Molecular Breeding

, 35:106 | Cite as

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

Article

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.

Keywords

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

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

He

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

Supplementary material

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Supplementary material 1 (XLSX 23 kb)
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Supplementary material 2 (DOCX 18 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)
11032_2015_302_MOESM6_ESM.pdf (160 kb)
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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