GenoTriplo: A SNP genotype calling method for triploids
Authors: Julien Roche , Mathieu Besson , François Allal , Pierrick Haffray , Pierre Patrice , Marc Vandeputte , Florence Phocas 
Published: March 2024

Triploidy is very useful in both aquaculture and some cultivated plants as the induced sterility helps to enhance growth and product quality, as well as acting as a barrier against the contamination of wild populations by escapees. To use genetic information from triploids for academic or breeding purposes, an efficient and robust method to genotype triploids is needed. We developed such a method for genotype calling from SNP arrays, and we implemented it in the R package named GenoTriplo. Our method requires no prior information on cluster positions and remains unaffected by shifted luminescence signals. The method relies on starting the clustering algorithm with an initial higher number of groups than expected from the ploidy level of the samples, followed by merging groups that are too close to each other to be considered as distinct genotypes. Accurate classification of SNPs is achieved through multiple thresholds of quality controls. We compared the performance of GenoTriplo with that of fitPoly, the only published method for triploid SNP genotyping with a free software access. This was assessed by comparing the genotypes generated by both methods for a dataset of 1232 triploid rainbow trout genotyped for 38,033 SNPs. The two methods were consistent for 89% of the genotypes, but for 26% of the SNPs, they exhibited a discrepancy in the number of different genotypes identified. For these SNPs, GenoTriplo had >95% concordance with fitPoly when fitPoly genotyped better. On the contrary, when GenoTriplo genotyped better, fitPoly had less than 50% concordance with GenoTriplo. GenoTriplo was more robust with less genotyping errors. It is also efficient at identifying low-frequency genotypes in the sample set. Finally, we assessed parentage assignment based on GenoTriplo genotyping and observed significant differences in mismatch rates between the best and second-best couples, indicating high confidence in the results. GenoTriplo could also be used to genotype diploids as well as individuals with higher ploidy level by adjusting a few input parameters.

Author Summary

To cultivate plants, fish and shellfish more profitable for both farmers and consumers, one can utilize individuals one can utilize individuals with three chromosome sets instead of the two found in fertile populations that are diploids. These individuals, called triploids, are generally sterile and then often exhibit higher growth and quality of products, such as seedless fruits or better flesh quality for fish and shellfish. To be able to improve performances of the sterile triploids by selective breeding, it is important to know the versions of the genes present in the three chromosome sets of triploids. Until now, few methods existed to identify these three versions, and none have been demonstrated as sufficiently effective. It is the reason why we developed the GenoTriplo software. We demonstrate in this paper the possibility to accurately genotype triploids, as well as how it can be used to reconstruct pedigree information of triploid progeny. Ultimately, we expect that it can help select for reproduction the parents that have the best triploid progeny for the traits of interest such as growth, vigour or product quality.