Publications
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2026
Yang H, Pakhomov SV, Morrell PL (2026). Language modeling in genetics: A Swiss Army knife for a modern biologist.. In review.• 0 citations
Gaut BS, Wright SI, Wang T, Morrell PL (2026). What has populations genomics told us about the dynamics of selection and plant adaptation?. Molecular Biology and Evolution.
• 0 citations • Github
Akakpo R, Lee EJ, Pacheco JB, Rios EF, Kantar MB, Ousmane B, Volz KM, Akinmade H, Getino L, Boote KJ, Muñoz-Amatriaín M, Morrell PL (2026). Identification of genetic variation associated with high-temperature tolerance in cowpea. Molecular Ecology.
• 0 citations • Preprint version • Associated dataset • Github
Liu C, Lei L, Shao M, Franckowiak JD, Pacheco JB, Scott JC, Gavin RT, Roy JK, Sallam AH, Steffenson BJ, Morrell PL (2026). Phenotypically wild barley shows evidence of introgression from cultivated barley. Molecular Ecology.
• 0 citations • Preprint version • Associated dataset • Github
2025
Spanner R, Sallam AH, Guo Y, Jayakodi M, Himmelbach A, Fiebig A, Simmons J, et al. (2025). Whole-genome sequencing of the Wild Barley Diversity Collection: a resource for identifying and exploiting genetic variation for cultivated barley improvement. G3: Genes, Genomes, Genetics.• 10 citations • Preprint version • Associated dataset • Github
Morrell PL, Pakhomov SV (2025). Decoding nature’s grammar with DNA language models. Proceedings of the National Academy of Sciences 122(29) e2512889122.
• 1 citations
Liu C, Frascarelli G, Stec AO, Heinen S, Lei L, Wyant SR, Legg E, Spiller M, Muehlbauer GJ, Smith KP, Morrell PL (2025). Sodium azide mutagenesis induces a unique pattern of mutations. PLOS Genetics 21(6) e1011634.
• 8 citations • Preprint version • Associated dataset • Github
Halpin-McCormick A, Campbell Q, Negrão S, Morrell PL, Hübner S, Neyhart JL, Kantar MB (2025). Environmental genomic selection to leverage polygenic local adaptation in barley landraces. Communications Biology 8(1): 618.
• 14 citations • Preprint version • Associated dataset • Github
2024
Cortinovis G, Vincenzi L, Anderson R, Marturano G, Marsh JI, Bayer PE, Rocchetti L, Frascarelli G, Lanzavecchia G, Pieri A, Benazzo A, Bellucci E, Di Vittori V, Nanni L, Ferreira Fernández JJ, Rosatto M, Aguilar OM, Morrell PL, Rodriguez M, Gioia T, Neumann K, Alvarez Diaz JC, Gratias-Weill A, Klopp C, Geffroy V, Bitocchi E, Delledonne M, Edwards D, Papa R (2024). Adaptive gene loss in the common bean pan-genome during range expansion and domestication. Nature Communications 15: 6698.• 49 citations • Preprint version
Landis JB, Guercio AM, Brown KE, Fiscus CJ, Morrell PL, Koenig D (2024). Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley. Science 385(6705) eadl0038.
• 22 citations • Preprint version • Associated dataset • Github
2023
Bethke G, Huang Y, Hensel G, Heinen S, Liu C, Wyant SR, Li X, Quin M, McCormick S, Morrell PL, Dong Y, Kumlehn J, Salvi S, Berthiller F, Muehlbauer GJ (2023). UDP-glucosyltransferase HvUGT13248 confers type II resistance to Fusarium graminearum in barley. Plant Physiol 193 (4): 2691-2710.• 22 citations • Github
Wang N, Xu X, Zhongjie L, Hu J, Xiao H, Chen P, Wu X, Wang Y, Ye J, Chai L, Xu Q, Morrell PL, Zhou Y, Deng X (2023). Genomic conservation of citrus wild relatives: a case study of citrus. PLOS Genetics 19(6) e1010811.
• 0 citations
Flint-Garcia S, Feldman MJ, Dempewolf H, Morrell PL, Ross-Ibarra J (2023). Diamonds in the not-so-rough: wild relative diversity hidden in crop genomes. PLOS Biology 21(7) e3002235.
