Skip to main content

Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines


To help support utilization of germplasm resources for tomatillo (Physalis philadelphica) crop improvement, we characterized genetic diversity in the National Plant Germplasm System collection. Genotyping by sequencing, a method of high-throughput DNA sequencing of reduced representation genomic libraries, was performed on 190 plant samples. This yielded 77,340 high-quality filtered single nucleotide polymorphisms from 179 plants sampled from 125 accessions. Geographical information systems data on geospatial references were verified using web- and PC-based software tools. We found that multiple plants sampled per accession were closely related to each other, but there was no apparent pattern related to original sampling location with respect to state in Mexico. There was no evidence for isolation by distance in a 15-accession, 53 plant geodiversity panel. Average proportion of heterozygous sites was halved in samples from nine inbred lines relative to samples from open-pollinated accessions (0.04 vs. 0.08). The genetic characterization of these accessions can help end users choose germplasm to support increased production of fresh and processed tomatillo products for expanding niche markets.

This is a preview of subscription content, access via your institution.

Fig. 1



Agricultural Marketing Service


Burrows–Wheeler alignment


Computational Biology Service Unit


Food and Agriculture Organization


Genotyping by sequencing


Single nucleotide polymorphism


Geographical information systems

H e :

Expected heterozygosity


Simple sequence repeat


National Center for Biotechnology Information


Neighbor joining


National Plant Germplasm System


Sequence read archive


Plant Genetic Resources Unit


Germplasm Resources Information Network


Universal Network Enabled Analysis Kit


United States Department of Agriculture


  1. Anonymous (2014) Mexico: broad and deep agricultural trade relationship. USDA Foreign Agricultural Service, Global Agricultural Information Network Report Number MX4019

  2. Barrett T, Clark K, Gevorgyan R, Gorelenkov V, Gribov E, Karsch-Mizrachi I, Kimelman M, Pruitt KD, Resenchuk S, Tatusova T (2012) BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res 40(D1):D57–D63

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  3. Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA (2011) The Sol Genomics Network ( growing tomatoes using Perl. Nucleic Acids Res 39(Database issue):D1149–1155

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Choi JK, Murillo G, Su BN, Pezzuto JM, Kinghorn AD, Mehta RG (2006) Ixocarpalactone A isolated from the Mexican tomatillo shows potent antiproliferative and apoptotic activity in colon cancer cells. FEBS J 273:5714–5723

    Article  CAS  PubMed  Google Scholar 

  5. Elizalde-Gonzalez MP, Hernandez-Ogarcia SG (2007) Effect of cooking processes on the contents of two bioactive carotenoids in Solanum lycopersicum tomatoes and Physalis ixocarpa and Physalis philadelphica tomatillos. Molecules 12:1829–1835

    Article  CAS  PubMed  Google Scholar 

  6. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567

    Article  PubMed  Google Scholar 

  8. Felsenstein J (1989) PHYLIP—phylogeny inference package (version 3.2). Cladistics 5:164–166

    Google Scholar 

  9. Freeling M, Walbot V, Lee M (1994) Inbred lines of maize and their molecular markers. In: The maize handbook. Springer Lab Manuals. Springer, New York, pp 423–432

  10. Freyre R, Loy JB (2000) Evaluation and yield trials of tomatillo in New Hampshire. HortTechnology 10:374–377

    Google Scholar 

  11. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS ONE 9:e90346

    Article  PubMed Central  PubMed  Google Scholar 

  12. Grills G, Schweitzer P, Sun Q, Pillardy J, Wang W, Stelick T, Bukowski R, Ponnala L, VanEe J, Grills G (2011) Integrated core facility support and optimization of next generation sequencing technologies. J Biomol Tech 22(Supplement):S32

    PubMed Central  Google Scholar 

  13. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620

    Article  Google Scholar 

  14. Heled J, Drummond AJ (2010) Bayesian inference of species trees from multilocus data. Mol Biol Evol 27:570–580

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Howard N, Wright S (2012) Tomatillo. University of Kentucky Cooperative Extension Service. CCD Crop Profiles

  16. Hudson WD Jr (1986) Relationships of domesticated and wild Physalis philadelphica. In: D’Arcy WG (ed) Solanaceae biology and systematics. Columbia University Press, New York, pp 416–432

    Google Scholar 

  17. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro H (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132

    Chapter  Google Scholar 

  18. Labate JA, Robertson LD, Strickler SR, Mueller LA (2014) Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex. Genome 57:169–180

    Article  CAS  PubMed  Google Scholar 

  19. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25(14):1754–1760

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Liu HY, Koike ST, Xu D, Li R (2012) First report of Turnip mosaic virus in tomatillo (Physalis philadelphica) in California. Plant Dis 96(2):296

    Article  Google Scholar 

  21. Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE (2013) Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 9(1):e1003215

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Maldonado E, Perez-Castorena AL, Garces C, Martinez M (2011) Philadelphicalactones C and D and other cytotoxic compounds from Physalis philadelphica. Steroids 76(7):724–728

    Article  CAS  PubMed  Google Scholar 

  23. Marchini J, Howie B (2010) Genotype imputation for genome-wide association studies. Nat Rev Genet 11:499–511

    Article  CAS  PubMed  Google Scholar 

  24. Melchinger AE (1990) Use of molecular markers in breeding for oligogenic disease resistance. Plant Breed 104:1–19

    Article  Google Scholar 

  25. Menzel MY (1951) The cytotaxonomy and genetics of Physalis. Proc Am Philos Soc 95:132–183

  26. Montes Hernández S, Aguirre Rivera J (1994) Tomatillo, husk-tomato (Physalis philadelphica). In: Hernándo Bermejo J, León J (eds) Neglected crops: 1492 from a different perspective. Plant Production and Protection Series No. 26. FAO, Rome, Italy, pp 117–122

