Aquatic and Crop Resource Development: Strategic Agri-Food Genomics Research

Berraies S, Ruan Y, Knox R, DePauw R, Bokore F, Cuthbert R, Blackwell B, Henriquez MA, Konkin D, Yu B, Pozniak C, Meyer B. 2024. Genetic mapping of deoxynivalenol and fusarium damaged kernel resistance in an adapted durum wheat population. BMC Plant Biol 24(1):183. https://doi.org/10.1186/s12870-023-04708-8

Bhowmik P, Yan W, Hodgins C, Polley B, Warkentin T, Nickerson M, Ro D-K, Marsolais F, Domoney C, Shariati-Ievari S, Aliani M. 2023. CRISPR/Cas9-mediated lipoxygenase gene-editing in yellow pea leads to major changes in fatty acid and flavor profiles. Front Plant Sci 14:1246905. https://doi.org/10.3389/fpls.2023.1246905

Bokore FE, Ruan Y, Mccartney C, Knox RE, Pei X, Aboukhaddour R, Randhawa H, Ammar K, Meyer B, Cuthbert RD, Berraies S, Depauw R, Fobert P. 2021. High density genetic mapping of stripe rust resistance in a 'Strongfield' / 'Blackbird' durum wheat population. Can J Plant Pathol 43(sup2):S242. https://doi.org/10.1080/07060661.2021.1968036

Buhrow LM, Liu Z, Cram D, Sharma T, Foroud NA, Pan Y, Loewen MC. 2021. Wheat transcriptome profiling reveals abscisic and gibberellic acid treatments regulate early-stage phytohormone defense signaling, cell wall fortification, and metabolic switches following Fusarium graminearum-challenge. BMC Genomics 22(1):798. https://doi.org/10.1186/s12864-021-08069-0

Cabral AL, Ruan Y, Cuthbert RD, Li L, Zhang W, Boyle K, Berraies S, Henriquez MA, Burt A, Kumar S, Fobert P, Piche I, Bokore FE, Meyer B, Sangha J, Knox RE. 2023. Multi-locus genome-wide association study of fusarium head blight in relation to days to anthesis and plant height in a spring wheat association panel. Front Plant Sci 14:1166282. https://doi.org/10.3389/fpls.2023.1166282

Da Ros L, Bollina V, Soolanayakanahally R, Pahari S, Elferjani R, Kulkarni M, Vaid N, Risseuw E, Cram D, Pasha A, Esteban E, Konkin D, Provart N, Nambara E, Kagale S. 2023. Multi-omics atlas of combinatorial abiotic stress responses in wheat. Plant J 116(4):1118. https://doi.org/10.1111/tpj.16332

Das PP, Xu C, Lu Y, Khorsandi A, Tanaka T, Korber D, Nickerson M, Rajagopalan N. 2023. Snapshot of proteomic changes in Aspergillus oryzae during various stages of fermentative processing of pea protein isolate. Food Chem Mol Sci 6:100169. https://doi.org/10.1016/j.fochms.2023.100169

Ficht A, Konkin DJ, Cram D, Sidebottom C, Tan Y, Pozniak C, Rajcan I. 2023. Genomic selection for agronomic traits in a winter wheat breeding program. Theor Appl Genet 136(3):38. https://doi.org/10.1007/s00122-023-04294-1

Gao P, Quilichini TD, Yang H, Li Q, Nilsen KT, Qin L, Babic V, Liu L, Cram D, Pasha A, Esteban E, Condie J, Sidebottom C, Zhang Y, Huang Y, Zhang W, Bhowmik P, Kochian LV, Konkin D, Wei Y, Provart NJ, Kagale S, Smith M, Patterson N, Gillmor CS, Datla R, Xiang D. 2022. Evolutionary divergence in embryo and seed coat development of U's Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas. New Phytol 233(1):30. https://doi.org/10.1111/nph.17759

Gao P, Quilichini TD, Zhai C, Qin L, Nilsen KT, Li Q, Sharpe AG, Kochian LV, Zou J, Reddy ASN, Wei Y, Pozniak C, Patterson N, Gillmor CS, Datla R, Xiang D. 2021. Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species. Plant Biotechnol J 19(8):1624. https://doi.org/10.1111/pbi.13579

Haile JK, Sertse D, N'Diaye A, Klymiuk V, Wiebe K, Ruan Y, Chawla HS, Henriquez M-A, Wang L, Kutcher HR, Steiner B, Buerstmayr H, Pozniak CJ. 2023. Multi-locus genome-wide association studies reveal the genetic architecture of Fusarium head blight resistance in durum wheat. Front Plant Sci 14:1182548. https://doi.org/10.3389/fpls.2023.1182548