• 13 citations
Agha HI, Shannon LM, Morrell PL (2023). Unloading potatoes: potato breeding moves forward with only half the genome. Cell Genomics 3(6) 100343.
• 1 citations
Bellucci E, Benazzo A, Xu C, Bitocchi E, Rodriguez M, Alseekh S, Di Vittori V, Gioia T, Neumann K, Cortinovis G, Frascarelli G, Murube E, Trucchi E, Nanni L, Ariani A, Logozzo G, Shin JH, Liu C, Jiang L, Ferreira JJ, Campa A, Attene G, Morrell PL, Bertorelle G, Graner A, Gepts P, Fernie AR, Jackson SA, Papa R (2023). Selection and adaptive introgression guided the complex evolutionary history of European common bean. Nature Communications 14(1) 1908.
• 15 citations • Preprint version • Associated dataset • Github
Liang Q, Muñoz-Amatriaín M, Shu S, Lo S, Wu X, Carlson JW, Davidson P, Goodstein DM, Phillips J, Janis NM, Lee EJ, Liang C, Morrell PL, Farmer AD, Xu P, Close TJ, Lonardi S (2023). A view of the pan-genome of domesticated cowpea (Vigna unguiculata [L.] Walp.). The Plant Genome 17:e20319.
• 56 citations • Preprint version • Associated dataset • Github
2022
Chen Y-Y, Schreiber M, Bayer MM, Dawson IK, Hedley PE, Lei L, Akhunov A, Liu C, Smith KP, Muehlbauer GJ, Steffenson BJ, Morrell PL, Waugh R, Russell JR (2022). The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication. Plant J 111 1580-1594.• 9 citations • Associated dataset
He, F,, Wang, W, Rutter, WB, Jordan, KW, Ren, J, Taagen, E, DeWitt, N, Sehgal, D, Sukumaran, S, Dreisigacker, S, Reynolds, M, Halder, J, Sehgal, SK, Liu, S, Chen, J, Fritz, A, Cook, J, Brown-Guedira, G, Pumphrey, M, Carter, A, Sorrells, M, Dubcovsky, J, Hayden, M, Akhunova, A, Morrell, PL, Szabo, L, Rouse, M, Akhunov, E (2022). Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat. Nature Communications 13(1) 826.
• 44 citations
2021
Wyant SR, Rodriguez MF, Carter CK, Parrott WA, Jackson SA, Stupar RM, Morrell PL (2021). Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations. G3 12(2): jkab431.• 10 citations • Preprint version • Associated dataset • Github
2020
Graham N, Patil G, Bubeck DM, Dobert RC, Glenn KC, Gutsche AT, Kumar S, Lindbo JA, Maas L, May GD, Vega-Sanchez ME, Stupar RM, Morrell PL (2020). Plant genome editing and the relevance of off-target changes. Plant Physiology 183(4): 1453-1471.• 68 citations
2019
Kono TJY, Liu C, Vonderharr EE, Koenig D, Fay JC, Smith KP, Morrell PL (2019). The fate of deleterious variants in a barley genomic prediction population. Genetics 213(4): 1531-1544.• 22 citations • Preprint version • Associated dataset • Github
Lei L, Poets AM, Liu C, Wyant SR, Hoffman PJ, Carter CK, Shaw BG, Li X, Muehlbauer GJ, Katagiri F, Morrell PL (2019). Environmental association identifies candidates for tolerance to low temperature and drought. G3 9: 3423-3438.
• 25 citations • Preprint version • Associated dataset • Github
Hemshrot A, Poets AM, Tyagi P, Lei L, Carter CK, Hirsch CN, Li L, Brown-Guedira G, Morrell PL, Muelbauer GJ, Smith KP (2019). Development of a multi-parent population for genetic mapping and allele discovery in six-row barley. Genetics 213: 595-613.
• 23 citations • Associated dataset • Github
He F, Pasam R, Shi F, Kant S, Keeble-Gagnere G, Kay P, Forrest K, Fritz A, Hucl P, Wiebe K, Knox R, Cuthbert R, Pozniak C, Akhunova A, Morrell PL, Davies JP, Webb SR, Spangenberg G, Hayes B, Daetwyler H, Tibbits J, Hayden M, Akhunov E (2019). Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nature Genetics 51: 896–904.
