Christopher Saski

Professor of Systems Biology
Plant and Environmental Sciences Department

Office: 306B Biosystems Research Complex
Phone: 864-656-6929

Email: SASKI@clemson.edu

Educational Background

Ph.D. Genetics
Clemson University 2007

B.S. Microbiology
Clemson University 1999

Courses Taught

PES 4050/6050 Introduction to Plant Breeding (Spring semesters)
PES 3500 Practicum
PES 4550/8250 PES/ENT Seminar

Profile

Dr. Christopher Saski joined the Department of Plant and Environmental Sciences at Clemson University in the Spring of 2018. Dr. Saski is a systems geneticist and translational scientist at the frontier of discovery to develop and deliver new ways to understand and exploit the crop genome and germplasm collections to advance crop breeding, productivity, horticultural traits, and resilience to abiotic/biotic stresses. Dr. Saski brings an array of disciplinary expertise to the PES department that includes genomics, bioinformatics, computational biology, functional genomics, and genome engineering. His research transcends basic and applied sciences, and these experiences are recapitulated in the classroom. Dr. Saski recently received a highly competitive research award from Target, NASA, and CASIS to conduct cotton research aboard the International Space Station. He also serves as the Chair of the International Rosaceous Crop Executive Committee (ROSEXEC), and as an active member of the International Cotton Genome Sequencing Committee. Dr. Saski is also involved in developing and teaching courses, and advising and mentoring undergraduate and graduate students.

Research Interests

Dr. Saski's research interests include the use of systems-scale approaches to understand disease resistance and horticultural qualities in Rosaceous crops (peach, plum, cherry, apple, almond, and others). He also investigates fiber traits, genome evolution, somatic embryogenesis, and gene function in Upland cotton; and genome dynamics of rapid adaptation in weeds. Ultimately, Dr. Saski's research portfolio is aimed to deliver healthier foods, more sustainable agriculture, and environmental systems that support agriculture.

