College of Agriculture & Natural Resources Department of Horticulture

Current Projects

Transcriptional mechanisms driving development of multicellular organisms. As an organism develops, cells may proliferate to maintain a pool of stem cells, or differentiate to form specialized tissues. We are studying the mechanisms by which states of gene activity are propagated within and across mitotic boundaries, specifically in relation to chromatin-associated proteins and modifications of DNA and histones at specific genetic sites. In Arabidopsis, we identified a class of protein required for maintaining transcriptional activity of a subset of developmental regulatory genes by counteracting the repressive activity of the so-called Polycomb-group proteins.

Identity and function of genes influencing juvenility and flowering in apple. The transition from vegetative growth to flowering is a developmentally regulated process that is crucial for production of most horticultural crops. The molecular-genetic pathways of flowering have been extensively studied only in herbaceous model plants. We are developing the domestic apple, Malus x. domestica, as a reference for understanding the genetic and molecular control of flowering in woody perennials. This includes identifying important genes and processes associated with the switch from juvenile to adult phase, the seasonal timing of flowering, and repression of flowering by fruit and endogenous hormones including gibberellins.

Education

Ph.D., Cell and Molecular Biology, University of Wisconsin

B.S. Genetics, Cornell University

Teaching

HRT860 Scientific Writing: Workshop
This small-group workshop will train graduate students in scientific writing through reading and analysis of representative publications from a variety of general and plant-related journals. Optionally, students writing a paper, thesis or grant proposal may bring copies and distribute these to other students in the group. The writing will be discussed and suggestions for improvement will be made collectively by instructor and class members.

Publications

 (Recent; *under review)

Peer-reviewed publications (*under review)

 *Chen P, Duan S, Zhang D, Xie Y, Zhang J, Li C, Jiang L, Li X, Shen X, Geng D, Yang Z, Wang L, Niu C, Bao C, Yan M, Li H, Yan Y, Zou Y, LIang W, Chen W, van Nocker S, Tan Y, Ma J, Wang W, Ma F, Dong Y, Guan Q. Insights into the origin of the apple (Malus) genus and domestication from resequencing of 297 accessions. Nature Commun., submitted.

Liu Z, Zhu H, Chen P-Y, Zhong S, Dardick C, Callahan A, An Y-Q, van Nocker S, Yang Y, Zhong G-Y, Abbot A. 2020. Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral buds. Horticulture Research, in press.

Gao T, Zhang Z, Liu X, Wu Q, Chen Q, Liu Q, van Nocker S, Ma, F, Li C. 2020. Physiological and transcriptome analyses of the effects of exogenous dopamine on drought tolerance in apple. Plant Physiol Biochem 148 DOI 10.1016/j.plaphy.2020.01.022

Tang Y, Liu B, Li Y, van Nocker S., Wang Y, Zhan C. 2020. Differential expression of the seed-specific gene ABCG20 between seedless and seeded grapes and its roles in tomato seed development. South African Journal of Botany 131:428-436

Wang Q, Liu C, Huang D, Dong Q, Li P, van Nocker S, Ma F. 2020. Physiological evaluation of nitrogen use efficiency of different apple cultivars under various nitrogen and water supply conditions. J Integrative Agriculture 19(3):709-720.

Miles C, Alexander T, Peck G, Galinato S, Gottschalk C, van Nocker S. 2020. Growing apples for hard cider production in the U.S. - Trends and research opportunities. HortTechnology 30(2):148-155.

Li X, Xie Y, Lu L, Yan M, Fang N, Xu J, Wang L, Yan Y, Zhao T, van Nocker S, Ma F, Liang D, Guan Q. 2019. Contribution of methylation regulation of MpDREB2A promoter to drought resistance of Malus prunifolia. Plant and Soil 441. DOI 10.1007/s11104-019-04149-z

Huang D, Wang Q, Duan D, Dong Q, Zhao S, Zhang M, Jing G, Liu C, van Nocker S, Ma F, Li C. 2019. Overexpression of MdIAA9 confers high tolerance to osmotic stress in transgenic tobacco. PeerJ 7:e7935 DOI 10.7717/peerj.7935 https://doi.org/10.7717/peerj.7935