• 270 citations
2018
Kono TJY, Lei L, Shih C, Hoffman PJ, Morrell PL, Fay JC (2018). Comparative genomics approaches accurately predict deleterious variants in plants. G3 8: 3321-3329.• 47 citations • Preprint version • Associated dataset • Github
Moyers BT, Morrell PL, McKay JK (2018). Genetic costs of domestication and improvement. Journal of Heredity 109: 103-116.
• 209 citations • Preprint version
2017
Allen MF, Morrell PL, Rice CW, Vaux HJ, Dahm CN, Hernandez RR (2017). Food and nutrition security in the United States of America. Challenges and opportunities for this century. InterAmerican Network of Academies of Science (IANAS).Liu Q, Zhou Y, Morrell PL, Gaut BS (2017). Deleterious variants in Asian rice and the potential cost of domestication. Molecular Biology and Evolution 34: 908-924.
• 40 citations • Preprint version • Associated dataset
2016
Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J (2016). ANGSD-wrapper: utilities for analyzing next generation sequencing data. Molecular Ecology Resources 16: 1449-1454.• 21 citations • Preprint version • Github
Fang Z, Morrell PL (2016). Domestication: Polyploidy boosts domestication. Nature Plants 2:16116.
• 4 citations
Nice LM, Steffenson BJ, Brown-Guedira GL, Akhunov ED, Liu C, Kono TJY, Morrell PL, Horsley RD, Smith KP, Muehlbauer GJ (2016). Development and genetic characterization of an Advanced Backcross – Nested Association Mapping (AB-NAM) population of wild x cultivated barley. Genetics 203: 1453-1467.
• 38 citations
Kono TJY, Fu F, Mohammadi M, Hoffman PJ, Liu C, Stupar RM, Smith KP, Tiffin P, Fay JC, Morrell PL (2016). The role of deleterious substitutions in crop genomes. Molecular Biology and Evolution 33: 1669-1678.
• 40 citations • Preprint version • Associated dataset • Github
Anderson JE, Kono TJ, Stupar RM, Kantar MB, Morrell PL (2016). Environmental association analyses identify candidates for abiotic stress tolerance in Glycine soja, the wild progenitor of cultivated soybeans. G3 6: 835-843.
• 21 citations • Resumen en español
2015
Poets AM, Mohammadi M, Seth K, Wang H, Kono TJY, Fang Z, Muehlbauer GJ, Smith KP, Morrell PL (2015). The effects of both recent and long-term selection and genetic drift are readily evident in North American barley breeding populations. G3 6: 609-622.• 13 citations • Preprint version • Associated dataset • Github • Resumen en español
Gaut BS, Diez CM, Morrell PL (2015). Genomics and the contrasting dynamics of annual and perennial domestication. Trends in Genetics 31:709-719.
• 161 citations
He SL, Yang Y, Morrell PL, Yi TS (2015). Nucleotide sequence diversity and linkage disequilibrium of four nuclear loci in foxtail millet (Setaria italica). PLoS One 10: e0137088.
• 3 citations
Poets AM, Fang Z, Clegg MT, Morrell PL (2015). Barley landraces are characterized by geographically heterogeneous genomic origins. Genome Biology 16: 173.
• 72 citations • Associated dataset • Github
Research highlight by Robin Allaby: Barley domestication: the end of a central dogma?
2014
Fang Z, Gonzales AM, Clegg MT, Muehlbauer GJ, Smith KP, Steffenson BJ, Morrell PL (2014). Two genomic regions contribute disproportionately to geographic differentiation in wild barley. G3 4: 1193-1203.• 33 citations • Associated dataset
Kantar MB, Betts K, Michno J-MS, Luby JJ, Morrell PL, Hulke BS, Stupar RM, Wyse DL (2014). Evaluating an interspecific Helianthus annuus x Helianthus tuberosus population for use in a perennial sunflower breeding program. Field Crops Research 155: 254-264.
• 41 citations
Morrell PL, Gonzales AM, Meyer KK, Clegg MT (2014). Resequencing data indicate a modest effect of domestication on diversity in barley: a cultigen with multiple origins. Journal of Heredity 105: 253-264.
