Publications 2022-24

Publications acknowledging WheatCAP support

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Publications reported in 2022 (47)

  1. Alarcón-Reverte R, Xie Y, Stromberger J, Cotter JD, Mason RE, Pearce S (2022) Induced mutations in ASPARAGINE SYNTHETASE-A2 reduce free asparagine concentration in the wheat grain. Crop Science 62:1484–1496. https://doi.org/10.1002/csc2.20760
  2. Baenziger PS, Frels KA, Boehm J, Belamkar V, Rose DJ, Xu L, Wegulo SN, Regassa T, Easterly AC, Creech CF, Santra DK, Klein RN, Jin Y, Kolmer J, Chen MS, Guttieri MJ, Bai G, El-Basyoni Salah I, Masterson SD, Poland J (2022) Registration of ‘Epoch’ hard red winter wheat. Journal of Plant Registrations 16:613–621. https://doi.org/10.1002/plr2.20247
  3. Chen H, Su Z, Tian B, Liu Y, Pang Y, Kavetskyi V, Trick HN, Bai G (2022) Development and optimization of a Barley stripe mosaic virus-mediated gene editing system to improve Fusarium head blight resistance in wheat. Plant Biotechnology Journal 20:1018–1020. https://doi.org/10.1111/pbi.13819
  4. Chen H, Su Z, Tian B, Hao G, Trick HN, Bai G (2022) TaHRC suppresses the calcium-mediated immune response and triggers wheat Fusarium head blight susceptibility. Plant Physiology 190:1566–1569. https://doi.org/10.1093/plphys/kiac352
  5. Chen Y, Liu Y, Zhang J, Torrance A, Watanabe N, Adamski NM, Uauy C (2022) The Triticum ispahanicum elongated glume locus P2 maps to chromosome 6A and is associated with the ectopic expression of SVP-A1. Theor Appl Genet 135:2313–2331.
    https://doi.org/10.1007/s00122-022-04114-y
  6. Chu C, Wang S, Rudd JC, Ibrahim AMH, Xue Q, Devkota RN, Baker JA, Baker S, Simoneaux B, Opena G, Dong H, Liu X, Jessup KE, Chen MS, Hui K, Metz R, Johnson CD, Zhang ZS, Liu S (2022) A new strategy for using historical imbalanced yield data to conduct genome-wide association studies and develop genomic prediction models for wheat breeding. Mol Breeding 42:18. https://doi.org/10.1007/s11032-022-01287-8
  7. Debernardi JM, Woods DP, Li K, Li C, Dubcovsky J (2022) MiR172-APETALA2-like genes integrate vernalization and plant age to control flowering time in wheat. PLoS Genetics, 18: e1010157. https://doi.org/10.1371/journal.pgen.1010157
  8. Dang C, Zhang J, Dubcovsky J (2022) High-resolution mapping of Yr78, an adult plant resistance gene to wheat stripe rust. The Plant Genome, 15: e20212. https://doi.org/10.1002/tpg2.20212
  9. Fan M, Zhang X, Nagarajan R, Fan M, Zhang X, Nagarajan R, Zhai W, Rauf Y, Jia H, Ma Z, Yan LL (2023) Natural variants and editing events provide insights into routes for spike architecture modification in common wheat. The Crop Journal, 11:148-156 https://doi.org/10.1016/j.cj.2022.04.009
  10. Gill HS, Halder J, Zhang J, Rana A, Kleinjan J, St. Amand P, Bernardo A, Bai G, Sehgal SK (2022) Whole-genome analysis of hard winter wheat germplasm identifies genomic regions associated with spike and kernel traits. Theor Appl Genet 135:2953–2967.
    https://doi.org/10.1007/s00122-022-04160-6
  11. Glenn P, Zhang J, Brown-Guedira G, DeWitt N, Cook JP, Li K, Akhunov E, Dubcovsky J (2022) Identification and characterization of a natural polymorphism in FT-A2 associated with increased number of grains per spike in wheat. Theor Appl Genet 135:679-692. https://doi.org/10.1007/s00122-021-03992-y
  12. He F, Wang W, Rutter WB, KW Jordan, Ren J, Taagen E, DeWitt N, Sehgal D, Sukumaran S, Dreisigacker S, Reynolds M, Liu S, Chen J, Fritz A, Cook J, Brown-Guedira G, Pumphrey M, Carter A, Sorrells M, Dubcovsky J, Hayden MJ, 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. Nat Commun 13:826. https://doi.org/10.1038/s41467-022-28453-y
  13. Jiang D, Hua L, Zhang C, Li H, Wang Z, Li J, Wang G, Song R, Shen T, Li H, Bai S, Liu Y, Wanga J, Li H, Dubcovsky J, Chen S 2023. Mutations in the miRNA165/166 binding site of the HB2 gene result in pleiotropic effects on morphological traits in wheat. The Crop Journal, 11:19-20 https://doi.org/10.1016/j.cj.2022.05.002
  14. Kissing Kucek L, Dawson JC, Darby H, Mallory E, Davis M, Sorrells ME (2021) Breeding wheat for weed-competitive ability: II–measuring gains from selection and local adaptation. Euphytica 217:203. https://doi.org/10.1007/s10681-021-02905-w
  15. Kissing Kucek L, Mallory EB, Darby HM, Dawson JC, Sorrells ME (2021) Breeding wheat for weed-competitive ability: I. Correlated traits. Euphytica 217:202.