Zhang S, Gottschalk C, van Nocker S. 2019. Genetic mechanisms in the repression of flowering by gibberellins in apple (Malus x domestica Borkh.). BMC Genomics 20-747. doi:10.1186/s12864-019-6090-6

Li Y, Zhang S, Dong R, Wang L, Yao J, van Nocker S, Wang X. 2019. The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways. BMC Plant Biology 19. DOI 10.21203/rs.2.11184/v4 DOI 10.1186/s12870-019-2144-9

Zhang G, Yan X, Zhang S, Zhu Y, Zhang X, Qiao  H, van Nocker S, Li Z, Wang X. 2019. The jasmonate-ZIM domain gene VqJAZ4 from the Chinese wild grape Vitis quinquangularis improves resistance to podery mildew in Arabidopsis thaliana. Plant Physiol Biochem 143. DOI 10.1016/j.plaphy.2019.09.018

Zhang S, Wang L, Sun X, Li Y, Yao J, van Nocker S, Wang X. 2019. Genome-wide analysis of the YABBY gene family in grapevine and functional characterization of VvYABBY4. Frontiers in Plant Science, published online Oct 8, 2019  https://doi.org/10.3389/fpls.2019.01207

Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, Cornille A, Durel CE, Myles S, Migicovsky Z, Schaffer RJ, Costes E, Fazio G, Yamane H, van Nocker S, Gottschalk C, Costa F, Chagné D, Zhang X, Patocchi A, Gardiner SE, Hardner C, Kumar S, Laurens F, Bucher E, Main D, Jung S, Vanderzande S. 2019. Apple whole genome sequences: recent advances and new prospects. Hortic Res. 6-59 doi:10.1038/s41438-019-0141-7

Guo T, Wang N, Xue Y, Guan Q, van Nocker S, Liu C, Ma F. 2019. Overexpression of the RNA binding protein MhYTP1 in transgenic apple enhances drought tolerance and WUE by imprvoing ABA level under drought conditions. Plant Sci 280:397-407.

Jia D, Jiang Q, van Nocker S, Gong X, Ma F. 2019. An apple (Malus domestica) NAC transcription factor enhances drought tolerance in transgenic apple plants. Plant Physiol Biochem 139:504-512.

Shao Y, Zhang X, van Nocker S, Gong X. Ma F. 2019. Overexpression of a protein kinase gene MpSnRK2.10 from Malus prunifolia confers tolerance to drought stress in transgenic Arabidopsis thaliana and apple. Gene 692:26-34.

Inês Pratas M, Aguiar B, Vieira J, Nunes V, Teixeira V, Fonseca N, Iezzoni AF, van Nocker S, Vieira C. 2018. Inferences on specificity recognition at the Malus × domestica gametophytic self-incompatibility system. Scientific Reports 8-1717. https://doi.org/10.1038/s41598-018-19820-1

Wang H, Dong Q, Duan D, Zhao S, Li M, van Nocker S, Ma F, Mao K. 2018. Comprehensive genomic analysis of the TYROSINE AMINOTRANSFERASE (TAT)genes in apple (Malus domestica) allows the identification of MdTAT2 conferring tolerance to drought and osmotic stress in plants. Plant Physiol Biochem. 133:81-91.

van Nocker, S. 2018. Hybrids without hybridization - can it revolutionize horticulture? Hortic Res 5:76

Xie Y, Chen P, yan Y, Bao C, Li X, Wang L, Shen X, Li H, Liu X, Niu C, Zhu C, Fang N, Shao Y, Zhao T, Yu J, Zhu J, Xu L, van Nocker S, Ma F, Guan Q. 2o18. An atypical R2R3 MYB transcription factor increases cold hardiness by CBF-dependent and CBF-independent pathways in apple. New Phytol 218:201-218.

Xu J, Zhou S, Gong X, Song Y, van Nocker S, Ma F, Guan Q. 2017. Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple. Plant Biotechnol J.