• 36 citations • Associated dataset
McCoy AM, Schaefer R, Petersen JL, Morrell PL, Slamka MA, Mickelson JR, Valberg SJ, McCue ME (2014). Evidence of positive selection for a glycogen synthase (GYS1) mutation in domestic horse populations. Journal of Heredity 105: 163-172.
• 23 citations
2013
Kono TJ, Seth K, Poland JA, Morrell PL (2013). SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Molecular Ecology Resources 14: 419-425.• 12 citations • Associated dataset • Github • Program documentation
Yi T, Morrell PL, Pei S-J, He S-A (2013). Chapter 20 - Major introduced economic plants. Plants of China - A companion to the Flora of China. Beijing, China.
Fang Z, Eule-Nashoba A, Powers C, Kono TKY, Takuno, S, Morrell PL, Smith KP (2013). Comparative analyses identify the contributions of exotic donors to disease resistance in a barley experimental population. G3 3: 1945-1953.
• 14 citations
Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D’Ascenzo M, Akhunov ED, Hedley P, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KFX, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N (2013). Barley whole exome capture: a new tool for genomic research in the genus Hordeum and beyond. The Plant Journal 76: 494-505.
• 186 citations • Associated dataset
Fang Z, Gonzales AM, Durbin ML, Meyer KKT, Miller BH, Volz KM, Clegg MT, Morrell PL (2013). Tracing the geographic origin of weedy Ipomoea purpurea (common morning glory) in the Southeastern United States. Journal of Heredity 104: 666-677.
• 9 citations • Associated dataset
Cavanagh CR, Chao S, Wang S, Huang BE, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira GL, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Reynolds M, da Silva ML, Bockelman H, Talbert L, Anderson JA, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell PL, Dubcovsky J, Morell MK, Sorrells ME, Hayden MJ, Akhunov E (2013). Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proceedings of the National Academy of Sciences of the United States of America 110: 8057-8062.
• 626 citations
2012
Gonzales AM, Fang Z, Durbin ML, Meyer KK, Clegg MT, Morrell PL (2012). Nucleotide sequence diversity of floral pigment genes in Mexican populations of Ipomoea purpurea (morning glory) accord with a neutral model of evolution. Journal of Heredity 103: 836-872.• 6 citations • Associated dataset • Poster
Yi, T and Morrell, PL (2012). Introduction of major exotic economic plants. Hong, D and Blackmore, S (eds.). Plants of China.
Fang Z, Pyhäjärvi T, Weber AL, Dawe RK, Glaubitz JC, Sanchez Gonzalez JD, Ross-Ibarra C, Doebley J, Morrell PL, Ross-Ibarra J (2012). Megabase-scale inversion polymorphism in the wild ancestor of maize. Genetics 191: 883-894.
• 69 citations • Associated dataset
Hufford MB, Xu X, van Heerwaarden J, Pyhajarvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J (2012). Comparative population genomics of maize domestication and improvement. Nature Genetics 44: 808-811.
• 523 citations
Nature Genetics News and Views
Morrell PL, Buckler ES, Ross-Ibarra J (2012). Crop genomics: advances and applications. Nature Reviews Genetics 13: 85-96.
• 358 citations
2011
Morrell, PL and Clegg, MT (2011). Hordeum. Wild Crop Relatives–Genomic and Breeding Resources: Legume Crops and Forages, edited by C. Kole, Springer-Verlag, Berlin.• citations
2010
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 (2010). Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BioMed Central Genomics 11: 702.• 144 citations • Associated dataset
Chen HF, Morrell PL, Toleno DM, Lundy KE, Clegg MT (2010). Allele-specific PCR can improve the efficiency of experimental resolution of heterozygotes in resequencing studies. Molecular Ecology Resources 10: 647-658.
• 4 citations
2009
Luo MC, Deal KR, Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo HY, Huo N, Lazo G, Ma Y, 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 (2009). Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proceedings of the National Academy of Sciences of the United States of America 106: 15780-15785.• 171 citations
Aguilar-Melendez A, Morrell PL, Roose ML, Kim SC (2009). Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico. American Journal of Botany 96: 1190-1202.