    https://doi.org/10.1007/s10681-021-02930-9
  16. Kuzay S, Lin H, Li C, Chen S, Woods D, Zhang J, Dubcovsky J (2022) WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat. PLOS Genetics 18:e1009747. https://doi.org/10.1371/journal.pgen.1009747
  17. Larkin DL, Mason RE, Moon DE, Holder AL, Ward BP, Brown-Guedira G (2021) Predicting Fusarium Head Blight Resistance for Advanced Trials in a Soft Red Winter Wheat Breeding Program with Genomic Selection. Frontiers in Plant Science 12: 715314. https://doi.org/10.3389/fpls.2021.715314
  18. Li H, Zhang F, Zhao J, Bai G, St. Amand P, Bernardo A, Ni Z, Sun Q, Su Z (2022) Identification of a novel major QTL from Chinese wheat cultivar Ji5265 for Fusarium head blight resistance in greenhouse. Theor Appl Genet 135:1867–1877. https://doi.org/10.1007/s00122-022-04080-5
  19. Lopez SR, Wiersma AT, Strauss NM, Watkins T, Baik BK, Zhang G, Sehgal SK, Kolb FL, Poland JA, Mason RE, Carter AH, Olson EL (2023) Description of U6719-004 wheat germplasm with YrAS2388R stripe rust resistance introgression from Aegilops tauschii. Journal of Plant Registrations. 17(1):26–33. https://doi.org/10.1002/plr2.20226
  20. Luo J, Rouse MN, Hua L, Li H, Li B, Li T, Zhang W, Gao C, Wang Y, Dubcovsky J, Chen S (2022). Identification and characterization of Sr22b, a new allele of the wheat stem rust resistance gene Sr22 effective against the Ug99 race group. Plant Biotechnology Journal. 20: 554–563. https://doi.org/10.1111/pbi.13737
  21. Morales N, Ogbonna AC, Ellerbrock BJ, Bauchet GJ, Tantikanjana T, et al. (57 co-authors including Jean-Luc Jannink, Clay Birkett, and David Waring) 2022. Breedbase: a digital ecosystem for modern plant breeding. G3. https://doi.org/10.1093/g3journal/jkac078
  22. Moriconi JI, Silva M, Zhang J, Tranquilli GE, Santa-María GE (2022) A genome-wide association study unveils key chromosome regions involved in determining sodium accumulation in wheat under conditions of low potassium supply. Journal of Plant Physiology 275:153739. https://doi.org/10.1016/j.jplph.2022.153739
  23. Peters Haugrud AR, Zhang Q, Green AJ, Xu SS, Faris JD (2023) Identification of stable QTL controlling multiple yield components in a durum × cultivated emmer wheat population under field and greenhouse conditions. G3 Genes|Genomes|Genetics 13: jkac281. https://doi.org/10.1093/g3journal/jkac281
  24. Prather S, Schneider T, Gaham Godoy J, Odubiyi S, Bosque-Perez NA, Rashed A, Rynearson S, Pumphrey MO (2022) Reliable DNA Markers for a Previously Unidentified, Yet Broadly Deployed Hessian Fly Resistance Gene on Chromosome 6B in Pacific Northwest Spring Wheat Varieties. Frontiers in Plant Science 13. https://doi.org/10.3389/fpls.2022.779096
  25. Rooney TE, Kunze KH, Sorrells ME (2022a) Genome-wide marker effect heterogeneity is associated with a large effect dormancy locus in winter malting barley. The Plant Genome:e20247. https://doi.org/10.1002/tpg2.20247
  26. Rooney TE, Sweeney DW, Sorrells ME (2022b) Time series barley germination is predictable and associated with known seed dormancy loci. Crop Science 62:100–119. https://doi.org/10.1002/csc2.20638
  27. Sandhu KS, Merrick LF, Sankaran S, Zhang Z, Carter AH (2022) Prospectus of Genomic Selection and Phenomics in Cereal, Legume and Oilseed Breeding Programs. Frontiers in Genetics 12. https://doi.org/10.3389/fgene.2021.829131
  28. Sandhu KS, Mihalyov PD, Lewien MJ, Pumphrey MO, Carter AH (2021) Genomic Selection and Genome-Wide Association Studies for Grain Protein Content Stability in a Nested Association Mapping Population of Wheat. Agronomy 11:2528. https://doi.org/10.3390/agronomy11122528
  29. Sandhu KS, Patil SS, Aoun M, Carter AH (2022) Multi-Trait Multi-Environment Genomic Prediction for End-Use Quality Traits in Winter Wheat. Frontiers in Genetics 13: 831020. https://doi.org/10.3389/fgene.2022.831020
  30. Sandro P, Kucek LK, Sorrells ME, Dawson JC, Gutierrez L (2022) Developing high-quality value-added cereals for organic systems in the US Upper Midwest: hard red winter wheat (Triticum aestivum L.) breeding. Theor Appl Genet. 135: 4005-4027. https://doi.org/10.1007/s00122-022-04112-0
  31. Sweeney DW, Kunze KH, Sorrells ME (2022) QTL x environment modeling of malting barley preharvest sprouting. Theor Appl Genet 135:217–232. https://doi.org/10.1007/s00122-021-03961-5
  32. Sweeney DW, Rooney TE, Sorrells ME (2021) Gain from genomic selection for a selection index in two-row spring barley. The Plant Genome 14:e20138. https://doi.org/10.1002/tpg2.20138
