PhD thesis
Assessment of genetic diversity in local breeds



Publication Details
Authors:
Addo, S.
Publication year:
2020

Abstract

The present study aimed at assessing genetic diversity in selected local
livestock breeds in Northern Germany, and furthermore, examining some
of the indices used in describing diversity in populations. The study
begun with an assessment of genetic diversity in the German Angler (RVA)
and Red-and-white dual-purpose (RDN) cattle breeds. Analyses of the RVA
and RDN pedigrees, consisting of 93,078 and 184,358 records,
respectively, revealed a number of Red Holstein (RH) sires that were
influential in these breeds. Even when the pedigrees were combined and
analysed, four RH individuals alone had a cumulative marginal genetic
contribution of over 9% and were at the top of the list. The results
also revealed low levels of classical inbreeding for RVA (1.39%) and RDN
(0.41%) with moderately high effective population size (Ne) estimates
of 156 and 170, respectively. However, using purging-based approaches
such as the ancestral history coefficient, the levels of inbreeding rose
slightly and the corresponding Ne values were reduced to 50 and 53 for
RVA and RDN, respectively. Additionally, estimates of effective number
of founders and ancestors indicated an unbalanced genetic contribution
in the founder populations, where some individuals had many more
offspring than others. Notably, the quality of pedigrees used for the
analyses was low with mean number of complete generation equivalent of
5.59 and 2.7 for RVA and RDN, respectively.

A follow-up study was
performed to assess genetic diversity at the genome level, investigate
gene flow events, and to shed light on the usefulness of runs of
homozygosity (ROH) as a means to estimate inbreeding. The Illumina
BovineSNP50 BeadChip information on RVA, RDN, RH and 11 outgroup breeds
were made available for the different analyses. For RVA, RDN and RH,
observed heterozygosity (Ho) estimates were 0.374, 0.356 and 0.363, and
the estimates of ROH-based genomic inbreeding (FROH) were 0.021, 0.045
and 0.053, respectively. Linkage disequilibrium-based Ne estimate for
five generation ago was highest in RVA (113) and lowest in RDN (67).
Population structure analyses found a high level of admixture between
RVA and RH than between RDN and RH, and for the first time,
connectedness between RVA and Norwegian Red cattle was uncovered.
Furthermore, the investigation showed moderate to high positive
correlations between FROH and pedigree-based inbreeding (FPED), and even
when FPED was zero, traces of inbreeding were detected by the ROH-based
measure.

A third investigation was launched to analyse genetic
diversity in the German White-headed mutton (GWM) sheep using both
pedigree (N = 19,000) and genotype (N = 46) data. Additionally,
different measures of ROH inbreeding were investigated. From the
pedigree analysis, average generation interval was 3.24. Estimate of
average FPED and Ne for the whole population were 0.01 and 132,
respectively, and differed from the estimates computed for a
subpopulation of animal born in the last four years of pedigree data,
which were 0.04 and 99, respectively. Only 59 ancestors explained 50% of
variation in the breed. Genome-based Ho and Ne were 0.389 and around
50, respectively. Based on 16,852 single nucleotide polymorphism (SNP)
markers, three separate population structure analyses pointed to the
flow of genes from other breeds, especially Berrichone du Cher to GWM.
To investigate different ROH inbreeding measures, FROH was calculated
based on either ROH length or on the number of SNPs in ROH. Inbreeding
estimates derived from the two measures were 0.045 and 0.046 and highly
correlated (rp = 0.99). Furthermore, total FROH was effectively
partitioned into values for specific chromosomes.

In a final
investigation, the outcomes of two ROH detection software including
PLINK and RZOOROH were compared to address the lack of consensus on the
choice of parameter thresholds in calling ROH across studies. With array
data on 52 Mangalitza pigs and whole genome sequence (WGS) data on six
Schleswig Draught horses, the analyses showed comparable estimates of
FROH across different models and detection software, although the number
of ROH detected varied greatly. In the horse, an array-like dataset
consisting of 26,932 SNPs was compared to the WGS data and the latter
proved to be more efficient in detecting small size ROH.



Authors/Editors

Last updated on 2021-13-07 at 12:08