Haldar A, Tekieh F, Balcerzak M, Wolfe D, Lim D, Joustra K, Konkin D, Han F, Fedak G, Ouellet T. 2021. Introgression of thinopyrum elongatum dna fragments carrying resistance to fusarium head blight into triticum aestivum cultivar chinese spring is associated with alteration of gene expression. Genome 64(11):1009. https://doi.org/10.1139/gen-2020-0152

Han X, Akhov L, Ashe P, Lewis C, Deibert L, Irina Zaharia L, Forseille L, Xiang D, Datla R, Nosworthy M, Henry C, Zou J, Yu B, Patterson N. 2023. Comprehensive compositional assessment of bioactive compounds in diverse pea accessions. Food Res Int 165:112455. https://doi.org/10.1016/j.foodres.2022.112455

Hodgins CL, Salama EM, Kumar R, Zhao Y, Roth SA, Cheung IZ, Chen J, Arganosa GC, Warkentin TD, Bhowmik P, Ham B-K, Ro D-K. 2024. Creating saponin-free yellow pea seeds by CRISPR/Cas9-enabled mutagenesis on β-amyrin synthase. Plant Direct 8(1):e563. https://doi.org/10.1002/pld3.563

Jiang Y, N'Diaye A, Koh CS, Quilichini TD, Shunmugam ASK, Kirzinger MW, Konkin D, Bekkaoui Y, Sari E, Pasha A, Esteban E, Provart NJ, Higgins JD, Rozwadowski K, Sharpe AG, Pozniak CJ, Kagale S. 2023. The coordinated regulation of early meiotic stages is dominated by non-coding RNAs and stage-specific transcription in wheat. Plant J 114(1):209. https://doi.org/10.1111/tpj.16125

Konkin D, Hsueh Y-C, Kirzinger M, Kubaláková M, Haldar A, Balcerzak M, Han F, Fedak G, Doležel J, Sharpe A, Ouellet T. 2022. Genomic sequencing of Thinopyrum elongatum chromosome arm 7EL, carrying fusarium head blight resistance, and characterization of its impact on the transcriptome of the introgressed line CS-7EL. BMC Genomics 23(1):228. https://doi.org/10.1186/s12864-022-08433-8

Links MG, Dumonceaux TJ, Luke Mccarthy E, Hemmingsen SM, Topp E, Town JR. 2021. Captureseq: Hybridization-based enrichment of cpn60 gene fragments reveals the community structures of synthetic and natural microbial ecosystems. Microorg 9(4):816. https://doi.org/10.3390/microorganisms9040816

Mahesh HB, Prasannakumar MK, Manasa KG, Perumal S, Khedikar Y, Kagale S, Soolanayakanahally RY, Lohithaswa HC, Rao AM, Hittalmani S. 2021. Genome, Transcriptome, and Germplasm Sequencing Uncovers Functional Variation in the Warm-Season Grain Legume Horsegram Macrotyloma uniflorum (Lam.) Verdc. Front Plant Sci 12:758119. https://doi.org/10.3389/fpls.2021.758119

Moghaddam SM, Oladzad A, Koh C, Ramsay L, Hart JP, Mamidi S, Hoopes G, Sreedasyam A, Wiersma A, Zhao D, Grimwood J, Hamilton JP, Jenkins J, Vaillancourt B, Wood JC, Schmutz J, Kagale S, Porch T, Bett KE, Buell CR, McClean PE. 2021. The tepary bean genome provides insight into evolution and domestication under heat stress. Nat Commun 12(1):2638. https://doi.org/10.1038/s41467-021-22858-x

Pan Y, Li Y, Liu Z, Zou J, Li Q. 2022. Computational genomics insights into cold acclimation in wheat. Front Genet 13:1015673. https://doi.org/10.3389/fgene.2022.1015673

Pandey PK, Bhowmik P, Kagale S. 2022. Optimized methods for random and targeted mutagenesis in field pea (Pisum sativum L.). Front Plant Sci 13:995542. https://doi.org/10.3389/fpls.2022.995542

Quiza L, Tremblay J, Greer CW, Hemmingsen SM, St-Arnaud M, Pozniak CJ, Yergeau E. 2021. Rhizosphere shotgun metagenomic analyses fail to show differences between ancestral and modern wheat genotypes grown under low fertilizer inputs. FEMS Microbiol Ecol 97(6):fiab071. https://doi.org/10.1093/femsec/fiab071

