Research Project: New Genetic Resources for Breeding Better Wheat and Bioenergy Crops

Location: Crop Improvement and Genetics Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Linkage drag analysis in three Aegilops speltoides introgressions carrying Sr47 in modern durum and hard red spring wheat germplasm - (Peer Reviewed Journal)
Klindworth, D.L., Salsman, E., Underdahl, J., Elias, E.M., Green, A.J., Dykes, L., Faris, J.D., Xu, S.S. 2023. Linkage drag analysis in three Aegilops speltoides introgressions carrying Sr47 in modern durum and hard red spring wheat germplasm. Theoretical and Applied Genetics. 136. Article 168. https://doi.org/10.1007/s00122-023-04409-8.

Mixed-linkage glucan is the main carbohydrate source and starch is an alternative source during Brachypodium grain germination - (Peer Reviewed Journal)
Francin-Allami, M., Bouder, A., Geairon, A., Alvarado, C., Le-Bot, L., Daniel, S., Shao, M., Chingcuanco, D.L., Vogel, J.P., Guillon, F., Bonnin, E., Saulnier, L., Sibout, R. 2023. Mixed-linkage glucan is the main carbohydrate source and starch is an alternative source during Brachypodium grain germination. International Journal of Molecular Sciences. 24(7). Article 6821. https://doi.org/10.3390/ijms24076821.

PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon - (Peer Reviewed Journal)
Woods, D., Li, W., Sibout, R., Shao, M., Chingcuanco, D.L., Vogel, J., Dubcovsky, J., Amasino, R. 2023. PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon. PLoS Genetics. 19(5). Article e1010706. https://doi.org/10.1371/journal.pgen.1010706.

Elimination of the yellow pigment gene PSY-E2 tightly linked to the Fusarium head blight resistance gene Fhb7 from Thinopyrum ponticum - (Peer Reviewed Journal)
Li, X., Li, D., Xuan, Y., He, Z., Zhao, L., Hao, Y., Ge, W., Xu, S., Hou, B., Wang, B., Guo, J., Liu, W., Li, M., Han, Y., Bo, C., Bao, Y., Qi, Z., Xu, S.S., Bai, G., Wang, H., Kong, L. 2023. Elimination of the yellow pigment gene PSY-E2 tightly linked to the Fusarium head blight resistance gene Fhb7 from Thinopyrum ponticum. The Crop Journal. 11(3):957-962. https://doi.org/10.1016/j.cj.2022.12.005.

Toward reducing the immunogenic potential of wheat flour: Identification and characterization of wheat lines missing omega-5 gliadins encoded by the 1D chromosome - (Peer Reviewed Journal)
Kim, S., Sim, J., Gu, Y.Q., Altenbach, S.B., Denery-Papini, S., Pineau, F., Tranquet, O., Yang, Y., Ji Park, E., Lim, S., Kang, C., Choi, C., Lee, J. 2023. Toward reducing the immunogenic potential of wheat flour: Identification and characterization of wheat lines missing omega-5 gliadins encoded by the 1D chromosome. Theoretical and Applied Genetics. 136. Article 33. https://doi.org/10.1007/s00122-023-04295-0.

Genome-wide association analyses of leaf rust resistance in cultivated emmer wheat - (Peer Reviewed Journal)
Lhamo, D., Sun, Q., Zhang, Q., Li, X., Fiedler, J.D., Xia, G., Faris, J.D., Gu, Y.Q., Gill, U., Cai, X., Acevedo, M., Xu, S.S. 2023. Genome-wide association analyses of leaf rust resistance in cultivated emmer wheat. Theoretical and Applied Genetics. 136. Article 20. https://doi.org/10.1007/s00122-023-04281-6.

Updated annotation of Affymetrix wheat genome array microarray probes - (Research Notes)
Waymack, R.V., Chingcuanco, D.L. 2022. Updated annotation of Affymetrix wheat genome array microarray probes. Annual Wheat Newsletter. 68:32-33. Available: https://wheat.pw.usda.gov/ggpages/awn/68/AWN_VOL_68.pdf

Haplotype variants of Sr46 in Aegilops tauschii, the diploid D genome progenitor of wheat - (Peer Reviewed Journal)
Athiyannan, N., Long, Y., Kang, H., Chandramohan, S., Bhatt, D., Zhang, Q., Klindworth, D.L., Rouse, M.N., Friesen, T.L., MciIntosh, R., Zhang, P., Forrest, K., Hayden, M., Patpour, M., Hovmoller, M.S., Hickey, L.T., Ayliffe, M., Cai, X., Lagudah, E.S., Periyannan, S., Xu, S.S. 2022. Haplotype variants of Sr46 in Aegilops tauschii, the diploid D genome progenitor of wheat. Theoretical and Applied Genetics. 135: 2627-2639. https://doi.org/10.1007/s00122-022-04132-w.

