Exploring the molecular basis of dairy production and viability traits in murciano-granadina goats with genomic, metagenomic and transcriptomic approaches

Abstract

In this thesis, we aimed to investigate the genetic basis of milk and morphological traits in Murciano-Granadina goats as well as to explore the microbial composition of several types of caprine cheeses. Moreover, we wanted to assess the consequences of inbreeding on dairy performance and to study the molecular basis of traits related with the biological viability of goats. In study 1, we have identified several genetic determinants of milk yield and composition traits in Murciano-Granadina goats with records for three lactations by performing three independent GWAS (one for each lactation) and a longitudinal GWAS. Both approaches consistently revealed a genome-wide significant QTL for protein percentage on a chromosome 6 (74.8;94.6 Mb) region which harbours the four casein genes. Another QTL on chromosome 2 (129.77;131.01 Mb) for lactose percentage was also consistently detected. More QTL were identified in the longitudinal GWAS than in the three independent GWAS, possibly because the former has more statistical power than the latter. In study 2, we also used a GWAS approach to identify genomic regions associated with the variation of morphological traits in Murciano-Granadina goats. In this analysis, few significant associations were found and positional coincidence with morphology QTL detected in other breeds was low. These results are compatible with a highly polygenic determinism of morphological traits in goats. Since dairy production in goats is focused to the cheesemaking and the technological and organoleptic properties of this food are largely determined by its microbiota, in study 3, we characterised the microbiota of six different goat cheeses by sequencing hyper-variable regions of the bacterial 16S rRNA gene. We have identified lactic acid bacteria as the predominant microbial community in all six cheeses. Besides, we detected an abundance of psychrophilic bacteria, which are common post-pasteurisation contaminants of milk, in fresh cheeses. Regarding viability traits, in study 4, we detected low levels of inbreeding in the Murciano-Granadina population under study (FROH = 0.053±0.04). Despite this, a significant inbreeding depression on the logarithm of the somatic cell score (lnSCC), an important trait for udder health and milk quality, was detected and its determinants were finely mapped to a few chromosome 8 and 25 regions containing immunity genes. To ascertain genomic regions harbouring potentially harmful mutations (that are not expected to show a Mendelian segregation in the offspring of carrier individuals), in study 5 we carried out a scan to detected transmission ratio distortion (TRD) in Murciano-Granadina goats at a genome-wide scale. From the 36 SNPs displaying significant TRD, 25 had low GenTrain scores (< 0.8) indicating poor assignment of the genotypes. This result implies that most of the TRD signals detected by us are artifacts attributable to defective genotyping and stress the importance of filtering SNPs according to their GenTrain scores when carrying out TRD scans. As maternal care has an important influence on offspring viability, in study 6, we characterised the mRNA expression profiles of 12 brain tissues in 7 goats, of which 3 were 1 month-pregnant. Principal component analysis of the data revealed that most tissues tend to cluster according to their neural vesicle of origin, suggesting that embryonic development leaves a durable footprint that affects gene expression in the adult goat. Exceptions to this trend were cerebellum and glandular tissues, possibly because of their highly specialised functions. Important gene expression changes associated with 1-month gestation were observed in the adenohypophysis, frontal neocortex, hippocampus, pineal gland, pons and particularly in the olfactory bulb. Many of the genes differentially expressed in the olfactory bulb are related to human behavior, and there is evidence that this anatomical structure has a key role in the development of maternal care.