Intra- and Interspecies RNA-Seq Based Variants in the Lactation Process of Ruminants

SIMPLE SUMMARY: RNA-Seq data provide a new chance to find transcriptome variants. We used RNA-Seq data to detect the variants involved in the three different stages (before peak = BP, peak = P, and after peak = AP) of the lactation process in two sheep and two cow breeds. Furthermore, several KEGG pathways and enriched gene ontologies associated with immune system activation and the metabolic process were demonstrated by analyzing the functional enrichment of the genes that were affected. Findings of the present study also suggest that milk yield and milk composition in sheep and cow breeds at different stages of lactation can be related to known and novel variants of specific genes related to milk fat and protein synthesis. The results pave the way for further studies on determining the genetic basis of milk production. The novel variants discovered here using RNA-seq data may be central and crucial when it comes time to design new SNP chips used as guides for selective breeding programs. ABSTRACT: The RNA-Seq data provides new opportunities for the detection of transcriptome variants’ single nucleotide polymorphisms (SNPs) in various species and tissues. Herein, milk samples from two sheep breeds and two cow breeds were utilized to characterize the genetic variation in the coding regions in three stages (before-peak (BP), peak (P), and after-peak (AP)) of the lactation process. In sheep breeds Assaf and Churra, 100,462 and 97,768, 65,996 and 62,161, and 78,656 and 39,245 variants were observed for BP, P, and AP lactation stages, respectively. The number of specific variants was 59,798 and 76,419, 11,483 and 49,210, and 104,033 and 320,817 in cow breeds Jersy and Kashmiri, respectively, for BP, P, and AP stages. Via the transcriptome analysis of variation in regions containing QTL for fat, protein percentages, and milk yield, we detected a number of pathways and genes harboring mutations that could influence milk production attributes. Many SNPs detected here can be regarded as appropriate markers for custom SNP arrays or genotyping platforms to conduct association analyses among commercial populations. The results of this study offer new insights into milk production genetic mechanisms in cow and sheep breeds, which can contribute to designing suitable breeding systems for optimal milk production.