Biochemical Evolution of Specialized Metabolism within the Solanaceae Family; Genetic Determinants of Fruit Quality and Ripening
Faced with the reality of an increasing poulation, the postharvest handling and storage of crops is a critical component of the global food system that helps to promote nutritional and food security. HRT403 is a middle level course that describes the basic principles of postharvest biology and technology. The aim of the course is to outline the biological processes that occur in horticultural crops following harvest and describe how these processes impact product quality. In addition, practical strategies that are employed by the fresh produce industry to reduce rates of postharvest decay and maintain quality are discussed. The course integrates basic biological knowledge with industry practices and introduces current research topics. The course runs during the fall semester each year and is comprised of a lecture and a laboratory format. The laboratory time is used to demonstrate principles discussed during the lectures, for student presentations and field trips. Following completion of the course, students will have gained knowledge of postharvest handling systems for fruits, vegetables and ornamental crops and be able to relate the perishable nature of these crops to their underlying biology.
It is estimated that we will have to feed an extra 2 billion people by 2050 and to achieve this goal, crop yields will have to double. At the same time, climate change will alter growing regions and resources such as fertile land, water, and nutrient inputs will be limiting. Research in basic and applied plant sciences is of fundamental importance in feeding the world population. Modern day crop plants were domesticated from wild ancestors and have undergone selection to improve yield, architecture, abiotic and biotic stress tolerance, nutrient content and flavor. Plant breeders have been instrumental in developing new crop varieties with increased yields and improved quality that help to reduce hunger. Applied Crop Improvement teaches the basic principles of genetics and plant breeding and provides students with insight into what plant breeders do through exposure to several MSU plant breeding programs.
I serve as the PI and Director of the NSF REU Site: Plant Genomics @ MSU http://www.plantgenomics.msu.edu
This program provides a 10-week research intensive experience in plant genomics to undergraduates entering their sophomore, junior or senior years. The program is designed to enrich the professional development of participants and provide an insight to what life is like in graduate school.
Plants are master chemists that collectively synthesize thousands of metabolites. These metabolites fall into two distinct classes; primary metabolites that are common to most plant lineages such as sugars, amino acids and fatty acids together with specialized metabolites (formerly, secondary metabolites) that are often lineage or species specific. Specialized metabolites are chemically diverse and include broad classes of structurally distinct molecules such as terpenoids, flavonoids and alkaloids. Many specialized metabolites are implicated in plant responses to abiotic or biotic stress and can serve directly as toxins or repellants. Alternatively, specialized metabolites, particularly those associated with the color and aroma of flowers and fruits serve as attractants to pollinators or seed dispersing fauna. As such, specialized metabolites are often synthesized in specific organs or cell types at particular stages of development or in response to environmental perturbation. Humans have exploited plant specialized metabolites for millennia for use as flavorings, fragrances, medicines, and poisons.
The Solanaceae (nightshade family) is a large and diverse family of approximately 3000 species that occupy varied ecological niches including species that thrive in tropical rain forests, at high altitudes in the mountain ranges of the Andes, and in desert environments. In addition, several Solanaceae species are important crop plants including potato, tomato, pepper, eggplant, tobacco and petunia. The Solanaceae family also exhibits tremendous phenotypic variation, including prolific diversity of specialized metabolites that often show restricted distribution to particular genera or species, or even to specific accessions within a species. This chemical diversity is fueled by rapid gene evolution that generates copy number variation leading to relaxed selection and subsequent neofunctionalization. We are utilizing an integrated approach involving genomics, metabolite profiling, gene-silencing biochemical analyses and synthetic biology to investigate the biosynthesis and evolution of specialized metabolite pathways within the Solanaceae. Current research is focused on the synthesis of defense compounds such as terpenes and acylsugars in the glandular trichomes and the biosynthesis of the medicinally important tropane alkaloids that occurs within the roots of selected members of the Solanaceae family. More information about our research can be found here: https://trichome.natsci.msu.edu/
Fleshy fruits have evolved to perform two complementary functions. Firstly, they protect the developing seeds from predation using a range of chemical and physical barriers. Then, once the seeds are fully developed and mature, fleshy fruits facilitate seed dispersal through the initiation of ripening. Fleshy fruits are highly diverse, they differ in size, shape, color, texture and flavor. However, despite this diversity there are evolutionary conserved changes that accompany ripening in many species including changes in color, increased softening, accumulation of sugars and the production of aroma compounds. The commonality of these processes suggest that there are underlying genetic mechanisms that regulate ripening in diverse species. We have a long standing interest in understanding of the genetic mechanisms that influence fruit ripening and quality and have used tomato as a model system coupled with genetic and genomics based approaches to identify and characterize loci that influence ethylene responses, pigment synthesis and degradation, ripening time and cuticle biosynthesis.