Publications

1. Wang Z, Saski C, Williamson C, Campbell B, Ye R. 2024. Crop cover and manure compost: Their varied effects on nitrogen availability and nitrogen cycling functional gene abundances in sandy soils for organic farming. Applied Soil Ecology. 200:105446. doi: https://doi.org/10.1016/j.apsoil.2024.105446.
2. Sreedasyam A, Lovell JT, Mamidi S, Khanal S, Jenkins JW, Plott C, Bryan KB, Li Z, Shu S, Carlson J, Goodstein D, De Santiago L, Kirkbride RC, Calleja S, Campbell T, Koebernick JC, Dever JK, Scheffler JA, Pauli D, Jenkins JN, McCarty JC, Williams M, Boston L, Webber J, Udall JA, Chen ZJ, Bourland F, Stiller WN, Saski CA, Grimwood J, Chee PW, Jones DC, Schmutz J. 2024. Genome resources for three modern cotton lines guide future breeding efforts. Nat Plants. doi: 10.1038/s41477-024-01713-z.
3. Lawrence BT, Calle A, Saski CA, Melgar JC, Du JB. 2024. Differential Gene Expression Patterns in Peach Roots under Non-Uniform Soil Conditions in Response to Organic Matter. Genes. 15(1). doi: ARTN 70
10.3390/genes15010070.
4. Asgari D, Purvis T, Pickens V, Saski C, Meisel RP, Nayduch D. 2024. Expression of defensin genes across house fly (Musca domestica) life history gives insight into immune system subfunctionalization. Genome. doi: 10.1139/gen-2024-0016.
5. Wilkes JE, Fallen B, Saski C, Agudelo P. 2023. Development of SNP molecular markers associated with resistance to reniform nematode in soybean using KASP genotyping. Euphytica. 219(2). doi: ARTN 27
10.1007/s10681-022-03144-3.
6. Parris S, Huang W, Jones D, Bridges W, Olvey J, Olvey M, Saski C. 2023. Geostatistical techniques to account for the heterogeneity of
wilt inoculum distribution in upland cotton field screening studies. Crop Science. 63(3):1316-1329. doi: 10.1002/csc2.20961.
7. LaFave Q, Etukuri SP, Courtney CL, Kothari N, Rife TW, Saski CA. 2023. A Simplified Microscopy Technique to Rapidly Characterize Individual Fiber Traits in Cotton. Methods Protoc. 6(5). doi: 10.3390/mps6050092.
8. Kumar R, Brar MS, Kunduru B, Ackerman AJ, Yang Y, Luo F, Saski CA, Bridges WC, de Leon N, McMahan C, Kaeppler SM, Sekhon RS. 2023. Genetic architecture of source-sink-regulated senescence in maize. Plant Physiol. doi: 10.1093/plphys/kiad460.
9. Fu W, MacGregor DR, Comont D, Saski CA. 2023. Sequence Characterization of Extra-Chromosomal Circular DNA Content in Multiple Blackgrass (Alopecurus myosuroides) Populations. Genes (Basel). 14(10). doi: 10.3390/genes14101905.
10. Fletcher E, Patterson R, Dunne J, Saski C, Fallen B. 2023. Evaluating the Effects of Flooding Stress during Multiple Growth Stages in Soybean. Agronomy. 13(5):1243.
11. Chitwood DG, Wang Q, Klaubert SR, Green K, Wu CH, Harcum SW, Saski CA. 2023. Microevolutionary dynamics of eccDNA in Chinese hamster ovary cells grown in fed-batch cultures under control and lactate-stressed conditions. Sci Rep. 13(1):1200. doi: 10.1038/s41598-023-27962-0.
12. Chitwood DG, Uy L, Fu W, Klaubert SR, Harcum SW, Saski CA. 2023. Dynamics of Amino Acid Metabolism, Gene Expression, and Circulomics in a Recombinant Chinese Hamster Ovary Cell Line Adapted to Moderate and High Levels of Extracellular Lactate. Genes (Basel). 14(8). doi: 10.3390/genes14081576.
13. Chavan S, Schnabel E, Saski C, Frugoli J. 2023. Fixation and Laser Capture Microdissection of Plant Tissue for RNA Extraction and RNASeq Library Preparation. Curr Protoc. 3(7):e844. doi: 10.1002/cpz1.844.