  33. Sweeney DW, Rooney TE, Walling JG, Sorrells ME (2022) Interactions of the barley SD1 and SD2 seed dormancy loci influence preharvest sprouting, seed dormancy, and malting quality. Crop Science 62:120–138. https://doi.org/10.1002/csc2.20641
  34. Taagen E, Jordan K, Akhunov E, Sorrells ME, Jannink JL (2022) If It Ain’t Broke, Don’t Fix It: Evaluating the Effect of Increased Recombination on Response to Selection for Wheat Breeding. G3 Genes|Genomes|Genetics jkac291. https://doi.org/10.1093/g3journal/jkac291
  35. Venegas J, Guttieri MJ, Boehm Jr. JD, Graybosch R, Bai G, St. Amand PC, Palmer N, Hussain W, Blecha S, Baenziger PS (2022) Genetic architecture of the high-inorganic phosphate phenotype derived from a low-phytate mutant in winter wheat. Crop Science 62:1228–1241. https://doi.org/10.1002/csc2.20738
  36. Wu J, Qiao L, Liu Y, Fu B, Nagarajan R, Rauf Y, Jia H, Yan LL (2022) Rapid identification and deployment of major genes for flowering time and awn traits in common wheat. Frontiers in Plant Science 13:992811. https://doi.org/10.3389/fpls.2022.992811
  37. Xu Y, La G, Fatima N, Liu Z, Zhang L, Zhao L, Chen MS, Bai G (2021) Precise mapping of QTL for Hessian fly resistance in the hard winter wheat cultivar ‘Overland’. Theor Appl Genet 134:3951–3962. https://doi.org/10.1007/s00122-021-03940-w
  38. Zhang G, Martin TJ, Fritz AK, Li Y, Seabourn BW, Chen RY, Bai G, Bowden RL, Chen MS, Rupp J, Jin Y, Chen X, Kolmer JA, Marshall DS (2022) Registration of ‘KS Hamilton’ hard red winter wheat. Journal of Plant Registrations 16:73–79. https://doi.org/10.1002/plr2.20190
  39. Zhang J (2022) Check CRISPR editing events in transgenic wheat with next-generation sequencing. In: Wani SH, Kumar A (eds) Genomics of Cereal Crops. Springer US, New York, NY, pp 95–106
  40. Zhang J, Gill HS, Brar NK, Halder J, Ali S, Liu X, Bernardo A, St. Amand P, Bai G, Gill US, Turnipseed B, Sehgal SK (2022) Genomic prediction of Fusarium head blight resistance in early stages using advanced breeding lines in hard winter wheat. The Crop Journal 10:1695-1704. https://doi.org/10.1016/j.cj.2022.03.010
  41. Zhang J, Gill HS, Halder J, Brar NK, Ali S, Bernardo A, St. Amand P, Bai G, Turnipseed B, Sehgal SK (2022) Multi-locus genome-wide association studies to characterize Fusarium Head Blight (FHB) resistance in Hard Winter Wheat. Frontiers in Plant Science 13: 946700. https://doi.org/10.3389/fpls.2022.946700
  42. Zhang L, Xu Y, Chen M-S, Su Z, Liu Y, Xu Y, La G, Bai G (2022) Identification of a major QTL for Hessian fly resistance in wheat cultivar ‘Chokwang’. The Crop Journal 10:775–782. https://doi.org/10.1016/j.cj.2021.08.004
  43. Zhang XY, Jia HY, Li T, Wu JZ, Nagarajan R, Lei L, Powers C, Kan CC, Hua W, Liu ZY, Chen C, Carver BF, Yan LL (2022) TaCol-B5 modifies spike architecture and enhances grain yield in wheat. Science 376:180–183. https://doi.org/10.1126/science.abm0717
  44. Zhao L, Ge W, Lyu Z, Xu S, Xu Y, Bernardo A, Zhang Q, Xu S, Wang H, Kong L, Bai G (2022) Development and validation of diagnostic markers for the wheat Fusarium head blight resistance gene Fhb7. Crop Science 62:1903–1911. https://doi.org/10.1002/csc2.20754
  45. Zhao L, Su P, Hou B, Wu H, Fan Y, Li W, Zhao J, Ge W, Xu S, Wu S, Ma X, Li A, Bai G, Wang H, Kong L (2022) The Black Necrotic Lesion Enhanced Fusarium graminearum Resistance in Wheat. Frontiers in Plant Science 13: 926621. https://doi.org/10.3389/fpls.2022.926621
  46. DeWitt N, Guedira M, Murphy JP, Marshall D, Mergoum M, Maltecca C, Brown-Guedira G (2022) A network modeling approach provides insights into the environment-specific yield architecture of wheat. Genetics 221(3) iyac076. https://doi.org/10.1093/genetics/iyac076
  47. Rivera-Burgos LA, Brown-Guedira G, Johnson J, Mergoum M, Cowger, C (2022) Accounting for heading date gene effects allows detection of small-effect QTL associated with resistance to Septoria nodorum blotch in wheat. PloS one 17(5) p.e0268546. https://doi.org/10.1371/journal.pone.0268546

Publications reported in 2023 (50)

  1. Yu S, Li M, Dubcovsky J, Tian L (2022). Mutant combinations of lycopene ɛ-cyclase and β-carotene hydroxylase 2 homoeologs increased beta-carotene accumulation in endosperm of tetraploid wheat (Triticum turgidum L.) grains. Plant Biotech. J. 20, 564–576. https://doi.org/10.1111/pbi.13738
