Genome-wide differential mRNA expression profiles in follicles of two breeds and at two stages of estrus cycle of gilts

Abstract

Estrus expression by gilts and sows is hereditable and important for heat detection. To better understand the molecular biological mechanisms of estrus expression in gilts, the mRNA expression profiles of follicular tissue from Large White gilts in diestrus (LD, n = 3) and estrus (LE, n = 3), and Chinese indigenous Mi gilts in diestrus (MD, n = 2) and estrus (ME, n = 3) were investigated using RNA sequencing. We detected 122,804-335,295 SNPs, 6,140-14,947 InDel and 12 types of AS events (39.57% TSS, 34.90% TTS) in 11 samples. A total of 2,838 differentially expressed genes (DEGs) were found in LD vs MD, LE vs ME, LE vs LD, or ME vs MD comparisons. Two DEGs (ACP5 and PIGS) were observed in all comparisons. Two new genes (ENSSSCG00000028235 and ENSSSCG00000021903) were exclusively expressed in Mi and Large White gilts, respectively. Bioinformatics analyses indicate that these DEGs are involved in single-organism process, catalytic activity, cell adhesion and enriched in ECM-receptor interaction, olfactory transduction, ovarian steroidogenesis, steroid biosynthesis and CAMs signaling pathways. These results of RNA-Seq have provided important information for screening the key functional genes or molecular markers of estrus expression in gilts.

Transcriptomic and computational analysis identified LPA metabolism, KLHL14 and KCNE3 as novel regulators of Epithelial-Mesenchymal Transition

“…This depicted the transcriptional landscapes of mAEC and eAEC, detailing both common (15,708) and populations-specific genes (481 genes in mAEC and 658 in eAEC). Retaining only those genes with confidence (q-value ≤ 0.05) and exhibiting a fold change higher than |log2fold| ≥ 1 33 (Fig. 2C), a reliable subset of 1,248 differentially expressed genes (DEGs) was identified.…”

Changes in Ovary Transcriptome and Alternative splicing at estrus from Xiang pigs with Large and Small Litter Size

“…Reddening and swelling of the vulva were measured visually. The expression of estrus was scored according to a standard scoring system [14, 27]. In this study, we randomly chose six Xiang gilts from the XL (n = 3; TNB mean = 16.16) and XS (n = 3; TNB mean = 6.78) groups to perform the genome-wide analysis of transcriptomes by RNA-seq.…”

“…To find the quantitative trait loci (QTL) and causal genes for these traits, several studies for linkages [11-13] and candidate genes ([14-17] have been conducted by using modern molecular information. Many of the major genes involved in the prolificacy of pig, such as ESR , FSHB , RBP4 , PRLR , MTNR1A , OPN , BMP families, and GDF9 genes have been characterized [18, 19].…”

“…Genetic studies have revealed an increasing number of associated QTLs and candidate genes involved in pig litter size [20-22]. Recently, several studies of the transcriptome for reproductive organs reveals differentially expressed genes affecting reproduction and candidate genes for litter size in European pig breeds [9, 15, 17] and Chinese indigenous pig breeds [14, 23]. Although QTLs and candidate genes have been reported to affect the litter size in many pig breeds, however, the studies were only focused on specific species or breeds and the findings cannot elucidate the marked differences of the reproductive traits between Asian and European pig breeds and the variations of litter size between pigs.…”

Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

“…RNA-Seq has been applied to study ovarian follicle development of several livestock animals, such as goat [ 9 , 10 ], sheep [ 11 , 12 ], and cattle [ 13 ]. The use of the RNA-Seq technique identified many DEGs that were associated with pig fecundity [ 14 – 17 ]. A total of 11 genes identified in ovaries might be related to litter size in Yorkshire pigs [ 14 ].…”