Combining conventional QTL analysis and whole-exome capture-based bulk-segregant analysis provides new genetic insights into tuber sprout elongation a

A study conducted by the James Hutton Institute, University of Greenwich, Cranfield University, and Imperial College London has conducted an in-depth genetic analysis of tuber sprout growth. The study utilized a diploid potato population that originated from two highly heterozygous parents. Here is a summary of their findings.

by Jorge Luis Alonso with ChatGPT-4

Key Points

• The study discusses the importance of tuber dormancy and sprouting in potatoes, as these traits are key to maintaining product quality during long-term storage.
• In Europe, the absence of the main chemical sprout suppressant chlorpropham (CIPC) creates a demand for the breeding of potato varieties with longer dormancy and slower sprout growth. Despite this, the need for rapid emergence in the seed potato industry requires a delicate equilibrium.
• The researchers conducted a genetic analysis of tuber sprout growth using a diploid potato population derived from two highly heterozygous parents.
• Utilizing conventional QTL analysis in conjunction with bulk segregant analysis (BSA), the study implemented a novel potato whole exome capture (WEC) platform.
• Tubers were evaluated for sprout growth in storage at six different time points over two consecutive growing seasons.
• The study identified major QTLs on five chromosomes, several of which were consistent across two growing seasons.
• Using a combined BSA and WEC approach confirmed QTL locations, narrowed the associated genomic regions, and identified new QTL for further investigation.

Below there are some explanations of the technical and complex terms used in this article

Potato, an important non-cereal food crop, is often subject to genetic analysis using heterozygous diploid parental crosses. Recent advances in linkage mapping tools and quantitative trait locus (QTL) analysis have made this process more manageable, especially for tetraploid potato. The publication of the potato genome, along with dense SNP platforms, now supports candidate gene approaches to trait identification, despite the inherent challenges of complex trait analysis.

After maturation, potato tubers enter a state of endodormancy, a trait that significantly affects their post-harvest storage life and varies between cultivars. This dormancy period has significant economic implications as it determines the length of time potatoes must be stored before they can be processed or sold. However, premature release from dormancy can lead to a reduction in product quality. Given the limitations of current storage methods, such as the EU’s withdrawal of chlorpropham and the disadvantages of low-temperature storage, it’s necessary to develop new storage strategies and breed varieties with modified dormancy or sprouting vigor.

Previous studies on tuber dormancy at the diploid level have revealed QTL effects on different potato chromosomes. However, the low resolution of genetic maps generated by pre-modern marker technology hindered the identification of genes controlling potato tuber dormancy and sprouting. The focus of the current research was to further explore the genetic structure of tuber sprout elongation using an extensive diploid mapping population. This investigation assessed tuber sprout growth in storage at six intervals over two seasons and implemented both QTL analysis and bulk segregant analysis (BSA) complemented by whole exome capture (WEC) sequencing.

The extensive genetic study was based on a unique diploid potato population derived from two highly heterozygous parents. This population is characterized by below-average tuber dormancy and late maturation. Using a pre-existing SNP map, the study expanded the number of progeny clones from 186 to 249 and increased the number of mapped loci to 3076.

Using both nonparametric (KW) and CIM approaches, the QTL analysis was largely concordant, locating QTL in similar regions on chromosomes 2, 3, 4, 5, and 10. These data suggest that tuber dormancy break and sprout growth are incredibly complex genetic traits, with differences in direction and magnitude of effect.

In addition to the traditional QTL approach, the study piloted an innovative BSA method combined with a WEC platform. This method identified QTL on chromosomes 1–8, consistent with the results of the CIM QTL analyses. The integration of BSA-WEC improved the precision and resolution of genetic studies in potatoes, facilitating the identification of genetic factors in smaller genomic regions.

The researchers identified a candidate gene, CENTRORADIALIS (StCEN), located in the CIM QTL region on chromosome 3. This gene is known to influence bud maturation and outgrowth. By manipulating the expression level of StCEN in a potato genotype, the rate of tuber sprout growth could be influenced.

The results of this current study correlate well with previous genetic research on potato tuber dormancy and sprout growth. Despite differences in methodology, the same loci were often found to be significant in different studies, suggesting a common genetic basis for these traits. Given the complexity of these traits, a genomic selection approach may be essential for future improvements in tuber dormancy and sprout growth in breeding programs.

The WEC-BSA approach allowed the identification of more than 500 candidate genes, highlighting the difficulty in identifying the causative genes behind complex trait QTLs. Additional methods, such as network modeling, may be needed to refine the candidate gene list. This research also highlights the effectiveness of sequence-based genotyping, which provides high SNP density and allows the study of a wide range of polymorphisms.

Source: Sharma, S. K., McLean, K., Colgan, R. J., Rees, D., Young, S., S?nderk?r, M., Terry, L. A., Turnbull, C., Taylor, M. A., & Bryan, G. J. (2021). Combining conventional QTL analysis and whole-exome capture-based bulk-segregant analysis provides new genetic insights into tuber sprout elongation and dormancy release in a diploid potato population. Heredity, 127(3), 253–265. https://doi.org/10.1038/s41437-021-00459-0

Some explanations of the technical and complex terms used in the text?above

Diploid potato population: Potatoes, like humans, are diploid organisms, meaning they have two sets of chromosomes, one from each parent. By using a diploid population, researchers can more easily track which traits come from which parent.

QTL analysis: QTL stands for Quantitative Trait Locus. It is a section of DNA (the genetic material) that correlates with variation in a phenotype (the observable characteristics of an organism). The QTL is the genetic “source” of a trait.

Bulk Segregant Analysis (BSA): This is a method for identifying candidate genes associated with a trait. It involves creating two groups (or “bulks”) of individuals, one with the trait of interest and one without. The genomes of these groups are then compared to identify regions that differ.

Whole Exome Capture (WEC): Employing this particular method allows for the isolation of all exons (the parts of the genome that directly code for proteins) in a genome. This technique is widely used in genetic research because although the exome represents a small fraction of the genome, mutations in the exome are thought to harbor 85% of disease-causing mutations.

Non-grain crop: This is a term for a type of crop that is not a member of the grass family. For example, potatoes are a non-cereal food crop.

Endodormancy: This is a phase in the life of a plant when growth is temporarily arrested. In potatoes, endodormancy is critical for the long-term storage of tubers.

SNP: SNP stands for single nucleotide polymorphism. It is a change at a single site in the DNA. SNPs can be used as biological markers to help scientists locate genes associated with certain diseases.

CENTRORADIALIS (StCEN): This is a gene found in plants that is known to influence bud maturation and outgrowth. In the context of this study, manipulating the expression of StCEN could potentially influence the rate of growth of potato tuber sprouts..

For more research on potato storage, click here: https://bit.ly/3u8OCtU.

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