  2. Zhang J, Nirmala J, Chen S, Jost M, Steuernagel B, Karafiatova M, Hewitt T, Li H, Edae E, Sharma K, Hoxha S, Bhatt D, Antoniou-Kourounioti R, Dodds P, Wulff BBH, Dolezel J, Ayliffe M, Hiebert C, McIntosh R, Dubcovsky J, Zhang P, Rouse MN, Lagudah E (2023) Single amino acid change alters specificity of the multi-allelic wheat stem rust resistance locus SR9. Nature Communications 14: 7354. https://doi.org/10.1038/s41467-023-42747-9
  3. Glenn P, Woods DP, Zhang J, Gabay G, Odle N, Dubcovsky J (2023) Wheat bZIPC1 interacts with FT2 and contributes to the regulation of spikelet number per spike. Theoretical and Applied Genetics 136: 237. https://doi.org/10.1007/s00122-023-04484-x
  4. Zhang J, Xiong H, Burguener GF, Vasquez-Gross H, Liu Q, Debernardi JM, Akhunova A, Garland-Campbell K, Kianian SF, Brown-Guedira G, Pozniak C, Faris JD, Akhunov E, Dubcovsky J (2023) Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression. Proceedings of the National Academy USA 120: e2306494120. https://doi.org/10.1073/pnas.2306494120
  5. Li H, Hua L, Zhao S, Hao M, Song R, Pang S, Liu Y, Chen H, Zhang W, Shen T, Gou J-Y, Mao H, Wang G, Hao X, J. L, Song B, C. L, Li Z, Wang Deng X, Dubcovsky J, Wang X, Chen S (2023) Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides. Nature Communications: 6072. https://doi.org/10.1038/s41467-023-41833-2
  6. Bekkering CS, Yu S, Isaka NN, Sproul BW, Dubcovsky J, Tian L (2023) Genetic dissection of the roles of beta-hydroxylases in carotenoid metabolism, photosynthesis, and plant growth in tetraploid wheat (Triticum turgidum L.). Theor Appl Genet 136:8. https://doi.org/10.1007/s00122-023-04276-3
  7. Li H, Luo J, Zhang W, Hua L, Li K, Wang J, Xu B, Yang C, Wang G, Rouse MN, Dubcovsky J, Chen S (2023) High-resolution mapping of SrTm4, a recessive resistance gene to wheat stem rust. Theor. Appl. Genet. 136: 120. https://doi.org/10.1007/s00122-023-04276-3
  8. Boden SA, McIntosh RA, Uauy C, Krattinger SG, Dubcovsky J, Rogers WJ, Xia XC, Badaeva ED, Bentley AR, Brown-Guedira G, Caccamo M, Cattivelli L, Chhuneja P, Cockram J, Contreras-Moreira B, Dreisigacker S, Edwards D, Gonzalez FG, Guzman C, Ikeda TM, Karsai I, Nasuda S, Pozniak C, Prins R, Sen TZ, Silva P, Simkova H, Zhang Y, Wheat I (2023) Updated guidelines for gene nomenclature in wheat. Theor. Appl. Genet. 136:72. https://doi.org/10.1007/s00122-023-04253-w
  9. Debernardi JM, Burguener G, Bubb K, Liu Q, Queitsch C, Dubcovsky J (2023) Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei. BMC Plant Biology 23:270. https://doi.org/10.1186/s12870-023-04281-0
  10. Zhang J, Li C, Zhang W, Zhang X, Mo Y, Tranquilli GE, Vanzetti LS, Dubcovsky J (2023) Wheat plant height locus RHT25 encodes a PLATZ transcription factor that interacts with DELLA (RHT1). Proc. Natl. Acad. Sci. USA. 120: e2300203120. https://doi.org/10.1073/pnas.2300203120
  11. Alvarez MA., Li C, Lin H, Joe A, Padilla M, Woods DP, Dubcovsky J. (2023). EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time. PLoS Genetics 19: e1010655. https://doi.org/10.1371/journal.pgen.1010655
  12. Gabay G, Wang HC, Zhang JL, Moriconi JI, Burguener GF, Gualano LD, Howell T, Lukaszewski A, Staskawicz B, Cho MJ, Tanaka J, Fahima T, Ke HY, Dehesh K, Zhang GL, Gou JY, Hamberg M, Santa-María GE, Dubcovsky J (2023) Dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat primary root growth. Nature Communications. 14:539. https://doi.org/10.1038/s41467-023-36248-y
  13. Chen Z, Debernardi JM, Dubcovsky J, Gallavotti A (2022). Recent advances in crop transformation technologies. Nature Plants. 8: 1343–1351. https://doi.org/10.1038/s41477-022-01295-8
  14. Zhang J, Debernardi JM, Burguener GF, Choulet F, Paux E, O’Connor L, Enk J, Dubcovsky J (2023) A second generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives. The Plant Genome. 16:e20296. https://doi.org/10.1002/tpg2.20296
  15. Wong ML, Bruckner PL, Berg JE, Lamb PF, Hofland ML, Caron CG, Heo H-Y., Blake NK, Weaver DK, Cook JP (2023). Evaluation of wheat stem sawfly-resistant solid stem Qss.msub-3BL alleles in hard red winter wheat. Crop Science, 63, 556–567. https://doi.org/10.1002/csc2.20866
  16. Bian R, Liu N, Xu Y, Su Z, Chai L, Bernardo A, St. Amand P, Fritz A, Zhang G, Rupp J, Akhunov E, Jordan KW, Bai G (2023) Quantitative trait loci for rolled leaf in a wheat EMS mutant from Jagger. Theor Appl Genet 136(3):52. https://doi.org/10.1007/s00122-023-04284-3
  17. Chen J, Wheeler JJ, Marshall JM, Chen X, Windes S, Wilson C, Su M, Yimer B, Schroeder K, Jackson C (2023) Release of ‘UI Gold’ hard white spring wheat. Journal of Plant Registrations. https://doi.org/10.1002/plr2.20309
