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

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Abstract

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.

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Abbreviations

AMS:

Agricultural Marketing Service

BWA:

Burrows–Wheeler alignment

CBSU:

Computational Biology Service Unit

FAO:

Food and Agriculture Organization

GBS:

Genotyping by sequencing

SNP:

Single nucleotide polymorphism

GIS:

Geographical information systems

H e :

Expected heterozygosity

SSR:

Simple sequence repeat

NCBI:

National Center for Biotechnology Information

NJ:

Neighbor joining

NPGS:

National Plant Germplasm System

SRA:

Sequence read archive

PGRU:

Plant Genetic Resources Unit

GRIN:

Germplasm Resources Information Network

UNEAK:

Universal Network Enabled Analysis Kit

USDA:

United States Department of Agriculture

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Acknowledgments

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.

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  1. Plant Genetic Resources Unit, United States Department of Agriculture, Agricultural Research Service, 630 W. North St., Geneva, NY, 14456, USA

    Joanne A. Labate & Larry D. Robertson

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  1. Joanne A. Labate
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  2. Larry D. Robertson
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Correspondence to Joanne A. Labate.

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Labate, J.A., Robertson, L.D. Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines. Mol Breeding 35, 106 (2015). https://doi.org/10.1007/s11032-015-0302-9

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