Transcriptomics–genomics data integration and expression quantitative trait loci analyses in oocyte donors and embryo recipients for improving invitro production of dairy cattle embryos

Abstract

In this paper we first provide a brief review of main results from our previously published studies on genome-wide gene expression (transcriptomics) in donor and recipient cattle used in invitro production (IVP) of embryos and embryo transfer (ET). Then, we present novel results from applying integrative systems genomics and biological analyses where transcriptomics data are combined with genomic data in both donor and recipient cattle to map expression quantitative trait loci (eQTLs). The eQTLs are genetic markers that can regulate or control the expression of genes in the entire genome, via complex molecular mechanisms, and thus can act as a powerful tool for genomic and gene-assisted selection. We identified significant eQTLs potentially controlling the expression of 13 candidate genes for donor cow quality (IVP parameters; e.g. cyclin B1 (CCNB1), outer dense fiber of sperm tails 2 like (ODF2L)) and 19 candidate genes for recipient cows quality (endometrial receptivity; e.g. ER membrane protein complex subunit 9 (EMC9), mannosidase beta (MANBA), peptidase inhibitor 16 (PI16)). Annotation and colocation of detected eQTLs show that some of the eQTLs are in the same genomic regions previously reported as QTLs for reproduction-related traits. However, eQTLs and the candidate genes identified should be further validated in larger populations before implementation as genetic markers or used in genomic selection for improving IVP and ET performance.

Outstanding Gir oocyte donors: How does individual factor affect in vitro embryo production efficiency?

“…The identification of biomarkers associated to increased performance in oocyte donors would be a major step for IVP efficiency improvement and has been the focus of many studies (Kadarmideen & Mazzoni, 2019; Kussano et al, 2016; Labrecque & Sirard, 2014; Mazzoni et al, 2017). Oocyte developmental capacity is affected by several factors, such as chromosomal aneuploidies (Mikwar et al, 2020; Patrizio et al, 2007), mitochondrial dysfunction (Cimadomo et al, 2018), extracellular vesicles lipid profile (da Silveira et al, 2021), and follicular fluid contents such as glucose, pyruvate, cholesterol, and oestradiol (Alves et al, 2019).…”

“…Differences between oocytes showing distinct performance have been described regarding RNA content and early atresia (Mazzoni et al, 2017). An interesting study associated genomic eQTLs to IVP performance (Kadarmideen & Mazzoni, 2019), but to date, no application is available in genomic selection approaches, and broader studies confirming candidate genes and superior donor performance are required.…”

Restraint stress of female mice during oocyte development facilitates oocyte postovulatory aging

“…This study evidenced that FRSOD downregulated expression of cyclin B1 ( Ccnb1 ) and zygote arrest 1 ( Zar1 ) genes. The Ccnb1 gene has been identified as in vitro embryo production (IVP) parameter of donor cow quality [ 35 ], and increased expression of Ccnb1 is associated with improved oocyte maturation in vitro and post-maturation development [ 36 , 37 ]. In contrast, a decrease in Ccnb1 expression has been observed in aged porcine oocytes [ 38 , 39 ].…”

Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows

“…Expression QTL studies have been reported for several complex traits; however, only a few of them have focused on fertility in cattle. Kadarmideen and Mazzoni [19] reported eQTLs affecting genes in the bovine follicular cells and the endometrium of dairy cows. The eQTL-modulated genes were associated with the quality of in vitro-produced embryos and endometrial receptivity [19].…”