  18. Crutcher FK, Lamb PF, Nash D, Fiedler JD, Eberly J, Kephart KD, McVay K, Torrion J, Beiermann CW, Vetch JM, Chen C, Holen D, Blake NK, Heo H-Y, Cook JP (2023) Registration of ‘MT Sidney’ hard red spring wheat. Journal of Plant Registrations 17(2):368–375. https://doi.org/10.1002/plr2.20268
  19. DeWitt N, Lyerly J, Guedira M, Holland JB, Murphy JP, Ward BP, Boyles RE, Mergoum M, Babar MA, Shakiba E, Sutton R, Ibrahim A, Tiwari V, Santantonio N, Van Sanford DA, Howell K, Smith JH, Harrison SA, Brown-Guedira G (2023) Bearded or smooth? Awns improve yield when wheat experiences heat stress during grain fill in the southeastern United States. Journal of Experimental Botany: 74(21): 6749-6759. https://doi.org/10.1093/jxb/erad318
  20. Dixon L, Bellinger B, Carter AH (2023) A gravimetric method to monitor transpiration under water stress conditions in wheat. The Plant Phenome Journal 6(1):e20078. https://doi.org/10.1002/ppj2.20078
  21. Dogan M, Wang Z, Cerit M, Valenzuela-Antelo JL, Dhakal S, Chu C, Xue Q, Ibrahim AMH, Rudd JC, Bernardo A, St. Amand P, Bai G, Zhang H, Liu S (2023) QTL Analysis of Yield and End-Use Quality Traits in Texas Hard Red Winter Wheat. Agronomy 13(3):689. https://doi.org/10.3390/agronomy13030689
  22. Garst N, Belamkar V, Easterly A, Guttieri MJ, Stoll H, Ibrahim AMH, Baenziger PS (2023) Evaluation of pollination traits important for hybrid wheat development in Great Plains germplasm. Crop Science 63(3):1169–1182. https://doi.org/10.1002/csc2.20926
  23. Gill HS, Brar N, Halder J, Hall C, Seabourn BW, Chen YR, St. Amand P, Bernardo A, Bai G, Glover K, Turnipseed B, Sehgal SK (2023) Multi-trait genomic selection improves the prediction accuracy of end-use quality traits in hard winter wheat. The Plant Genome:e20331. https://doi.org/10.1002/tpg2.20331
  24. Guttieri MJ, Bowden RL, Zhang G, Haley S, Frels K, Hein GL, Jordan KW (2023) Agronomic and quality impact of a shortened translocation for wheat streak mosaic virus resistance. Crop Science 63(2):622–634. https://doi.org/10.1002/csc2.20876
  25. Halder J, Gill HS, Zhang J, Altameemi R, Olson E, Turnipseed B, Sehgal SK (2023) Genome-wide association analysis of spike and kernel traits in the U.S. hard winter wheat. The Plant Genome 16(1):e20300. https://doi.org/10.1002/tpg2.20300
  26. Hammers M, Winn ZJ, Ben-Hur A, Larkin D, Murry J, Mason RE (2023) Phenotyping and predicting wheat spike characteristics using image analysis and machine learning. The Plant Phenome Journal 6(1):e20087. https://doi.org/10.1002/ppj2.20087
  27. Herr AW, Adak A, Carroll ME, Elango D, Kar S, Li C, Jones SE, Carter AH, Murray SC, Paterson A, Sankaran S, Singh A, Singh AK (2023) Unoccupied aerial systems imagery for phenotyping in cotton, maize, soybean, and wheat breeding. Crop Science 63(4):1722–1749. https://doi.org/10.1002/csc2.21028
  28. Herr AW, Carter AH (2023) Remote sensing continuity: a comparison of HTP platforms and potential challenges with field applications. Frontiers in Plant Science 14:1233892. https://doi.org/10.3389/fpls.2023.1233892
  29. Kaur S, Gill HS, Breiland M, Kolmer JA, Gupta R, Sehgal SK, Gill U (2023) Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis. Frontiers in Plant Science 14:1090163. https://doi.org/10.3389/fpls.2023.1090163
  30. Liu Z, Li Y, Bernardo A, Amand PSt, Zhang P, Sehgal S, Bai G (2023) Development of diagnostic SNP markers for identification of rye 1RS translocations in wheat. Crop Science 63(1):255–265. https://doi.org/10.1002/csc2.20841
  31. Merrick LF, Burke AB, Zhang Z, Carter AH (2022) Comparison of single-trait and multi-trait genome-wide association models and inclusion of correlated traits in the dissection of the genetic architecture of a complex trait in a breeding program. Frontiers in Plant Science 12: 772907. https://doi.org/10.3389/fpls.2021.772907
  32. Merrick LF, Herr AW, Sandhu KS, Lozada DN, Carter AH (2022) Optimizing plant breeding programs for genomic selection. Agronomy 12(3):714. https://doi.org/10.3390/agronomy12030714
  33. Merrick LF, Herr AW, Sandhu KS, Lozada DN, Carter AH (2022) Utilizing genomic selection for wheat population development and improvement. Agronomy 12(2):522. https://doi.org/10.3390/agronomy12020522
  34. Merrick LF, Lozada DN, Chen X, Carter AH (2022) Classification and regression models for genomic selection of skewed phenotypes: A case for disease resistance in winter wheat (Triticum aestivum L.). Frontiers in Genetics 13:835781. https://doi.org/10.3389/fgene.2022.835781
