Molecular Breeding

, 35:106 | Cite as

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.


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



Agricultural Marketing Service


Burrows–Wheeler alignment


Computational Biology Service Unit


Food and Agriculture Organization


Genotyping by sequencing


Single nucleotide polymorphism


Geographical information systems


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

Supplementary material

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Supplementary material 1 (XLSX 23 kb)
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Supplementary material 3 (PPTX 774 kb)
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Supplementary material 4 (DOCX 16 kb)
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Supplementary material 5 (XLSX 9426 kb)
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Supplementary material 6 (PDF 159 kb)
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Supplementary material 7 (XLSX 78 kb)


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Copyright information

© Springer Science+Business Media Dordrecht (outside the USA) 2015

Authors and Affiliations

  1. 1.Plant Genetic Resources Unit, United States Department of AgricultureAgricultural Research ServiceGenevaUSA

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