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bioRxiv · 10.1101/2024.09.15.613137

PREDICTION OF SINGLE NUCLEOTIDE VARIANT EFFECTS RELATED TO SEX DETERMINATION IN Carica papaya (Caricaceae)

Spelta, J. V. V. B.·Sakamoto, T.
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Abstract

Papaya (Carica papaya) produces one of the most consumed fruits worldwide, holding great economic importance, especially in tropical regions. Papaya trade mainly involves gynodioecious cultivars with a ratio of 1:1 or 2:1 of hermaphrodites to females. For commercial reasons and also inherent to cultivation, it is preferable to have as many hermaphrodites as possible. In general, it is still not possible to produce only hermaphrodite seeds, so the sex of the plant is usually identified by conventional methods after the first flowering of the papaya plant. This occurs about 4-6 months after planting the seedling, with the females typically being discarded at the end. To avoid wasting resources and achieve higher harvest yields, producers may also resort to molecular methods using sex markers. However, this alternative also has its limitations, including high costs. Given these challenges, many researchers have focused on studying the process of sex determination in C. papaya, but the factors directly influencing this process remain unknown. The elucidation of this mechanism is not only of great agronomic interest, but also represents a significant opportunity for C. papaya to establish itself as a model organism for studying sexual chromosomes of recent evolutionary origin. Therefore, in this work, a bioinformatics strategy was used to address the topic. A genotype-phenotype association study was conducted to find possible genetic factors involved in sex determination using resequencing data from 36 individuals (24 male papaya plants and 12 hermaphrodites) obtained from public databases. The association study was preceded by a variant calling performed with BCFTOOLS, which found 75,607 variants, leaving 37,027 after filtering. Association studies were then carried out using the PLINK program with the filtered variants, and among these, 251 of the most statistically significant variants were applied to the SnpEff program for variant annotation, returning 449 effects, including 402 with a modifier level of impact, 22 with a low impact, and 25 with a moderate effect. Inferences and gene annotations were also performed using the Augustus software and BLASTP alignments with the gene sequences that had moderate effects predicted by SnpEff, as well as de novo genome assemblies of a male sample and its alignment with the hermaphrodite sex-determining region. These results were recorded and compared with previous studies in the literature. This allowed for the conclusion that the specific results obtained serve as a starting point for more robust studies to understand the molecular mechanisms of sex determination in C. papaya.

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Spelta, J. V. V. B., Sakamoto, T.. 2024-09-19. PREDICTION OF SINGLE NUCLEOTIDE VARIANT EFFECTS RELATED TO SEX DETERMINATION IN Carica papaya (Caricaceae). https://doi.org/10.1101/2024.09.15.613137

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