  35. Montesinos-López OA, Herr AW, Crossa J, Carter AH (2023) Genomics combined with UAS data enhances prediction of grain yield in winter wheat. Frontiers in Genetics 14. https://doi.org/10.3389/fgene.2023.1124218
  36. Mustahsan W, Guttieri MJ, Bowden RL, Garland-Campbell K, Jordan K, Bai G, Zhang G (2023) Mapping the quantitative field resistance to stripe rust in a hard winter wheat population “Overley” × “Overland”. Crop Science 63(4):2050–2066. https://doi.org/10.1002/csc2.20977
  37. Peters Haugrud AR, Sharma JS, Zhang Q, Green AJ, Xu SS, Faris JD (2023) Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement. The Plant Genome:e20398. https://doi.org/10.1002/tpg2.20398
  38. Wang H, Bernardo A, St. Amand P, Bai G, Bowden RL, Guttieri MJ, Jordan KW (2023) Skim exome capture genotyping in wheat. The Plant Genome:e20381. https://doi.org/10.1002/tpg2.20381
  39. Winn ZJ, Amsberry AL, Haley SD, DeWitt ND, Mason RE (2023) Phenomic versus genomic prediction-A comparison of prediction accuracies for grain yield in hard winter wheat lines. The Plant Phenome Journal 6(1):e20084. https://doi.org/10.1002/ppj2.20084
  40. Winn ZJ, Larkin DL, Lozada DN, DeWitt N, Brown-Guedira G, Mason RE (2023) Multivariate genomic selection models improve prediction accuracy of agronomic traits in soft red winter wheat. Crop Science 63(4):2115–2130. https://doi.org/10.1002/csc2.20994
  41. Winn ZJ, Lyerly JH, Brown-Guedira G, Murphy JP, Mason RE (2023) Utilization of a publicly available diversity panel in genomic prediction of Fusarium head blight resistance traits in wheat. The Plant Genome 16(3):e20353. https://doi.org/10.1002/tpg2.20353
  42. Wold-McGimsey F, Krosch C, Alarcón-Reverte R, Ravet K, Katz A, Stromberger J, Mason RE, Pearce S (2023) Multi-target genome editing reduces polyphenol oxidase activity in wheat (Triticum aestivum L.) grains. Frontiers in Plant Science 14: 1247680. https://doi.org/10.3389/fpls.2023.1247680
  43. Wu J, Jia H, Qiao L, Fu B, Brown-Guedira G, Nagarajan R, Yan L (2023) Genetic basis of resistance against powdery mildew in the wheat cultivar “Tabasco”. Mol Breeding 43(7):56. https://doi.org/10.1007/s11032-023-01402-3
  44. Xu Y, Li Y, Bian R, Zhang G, Fritz AK, Dong Y, Zhao L, Xu Y, Ghori N, Bernardo A, St. Amand P, Rupp JLS, Bruce M, Wang W, Akhunov E, Carver B, Bai G (2023) Genetic architecture of quantitative trait loci (QTL) for FHB resistance and agronomic traits in a hard winter wheat population. The Crop Journal. Online first. https://doi.org/10.1016/j.cj.2023.09.004
  45. Rebollo I, Aguilar I, Pérez de Vida F, Molina F, Gutiérrez L, Rosas JE (2023) Genotype by environment interaction characterization and its modeling with random regression to climatic variables in two rice breeding populations. Crop Science 63(4):2220–2240. https://doi.org/10.1002/csc2.21029
  46. Bhandari M, Chang A, Jung J, Ibrahim AM, Rudd JC, Baker S, Landivar J, Liu S, Landivar J (2023) Unmanned aerial system‐based high‐throughput phenotyping for plant breeding. The Plant Phenome Journal 6: e20058. https://doi.org/10.1002/ppj2.20058
  47. Cerit M, Wang Z, Dogan M, Yu S, Valenzuela-Antelo JL, Chu C, Wang S, Xue Q, Ibrahim AMH, Rudd JC, Metz R, Johnson CD, Liu S (2023) Mapping QTL for Yield and Its Component Traits Using Wheat (Triticum aestivum L.) RIL Mapping Population from TAM 113 x Gallagher. Agronomy 13:2402. https://doi.org/10.3390/agronomy13092402
  48. Wang Z, Dhakal S, Cerit M, Wang S, Rauf Y, Yu S, Maulana F, Huang W, Anderson JD, Ma X-F, Rudd JC, Ibrahim AMH, Xue Q, Hays DB, Bernardo A, St. Amand P, Bai G, Baker J, Baker S, Liu S (2022) QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster. Frontiers in Plant Science 13:1057701. https://doi.org/10.3389/fpls.2022.1057701
  49. Rooney TE, Sweeney DW, Kunze KH, Sorrells ME, Walling JG (2023) Malting quality and preharvest sprouting traits are genetically correlated in spring malting barley. Theor Appl Genet 136(3):59. https://doi.org/10.1007/s00122-023-04257-6
  50. Jordan KW, Fernandez-de Soto M, Korol A, Akhunova A, Akhunov E (2023). Allelic variation in the wheat homolog of topoisomerase II is associated with crossover rate. BioRxiv, https://doi.org/10.1101/2023.07.06.548017

Publications reported in 2024 (29)

  1. Zhang, J.,  G.F. Burguener, F. Paraiso, J. Dubcovsky. 2024. Natural alleles of LEAFY and WAPO1 interact to regulate spikelet number per spike in wheat. bioRxiv https://doi.org/10.1101/2024.08.17.608376 accepted in Theoretical and Applied Genetics.