Haploidy and aneuploidy in switchgrass mediated by misexpression of CENH3 - (Peer Reviewed Journal)
Yoon, S., Bragg, J.N., Aucar-Yamato, S., Chanbusarakum, L.J., Dluge, K., Cheng, P., Blumwald, E., Gu, Y.Q., Tobias, C.M. 2022. Haploidy and aneuploidy in switchgrass mediated by misexpression of CENH3. The Plant Genome. Article e20209. https://doi.org/10.1002/tpg2.20209.

KARRIKIN INSENSITIVE2 regulates leaf development, root system architecture and arbuscular-mycorrhizal symbiosis in Brachypodium distachyon - (Peer Reviewed Journal)
Meng, Y., Varshney, K., Incze, N., Badics, E., Kamran, M., Davies, S., Oppermann, L.M., Magne, K., Dalmais, M., Bendahmane, A., Sibout, R., Vogel, J., Chingcuanco, D.L., Bond, C.S., Soos, V., Gutjahr, C., Waters, M. 2021. KARRIKIN INSENSITIVE2 regulates leaf development, root system architecture and arbuscular-mycorrhizal symbiosis in Brachypodium distachyon. The Plant Journal. 109(6):1559-1574. https://doi.org/10.1111/tpj.15651.

Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation - (Peer Reviewed Journal)
Wang, L., Zhu, T., Rodriguez, J.C., Deal, K.R., Dubcovsky, J., McGuire, P.E., Lux, T., Spannagl, M., Mayer, K.F., Baldrich, P., Meyers, B.C., Huo, N., Gu, Y.Q., Zhou, H., Devos, K.M., Bennetzen, J.L., Unver, T., Budak, H., Gulick, P.J., Galiba, G., Kalapos, B., Nelson, D.R., Li, P., You, F.M., Ming-Cheng, L., Dvorak, J. 2021. Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation. G3, Genes/Genomes/Genetics. 11(12). Article jkab325. https://doi.org/10.1093/g3journal/jkab325.

Heterosis for biomass yield and other traits in alamo x kanlow switchgrass populations - (Peer Reviewed Journal)
Shrestha, S.L., Bhandari, H.S., Allen, F., Tobias, C.M., Santosh, N., Goddard, K., Senseman, S.A. 2021. Heterosis for biomass yield and other traits in alamo x kanlow switchgrass populations. Crop Science. https://doi.org/10.1002/csc2.20618.

Proteomic determination of low-molecular-weight glutenin subunit composition in Aroona near-isogenic lines and standard wheat cultivars - (Peer Reviewed Journal)
Cho, K., Jang, Y., Lim, S., Altenbach, S.B., Gu, Y.Q., Simon-Buss, A., Lee, J. 2021. Proteomic determination of low-molecular-weight glutenin subunit composition in Aroona near-isogenic lines and standard wheat cultivars. International Journal of Molecular Sciences. 22(14). Article: 7709. https://doi.org/10.3390/ijms22147709.

Optical maps refine the bread wheat Triticum aestivum vc. Chinese Spring genome assembly - (Peer Reviewed Journal)
Zhu, T., Wang, L., Rimbert, H., Rodriguez, J., Deal, K.R., De Oliveira, R., Choulet, F., Keeble-Gagnere, G., Tibbits, J., Rogers, J., Eversole, K., Appels, R., Gu, Y.Q., Mascher, M., Dvorak, J., Luo, M. 2021. Optical maps refine the bread wheat Triticum aestivum vc. Chinese Spring genome assembly. The Plant Journal. 107(1):303-314. https://doi.org/10.1111/tpj.15289.

BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon - (Peer Reviewed Journal)
Sakai, K., Citerne, S., Antelme, S., Le Bris, P., Daniel, S., Boulder, A., D'Orlando, A., Cartwright, A., Tellier, F., Pateyron, S., Delannoy, E., Chingcuanco, D.L., Mouille, G., Palauqui, J., Vogel, J., Sibout, R. 2021. BdERECTA drives vasculature patterning and phloem-xylem organization in Brachypodium distachyon. Biomed Central (BMC) Plant Biology. 21. Article 196. https://doi.org/10.1186/s12870-021-02970-2.

