South African communal indigenous goats

Indigenous goats form the majority of populations in smallholder; low
input, low output production systems and are considered an important
genetic resource due to their adaptability to different production
environments and support communal farming. Effective population size (Ne),
inbreeding levels, and the runs of homozygosity (ROHs) are effective tools
for exploring the genetic diversity and understanding the demographic
history in efforts to support breeding strategies to use and conserve
genetic resources. Across populations, the current Ne of Gauteng was the
lowest at 371 animals, while the historical Ne across populations suggests
that the ancestor Ne has decreased by 53.86%, 44.58%, 42.16% and
41.16% in Free State (FS), North West (NW), Limpopo (LP) and Gauteng (GP),
respectively, over the last 971 generations. Genomic inbreeding levels
related to ancient kinship (FROH >5Mb) was highest in FS
(0.08±0.09) and lowest for Eastern Cape (EC) (0.02±0.02). A total of 871
ROH island regions which include important environmental adaptation and
hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR and
MAPK3 were identified (occurring in over 20% of the samples) in FS (n =
37), GP (n = 42), NW (n = 2) populations only. The mean length of ROH
across populations was 7.76Mb and ranged from 1.61Mb KwaZulu-Natal (KZN)
to 98.05Mb (GP and NW). Distribution of ROH according to their size showed
that the majority (n = 1949) of the detected ROH were >5Mb in
length than the other categories. Assuming two hypothetical ancestral
populations, the population from KZN and LP are revealed, supporting PC 1.
The genomes of KZN and LP shared an origin but have substantial admixture
from the EC and NW populations. The findings revealed that the occurrence
of high Ne and autozygosity varied largely across breeds in communal
indigenous goat populations at recent and ancient events when a
genome-wide Single nucleotide polymorphism (SNP) marker was used. The use
of Illumina goat SNP50K BeadChip shows that there was a migration route of
communal indigenous goat populations from the northern part (LP) of South
Africa to the eastern areas of the KZN, that confirmed their historical
relatedness and which coincide with the migration periods of the Bantu
nation.