14. Cai L, Comont D, MacGregor D, Lowe C, Beffa R, Neve P, Saski C. 2023. The blackgrass genome reveals patterns of non-parallel evolution of polygenic herbicide resistance. New Phytol. 237(5):1891-1907. doi: 10.1111/nph.18655.
15. Cai L, Adelberg J, Naylor-Adelberg J, Schnabel G, Calle A, Li Z, Reighard G, Gasic K, Saski CA. 2023. Transcriptomics reveal the genetic coordination of early defense to Armillaria root rot (ARR) in Prunus spp. Frontiers in plant science. 14:1181153. doi: 10.3389/fpls.2023.1181153.
16. Cai L, Adelberg J, Naylor-Adelberg J, Schnabel G, Calle A, Li Z, Reighard G, Gasic K, Saski CA. 2023. Transcriptomics reveal the genetic coordination of early defense to Armillaria root rot (ARR) in Prunus spp. Frontiers in plant science. 14. doi: 10.3389/fpls.2023.1181153.
17. Spier Camposano H, Molin WT, Saski CA. 2022. Sequence characterization of eccDNA content in glyphosate sensitive and resistant Palmer amaranth from geographically distant populations. PloS one. 17(9):e0260906. doi: 10.1371/journal.pone.0260906.
18. Rangani G, Rouse CE, Saski C, Noorai RE, Shankar V, Lawton-Rauh AL, Werle IS, Roma-Burgos N. 2022. High Resistance to Quinclorac in Multiple-Resistant Echinochloa colona Associated with Elevated Stress Tolerance Gene Expression and Enriched Xenobiotic Detoxification Pathway. Genes (Basel). 13(3). doi: 10.3390/genes13030515.
19. Parris SM, Jeffers SN, Olvey JM, Olvey JM, 2nd, Adelberg JW, Wen L, Udall JA, Coleman JJ, Jones DC, Saski CA. 2022. An In Vitro Co-Culture System for Rapid Differential Response to Fusarium oxysporum f. sp. vasinfectum Race 4 in Three Cotton Cultivars. Plant Dis. 106(3):990-995. doi: 10.1094/PDIS-08-21-1743-RE.
20. Guajardo V, Martinez-Garcia PJ, Solis S, Calleja-Satrustegui A, Saski C, Moreno MA. 2022. QTLs Identification for Iron Chlorosis in a Segregating Peach-Almond Progeny Through Double-Digest Sequence-Based Genotyping (SBG). Frontiers in plant science. 13:872208. doi: 10.3389/fpls.2022.872208.
21. Fleming MB, Miller T, Fu W, Li Z, Gasic K, Saski C. 2022. Ppe.XapF: High throughput KASP assays to identify fruit response to Xanthomonas arboricola pv. pruni (Xap) in peach. PloS one. 17(2):e0264543. doi: 10.1371/journal.pone.0264543.
22. Calle A, Saski C, Wünsch A, Grimplet J, Gasic K. 2022. Identification of Key Genes Related to Dormancy Control in Prunus Species by Meta-Analysis of RNAseq Data. Plants. 11(19):2469.
23. Asgari D, Saski CA, Meisel RP, Nayduch D. 2022. Constitutively-expressed and induced immune effectors in the house fly (Musca domestica) and the transcription factors that may regulate them. Insect molecular biology. 31(6):782-797. doi: 10.1111/imb.12804.
24. Neupane S, Saski C, Nayduch D. 2021. House fly larval grazing alters dairy cattle manure microbial communities. BMC Microbiol. 21(1):346. doi: 10.1186/s12866-021-02418-5.
25. Lovell JT, MacQueen AH, Mamidi S, Bonnette J, Jenkins J, Napier JD, Sreedasyam A, Healey A, Session A, Shu S, Barry K, Bonos S, Boston L, Daum C, Deshpande S, Ewing A, Grabowski PP, Haque T, Harrison M, Jiang J, Kudrna D, Lipzen A, Pendergast TH, Plott C, Qi P, Saski CA, Shakirov EV, Sims D, Sharma M, Sharma R, Stewart A, Singan VR, Tang Y, Thibivillier S, Webber J, Weng X, Williams M, Wu GA, Yoshinaga Y, Zane M, Zhang L, Zhang J, Behrman KD, Boe AR, Fay PA, Fritschi FB, Jastrow JD, Lloyd-Reilley J, Martínez-Reyna JM, Matamala R, Mitchell RB, Rouquette FM, Ronald P, Saha M, Tobias CM, Udvardi M, Wing RA, Wu Y, Bartley LE, Casler M, Devos KM, Lowry DB, Rokhsar DS, Grimwood J, Juenger TE, Schmutz J. 2021. Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature. doi: 10.1038/s41586-020-03127-1.
