Abstract
BackgroundWater buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited knowledge on buffalo embryonic development, especially during the preimplantation period. Assembly of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED).MethodsWe revealed transcriptomic profile of four stages (2-cell, 8-cell, Morula and Blastocyst) of PED via RNA-seq (Illumina HiSeq4000). Each stage comprised three biological replicates. The data were analyzed according to the basic RNA-seq analysis process. Ingenuity analysis of cell lineage control, especially transcription factor (TF) regulatory networks, was also performed.ResultsA total of 21,519 expressed genes and 67,298 transcripts were predicted from approximately 81.94 Gb of raw data. Analysis of transcriptome-wide expression, gene coexpression networks, and differentially expressed genes (DEGs) allowed for the characterization of gene-specific expression levels and relationships for each stage. The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo.
Highlights
Water buffalo (Bubalus bubalis) is a species of the Bubalus genus in the Bovidae family; these buffalo are primarily distributed in tropical and subtropical regions (Nanda & Nakao, 2003)
Studies concerning the reproduction of river buffalo have primarily focused on selection of optimal fertility through methods such as good nutrition condition and short-day fertility (Campanile, 2007; Campanile et al, 2010), with a goal of avoiding embryonic mortality, which is highly correlated withmaternal progesterone concentrations (Neglia et al, 2008)
Expression patterns, transcriptional regulators, and epigenomic reprogramming mechanisms have been revealed at representative stages of preimplantation embryo development (PED) in these species (Xie et al, 2010; Biase, Cao & Zhong, 2014; Graf et al, 2014; Fan et al, 2015; Guo et al, 2017), resulting in successive waves of signal regulators and gene regulatory networks being established in PED (Xie et al, 2010; Vassena et al, 2011; Zuo et al, 2016)
Summary
Water buffalo (Bubalus bubalis) is a species of the Bubalus genus in the Bovidae family; these buffalo are primarily distributed in tropical and subtropical regions (Nanda & Nakao, 2003). Of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED). The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo
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