# Transcriptomic Profiling Provides Insight into the Molecular Basis of Heterosis in Philippine-Reared Bombyx mori Hybrids

## TL;DR

This study explores the genetic basis of hybrid vigor in Philippine silkworms to improve breeding and silk production.

## Contribution

The study identifies genes linked to hybrid vigor in Philippine Bombyx mori hybrids using transcriptomic profiling.

## Key findings

- Reference-based transcriptome assembly outperformed de novo assembly in quality metrics.
- Hybrid silkworms showed differential expression of genes related to stress resistance and silk production.
- Heat shock proteins and antimicrobial peptides were identified as potential molecular markers for breeding.

## Abstract

Hybridization among Philippine-reared Bombyx mori strains is a common practice locally and is aimed at producing hybrids that exhibit improved silkworm traits and hence enhanced performance due to the phenomenon of heterosis. Despite the observed improvements in these hybrids, the underlying molecular mechanisms responsible for the enhanced traits remain largely unexplored. This study seeks to address this knowledge gap through sequencing, assembly, and annotation of the transcriptomes of parental and hybrid B. mori strains reared in the Philippines. Differentially expressed genes (DEGs) were also identified to find genes associated with desirable traits, including disease resistance, tolerance to extreme temperatures, and high silk production. The identification of these genes holds significant potential, as they may serve as molecular markers for silkworm core germplasm selection and marker-assisted breeding, thereby increasing the efficiency of breeding programs aimed at improving strain performance.

In the Philippines, Bombyx mori parental strains Lat21 and B221 are crossed to yield NC144 and CN144, which demonstrate hybrid vigor. The molecular basis of the observed vigor in the hybrids is warranted, as it may assist in improving local sericulture programs. This study, therefore, aims to investigate the basis of hybrid vigor and generate molecular resources through whole-silkworm larvae transcriptome sequencing, assembly, and analysis. Differential gene expression was also conducted among the parental strains and hybrids. Assembly of the pre-processed reads was also performed using de novo and reference-based protocols. As expected, the reference-based assembly was better than de novo, based on E90N50, N50, and BUSCO assembly completeness metrics. The Analysis of the differentially expressed genes (DEGs) revealed 202 upregulated and 182 downregulated genes in the hybrids (with the parents as the reference) and 66 upregulated and 753 downregulated genes in NC144 (with CN144 as the reference). Among these were genes encoding heat shock proteins and antimicrobial peptides, which may serve as markers for marker-assisted breeding. The genes were further validated using quantitative real-time PCR. Moreover, the inducible nature of these genes under stressors like extreme temperature and bacterial exposure suggests their potential as diagnostic tools for stress assessment.