Xu H, Moghe G, Wiegert-Rininger KE, Schilmiller AL, Barry CS, Last RL, Pichersky E (2018) Coexpression analysis identifies two oxidoreductases involved in the biosynthesis of the monoterpene acid moiety of natural pyrethrin insecticides in Tanacetum cinerariifolium. Plant Physiology: 176: 524-537. DOI: https://doi.org/10.1104/pp.17.01330
Nadakuduti SS, Uebler JB, Liu X, Jones AD, Barry CS (2017) Characterization of trichome-expressed BAHDs in Petunia reveals distinct acylsugar assembly mechanisms. Plant Physiology 175: 36-50. DOI: https://doi.org/10.1104/pp.17.00538
Liu X, Enright M, Barry CS, Jones A (2017) Profiling, isolation and structure elucidation of specialized acylsucrose metabolites accumulating in trichomes of Petunia species. Metabolomics 13: article 85. doi:10.1007/s11306-017-1224-9
Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS et al., (2016) Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants Article Number 16074.
Guo Y, Wiegert-Rininger KE, Vallejo VA, Barry CS, Warner RM (2015) Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp. BMC Genomics 16: 726
Vallejo VA, Tychonievich J, Lin W-K, Wangchu L, Barry CS, Warner RM (2015) Identification of QTL for crop timing and quality traits in an interspecific Petunia population. Molecular Breeding 35: 2 DOI 10.1007/s11032-015-0218-4.
Bedewitz MA, Góngora-Castillo E, Uebler JB, Gonzales-Vigil E, Wiegert-Rininger KE, Childs KL, Hamilton JP, Vaillancourt B, Yeo YS, Chappell J, DellaPenna D, Jones AD, Buell CR, Barry CS (2014) A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna. Plant Cell 26: 3745-3762.
Nadakuduti SS, Holdsworth WL, Klein CL, Barry CS (2014) KNOX genes influence a gradient of fruit chloroplast development through regulation of GOLDEN2-LIKE expression in tomato. Plant Journal 78: 1022-1033.
Kang J-H, Gonzales-Vigil E, Matsuba Y, Pichersky E, Barry CS (2014) Determination of residues responsible for substrate and product specificity of Solanum habrochaites short-chain cis-prenyltransferases. Plant Physiology 164: 80-91.
Tychonievich J, Wangchu L, Barry C, Warner RM (2013) Utilizing wild species for marker-assisted selection of crop timing and quality traits in petunia. Acta Horticulturae 1000: 465-470.
Matsuba Y, Nguyen TTH, Wiegert K, Falara V, Gonzales-Vigil E, Leong B, Schäfer P, Kudrna D, Wing RA, Bolger AM, Usadel B, Tissier A, Fernie AR, Barry CS, Pichersky E (2013) Evolution of a complex locus for terpene biosynthesis in Solanum. Plant Cell 25: 2022-2036.
Kim J, Kang K, Gonzales-Vigil E, Shi F, Jones AD, Barry CS, Last RL (2012) Striking natural diversity in glandular trichome acylsugar composition is shaped by variation at the Acyltransferase 2 locus in the wild tomato Solanum habrochaites. Plant Physiology 160: 1854-1870.
Ma Q, Du W, Brandizzi F, Giovannoni JJ, Barry CS (2012) Differential control of ethylene responses by GREEN-RIPE and GREEN-RIPE LIKE1 provides evidence for distinct ethylene signaling modules in tomato. Plant Physiology 160: 1968-1984.
Powell ALT, Nguyen CV, Hill T, Cheng KLL, Figueroa‐Balderas R, Aktas H, Ashrafi H, Pons C, Fernández‐Muñoz R, Vicente A, Lopez‐Baltazar J, Barry CS, Liu Y, Chetelat R, Granell‐Richart A, Van Deynze A, Giovannoni JJ, Bennett AB (2012) Uniform ripening (U) encodes a Golden 2‐like transcription factor regulating tomato fruit chloroplast development. Science 336: 1711-1715.
Barry CS, Aldridge GM, Herzog G, Ma Q, McQuinn RP, Hirschberg J, Giovannoni JJ (2012) Altered chloroplast development and delayed fruit ripening caused by mutations in a chloroplast targeted zinc metalloprotease at the lutescent 2 locus of tomato. Plant Physiology 159: 1086-1098.
Nadakuduti SS, Pollard M, Kosma DK, Allen C Jr., Ohlrogge JB, Barry CS (2012) Pleiotropic phenotypes of the sticky peel (pe) mutant of tomato provide new insight into the role of CUTIN DEFICIENT 2. Plant Physiology 159: 945-960.
Gonzales-Vigil E, Hufnagel DE, Kim J, Last RL, Barry CS (2012) Evolution of TPS20-related terpene synthases influences chemical diversity in the glandular trichomes of the wild tomato relative Solanum habrochaites. Plant Journal 71: 921-935.
Barry CSand Pandey P (2009) A survey of cultivated heirloom tomato varieties identifies four new mutant alleles at the green-flesh locus. Molecular Breeding 24: 269-276.
Barry CS (2009) The stay-green revolution: recent progress in deciphering the mechanisms of chlorophyll degradation in higher plants. Plant Science 176: 325 - 333.
Barry CS, McQuinn R, Chung M-Y, Besuden A, Giovannoni JJ (2008) Amino acid substitutions in homologs of the STAY-GREEN protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper. Plant Physiology 147: 179 - 187.
