FUNCTIONAL TRANSCRIPTOME ANALYSIS UNDER THERMAL STRESS THROUGH RNA SEQUENCING IN KARAN FRIES CATTLE
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Date
2022
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Publisher
ICAR-NDRI, KARNAL
Abstract
Animal geneticists and breeders have the impending challenge of enhancing the resilience
of Indian livestock to heat stress through better selection strategies. Climate change’s
impact on livestock is more intense in tropical countries like India where prolific dairy
cattle crossbreeds are more sensitive to heat stress. So, the present study was planned to
identify global transcriptome variations in Karan Fries cattle during heat stress conditions
in comparison to the thermo-neutral environment using RNA sequencing. Blood samples
were collected from two and three animals, as control and treatment, respectively from
two seasons and total RNA was isolated. Good quality RNA was used for library
preparation and whole transcriptome sequencing. Quality assessment of the raw reads was
carried out and trimming was done using Fastp. Further, good quality reads were mapped
into Bos taurus genome (ARS-UCD1.2) using HISAT2 package. The aligned reads were
quantified using feature count and further differentially expressed genes (DEGs) were
identified using the DESeq2 R package. A total of 2741 genes were found to be
dysregulated in heat stress on the basis of the minimum log2 fold change and false
discovery rate of 1 and 0.05, respectively, of which 468 were up-regulated. Functional
annotation and pathway analysis of these DEGs were done on the basis of Gene Ontology
(Biological process), KEGG and Reactome pathways using g: Profiler, ShinyGO v0.76,
and iDEP.951. The most over-represented pathways from upregulated genes were
neuronal and sensory organ development, collagen formation, MAPK and Rap 1 signaling
pathways, apoptosis, and oxidative stress. Similarly, mRNA processing, immune system,
B-cell receptor signaling pathway, ribosome, and Nonsense-mediated decay (NMD)
pathway were identified from downregulated genes. Further co-expression network
analysis revealed CHD4, RPS14, EIF4A3, HNRNPH1, DENND5A, EDEM1, HNRNPH1,
and MSN as top genes. So, the results of the present study indicated the susceptibility of
Karan Fries cattle to heat stress due to altered gene expression levels in pathways such as
neuron and sensory development, apoptosis, and oxidative stress. Further, a detailed study
on the upregulated pathways is suggested for better understanding of the systems biology
of Karan Fries cattle under heat stress.