The Impact of Ploidy on Apple Varieties

In plants, the number of complete sets of chromosomes can vary. This is known as Ploidy level. It is common in plants and affects their evolution, reproduction, and improvements for farming. Plants can have different ploidy levels, ranging from single sets (haploid) to multiple sets like double (diploid), four times (tetraploid), and eight times (octoploid). For example, there are haploid cotton plants and octoploid strawberries. Triploid plants, which have three sets of chromosomes, often show advantages in many plant types. Triploid Populus trees grow faster and have larger leaves compared to diploid ones. The reasons for these benefits are not entirely clear, but they may be linked to more organelle production in the plant cells.

In agriculture, some triploid plants have been chosen for their unique traits, like the high-yield cassava and seedless mandarins, but triploid plants usually have lower fertility. The effects of triploidy on different fruit traits in agricultural plants need more study.

#The Apple Tree and Its Importance

The apple tree is a key fruit crop around the world, and many breeding efforts are ongoing. Most apples have two sets of chromosomes (diploid), but there are also triploid and tetraploid varieties. Notable commercial triploid apples include ‘Ribston Pippin’, ‘Mutsu’, and ‘Jonagold’. These triploid apples are often larger, more resistant to diseases, and show more vigorous growth compared to diploid apples. Breeding programs sometimes focus on these improvements to create new apple varieties. However, because Triploids produce fewer balanced gametes, they face challenges in breeding.

While historical records suggest triploids were essential in developing modern apples, this is contradicted by recent genetic studies. These studies show that triploid apples have rarely produced offspring, leading them to be called "dead ends" in breeding. Hence, the advantages of using triploids in apple breeding remain unclear.

#Comparing Diploid and Triploid Apples

Despite some reports of improved traits in triploid apples, there have been few thorough comparisons between diploid and triploid varieties. Understanding the differences in fruit quality across these types of apples can help breeders make better choices. This study looked at around 100,000 Genetic Markers called single nucleotide polymorphisms (SNPs) to distinguish between diploid and triploid apples. The study examined ten important traits in agriculture and linked apple ploidy to the year they were released, highlighting differences in fruit quality over time.

#Canada's Apple Biodiversity Collection

Canada's Apple Biodiversity Collection (ABC) is home to 1,119 unique apple types at a research station in Nova Scotia. The trees were planted in 2013 after being grafted onto a specific rootstock. The orchard is maintained according to industry standards.

#How Genetic Data Was Collected

The process of collecting genetic data and identifying SNPs in the apple accessions has been previously documented. Genotyping was performed using specific restriction enzymes, allowing for the identification of over 278,000 SNPs across many apple types. For this study, the dataset was narrowed down to only include 970 Malus domestica accessions harvested in recent years. A minor allele frequency (MAF) threshold was used to filter SNPs, yielding over 105,000 markers. Additional steps were taken to remove markers with excessive heterozygosity and to refine the dataset based on genetic linkage.

Heterozygosity was calculated for each apple type, and comparisons were made between known diploid and triploid accessions. This information was used to create plots and compare the two groups using statistical tests.

#Evaluating Traits in Apples

This study also looked at how ploidy impacts various traits in apples. Researchers evaluated ten interesting traits from previously published data. Some traits were measured in both 2016 and 2017, but more accessions were available for 2017 measurements.

The chosen traits included flowering date, harvest date, time to ripen, weight, acidity, soluble solids content (SSC), the ratio of SSC to acidity, total phenolic content, firmness, and how much the apples softened during storage. Each trait was measured carefully to ensure accuracy.

The study found only minor differences between diploid and triploid apples across the evaluated traits. Even though some traits like weight and firmness showed trends in favor of triploid apples, the only statistically significant difference was in phenolic content, which was higher in triploids.

#Release Year Comparison

The release years of diploid and triploid apples were also analyzed. The oldest diploid in the dataset was released in 1804, while the oldest triploid was released in 1720. Overall, diploid apples tended to have later release years compared to triploids. The study revealed that triploid apples were more likely to be released before 1900 compared to diploid apples. This difference could be due to the challenges faced in breeding triploid varieties, which often struggle with fertility.

#Genetic Variation in Apples

The level of ploidy can affect growth and reproductive traits in apples. To compare diploid and triploid apples, the ABC accessions were categorized based on heterozygosity. This method helped identify ploidy levels accurately in most cases. However, there were some misclassifications where Diploids were labeled as triploids and vice versa.

As the study looked at genetic similarity through principal components analysis (PCA), it showed that diploid apples captured more genetic variation compared to triploids. Triploids appeared to cluster more closely based on their genetic data, suggesting they share more similarities within their group.

#Findings on Traits in Apples

When analyzing the trait data, four traits showed some differences between diploid and triploid apples, including weight and firmness, but after correction for multiple comparisons, only the phenolic content remained significantly different. Triploid apples had a higher phenolic content, which could be beneficial for intended uses, such as cider making.

This study's findings align with previous observations that triploid apples can be larger and more vigorous, but the results indicate that over a large collection, the observed differences are not profound.

#Conclusion on Ploidy and Breeding

Although there are minor differences in traits between diploid and triploid apples, triploids have been grown and sold for over two centuries. This study highlights that while triploid apples may have had historical significance, contemporary breeding efforts tend to favor diploid varieties.

The results suggest that using heterozygosity can effectively differentiate between diploids and triploids. The only significant trait difference identified was in phenolic content, which could be used in specific breeding programs, particularly for cider apples. Overall, the study raises questions about the best practices in apple breeding, particularly concerning the role of triploids.