SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids

Abstract

Many plant species of great economic value (e.g., potato, wheat, cotton, and sugarcane) are polyploids. Despite the essential roles of autopolyploid plants in human activities, our genetic understanding of these species is still poor. Recent progress in instrumentation and biochemical manipulation has led to the accumulation of an incredible amount of genomic data. In this study, we demonstrate for the first time a successful genetic analysis in a highly polyploid genome (sugarcane) by the quantitative analysis of single-nucleotide polymorphism (SNP) allelic dosage and the application of a new data analysis framework. This study provides a better understanding of autopolyploid genomic structure and is a sound basis for genetic studies. The proposed methods can be employed to analyse the genome of any autopolyploid and will permit the future development of high-quality genetic maps to assist in the assembly of reference genome sequences for polyploid species.

Microsatellites and the Polyploid Guarana Plant: Diversity under a Sea of Alleles

“…Some work using the areas below the peaks can be useful to accomplish this type of analysis, which depends on information about the ancestors as demonstrated for hemisexual and polyploid Rosa L. Sect. Caninae D.C. [37] or on the assessment of information about the different dosages of the same alleles in genitors and the resultant hybrid progenies by other means [16]. Two tendencies were observed regarding the number of alleles in each locus: two alleles and multiples of two (Figure 3(a)) or three alleles and multiples of three (Figure 3(b)) per plant.…”

“…The advent of the polyploidization is thought to be recent [3] and extremely impacting, taking into account that additional seven species in the genus Paullinia have all 2n = 24 chromosomes [11] and genera on tribe Paullinieae have basal numbers of chromosomes (x) of 7, 10, 11, 12 or 14 [12]. Among complex polyploids, breeding assisted by co-dominant markers has been used, for instance, in sugarcane and wheat, but experimentation has been greatly improved by the identification of the ancestors and/or the knowledge about the contributions of different genomic complements for cultivated genotypes, by the existence of highly saturated linkage maps and, by the access to whole-genome data that were recently made available [13]- [16].…”

Probabilistic Multilocus Haplotype Reconstruction in Outcrossing Tetraploids

“…This is so because each score (gel band pattern) may correspond to multiple allelic dosages, and some alleles may not be revealed in a gel band pattern (the null alleles). However, new genotyping technologies, e.g., the Illumina Infinium platform and sequencing-based methods such as genotyping-by-sequencing, allow accurate estimation of the dosage of high-density singlenucleotide polymorphisms (SNPs) throughout the genome (Voorrips et al 2011;Garcia et al 2013;Hackett et al 2013;Li et al 2014). We focus on analyzing the increasingly available SNP dosage data.…”

Analysis of genes controlling biomass traits in the genome of sugarcane (Saccharum spp. hybrids)

“…These common markers have been applied for genetic studies, such as diversity, mapping, quantitative trait loci (QTL) and synteny definition; however, these systems have been developed mostly for well-established diploid species and are less effective for polyploidy plants (Garcia et al, 2013). Markers like AFLP, SSR and RFLP are unable to estimate the number of allelic copies and level of polyploidy in such complicated genomes as potato, strawberry and sugarcane (Garcia et al, 2013).…”

“…These common markers have been applied for genetic studies, such as diversity, mapping, quantitative trait loci (QTL) and synteny definition; however, these systems have been developed mostly for well-established diploid species and are less effective for polyploidy plants (Garcia et al, 2013). Markers like AFLP, SSR and RFLP are unable to estimate the number of allelic copies and level of polyploidy in such complicated genomes as potato, strawberry and sugarcane (Garcia et al, 2013). More recently, the use of SNPs markers, which are distributed at high density across the genome for complex genomes, can allow the estimation of the number of allelic copies and the ploidy level of genomes (Zhu et al, 2008, Hall et al, 2010.…”