26. Kumar S, Ruggles A, Logan S, Mazarakis A, Tyson T, Bates M, Grosse C, Reed D, Li Z, Grimwood J, Schmutz J, Saski C. 2021. Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines. Plants. 10(9):1775.
27. Kumar R, Gyawali A, Morrison GD, Saski CA, Robertson DJ, Cook DD, Tharayil N, Schaefer RJ, Beissinger TM, Sekhon RS. 2021. Genetic Architecture of Maize Rind Strength Revealed by the Analysis of Divergently Selected Populations. Plant and Cell Physiology. doi: 10.1093/pcp/pcab059.
28. Herbert A, Wang H, Saski C, Turechek W. 2021. Draft Genome Sequences of Two Xanthomonas fragariae Strains. Microbiol Resour Announc. 10(16). doi: 10.1128/MRA.00138-21.
29. Gasic K, Saski C, Adelberg J, Baumgartner K, Brannen P, Chavez DJ, Gradzielt TM, Hammerschmid R, Lezzonib AF, Koc B, Mark T, Melgar JC, Reighard GL, Schnabel G, Tharayil N, Vassalos M. 2021. Solutions to the Armillaria Root Rot Affecting the US Stone Fruit Industry. Hortscience. 56(9):S265-S265.
30. Chitwood DG, Wang Q, Elliott K, Bullock A, Jordana D, Li Z, Wu C, Harcum SW, Saski CA. 2021. Characterization of metabolic responses, genetic variations, and microsatellite instability in ammonia-stressed CHO cells grown in fed-batch cultures. BMC Biotechnol. 21(1):4. doi: 10.1186/s12896-020-00667-2.
31. Carey SB, Jenkins J, Lovell JT, Maumus F, Sreedasyam A, Payton AC, Shu S, Tiley GP, Fernandez-Pozo N, Healey A, Barry K, Chen C, Wang M, Lipzen A, Daum C, Saski CA, McBreen JC, Conrad RE, Kollar LM, Olsson S, Huttunen S, Landis JB, Burleigh JG, Wickett NJ, Johnson MG, Rensing SA, Grimwood J, Schmutz J, McDaniel SF. 2021. Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. Sci Adv. 7(27). doi: 10.1126/sciadv.abh2488.
32. Caputo GA, Wadl PA, McCarty L, Adelberg J, Saski C, Cutulle M. 2021. Impact of tank mixing plant hormones with bentazon and mesotrione on sweetpotato injury and weed control. Agrosystems, Geosciences & Environment. 4(3):e20185. doi: https://doi.org/10.1002/agg2.20185.
33. Cao X, Wang S, Ge L, Zhang W, Huang J, Sun W. 2021. Corrigendum: Extrachromosomal Circular DNA: Category, Biogenesis, Recognition, and Functions. Front Vet Sci. 8:784611. doi: 10.3389/fvets.2021.784611.
34. Callahan AM, Zhebentyayeva TN, Humann JL, Saski CA, Galimba KD, Georgi LL, Scorza R, Main D, Dardick CD. 2021. Defining the 'HoneySweet' insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica). Horticulture Research. 8(1). doi: ARTN 8
10.1038/s41438-020-00438-2.
35. Adelberg J, Naylor-Adelberg J, Miller S, Gasic K, Schnabel G, Bryson P, Saski C, Parris S, Reighard G. 2021. In vitro co-culture system for Prunus spp. and Armillaria mellea in phenolic foam rooting matric. In Vitro Cellular & Developmental Biology - Plant. 57(3):387-397. doi: 10.1007/s11627-020-10136-2.
36. Wu Y, Saski C, Schnabel G, Xiao S, Hu M. 2020. A High-Quality Genome Resource of Botrytis fragariae, a New and Rapidly Spreading Fungal Pathogen Causing Strawberry Gray Mold in the United States. Phytopathology.PHYTO05200204IA. doi: 10.1094/PHYTO-05-20-0204-IA.
