Use of continuous genotypes for genomic prediction in sugarcane

Abstract

Genomic selection in sugarcane faces challenges due to limited genomic tools and high genomic complexity, particularly because of its high and variable ploidy. The classification of genotypes for single nucleotide polymorphisms (SNPs) becomes difficult due to the wide range of possible allele dosages. Previous genomic studies in sugarcane used pseudo‐diploid genotyping, grouping all heterozygotes into a single class. In this study, we investigate the use of continuous genotypes as a proxy for allele‐dosage in genomic prediction models. The hypothesis is that continuous genotypes could better reflect allele dosage at SNPs linked to mutations affecting target traits, resulting in phenotypic variation. The dataset included genotypes of 1318 clones at 58K SNP markers, with about 26K markers filtered using standard quality controls. Predictions for tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and fiber content (Fiber) were made using parametric, non‐parametric, and Bayesian methods. Continuous genotypes increased accuracy by 5%–7% for CCS and Fiber. The pseudo‐diploid parametrization performed better for TCH. Reproducing kernel Hilbert spaces model with Gaussian kernel and AK4 (arc‐cosine kernel with hidden layer 4) kernel outperformed other methods for TCH and CCS, suggesting that non‐additive effects might influence these traits. The prevalence of low‐dosage markers in the study may have limited the benefits of approximating allele‐dosage information with continuous genotypes in genomic prediction models. Continuous genotypes simplify genomic prediction in polyploid crops, allowing additional markers to be used without adhering to pseudo‐diploid inheritance. The approach can particularly benefit high ploidy species or emerging crops with unknown ploidy.

Sugarcane breeding: a fantastic past and promising future driven by technology and methods

“…The genome has different ploidy levels and allele dosages (Batista et al, 2021), and it has also been a huge challenge to appropriately read the sugarcane DNA and distinguish among the different genotypic classes, mainly those related to heterozygous individuals (Garcia et al, 2013). In this sense, the majority of genotypic data, obtained for sugarcane to date, does not consider its ploidy levels, allele dosages and, therefore, does not provide a reliable genetic information about its genome (Yadav et al, 2023). At the same time, the statistical approaches are not fully developed to take into account the genotypic data obtained from the complex context of sugarcane, including the methods for GWAS, GS, and other approaches related to MAS (Yadav et al, 2020;Batista et al, 2021;Mahadevaiah et al, 2021;Jackson et al, 2022).…”