Dataset Information

Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids.

ABSTRACT: Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by prickle pollination of two tetraploid cultivars with Solanum phureja and genotyped with the 12.8 k SolCAP single nucleotide polymorphism (SNP) array. We show that in a population of monoparental haploids, the number of biallelic SNP markers segregating in linkage to loci from the tetraploid donor genotype is much larger than in putative crosses of this genotype to a diverse selection of 125 tetraploid cultivars. Although this strategy is more laborious than conventional breeding, the generation of haploid progeny for efficient marker analysis is straightforward if morphological markers and flow cytometry are utilized to select true haploid progeny. The level of introgressed fragments from S. phureja, the haploid inducer, is very low, supporting its suitability for genetic analysis. Mapping with single-dose markers allowed the analysis of quantitative trait loci (QTL) for four phenotypic traits.

SUBMITTER: Bartkiewicz AM

PROVIDER: S-EPMC5949705 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids.

Bartkiewicz Annette M AM Chilla Friederike F Terefe-Ayana Diro D Lübeck Jens J Strahwald Josef J Tacke Eckhard E Hofferbert Hans-Reinhard HR Linde Marcus M Debener Thomas T

Frontiers in plant science 20180507

Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by p ...[more]

PMID: 29868076

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Project description:BackgroundTuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economic importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype. Here, we used capture sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis (GWAS) for tuber bruising. In addition, we collected transcriptomic data to enrich the GWAS results. However, there is currently no satisfactory method to represent both GWAS and transcriptomics analysis results in a single visualisation and to compare them with existing knowledge about the biological system under study.ResultsWhen investigating population structure, we found that the STRUCTURE algorithm yielded greater insights than discriminant analysis of principal components (DAPC). Importantly, we found that markers with the highest (though non-significant) association scores were consistent with previous findings on tuber bruising. In addition, new genomic regions were found to be associated with tuber bruising. The GWAS results were backed by the transcriptomics differential expression analysis. The differential expression notably highlighted for the first time the role of two genes involved in cellular strength and mechanical force sensing in tuber resistance to bruising. We proposed a new visualisation, the HIDECAN plot, to integrate the results from the genomics and transcriptomics analyses, along with previous knowledge about genomic regions and candidate genes associated with the trait.ConclusionThis study offers a unique genome-wide exploration of the genetic components of tuber bruising. The role of genetic components affecting cellular strength and resistance to physical force, as well as mechanosensing mechanisms, was highlighted for the first time in the context of tuber bruising. We showcase the usefulness of genomic data from breeding programmes in identifying genomic regions whose association with the trait of interest merit further investigation. We demonstrate how confidence in these discoveries and their biological relevance can be increased by integrating results from transcriptomics analyses. The newly proposed visualisation provides a clear framework to summarise of both genomics and transcriptomics analyses, and places them in the context of previous knowledge on the trait of interest.

Project description:In potato breeding, morphological tuber traits are important selection targets to meet the demands of the fresh and processing markets. Understanding the genetic basis of tuber traits should guide selection and improve breeding efficiencies. However, this is challenging in potato due to the complexity of the traits and the polyploid nature of the potato genome. High-throughput affordable molecular markers and new software specific for polyploid species have the potential to unlock previously unattainable levels of understanding of the genetic basis of tuber traits in tetraploid potato. In this study, we genotyped a diversity panel of 214 advanced clones with the 22 K SNP potato array and phenotyped it in three field environments in Texas. We conducted a genome-wide association study using the GWASpoly software package to identify genomic regions associated with tuber morphological traits. Some of the QTLs discovered confirmed prior studies, whereas others were discovered for the first time. The main QTL for tuber shape was detected on chromosome 10 and explained 5.8% of the phenotypic variance. GWAS analysis of eye depth detected a significant QTL on chromosome 10 and explained 3.9% of the phenotypic variance. Another QTL peak for eye depth on chromosome 5 was located near the CDF1 gene, an important regulator of maturity in potato. Our study found that multiple QTLs govern russeting in potato. A major QTL for flesh color on chromosome 3 that explained 26% of the phenotypic variance likely represents the Y locus responsible for yellow flesh in potato tubers. Several QTLs were detected for purple skin color on chromosome 11. Furthermore, genomic estimated breeding values were obtained, which will aid in the early identification of superior parental clones that should increase the chances of producing progenies with higher frequencies of the desired tuber traits. These findings will contribute to a better understanding of the genetic basis of morphological traits in potato, as well as to identifying parents with the best breeding values to improve selection efficiency in our potato breeding program.

Dataset Information

Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids.

Publications

Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids.

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