  27. Moriconi DN, Rush MC, Flores H (1990) Tomatillo: a potential vegetable crop for Louisiana. In: Janick J, Simon JE (eds) Advances in new crops. Timber Press, Portland, pp 407–413

    Google Scholar 

  28. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  29. Pandey KK (1957) Genetics of self-incompatibility in Physalis ixocarpa Brot.—A new system. Am J Bot 44:879–887

  30. Pluzhnikov A, Donnelly P (1996) Optimal sequencing strategies for surveying molecular genetic diversity. Genetics 144:1247–1262

    PubMed Central  CAS  PubMed  Google Scholar 

  31. Poland JA, Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5:92–102

    Article  CAS  Google Scholar 

  32. Rambaut A (2012) FigTree 1.4.0. Accessed 12 May 2014

  33. Ramirez-Godina F, Robledo-Torres V, Pournabav RF, Benavides-Mendoza A, Hernandez-Pinero JL, Reyes-Valdes MH, Alvarado-Vazquez MA (2013) Yield and fruit quality evaluation in husk tomato autotetraploids (Physalis ixocarpa) and diploids. Aust J Crop Sci 7(7):933–940

    Google Scholar 

  34. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145(4):1219–12228

    PubMed Central  CAS  PubMed  Google Scholar 

  35. Russell J, Hackett C, Hedley P, Liu H, Milne L, Bayer M, Marshall D, Jorgensen L, Gordon S, Brennan R (2014) The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences. Mol Breed 33:835–849

    Article  CAS  Google Scholar 

  36. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  37. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 39(Suppl. 1):D38–D51

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  38. Simon J, Park C, Ayeni A, Payne R, Nitzsche P, Sciarappa B, Van Vranken R, Komar S, Dager E, Wu Q, Schilling B, Govindasamy R, Kelley KM (2013) Producing and marketing ethnic herbs and greens. In: Infante-Casella ML, Kline WL (eds) 58th New Jersey Agricultural Convention and Trade Show, Atlantic City, NJ, February 5–7, 2013. Rutgers Cooperative Extension, pp 140–141

  39. Smith R, Jiminez M (1999) Tomatillo production in California. Vegetable Production Series, Pub. 7246. University of California, Division of Agriculture and Natural Resources

  40. Su B-N, Misico R, Jung Park E, Santarsiero BD, Mesecar AD, Fong HHS, Pezzuto JM, Douglas Kinghorn A (2002) Isolation and characterization of bioactive principles of the leaves and stems of Physalis philadelphica. Tetrahedron 58(17):3453–3466

    Article  CAS  Google Scholar 

  41. The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635–641

    Article  Google Scholar 

  42. Upadhyaya HD, Gowda CLL (2006) Enhancing utilization of plant genetic resources in crop improvement. In: Plant breeding in post genomics era. Proceedings of Second National Plant Breeding Congress, Coimbatore, India, 1–3 March, 2006. Indian Society of Plant Breeders, pp 34–51

  43. Vargas-Ponce O, Perez-Alvarez LF, Zamora-Tavares P, Rodriguez A (2011) Assessing genetic diversity in Mexican husk tomato species. Plant Mol Biol Rep 29(3):733–738

    Article  Google Scholar 

  44. Vision T, Chacon M, Tsompana M, Robertson L, Pena Lomeli A, Ponce O (2006) Microsatellite variation and population structure in tomatillo (Physalis philadelphica Lam.). In: PAA/Solanaceae abstract 408, July 23–27, Madison, WI

  45. Waterfall UT (1967) Physalis in Mexico, Central America and the West Indies. Rhodora 69:82–120, 203–239, 319–329

  46. Wei J, Hu X, Yang J, Yang W (2012) Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers. PLoS ONE 7(11):e50164

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  47. Willing E-M, Dreyer C, van Oosterhout C (2012) Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers. PLoS ONE 7:e42649

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  48. Wright S (1951) The genetical structure of populations. Ann Eugen 15:323–354

    Article  CAS  PubMed  Google Scholar 

  49. Zamora-Tavares P, Vargas-Ponce O, Sánchez-Martínez J, Cabrera-Toledo D (2015) Diversity and genetic structure of the husk tomato (Physalis philadelphica Lam.) in Western Mexico. Genet Resour Crop Evol 62:141–153

Download references


We thank Susan M. Sheffer, William Garman, Jonathan Spencer, Paul Kisly, Sherri Tennies and Bob Nearpass for their assistance and excellent technical support. Sharon Mitchell and Robert Bukowski (Cornell University) performed and analyzed the spike-in experiment to verify library optimization. USDA is an equal opportunity provider and employer. The use of trade, firm or corporation names in this publication is for the information and convenience of the reader. Such use does not constitute an official endorsement or approval by the United States Department of Agriculture or the Agricultural Research Service of any product or service to the exclusion of others that may be suitable. This research was supported by CRIS Project No. 1910-21000-024-00D. Part of this work was carried out using the resources of the Computational Biology Service Unit from Cornell University which is partially funded by Microsoft Corporation.

Author information



Corresponding author

Correspondence to Joanne A. Labate.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Labate, J.A., Robertson, L.D. Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines. Mol Breeding 35, 106 (2015).

Download citation


  • Husk tomato
  • Germplasm
  • Single nucleotide polymorphism
  • Genotyping by sequencing
  • Population genetics
  • Isolation by distance