Li Y, Zhu Y, Yao J, Zhang S, Wang L, Guo C, van Nocker S, Wang X. 2017. Genome-wide identification and expression analyses of the homeobox transcription factor family during ovule development in seedless and seeded grapes. Sci Rep. 7(1):12638

Wang Y, Wang D, Wang F, Huang L, Tian X, van Nocker S, Gao H, Wang X. 2017. Expression of the Grape VaSTS19 Gene in Arabidopsis Improves Resistance to Powdery Mildew and Botrytis cinerea but Increases Susceptibility to Pseudomonas syringe pv Tomato DC3000. Int J Mol Sci. 18(9) pii: E2000

Yang J, Gao M, Huang L, Wang Y, van Nocker S, Wan R, Guo C, Wang X, Gao H. 2017. Identification and expression analysis of the apple (Malus × domestica) basic helix-loop-helix transcription factor family. Sci Rep. 7(1):28

Li X, Kui L, Zhang J, Xie Y, Wang L, Yan Y, Wang N, Xu J, Li C, Wang W, van Nocker S, Dong Y, Ma F, Guan Q. 2016. Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica). Gigascience 5(1):35

Ren M, van Nocker S. 2016. In silico analysis of histone H3 gene expression during human brain development. Int J Dev Biol. 60(4-6):167-73

Aguiar B, Vieira J, Cunha AE, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP. 2015. Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus. PLoS One. 10(5):e0126138

van Nocker S and Gardiner SE. 2014. (Review). Breeding better cultivars, faster: Applications of new technologies for the rapid deployment of superior horticultural tree crops. Horticulture Research 1:14022

Alkio M, Jonas U, Declercq M, van Nocker S and Knoche M. 2014. Transcriptional dynamics of the developing sweet cherry (Prunus avium L. ) fruit: sequencing, annotation and expression profiling of exocarp-associated genes. Horticulture Research 1:11

Gottschalk C and van Nocker S. 2013. Diversity in seasonal bloom time and floral development among apple (Malus) species and hybrids. J Amer Soc Hort Sci 138:367-374

Park S, Oh S and van Nocker S. 2012. Genomic and gene-level distribution of histone H3 dimethyl lysine-27 (H3K27me2) in Arabidopsis. PLoS One 7(12):e52855

Alkio M, Jonas U, Sprink T, van Nocker S and Knoche M. 2012. Identification of putative candidate genes involved in cuticle formation in sweet cherry fruit. Ann Bot 110, 101-112

van Nocker S, Berry G, Najdowski J, Michelutti R, Luffman M, Forsline P, Smerirat N, Beaudry R, Nair M, Ordidge M. 2012. Genetic diversity of red-fleshed apples (Malus). Euphytica, 185, 281-293

Liu Y, Geyer R, van Zanten M, Carles A, Li Y, Hörold A, van Nocker S, and Soppe WJJ. 2011. Identification of the Arabidopsis REDUCED DORMANCY 2 gene uncovers a role for the Polymerase Associated Factor 1 complex in seed dormancy. PLoS ONE 6(7):e22241

Park S, Ek-Ramos J, Oh S and van Nocker S. 2011. Potential role of Arabidopsis PHP as an accessory subunit of the PAF1 transcriptional cofactor. Plant Signaling and Behavior 6:8, 1-3

Mookerjee S and van Nocker S. 2011. (Review). Genetics of flowering in apple. In Genomics of fruits and vegetable crops: Apples. Ed. Aldwinckle HS and Malnoy M. Science Publishers, Enfield NH.

Park S, Oh S, Ek-Ramos J and van Nocker S. 2010. PLANT HOMOLOGOUS TO PARAFIBROMIN is a Component of PAF1C and Assists in Regulating Expression of Genes within H3K27me3-Enriched Chromatin. Plant Physiol 153, 821-831

Sun L and van Nocker S. 2010. Analysis of promoter activity of members of the PECTATE LYASE-LIKE (PLL) gene family in cell separation in Arabidopsis. BMC Plant Biology 10:152

van Nocker S. 2009. (Review). Development of the abscission zone. Stewart Postharvest Review 5:1-5

Sun L, Bukovac MJ, Forsline PL and van Nocker S. 2009. Natural variation in fruit abscission-related traits in apple (Malus). Euphytica 165(1): 55-67

**Oh S, Park S and van Nocker S. 2008. Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet 4(8): e1000077