It is really fun this article just came out. Here is a link to it. It was fun to share data of some of our populations and contribute to it. https://acsess.onlinelibrary.wiley.com/doi/10.1002/tpg2.70044
SNPs are places where members of a species generally share the same sequence in areas in the DNA, but there is one DNA nucleotide (the building blocks of DNA) in that generally shared sequence where a difference can be found. An individual can be homozygous for one version of the SNP (one specific nucleotide) or heterozygous (have each of the different sequence possibilities with one version in one of the sets of chromosomes inherited from say mom and the other version in the chromosome inherited from dad). Certain nucleotides at a spot (SNP) has been found in some cases to be linked to certain things like disease or a specific feature/trait. Platforms like 23 & me for instance use SNPs to understand human ancestry and health issues. SNPs can be used to study variation in humans, other animals, plants, etc.
In roses there are about 68,000 SNPs that have been found and are part of what is called the rose array and available from a company that can run and rate rose genotypes for SNPs. We can test a rose for which nucleotide variation it has at all these SNPs (if its homozygous for one nucleotide or another or has copies of both across its sets of chromosomes).
Anyways, SNP data was generated for a number of parents and seedlings we crossed and raised to study inheritance of black spot and rose rosette resistance and a number of cultivars on the market were used too. With roses being polyploid, they can have more than 2 sets of chromosomes making things especially challenging. Folks at Texas A&M worked very hard to be able to develop a software program to tell relative copy number of each nucleotide version of a SNP. Which chromosome the ~68,000 SNPs are on is generally known as well, which is another part of the story that makes the incredible advancement possible too. SNPs are peppered across all the seven unique chromosomes of roses (diploids have two sets of 7 for 14 total in their cells, triploids have 21, tetraploids have 28, etc.). Let’s say for a SNP the nucleotides found can be either an A or a G at a spot (adenine or guanine). If you had a tetraploid you could have AAAA, AAAG, AAGG, AGGG, or GGGG depending on what the specific rose possesses/inherited. The ratios of 100%, 75%, 50%, 25% or 0% of any specific nucleotide at a SNP that we would find if the rose is tetraploid helps us know the plant is tetraploid as we look at all the SNPs (~68,000) and find ratios for the 2 nucleotides in only these relative percentages/ratios. If a rose is triploid we’d find at any particular SNP 100%, 66.6%, 33.3%, or 0% of the two nucleotides at the spot (AAA, AAG, AGG, or GGG). If a rose is diploid, we find just 100%, 50%, or 0% ratios at the SNPs (AA, AG, or GG). This allows us to use this analysis as a powerful way to leverage the data for all SNPs and all their nucleotide variations to detect ploidy (not all SNPs would have either an AG, but say a T or C, another A or C, etc. and we’d compare and contrast ratios for all those as well).
Since we generally know which chromosome each of the SNPs are on, we can also use the data to detect aneuploids and even learn what chromosome or part of a chromosome has an extra or missing copy. Aneuploids do not have complete sets and equal representation of all chromosomes. They typically have a an extra chromosome or two or are missing a chromosome or two or even just part of a chromosome. Aneuploids tend to have not be as robust as counterparts that do have full sets of chromosomes.
In our crosses where we saved all the seedlings for black spot or RRD research and didn’t throw any individuals away that would grow somewhat okay, we found 16% aneuploids! They tended to be the awkward growing and/or less vigorous growing plants. Among the cultivars aneuploidy was much lower at 2%. This is likely due to aneuploids being selected out during the breeding/selection process since they are poorer performers. This gives us some insights why we get some awkward slow growing seedlings at times. Using this program with SNP data that has been generated for a rose is also a powerful way to easily and confidently detect its ploidy and even if it an aneuploid and what chromosome or two is extra or missing.
On a special side note, this article is in a special edition of the journal with articles to honor the late Dr. Ronald Phillips. He was an amazing geneticist and was at the Univ. of Minnesota. He was part of many ground breaking understandings of plant genetics/genetics in general. Oscar did a post doc with him (Oscar came up with the overall direction of this research). I took Dr. Phillips Cytogenetics class in grad school and was his TA the next time he taught it and treasured the opportunity to learn more as I had the opportunity to help with the class.