Comparison of MALDI-TOF-MS and RP-HPLC as rapid screening methods for wheat lines with altered gliadin compositions - (Peer Reviewed Journal)
Jang, Y., Cho, K., Kim, S., Sim, J., Lee, S., Kim, B., Gu, Y.Q., Altenbach, S.B., Lim, S., Goo, T., Lee, J. 2020. Comparison of MALDI-TOF-MS and RP-HPLC as rapid screening methods for wheat lines with altered gliadin compositions. Frontiers in Plant Science. 11. Article 600489. https://doi.org/10.3389/fpls.2020.600489.

Development of an optimized MALDI-TOF-MS method for high-throughput identification of high-molecular-weight glutenin subunits in wheat - (Peer Reviewed Journal)
Jang, Y., Cho, K., Kim, S., Altenbach, S.B., Lim, S., Sim, J., Lee, J. 2020. Development of an optimized MALDI-TOF-MS method for high-throughput identification of high-molecular-weight glutenin subunits in wheat. Molecules. 25(18). https://doi.org/10.3390/molecules25184347.

Characterization of Pm68, a new powdery mildew resistance gene on chromosome 2BS of Greek durum wheat TRI 1796 - (Peer Reviewed Journal)
He, H., Liu, R., Ma, P., Du, H., Zhang, H., Wu, Q., Yang, L., Gong, S., Liu, T., Huo, N., Gu, Y.Q., Zhu, S. 2020. Characterization of Pm68, a new powdery mildew resistance gene on chromosome 2BS of Greek durum wheat TRI 1796. Journal of Theoretical and Applied Genetics. 134:53-62. https://doi.org/10.1007/s00122-020-03681-2.

Environmentally responsive QTL controlling surface wax load in switchgrass - (Peer Reviewed Journal)
Bragg, J.N., Tomasi, P., Zhang, L., Williams, T.G., Wood, D.F., Lovell, J.T., Healy, A., Schmutz, J., Bonnette, J.E., Cheng, P.K., Chanbusarakum, L.J., Juenger, T., Tobias, C.M. 2020. Environmentally responsive QTL controlling surface wax load in switchgrass. Theoretical and Applied Genetics. 1-9. https://doi.org/10.1007/s00122-020-03659-0.

Combing a new exome capture panel with an effective varBScore algorithm accelerates BSA-based gene cloning in wheat - (Peer Reviewed Journal)
Dong, C., Zhang, L., Chen, Z., Xia, C., Gu, Y.Q., Wang, J., Li, D.L., Xie, Z., Zhang, Q., Zhang, X., Gui, L., Liu, X., Kong, X. 2020. Combing a new exome capture panel with an effective varBScore algorithm accelerates BSA-based gene cloning in wheat. Frontiers in Plant Science. 11:1249. https://doi.org/10.3389/fpls.2020.01249.

Genotyping-by-sequencing to determine the genetic structure of a Tibetan medicinal plant Swertia mussotii franch - (Peer Reviewed Journal)
Yan, Q., Guo, F., Huo, N., Zhan, L., Sun, J., Zuo, Q., Guo, Z., Gu, Y.Q., Wang, Y., Liu, Y. 2020. Genotyping-by-sequencing to determine the genetic structure of a Tibetan medicinal plant Swertia mussotii franch. Genetic Resources and Crop Evolution. 68:469-484. https://doi.org/10.1007/s10722-020-00993-6.

A rare single nucleotide variant in Pm5e confers powdery mildew resistance in common wheat - (Peer Reviewed Journal)
Xie, J., Guo, G., Wang, Y., Hu, T., Wang, L., Li, J., Qiu, D., Li, Y., Wu, Q., Lu, P., Chen, Y., Dong, L., Li, M., Zhang, H., Zhang, P., Zhu, K., Li, B., Deal, K., Huo, N., Zhang, Y., Luo, M., Liu, S., Gu, Y.Q., Li, H., Liu, Z. 2020. A rare single nucleotide variant in Pm5e confers powdery mildew resistance in common wheat. New Phytologist. https://doi.org/10.1111/nph.16762.

A high-quality reference genome sequences of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizome - (Peer Reviewed Journal)
Song, Z., Lin, C., Xing, P., Fen, Y., Jin, H., Zhou, C., Gu, Y.Q., Wang, J., Li, X. 2020. A high-quality reference genome sequences of salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizome. The Plant Genome. 13(3). Article e20041. https://doi.org/10.1002/tpg2.20041.