Barry CS, Giovannoni JJ. (2007) Ethylene and fruit ripening. Journal of Plant Growth Regulation. 26: 143 - 159.
Barry CS, Giovannoni JJ. (2006) Ripening in the tomato Green-ripe mutant is inhibited by ectopic expression of a protein that disrupts ethylene signaling. Proc Natl Acad Sci USA. 103: 7923-7928.
Barry CS, McQuinn R, Thompson AJ, Seymour GB, Grierson D, Giovannoni JJ (2005) Ethylene insensitivity conferred by the Green-ripe (Gr) and Never-ripe 2 (Nr-2) mutants of tomato. Plant Physiol 138: 267-275.
Adams-Phillips L, Barry C, Giovannoni J. (2004) Signal transduction systems regulating fruit ripening. Trends In Plant Science 9: 331-338.
Adams-Phillips L, Barry C, Kannan P, Leclercq J, Bouzayen M, Giovannoni J (2004) Evidence that CTR1-mediated ethylene signal transduction in tomato is encoded by a multigene family whose members display distinct regulatory features. Plant Mol Biol 54: 387-404.
Liu Y, Roof S, Ye Z, Barry C, Van Tuinen A, Vrebalov J, Bowler C, Giovannoni J (2004) Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. Proc Natl Acad Sci USA 101: 9897-9902.
Moeder W, Barry CS, Tauriainen A, Betz C, Tuomainen J, Utriainen M, Grierson D, Sandermann H, Langebartels C, Kangasjärvi J (2002) Ethylene synthesis regulated by bi-phasic induction of ACC synthase and ACC oxidase genes is required for H2O2 accumulation and cell death in ozone-exposed tomato. Plant Physiol 130: 1918-1926.
Barry CS, Fox EA, Yen H-C, Lee S, Ying T-J, Grierson D, Giovannoni JJ (2001) Analysis of the ethylene response in the epinastic (epi) mutant of tomato. Plant Physiol 127: 58-66.
Barry CS, Llop-Tous I, Grierson D (2000) The regulation of 1-aminocyclopropane-1-carboxylic acid synthase gene expression during the transition from system-1 to system-2 ethylene synthesis in tomato. Plant Physiol 123: 979-986.
Llop-Tous I, Barry CS, Grierson D (2000) Regulation of ethylene biosynthesis in response to pollination in tomato flowers. Plant Physiol. 123: 971-978.
Thompson AJ, Tor M, Barry CS, Vrebalov J, Orfila C, Jarvis MC, Giovannoni JJ, Grierson D, Seymour GB (1999) Molecular and genetic characterisation of a novel pleiotropic tomato-ripening mutant. Plant Physiol. 120: 383-389.
Griffiths A, Barry CS, Alpuche-Solis A, Grierson D (1999) Ethylene and developmental signals regulate expression of lipoxygenase genes during tomato fruit ripening. J. Ex. Bot. 50: 793-798.
Cooper W, Bouzayen M, Hamilton AJ, Barry CS, Rossall S, Grierson D (1998) Use of transgenic plants to study the role of ethylene and polygalacturonase during infection of tomato fruit by Colletotrichum gloeosporioides. Plant Pathology 47: 308-316.
Blume B, Barry CS, Hamilton AJ, Bouzayen M, Grierson D (1997) Identification of transposon-like elements in non-coding regions of tomato ACC oxidase genes. Mol. Gen. Genet. 254: 297-303.
Barry CS, Blume B, Bouzayen M, Cooper W, Hamilton AJ, Grierson D (1996) Differential expression of the 1-aminocyclopropane-1-carboxylate oxidase gene family of tomato. Plant Journal 9: 525-535.
Barry CS, (2014) Ripening mutants. In Fruit Ripening: Physiology, Signalling and Genomics. Eds. P. Nath et al., CAB International, Wallingford, Oxfordshire, UK, pp 246-258.
Barry CS, (2012) Positional Cloning Strategies in Tomato. In Genetics, Genomics and Breeding in Fruit and Vegetable Crops: Tomato. Series Editor C. Kole, Science Publishers, Enfield NH, USA pp 304 - 326.
Barry CS, (2010) Factors influencing the ripening and quality of fleshy fruits. Annual Plant Reviews. 38: Editor L. Ostergaard, Wiley pp 296 - 325.
Adams-Phillips L, Alba R, Barry C, Giovannoni J, (2003) Genomics of ethylene signaling in tomato. In. Biology and Biotechnology of the Plant Hormone Ethylene III. Eds M Vendrell et al., IOS Press, The Netherlands, pp131-136.
Barry CS, Blume B, Hamilton AJ, Fray R, Payton S, Alpuche-Solis A, Grierson D, (1997) Regulation of ethylene synthesis and perception in tomato and its control using gene technology. In. Biology and Biotechnology of the Plant Hormone Ethylene. Eds AK Kanellis et al., Kluher Academic Press, The Netherlands, pp 299-306.
Krystle Wiegert-Rininger, 2012 - Present
Matthew Bedewitz, Plant Breeding, Genetics and Biotechnology, 2013 - Present