RNA-Seq Analysis of Heterosis Using Chicken Hybrids and Inbred Parental Lines

The superior performance of hybrids to parents, termed heterosis, has been utilized in animal and plant breeding programs for more than a century, but the understanding of the genetic basis and molecular mechanisms of heterosis remains inadequate and requires further study. RNA-seq provides a novel way to investigate the phenomenon of heterosis at the genome-wide level, because gene expression can be considered as an intermediate phenotype that conveys the genetic information to observable phenotypes. We compared embryonic gene expression between the chicken hybrids and their inbred parental lines using RNA-seq in order to understand the gene expression basis of heterosis for embryonic weight in chickens. Two genetically distinct and highly inbred chicken lines, Fayoumi and Leghorn, were crossed reciprocally to obtain F1 hybrid fertile eggs. The polyadenylated RNA of brain and liver from Day 12 embryos was converted to cDNA and sequenced on an Illumina HiSeq sequencer. The resultant reads were mapped to the reference genome assembly Gallus gallus 5.0 and the differentially expressed genes were identified, pairwise, among the hybrids and the parental lines. Preliminary results showed the majority of the differentially expressed genes presented a dominant expression pattern. Additive and overdominant patterns were second and third in frequency, respectively. Future analysis will focus on categorizing of the gene expression patterns in hybrids compared to parental lines and the functional relevance of genes in each category.