Plant developmental genetics
Developmental genetics of plants, traits important for production including flowering, chromatin regulation of gene expression
What are the underlying genetic mechanisms that determine plant form, and how are these controlled? What are the key genes that influence agriculturally important traits such as flowering? What parallels exist between plant and human development, and can studies in plants shed light on issues such as cancer and stem cell biology?
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.
Ph.D., Cell and Molecular Biology, University of Wisconsin
B.S. Genetics, Cornell University
HRT/PLB865 Plant Growth and Development
This course focuses on the genetic, molecular and biochemical mechanisms influencing development in higher plants, including the patterning, cellular organization, formation of tissues and organs, mechanisms underlying developmental diversity, and biosynthesis, regulation and activity of phytohormones. To be offered next in Fall 2018!
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.
Tang Y, Liu B, Li Y, van Nocker S., Wang Y, Zhan C. Differential expression of the seed-specific gene ABCG20 between seedless and seeded grapes and its roles in tomato seed development. Submitted.
Inês Pratas M, Aguiar B, Vieira J, NunesV, Teixeira V, Fonseca N, Iezzoni AF, van Nocker S, Vieira C. Inferences on specificity recognition at the Malus × domestica gametophytic self-incompatibility system. Scientific Reports, in press.
Thompson R, Sugimoto Y, Rogers S and van Nocker S. 2018. Histone H3 'deviants' in nature - an in silico analysis. Accepted, in revision.
DeVries B, Chiles K, Scazzero AM, Guist D, Ruppert O, van Nocker S. 2017. Spectrum of mutations in PAF cofactor components revealed through bulked-segregant analysis and high-throughput sequencing. J Genomics (in press)
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. 2017 (in press)
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. Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops. Horticulture Research 1:14022 (PDF)
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 (PDF)
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 (PDF)
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)e:52855
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, Alsmairat N, Beaudry R, Nair MG and 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, Hoerold 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.
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.
Mookerjee S and van Nocker S. 2010. Genetics of flowering in apple. In Genomics of fruits and vegetable crops: Apples. Ed. Aldwinckle HS and Malnoy M. Science Publishers, Enfield NH.
van Nocker S. 2009. 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.
van Nocker S and Ek-Ramos J. 2007. Control of flowering time. In Regulation of transcription in plants, Grasser KD Ed. Plant Reviews (Blackwell Publishing, Ltd.)
Mulabagal V, van Nocker S, Dewitt D and Nair M. 2007. Cultivars of apple fruits that are not marketed with potential for anthocyanin production. J Agric Food Chem 55, 8165-8169
Park S, Sugimoto N, Larson MD, Beaudry R and van Nocker S. 2006. Identification of genes with potential roles in apple fruit development and biochemistry through large-scale statistical analysis of expressed sequence tags. Plant Physiol 141, 811-824.
Oh S, Zhang H, Ludwig P and van Nocker S. 2004. A mechanism related to the yeast transcriptional regulator Paf1C is required for expression of the Arabidopsis FLC/MAF MADS-box gene family. Plant Cell 16, 2940-2953.
van Nocker S. 2003. CAF-1 and MSI1-related proteins: Linking nucleosome assembly with epigenetics. Trends Plant Sci 8, 471-473.
van Nocker S and Ludwig P. 2003. The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function. BMC Genomics 4, 50.
Yoo SD, Gao Z, Cantini C, Loescher WH and van Nocker S. 2003. Fruit ripening in sour cherry (P. cerasus L.): Changes in expression of genes encoding expansins and other cell-wall-modifying enzymes. J Amer Soc Hort Sci 128, 16-22.
Zhang H, Ransom C, Ludwig P and van Nocker S. 2003. Genetic analysis of early-flowering mutants in Arabidopsis defines a class of pleiotropic developmental regulator required for activity of the flowering-time switch FLC. Genetics 164, 347-358.
Gao Z, Maurousset L, Lemoine R, Yoo SD, van Nocker S and Loescher W. 2003 Cloning, expression, and characterization of sorbitol transporters from developing sour cherry fruit and leaf sink tissues. Plant Physiol 131, 1566-1575.
Zhang H and van Nocker S. 2002. The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of FLOWERING LOCUS C. Plant J 31, 663-673.
van Nocker S and Ransom C. 2002. Towards a Molecular Understanding of Vernalization: A Genetic Analysis of Pleiotropic Regulators of the Flowering-Time Switch FLC. Flowering Newsletter (G. Bernier, Ed.). 34, 37-44.
Liu J, Gilmour SJ, Thomashow MF and van Nocker S. 2002. Cold signalling associated with vernalization in Arabidopsis thaliana does not involve CBF1 or abscisic acid. Physiol Plant 114, 125-134.