  2. Zhang, C., Hegarty J., Padilla M., D.M. Tricoli D.M, Dubcovsky J.*, Debernardi J.M.*. 2024. Manipulation of the microRNA172 - AP2L2 interaction provides precise control of wheat and triticale plant height. bioRxiv  https://doi.org/10.1101/2024.08.05.606718. *Co-senior and corresponding author. Accepted in Plant Biotechnology Journal. 
  3. Rottersman, M.G., W. Zhang, J. Zhang, G. Grigorian, G.F. Burguener, Carter C., T. Vang, J. Hegarty, X. Zhang, and J. Dubcovsky. 2024. Deletion of wheat alpha-gliadins from chromosome 6D improves gluten strength and reduces immunodominant celiac disease epitopes. bioRxiv. https://doi.org/10.1101/2024.07.19.604379
  4. Paraiso F., H. Lin, C. Li, D.P. Woods, T. Lan, C. Tumelty, J.M. Debernardi, A. Joe, J. Dubcovsky. 2024. LEAFY and WAPO1 jointly regulate spikelet number per spike and floret development in wheat. Development 151:dev202803. https://doi.org/10.1242/dev.202803(in bioRxiv in previous report).
  5. Li, C., H. Lin, J.M. Debernardi, C. Zhong, and J. Dubcovsky. 2024. GIGANTEA accelerates wheat heading time through gene interactions converging on FLOWERING LOCUS T1. The Plant Journal. 118, 519–533. https://doi.org/10.1111/tpj.16622
  6. Winn, Z.J., E. Hudson-Arns, M. Hammers, N. DeWitt, J. Lyerly, G. Bai, P. St. Amand, P. Nachappa, S. Haley, R.E. Mason. 2024. HaploCatcher: An R package for prediction of haplotypes. The Plant Genome 17:e20412. https://doi.org/10.1002/tpg2.20412
  7. Wondifraw, M., Z.J. Winn, S.D. Haley, J.A. Stromberger, E.E. Hudson-Arns, R.E. Mason. 2024. Advancing water absorption capacity in hard winter wheat using a multivariate genomic prediction approach. Crop Science In press: https://doi.org/10.1002/csc2.21321
  8. Wondifraw, M.A., Z.J. Winn, S.D. Haley, J.A. Stromberger, E.E., R.E. Mason. 2024. Elucidation of the genetic architecture of water absorption capacity in hard winter wheat through genome wide association study. The Plant Genome 17:e20500. https://doi.org/10.1002/tpg2.20500
  9. Joshi P, G.S. Dhillon, Y. Gao, A. Kaur, J. Wheeler, and J. Chen. 2024. An optimal model to improve genomic prediction for protein content and test weight in a diverse spring wheat panel. Agriculture, 14:347.  https://doi.org/10.3390/agriculture14030347
  10. Zhao, L., A. Bernardo, F. Kong, W. Zhao, Y. Dong, H. Lee, H.N. Trick, J. Rupp Noller, G Bai. 2024. A glutathione S-transferase from Thinopyrum ponticum confers Fhb7 resistance to Fusarium head blight in wheat. Phytopathology 114 (7): 1458-1461 https://doi.org/10.1094/PHYTO-03-24-0106-SC 
  11. Kumar, P., H.S. Gill, M. Singh, K. Kaur, D. Koupal, S. Talukder, A. Bernardo, P. St Amand, G. Bai, S.K. Sehgal. 2024. Characterization of flag leaf morphology identifies a major genomic region controlling flag leaf angle in the US winter wheat (Triticum aestivum L.). Theor Appl Genet 137 (205): 1-17 https://doi.org/10.1007/s00122-024-04701-1
  12. Zhao, L., Y. Lu, X. Zhang, W. Zhao, X. Xu, H. Wang, G. Zhang, A.K. Fritz, J. Fellers, M. Guttieri, K.W. Jordan, G. Bai. 2024. Characterization of quantitative trait loci for leaf rust resistance from CI 13227 in three winter wheat populations. Phytopathology (First Look). https://doi.org/10.1094/PHYTO-03-24-0108-R
  13. Kaushal, S., H.S. Gill, M.M. Billah, S.N. Khan, J. Halder, A. Bernardo, P.S. Amand, G. Bai, K. Glover, M. Maimaitijiang, S.K Sehgal. 2024. Enhancing the potential of phenomic and genomic prediction in winter wheat breeding using high-throughput phenotyping and deep learning. Front Plant Sci 15, 1410249. https://doi.org/10.3389/fpls.2024.1410249
  14. Xu, Y., N. Ghori, S. Hussain, X. Xu, Z. Su, D. Zhang, L. Zhao, X. Liu, M.S. Chen, G.H. Bai. 2024. Evaluating a worldwide wheat collection for resistance to Hessian fly biotype ‘Great Plains’. Front Plant Sci 15, 1402218, https://doi.org/10.3389/fpls.2024.1402218
  15. Wang, W., Q. Pan, B. Tian, D. Davidson, G. Bai, A. Akhunova, H.N. Trick, E. Akhunov. 2024. Non-additive dosage-dependent effects of TaGS3 gene editing on grain size and weight in wheat. bioRxiv, https://doi.org/10.1101/2024.04.28.591550
  16. Zhang, F., H. Zhang, J. Liu, X. Ren, Y. Ding, F. Sun, Z. Zhu, X. He, Y. Zhou, G. Bai, Z. Ni, Q. Sun, Z Su. 2024. Fhb9, a major QTL for Fusarium head blight resistance improvement in wheat. J Integr Agric. https://doi.org/10.1016/j.jia.2024.03.045   
  17. Nyine M, Davidson D, Adhikari E, Clinesmith M, Wang H, Akhunova A, Fritz A, Akhunov E, 2024, Ecogeographic signals of local adaptation in a wild relative help to identify variants associated with improved wheat performance under drought stress. BioRxiv, https://doi.org/10.1101/2024.03.20.585976 (accepted to Genome Biology).
