Identification of SNPs associated with residual feed intake from the muscle of Litopenaeus vannamei using bulk segregant RNA-seq

Feed efficiency is one of the most important economic traits of Litopenaeus vannamei. Molecular breeding such as marker-assisted selection or genomic selection is becoming a promising method for genetic improvement of this trait, considering the difficulty in collecting individual feed efficiency data. In this study, we used residual feed intake (RFI) as the measure of feed efficiency, aiming to develop RFI-associated single nucleotide polymorphism (SNP) markers by an integrated method of pooled RNA-seq along with bulked segregant analysis. Based on a population consisted of multiple families, specifically, we constructed a high-efficiency bulk and a low-efficiency bulk for pooled RNA-seq of muscle samples. >200,000 SNPs were called from pooled RNA-seq data of each bulk, with 123,219 SNPs being shared. Among them, 11,026 SNPs showed significant allelic imbalance between bulks (adjusted P value <0.05). Differential expression analysis between bulks identified 4231 differentially expressed unigenes (DEGs), and 568 of the 11,026 significant SNPs were located in the DEGs. As shown by functional analysis, many DEGs harboring significant SNPs were involved in some basic metabolic processes and important biological pathways. The results of this study will provide some new resources for implementing molecular breeding of feed efficiency in L. vannamei and some new knowledge for elucidating the molecular mechanisms underlying this trait.