• 140 citations
Chen HF, Morrell PL, Ashworth VE, de la Cruz M, Clegg MT (2009). Tracing the geographic origins of major avocado cultivars. Journal of Heredity 100: 56-65.
• 122 citations • Associated dataset
2008
Chen H, Morrell PL, de la Cruz M, Clegg MT (2008). Nucleotide diversity and linkage disequilibrium in wild avocado (Persea americana Mill.). Journal of Heredity 99: 382-389.• 65 citations • Associated dataset
2007
Toleno DM, Morrell PL, Clegg MT (2007). Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations. Bioinformatics 23: 1807-1814.• 13 citations
Ross-Ibarra J, Morrell PL, Gaut BS (2007). Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proceedings of the National Academy of Sciences of the United States of America 104 Suppl 1: 8641-8648.
• 311 citations
Morrell PL, Clegg MT (2007). Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent. Proceedings of the National Academy of Sciences of the United States of America 104: 3289-3294.
• 399 citations • Associated dataset
2006
Morrell PL, Toleno DM, Lundy KE, Clegg MT (2006). Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity. Genetics 173: 1705-1723.• 54 citations • Associated dataset
2005
Morrell PL, Williams-Coplin TD, Lattu AL, Bowers JE, Chandler JM et al. (2005). Crop-to-weed introgression has impacted allelic composition of johnsongrass populations with and without recent exposure to cultivated sorghum. Molecular Ecology 14: 2143-2154.• 109 citations
Morrell PL, Toleno DM, Lundy KE, Clegg MT (2005). Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proceedings of the National Academy of Sciences of the United States of America 102: 2442-2447.
• 231 citations • Associated dataset
2004
Clegg, M. T. and P. L. Morrell (2004). Mutational processes. Encyclopedia of Plant and Crop Science, edited by R.M. Goodman, Marcel Dekker, New York.Clegg, M. T. and P. L. Morrell (2004). Bioinformatics. Encyclopedia of Plant and Crop Science, edited by R.M. Goodman, Marcel Dekker, New York.
2003
Durbin ML, Lundy KE, Morrell PL, Torres-Martinez CL, Clegg MT (2003). Genes that determine flower color: the role of regulatory changes in the evolution of phenotypic adaptations. Molecular Phylogenetics and Evolution 29: 507-518.• 100 citations
Morrell PL, Lundy KE, Clegg MT (2003). Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration. Proceedings of the National Academy of Sciences of the United States of America 100: 10812-10817.
• 123 citations • Associated dataset
2002
Lin JZ, Morrell PL, Clegg MT (2002). The influence of linkage and inbreeding on patterns of nucleotide sequence diversity at duplicate alcohol dehydrogenase loci in wild barley (Hordeum vulgare ssp. spontaneum). Genetics 162: 2007-2015.• 48 citations • Associated dataset
2001
Takebayashi N, Morrell PL (2001). Is self-fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach. American Journal of Botany 88: 1143-1150.• 382 citations
Draye X, Lin YR, Qian XY, Bowers JE, Burow GB et al. (2001). Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation. Plant Physiology 125: 1325-1341.
• 108 citations
2000
Jiang CX, Chee PW, Draye X, Morrell PL, Smith CW et al. (2000). Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton). Evolution 54: 798-814.• 189 citations
Morrell PL, Porter JM, Friar EA (2000). Intercontinental dispersal: the origin of the widespread South American plant species Gilia laciniata (Polemoniaceae) from a rare California and Oregon coastal endemic. Plant Systematics and Evolution 224: 13-32.
• 33 citations • Associated dataset
1998
Morrell PL, Rieseberg LH (1998). Molecular tests of the proposed diploid hybrid origin of Gilia achilleifolia (Polemoniaceae). American Journal of Botany 85: 1439-1453.• 57 citations • Associated dataset
1994
Rieseberg LH, Allan GJ, Bui Y, Greene J, Morrell PL et al. (1994). Genetic fingerprinting of various native California cultivars. Madrono 41: 30-38.• 5 citations
1993
Carlquist S, Manchester SSR, Morrell PL (1993). Wood anatomy of the Sabiaceae (sl); ecological and systematics implications. Aliso 13: 521-549.• 13 citations