Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array

Abstract

BackgroundCultivated chrysanthemum is an outcrossing hexaploid (2n = 6× = 54) with a disputed mode of inheritance. In this paper, we present a single nucleotide polymorphism (SNP) selection pipeline that was used to design an Affymetrix Axiom array with 183 k SNPs from RNA sequencing data (1). With this array, we genotyped four bi-parental populations (with sizes of 405, 53, 76 and 37 offspring plants respectively), and a cultivar panel of 63 genotypes. Further, we present a method for dosage scoring in hexaploids from signal intensities of the array based on mixture models (2) and validation of selection steps in the SNP selection pipeline (3). The resulting genotypic data is used to draw conclusions on the mode of inheritance in chrysanthemum (4), and to make an inference on allelic expression bias (5).ResultsWith use of the mixture model approach, we successfully called the dosage of 73,936 out of 183,130 SNPs (40.4%) that segregated in any of the bi-parental populations. To investigate the mode of inheritance, we analysed markers that segregated in the large bi-parental population (n = 405). Analysis of segregation of duplex x nulliplex SNPs resulted in evidence for genome-wide hexasomic inheritance. This evidence was substantiated by the absence of strong linkage between markers in repulsion, which indicated absence of full disomic inheritance. We present the success rate of SNP discovery out of RNA sequencing data as affected by different selection steps, among which SNP coverage over genotypes and use of different types of sequence read mapping software. Genomic dosage highly correlated with relative allele coverage from the RNA sequencing data, indicating that most alleles are expressed according to their genomic dosage.ConclusionsThe large population, genotyped with a very large number of markers, is a unique framework for extensive genetic analyses in hexaploid chrysanthemum. As starting point, we show conclusive evidence for genome-wide hexasomic inheritance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4003-0) contains supplementary material, which is available to authorized users.

Genetic mapping in polyploids

“…Lack of 1x0 markers on a homologue is possible if there is a high degree of inbreeding, the population is from a selfing, or if there is selection for a phenotype for which alleles have an additive effect. However, our experience in polyploid mapping to date has shown that low-dosage markers tend to be the most abundant marker type van Geest et al, 2017c). Nevertheless, we were not able to define one homologue on linkage group 4, even though all others each had 175 SNP markers or more.…”

“…Dosage scoring from array output was mainly performed as described by (van Geest et al, 2017c). Because genomic dosage was highly correlated with the number of reads per allele from our sequence data (van Geest et al, 2017c), we estimated dosage per SNP of the parents a-priori based on the sequence data, and used this information for SNP calling.…”

“…Genotyping was performed with a 183k Affymetrix SNP array, as described by (van Geest et al, 2017c). In short, the array was designed based on RNA-seq data of 13 cultivars, including both parents of the population.…”

“…Others have identified homologous chromosomes based on alignment to a reference genome (Shirasawa et al, 2017). Similar to sweet potato, chrysanthemum is an outcrossing hexaploid with polysomic inheritance (van Geest et al, 2017c). Pairing at meiosis is primarily through bivalents, but multivalents do occur (Roxas et al, 1995;Chen et al, 2009).…”

“…This has been to a large extent due to developments in high-density genotyping platforms for single nucleotide polymorphism (SNP) markers, which have found increasing application in polyploids. For example, high-density SNP arrays have been developed in potato (Felcher et al, 2012;Vos et al, 2015), rose , alfalfa (Li et al, 2014b) and chrysanthemum (van Geest et al, 2017c), enhancing the scope for genetic studies in these species.…”