Rabanus-Wallace MT, Hackauf B, Mascher M, Lux T, Wicker T, Gundlach H, Baez M, Houben A, Mayer KFX, Guo L, Poland J, Pozniak CJ, Walkowiak S, Melonek J, Praz CR, Schreiber M, Budak H, Heuberger M, Steuernagel B, Wulff B, Börner A, Byrns B, Čížková J, Fowler DB, Fritz A, Himmelbach A, Kaithakottil G, Keilwagen J, Keller B, Konkin D, Larsen J, Li Q, Myśków B, Padmarasu S, Rawat N, Sesiz U, Biyiklioglu-Kaya S, Sharpe A, Šimková H, Small I, Swarbreck D, Toegelová H, Tsvetkova N, Voylokov AV, Vrána J, Bauer E, Bolibok-Bragoszewska H, Doležel J, Hall A, Jia J, Korzun V, Laroche A, Ma X-F, Ordon F, Özkan H, Rakoczy-Trojanowska M, Scholz U, Schulman AH, Siekmann D, Stojałowski S, Tiwari VK, Spannagl M, Stein N. 2021. Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential. Nat Genet 53(4):564. https://doi.org/10.1038/s41588-021-00807-0

Rossato M, Marcolungo L, De Antoni L, Lopatriello G, Bellucci E, Cortinovis G, Frascarelli G, Nanni L, Bitocchi E, Di Vittori V, Vincenzi L, Lucchini F, Bett KE, Ramsay L, Konkin DJ, Delledonne M, Papa R. 2023. CRISPR-Cas9-based repeat depletion for highthroughput genotyping of complex plant genomes. Genome Res 33(5):787. https://doi.org/10.1101/gr.277628.122

Song J, Mavraganis I, Shen W, Yang H, Cram D, Xiang D, Patterson N, Zou J. 2022. Transcriptome dissection of candidate genes associated with lentil seed quality traits. Plant Biol 24(5):815. https://doi.org/10.1111/plb.13426

Song J, Xie X, Chen C, Shu J, Thapa RK, Nguyen V, Bian S, Kohalmi SE, Marsolais F, Zou J, Cui Y. 2021. LEAFY COTYLEDON1 expression in the endosperm enables embryo maturation in Arabidopsis. Nat Commun 12(1):3963. https://doi.org/10.1038/s41467-021-24234-1

Sridhar PS, Vasquez V, Monteil-Rivera F, Allingham JS, Loewen MC. 2023. A peroxidase-derived ligand that induces Fusarium graminearum Ste2 receptor-dependent chemotropism. Front Cell Infect Microbiol 13:1287418. https://doi.org/10.3389/fcimb.2023.1287418

Sun G, Ni P, Lam E, Hrapovic S, Bing D, Yu B, Ai Y. 2023. Exploring the functional attributes and in vitro starch and protein digestibility of pea flours having a wide range of amylose content. Food Chem 405:134938. https://doi.org/10.1016/j.foodchem.2022.134938

Yu B, Gao P, Song J, Yang H, Qin L, Yu X, Song H, Coulson J, Bekkaoui Y, Akhov L, Han X, Cram D, Wei Y, Zaharia LI, Zou J, Konkin D, Quilichini TD, Fobert P, Patterson N, Datla R, Xiang D. 2023. Spatiotemporal transcriptomics and metabolic profiling provide insights into gene regulatory networks during lentil seed development. Plant J 115(1):253. https://doi.org/10.1111/tpj.16205

Yu L, Shen W, Fan J, Sah SK, Mavraganis I, Wang L, Gao P, Gao J, Zheng Q, Meesapyodsuk D, Yang H, Li Q, Zou J, Xu C. 2023. A chloroplast diacylglycerol lipase modulates glycerolipid pathway balance in Arabidopsis. Plant J 115(2):335. https://doi.org/10.1111/tpj.16228

Zhang W, Boyle K, Brule-Babel A, Fedak G, Gao P, Djama ZR, Polley B, Cuthbert R, Randhawa H, Graf R, Jiang F, Eudes F, Fobert PR. 2021. Evaluation of genomic prediction for fusarium head blight resistance with a multi-parental population. Biology 10(8):756. https://doi.org/10.3390/biology10080756

Zhang W, Boyle K, Gao P, Polley B, Brost JM, Francis T, Sidebottom C, McCallum BD, Kutcher HR, Randhawa H, Fetch TG, Ferrie AMR, Fobert PR. 2023. Systematic Characterization of Multi-Rust Resistance Genes from a 'Parula × Thatcher' Population with a High-Density Genetic Map. Phytopathology 113(5):847. https://doi.org/10.1094/PHYTO-06-22-0238-FI