates of Recombination in the Medicago truncatula Genome. Genome Biol Evol 4(5):726-737 View Online
  • Peng Zhou, Kevin AT Silverstein, Liangliang Gao, Jonathan D Walton, Sumitha Nallu, Joseph Guhlin and Nevin D Young 2013 Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application) BMC Bioinformatics 14:335 doi:10.1186/1471-2105-14-335 View Online
  • Stanton-Geddes J, Paape T, Epstein B, Briskine R, Yoder, J, Mudge J, Bharti AK, Farmer AD, Zhou P, Denny R, May GD, Erlandson S, Sugawara M, Sadowsky MJ, Young ND, Tiffin P 2013 Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula PLoS ONE 8(5): e65688. doi:10.1371/journal.pone.0065688 View Online
  • Stanton-Geddes J, Yoder J, Briskine R, Young ND, Tiffin P 2013 Estimating heritability with whole-genome data Methods in Ecology and Evolution: 4 1151-1158. doi: 10.1111/2041-210X.12129. View Online
  • Sugawara M, Epstein B, Badgley B, Unno T, Xu L , Reese J, Gyaneshwar P, Denny R, Mudge J, Bharti AK, Farmer AD, May GD, Woodward JE, Médigue C, Vallenet D, Lajus A, Rouy Z, Martinez-Vaz B, Tiffin P, Young ND, Sadowsky MJ 2013 Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains spanning five genospecies. Genome Biology 14(2):R17, doi:10.1186/gb-2013-14-2-r17 View Online
  • Trujillo DI, Silverstein KAT, Young ND 2014 Genomic characterization of the LEED..PEEDs, a gene family unique to Medicago lineage G3: Genes | Genomes | Genetics 4(10) 2003-2012. doi:10.1534/g3.114.011874 View Online
  • Yoder JB, Briskine, R, Mudge J, Farmer A, Paape T, Steel K, Weiblen GD, Bharti A, Zhou P, May GD, Young ND, Tiffin P 2013 Phylogenetic signal variation in the genomes of the genus Medicago (Fabaceae) Systematic Biology 62:424-438doi:10.1093/sysbio/syt009 View Online
  • Yoder JB, Stanton-Geddes J, Zhou P, Briskine R, Young ND, Tiffin P 2014 Genomic signature of local adaptation to climate in Medicago truncatula Genetics 196(4):1263-1275 doi: 10.1534/genetics.113.159319 View Online
  • Young ND, Bharti AK 2012 Genome-enabled insights into legume biology. Annu Rev Plant Biol 63:283-305 View Online
  • Young ND, Debellé F, Oldroyd G, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KFX, Gouzy J, Schoof H, et al 2011 The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480: 520-524 View Online
  • Young ND, Zhou P, Silverstein KAT 2016 Exploring structural variants in environmentally-sensitive gene families Current Opinion in Plant Biology 30: 19-24, http://dx.doi.org/10.1016/j.pbi.2015.12.012 View Online
  • Zhou P, Silverstein KAT, Thiruvarangan R, Guhlin J, Denny RL, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin PL, Mudge J, Young ND 2017 Exploring structural variation and gene family architecture with de novo assemblies of 15 Medicago genomes BMC Genomics 18:261 doi 10.1186/s12864-017-3654-1 View Online

Site hosted by: Nevin Young's Lab at University of Minnesota. Managed By: Joseph Guhlin

Primary Collaborators: INRA - Montpellier | ENSAT - Toulouse | Noble Foundation

Co-Principal Investigators: University of Minnesota N. Young, P. Tiffin, M. Sadowsky, B. Stupar, K. Silverstein | NCGR J. Mudge, A. Farmer

Boyce Thompson Institute M. Harrison | Hamline University B. Martinez-Vaz