  18. Coombes B, Lux T, Akhunov E, Hall A. Introgressions lead to reference bias in wheat RNA-Seq analysis. BMC Biology. 2024, 22:56. https://doi.org/10.1186/s12915-024-01853-w (in bioRxiv in previous report).
  19. Xu Y, Li Y, Bian R, Zhang G, Fritz AK, Dong Y, Zhao L, Xu Y, Ghori N, Bernardo A, Amand P, Rupp JLS, Bruce M, Wang W, Akhunov E, Carver B, Bai B. 2023. Genetic architecture of quantitative trait loci (QTL) for FHB resistance and agronomic traits in a hard winter wheat population. Crop Journal, 11 (6), 1836-1845. https://doi.org/10.1016/j.cj.2023.09.004 (online 1st on previous report).
  20. Concepcion JS, Noble AD, Thompson AM, Dong Y, Olson EL. 2024. Genomic regions influencing the hyperspectral phenome of deoxynivalenol infected wheat. Sci Rep. 14: 19340. https://doi.org/10.1038/s41598-024-69830-5
  21. Anderson JA, Wiersma JJ, Reynolds SK, Conley EJ, Stuart N, Caspers R, Kolmer JA, Rouse MN, Jin Y, Dill-Macky R, Smith MJ, Dykes L. 2024. Registration of 'MN-Torgy' spring wheat with moderate resistance to Fusarium head blight and adult plant resistance to Ug99 stem rust. Journal of Plant Registrations 18:122-133. https://doi.org/10.1002/plr2.20321
  22. Rivera-Burgos L, VanGessel C, Guedira M, Smith J, Marshall D, Jin Y, Rouse M, Brown-Guedira G. 2024. Fine mapping of stem rust resistance derived from soft red winter wheat cultivar AGS2000 to an NLR gene cluster on chromosome 6D. Theor Appl Genet 137, 206 (2024). https://doi.org/10.1007/s00122-024-04702-0 
  23. Li H., W. Men,  C. Ma, Q. Liu, Z. Dong, X. Tian, C. Wang, C. Liu, H.S. Gill, P. Ma, Z. Zhang, B. Liu, Y. Zhao, S.K. Sehgal, W. Liu W. 2024. Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein. Nature Communications 15:2449 https://doi.org/10.1038/s41467-024-46814-7 
  24. Thapa, S., H.S. Gill, J. Halder, A. Rana, S. Ali, M. Maimaitijiang, U. Gill, A. Bernardo, P. St. Amand, G. Bai, S.K Sehgal. 2024. Integrating genomics, phenomics, and deep learning improves the predictive ability for Fusarium head blight–related traits in winter wheat. The Plant Genome:e20470 https://doi.org/10.1002/tpg2.20470
  25. Zhao ,Y., Z. Dong, J. Miao, Q. Liu, C. Ma, X. Tian, J. He, H. Bi, W. Yao, T. Li, H. Gill, Z. Zhang, A. Cao, B. Liu, H. Li, S.K. Sehgal, W. Liu. 2024. Pm57 from Aegilops searsii encodes a tandem kinase protein and confers wheat powdery mildew resistance. Nature Communications 15:4796 https://doi.org/10.1038/s41467-024-49257-2 
  26. Sangjan, W., A.H. Carter, M.O. Pumphrey, K. Hagemeyer, V. Jitkov, S. Sankaran. 2024. Effect of high-resolution satellite and UAV imagery plot pixel resolution in wheat crop yield prediction. Int J Remote Sens 45:1678-1698. https://doi.org/10.1080/01431161.2024.2313997
  27. Herr, A.W., P. Schmuker, A.H. Carter. 2024. Large-scale breeding applications of UAS enabled genomic prediction. Plant Phenome J 7:e20101 https://doi.org/10.1002/ppj2.20101

  28. Montesinos-Lopez, O.A., A.W. Herr, A. Montesinos-Lopez, J. Crossa, A.H. Carter. 2024. Enhancing winter wheat prediction with genomics, phenomics, and environmental data. BMC Genomics 25:544 https://doi.org/10.1186/s12864-024-10438-4