National Clonal Germplasm Database

I want to get back to a little bit more scientific content in my blog so today, I'm posting about a research paper that I am reading. I learned that the USDA keeps a Grape Germplasm Database for grapes.
On that page is the following article: Genetic structure and differentiation in cultivated grape, Vitis vinifera L. and explains how genetic relationships among grapevines were determined.¹
The study evaluated the genetic diversity, structure and differentiation in a grape germplasm collection using polymorphisms at eight microsatellite loci, VVS2, VVMD5, VVMD6, VVMD7, VVMD27, VVMD28, VVMD31 and VVMD32.
Just what are microsatellites and why are they so useful? Microsatellite markers or single sequence repeats (SSRs) contain from 1 to 10 nucleotides. They are:²

• Abundant
• Multi-allelic
• Highly polymorphic
• Efficient and accurate for detecting genetic polymorphism
• Co-dominant

All of the above attributes leads to SSRs being the markers of choice for population genetic analysis to assess genetic structure and differentiation in germplasm collections and natural populations.
For wild species SSRs are used:

• (i) in studies of diversity measured on the basis of genetic distance
• (ii) to estimate gene flow and crossing over rates
• (iii) in evolutionary studies, above all to infer infraspecific genetic relations

For cultivated plants SSRs are commonly used for:

• (i) constructing linkage maps
• (ii) mapping loci involved in quantitative traits (QTL)
• (iii) estimating the degree of kinship between genotypes
• (iv) using marker-assisted selection
• (v) defining cultivar DNA fingerprints

Using microsatellite loci information, the researchers examined the consequences of isolation of eastern and western populations during the glacial period and post-glacial proliferation for population differentiation, climatic adaptations and early selection and cultivation by man. They also elucidated the genetic relationship between cultivated and wild grapes to draw inferences about the history of domestication. This research resulted in the classification of grape cultivars by eco-geographic variation and resulted in the following groupings:

• Occidentalis, the small-berried wine grapes of western Europe
• Orientalis, the large-berried table grapes of West Asia
• Pontica, the intermediate type from the basin of the Black Sea and eastern Europe

The data resulted in the following unrooted tree (phenogram) with 16 recognizable groups structured into three major clusters:

One of the clusters included the Gouais Blanc X Pinot Noir relations that I blogged about in Determining Genetic Relationships Between Auxerrois and Chardonnay.
References:
1. Malikarjuna K. Aradhya, Gerald S. Dangl, Bernard H. Prins, Jean-Michel Boursiquot, M. Andrew Walker, Carole P. Meredith, and Charles J. Simon, Genetic structure and differentiation in cultivated grape, Vitis vinifera L., Genet. Res., Camb. (2003), 81, pp. 179–192.
2. Vieira MLC, Santini L, Diniz AL, Munhoz C de F., Microsatellite markers: what they mean and why they are so useful, Genetics and Molecular Biology, 2016;39(3):312-328, doi:10.1590/1678-4685-GMB-2016-0027.