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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 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. [ABSTRACT FROM AUTHOR]

Unraveling the evolutionary mechanisms and consequences of hybridization is a major concern in biology. Many studies have documented the interplay between recombination and selection in modulating the genomic landscape of introgression, but few have considered how associations with phenotype may affect this landscape. Here, we use the European seabass (Dicentrarchus labrax), a key species in marine aquaculture that undergoes natural hybridization, to determine how selection on phenotype modulates the introgression landscape between Atlantic and Mediterranean lineages. We use a high-density single nucleotide polymorphism array to assess individual local ancestry along the genome and improve the mapping of muscle fat content, a polygenic trait that is divergent between lineages. Taking into account variation in recombination rates, we reveal a purging of Atlantic ancestry in the admixed Mediterranean populations. While Atlantic individuals had higher muscle fat content, we observed that genomic regions associated with this trait in Mediterranean populations displayed reduced introgression of Atlantic ancestry. These results emphasize how selection against maladapted alleles shapes the genomic landscape of introgression. [ABSTRACT FROM AUTHOR]

In aquaculture, sterile triploids are commonly used for production as sterility gives them potential gains in growth, yields, and quality. However, they cannot be reproduced, and DNA parentage assignment to their diploid or tetraploid parents is required to estimate breeding values for triploid phenotypes. No publicly available software has the ability to assign triploids to their parents. Here, we updated the R package APIS to support triploids induced from diploid parents. First, we created new exclusion and likelihood tables that account for the double allelic contribution of the dam and the recombination that can occur during female meiosis. As the effective recombination rate of each marker with the centromere is usually unknown, we set it at 0.5 and found that this value maximizes the assignment rate even for markers with high or low recombination rates. The number of markers needed for a high true assignment rate did not strongly depend on the proportion of missing parental genotypes. The assignment power was however affected by the quality of the markers (minor allele frequency, call rate). Altogether, 96–192 SNPs were required to have a high parentage assignment rate in a real rainbow trout dataset of 1,232 triploid progenies from 288 parents. The likelihood approach was more efficient than exclusion when the power of the marker set was limiting. When more markers were used, exclusion was more advantageous, with sensitivity reaching unity, very low false discovery rate (<0.01), and excellent specificity (0.96–0.99). Thus, APIS provides an efficient solution to assign triploids to their diploid parents. [ABSTRACT FROM AUTHOR]