Modified acid-PAGE method for rapid screening and phenotyping of wheat gliadin mutant lines - (Peer Reviewed Journal)
Watry, H., Zerkle, A.J., Chingcuanco, D.L. 2020. Modified acid-PAGE method for rapid screening and phenotyping of wheat gliadin mutant lines . MethodsX. 7. https://doi.org/10.1016/j.mex.2020.100858.

Contributions of individual and combined Glu-B1x and Glu-B1y high-molecular-weight glutenin subunits to semolina functionality and pasta quality - (Peer Reviewed Journal)
Zhang, Y., Schonhofen, A., Zhang, W., Hegarty, J., Carter, C., Vang, T., Chingcuanco, D.L., Dubcovsky, J. 2020. Contributions of individual and combined Glu-B1x and Glu-B1y high-molecular-weight glutenin subunits to semolina functionality and pasta quality. Journal of Cereal Science. 93. https://doi.org/10.1016/j.jcs.2020.102943.

Mutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of Brachypodium distachyon - (Peer Reviewed Journal)
Woods, D.P., Dong, Y., Bouche, F., Mayer, K., Varner, L., Ream, T.S., Thrower, N., Wilkerson, C., Cartwright, A., Sibout, R., Chingcuanco, D.L., Vogel, J., Amasino, R.M. 2020. Mutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of Brachypodium distachyon. New Phytologist. 227(6):1725-1735. https://doi.org/10.1111/nph.16546.

Mutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of brachypodium distachyon - (Peer Reviewed Journal)
Woods, D., Dong, Y., Bouche, F., Mayer, K., Varner, L., Ream, T., Thrower, N., Wilkerson, C., Cartwright, A., Sibout, R., Chingcuanco, D.L., Vogel, J., Amasino, R. 2020. Mutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of brachypodium distachyon. New Phytologist. 227:1725-1735. https://doi.org/10.1111/nph.16546.

Gene expression and physiological differences in neo-octoploid switchgrass subjected to drought stress - (Peer Reviewed Journal)
Chanbusarakum, L.J., Bragg, J.N., Cheng, P.K., Aucar, S., Sarath, G., Palmer, N.A., Edme, S.J., Tobias, C.M. 2020. Gene expression and physiological differences in neo-octoploid switchgrass subjected to drought stress. BioEnergy Research. 13:63-78. https://doi.org/10.1007/s12155-020-10092-0.

Reducing the immunogenic potential of wheat flour: silencing of alpha gliadin genes in a U.S. wheat cultivar - (Peer Reviewed Journal)
Altenbach, S.B., Chang, H., Rowe, M., Yu, X.B., Simon-Buss, A., Seabourn, B.W., Green, P.H., Alaedini, A. 2020. Reducing the immunogenic potential of wheat flour: silencing of alpha gliadin genes in a U.S. wheat cultivar. Frontiers in Plant Science. 11:20. https://doi.org/10.3389/fpls.2020.00020.

Integrated genome-scale analysis and northern blot detection of retrotransposon siRNAs across plant species - (Book / Chapter)
Bohrer, M., Rymen, B., Himber, C., Gerbaud, A., Pflieger, D., Chingcuanco, D.L., Carwright, A., Vogel, J., Sibout, R., Blevins, T. 2020. Integrated genome-scale analysis and northern blot detection of retrotransposon siRNAs across plant species. Heinlein, H. editor. RNA Tagging Methods and Protocols Methods in Molecular Biology 2166., New York, N.Y., Springer Science + Business Media, LLC., p.387-411. https://doi.org/10.1007/978-1-0716-0712-1_23.

A rare gain of function mutation in a wheat tandem kinase confers resistance to powdery mildew - (Peer Reviewed Journal)
Lu, P., Guo, L., Wang, Z., Li, B., Li, J., Li, Y., Qiu, D., Shi, W., Yang, L., Wang, N., Guo, G., Xie, J., Wu, Q., Chen, Y., Li, M., Zhang, H., Dong, L., Zhang, P., Zhu, K., Yu, D., Zhang, Y., Deal, K., Huo, N., Liu, C., Luo, M., Dvorak, J., Gu, Y.Q., Li, H., Liu, Z. 2020. A rare gain of function mutation in a wheat tandem kinase confers resistance to powdery mildew. Nature Communications. 11. https://doi.org/10.1038/s41467-020-14294-0.

Exploiting the reference genome sequence of hexaploid wheat: a proteomic study of flour proteins from the cultivar Chinese Spring - (Peer Reviewed Journal)
Altenbach, S.B., Chang, H., Simon-Buss, A., Mohr, T.J., Huo, N., Gu, Y.Q. 2019. Exploiting the reference genome sequence of hexaploid wheat: a proteomic study of flour proteins from the cultivar Chinese Spring. Functional and Integrative Genomics. 1-16. https://doi.org/10.1007/s10142-019-00694-z.

