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ARS Home » Northeast Area » Geneva, New York » Plant Genetic Resources Unit (PGRU) » Research » Publications at this Location » Publication #307195
Title: Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines

Author
item Labate, Joanne
item Robertson, Larry

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/20/2015
Publication Date: 4/2/2015
Publication URL: http://dx.doi.org/10.1007/s11032-015-0302-9
Citation: Labate, J.A., Robertson, L.D. 2015. Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines. Molecular Breeding. Volume 35(4):106. DOI: 10.1007/s11032-015-0302-9.

Interpretive Summary: Tomatillo (Physalis philadelphica), also known as husk tomato, is native to Mexico and is widely grown in Mexico and Guatemala. It is primarily consumed in the form of relishes or sauces such as green salsa which are part of a rapidly growing niche market in the USA. The fruit contains many healthful properties such as cancer prevention agents, antioxidants and vitamin C. An evaluation of the crop in the USA reported it to be generally disease resistant but very labor intensive to harvest. New varieties that can be harvested mechanically would be desirable for production systems in the USA. To help support usage of new genetic sources for tomatillo crop improvement, we characterized genetic diversity in the National Plant Germplasm System (NPGS) collection. We identified 77,340 genetic markers by DNA sequencing libraries of 179 plants. We found that plants within populations were closely related to each other, but there was no apparent pattern related to original sampling location with respect to state in Mexico or latitude. Based on gene frequencies, 29% of pairs of populations were distinct from each other. The results of this study will help breeders and other researchers to support the expansion of production of fresh and processed tomatillo products for new markets.

Technical Abstract: To help support utilization of germplasm resources for tomatillo (Physalis philadelphica) crop improvement, we characterized genetic diversity in the National Plant Germplasm System (NPGS) collection. Genotyping by sequencing (GBS), 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 (SNPs) from 179 plants sampled from 125 accessions. Geographical Information Systems (GIS) 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 or latitude. There was no evidence for isolation by distance in a 15 accession geodiversity panel. Average proportion of heterozygous sites was halved in nine inbred lines relative to open-pollinated accessions (0.04 versus 0.08). Tests of 300 pairs of accessions for population differentiation showed that 86 (0.29) pairs of accessions were significantly differentiated from each other. A few accessions were relatively more divergent and at least one of these may be misidentified at the species level. 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.