37. Wu P, Cogill S, Qiu Y, Li Z, Zhou M, Hu Q, Chang Z, Noorai RE, Xia X, Saski C, Raymer P, Luo H. 2020. Comparative transcriptome profiling provides insights into plant salt tolerance in seashore paspalum (Paspalum vaginatum). BMC genomics. 21(1):131. doi: 10.1186/s12864-020-6508-1.
38. Wilkes J, Saski C, Klepadlo M, Fallen B, Agudelo P. 2020. Quantitative Trait Loci Associated with Rotylenchulus reniformis Host Suitability in Soybean. Phytopathology. 110(9):1511-1521. doi: 10.1094/PHYTO-02-20-0035-R.
39. Wen L, Li W, Parris S, West M, Lawson J, Smathers M, Li Z, Jones D, Jin S, Saski CA. 2020. Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.). BMC Dev Biol. 20(1):25. doi: 10.1186/s12861-020-00230-4.
40. Staton M, Addo-Quaye C, Cannon N, Yu JL, Zhebentyayeva T, Huff M, Islam-Faridi N, Fan SH, Georgi LL, Nelson CD, Bellis E, Fitzsimmons S, Henry N, Drautz-Moses D, Noorai RE, Ficklin S, Saski C, Mandal M, Wagner TK, Zembower N, Bodenes C, Holliday J, Westbrook J, Lasky J, Hebard FV, Schuster SC, Abbott AG, Carlson JE. 2020. "A reference genome assembly and adaptive trait analysis ofCastanea mollissima'Vanuxem,' a source of resistance to chestnut blight in restoration breeding". Tree Genetics & Genomes. 16(4). doi: ARTN 57
10.1007/s11295-020-01454-y.
41. Shang JZ, Tian JP, Cheng HH, Yan QM, Li L, Jamal A, Xu ZP, Xiang L, Saski CA, Jin SX, Zhao KG, Liu XQ, Chen LQ. 2020. The chromosome-level wintersweet (Chimonanthus praecox) genome provides insights into floral scent biosynthesis and flowering in winter. Genome biology. 21(1). doi: ARTN 200
10.1186/s13059-020-02088-y.
42. Olafson PU, Saski CA. 2020. Chemosensory-Related Gene Family Members of the Horn Fly, Haematobia irritans irritans (Diptera: Muscidae), Identified by Transcriptome Analysis. Insects. 11(11). doi: 10.3390/insects11110816.
43. Molin WT, Yaguchi A, Blenner MA, Saski CA. 2020. The eccDNA Replicon: A Heritable, Extra-Nuclear Vehicle that Enables Gene Amplification and Glyphosate Resistance in Amaranthus palmeri. Plant Cell. doi: 10.1105/tpc.20.00099.
44. Molin WT, Yaguchi A, Blenner M, Saski CA. 2020. Autonomous replication sequences from the Amaranthus palmeri eccDNA replicon enable replication in yeast. BMC research notes. 13(1):330. doi: 10.1186/s13104-020-05169-0.
45. Molin WT, Patterson EL, Saski CA. 2020. Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations. PloS one. 15(9):e0233813. doi: 10.1371/journal.pone.0233813.
46. Li Z, Parris S, Saski CA. 2020. A simple plant high-molecular-weight DNA extraction method suitable for single-molecule technologies. Plant Methods. 16:38. doi: 10.1186/s13007-020-00579-4.
47. Guajardo V, Solis S, Almada R, Saski C, Gasic K, Moreno MA. 2020. Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function. Sci Rep. 10(1):1467. doi: 10.1038/s41598-020-58271-5.
48. Gasic K, Miller S, Barac G, Saski C, Schnabel G, Reighard G, editors. Breeding for Prunus Rootstock Tolerance to Replant Diseases. Hortscience; 2020: AMER SOC HORTICULTURAL SCIENCE 113 S WEST ST, STE 200, ALEXANDRIA, VA 22314 ….
49. Chen ZJ, Sreedasyam A, Ando A, Song Q, De Santiago LM, Hulse-Kemp AM, Ding M, Ye W, Kirkbride RC, Jenkins J, Plott C, Lovell J, Lin YM, Vaughn R, Liu B, Simpson S, Scheffler BE, Wen L, Saski CA, Grover CE, Hu G, Conover JL, Carlson JW, Shu S, Boston LB, Williams M, Peterson DG, McGee K, Jones DC, Wendel JF, Stelly DM, Grimwood J, Schmutz J. 2020. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nat Genet. doi: 10.1038/s41588-020-0614-5.

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