Rapid evolution of alpha-gliadin gene family revealed by analyzing Gli-2 locus regions of wild emmer wheat - (Peer Reviewed Journal)
Huo, N., Zhu, T., Zhang, S., Mohr, T.J., Luo, M., Lee, J., Distelfeld, A., Altenbach, S.B., Gu, Y.Q. 2019. Rapid evolution of alpha-gliadin gene family revealed by analyzing Gli-2 locus regions of wild emmer wheat. Functional and Integrative Genomics. https://doi.org/10.1007/s10142-019-00686-z.

OrthoVenn2: a web server for the whole-genome comparison and annotation of orthologous clusters across multiple species - (Peer Reviewed Journal)
Xu, L., Dong, Z., Fang, L., Luo, Y., Wei, Z., Guo, H., Zhang, G., Gu, Y.Q., Coleman-Derr, D.A., Xia, Q., Wang, Y. 2019. OrthoVenn2: a web server for the whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 47(W1):W52-W58. https://doi.org/10.1093/nar/gkz333.

Elimination of omega-1,2 gliadins from bread wheat (Triticum aestivum) flour: effects on immunogenic potential and end-use quality - (Peer Reviewed Journal)
Altenbach, S.B., Chang, H., Yu, X.B., Seabourn, B.W., Green, P.H., Alaedini, A. 2019. Elimination of omega-1,2 gliadins from bread wheat (Triticum aestivum) flour: effects on immunogenic potential and end-use quality. Frontiers in Plant Science. 10:580. https://doi.org/10.3389/fpls.2019.00580.

Complete genome sequence of Agrobacterium fabrum strain 1D159 - (Peer Reviewed Journal)
Huo, N., Gu, Y.Q., McCue, K.F., Alabed, D., Thomson, J.G. 2019. Complete genome sequence of Agrobacterium fabrum strain 1D159. Microbiology Resource Announcements. 8(19):e00207-19. https://doi.org/10.1128/MRA.00207-19.

Towards reducing the immunogenic potential of wheat flour: Omega gliadins encoded by the D genome of hexaploid may also harbor epitopes for the serious food allergy WDEIA - (Peer Reviewed Journal)
Altenbach, S.B., Chang, H., Simon-Buss, A., Jang, Y., Denery-Papini, S., Pineau, F., Gu, Y.Q., Huo, N., Lim, S., Kang, C., Lee, J. 2018. Towards reducing the immunogenic potential of wheat flour: Omega gliadins encoded by the D genome of hexaploid may also harbor epitopes for the serious food allergy WDEIA. Biomed Central (BMC) Plant Biology. 18:291. https://doi.org/10.1186/s12870-018-1506-z.

Release of a new set of lines of an elite variety of wheat with deletions in Glu-B1 Locus (GluB1-S60E) - (Germplasm Registration)
Chingcuanco, D.L. 2017. Release of a new set of lines of an elite variety of wheat with deletions in Glu-B1 Locus (GluB1-S60E). Germplasm Release. 8(1):1-8.

Release of a new set of lines of an elite variety of wheat with deletions in Glu-B1 Locus (GluB1-S101A) - (Germplasm Registration)
Chingcuanco, D.L. 2017. Release of a new set of lines of an elite variety of wheat with deletions in Glu-B1 Locus (GluB1-S101A). Germplasm Release. 8(1):1-8.

Release of a new set of lines of an elite variety of wheat with deletions in Glu-B1 Locus (GluB1-S261A) - (Germplasm Registration)
Chingcuanco, D.L. 2017. Release of a new set of lines of an elite variety of wheat with deletions in Glu-B1 Locus (GluB1-S261A). Germplasm Release. 8(1):1-8.

Release of a new set of lines of an elite variety of wheat with deletions in Glu-B1 Locus (GluB1-S62D) - (Germplasm Registration)
Chingcuanco, D.L. 2017. Release of a new set of lines of an elite variety of wheat with deletions in Glu-B1 Locus (GluB1-S62D). Germplasm Release. 8(1):1-8.

Release of a new set of lines of an elite variety of wheat with deletions in Glu-B1 Locus (GluB1-S239F) - (Germplasm Registration)
Chingcuanco, D.L. 2017. Release of a new set of lines of an elite variety of wheat with deletions in Glu-B1 Locus (GluB1-S239F). Germplasm Release. 8(1):1-8.

New bread wheat gluten protein genes induced variants - (Abstract Only)