Linkage Disequilibrium, Haplotype Block Structures, Effective Population Size and Genome-Wide Signatures of Selection of Two Conservation Herds of the South African Nguni Cattle

Abstract

The Nguni cattle of South Africa are a Sanga breed, characterized by many eco-types and research populations that have been established in an effort to conserve the diversity within the breed. The aim of this study was to investigate the overall genetic diversity as well as similarities and differences within and between two conservation herds of the South African Nguni Cattle. Mean LD (r2) estimates were 0.413 ± 0.219 for Bartlow Combine and 0.402 ± 0.209 for Kokstad. Genome-wide average LD (r2) decreased with increasing genetic marker distance for both populations from an average of 0.76 ± 0.28 and 0.77 ± 0.27 at 0–1 kb bin to 0.31 ± 0.13 and 0.32 ± 0.13 at 900–1000 kb bin in Bartlow Combine and Kokstad populations, respectively. Variation in LD levels across autosomes was observed in both populations. The results showed higher levels of LD than previously reported in Nguni field populations and other South African breeds, especially at shorter marker distances of less than 20 kb. A total number of 77,305 and 66,237 haplotype blocks covering a total of 1570.09 Mb (61.99% genome coverage) and 1367.42 Mb (53.96% genome coverage) were detected in Bartlow Combine and Kokstad populations, respectively. A total of 18,449 haploblocks were shared between the two populations while 58,856 and 47,788 haploblocks were unique to Bartlow Combine and Kokstad populations, respectively. Effective population size (Ne) results demonstrated a rapid decrease in Ne across generations for both Bartlow Combine and Kokstad conservation herds. Two complementary methods, integrated haplotype score (iHS) and Extend Haplotype Homozygosity Test (XP-EHH), were implemented in this study to detect the selection signatures in the two herds. A total of 553 and 166 selected regions were identified in Bartlow Combine and Kokstad populations, respectively. DAVID and GO terms analysis of the regions under selection reported genes/QTLs associated with fertility, carcass weight, coat colour, immune response, and eye area pigmentation. Some genes, such as HCAR1, GNAI1, PIK3R3, WNT3, RAB5A, BOLA-N (Class IB MHC Antigen QA-2-Related), BOLA (Class IB MHC Antigen QA-2-Related), and Rab-8B, etc., were found in regions under selection in this study. Overall, the study implied reduced genetic diversity in the two herds calling for corrective measures to maintain the diversity of the South African Nguni cattle. This study presented a comprehensive analysis of the genomic architecture of South African Nguni cattle populations, providing essential genetic information of utility in the management of conservation flocks.

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America

“…As expected, the N e in the studied commercial and Creole populations declined over generations. The N e estimation in Latin American Creole cattle is scarce; however, this parameter was reported for several indigenous and highly selected commercial cattle breeds, showing similar decay of N e over generations (Biegelmeyer et al., 2016; Dlamini et al., 2022; Garcia et al., 2023; Jin et al., 2022; Sargolzaei et al., 2008; Strucken et al., 2021; Sudrajad et al., 2016; Xu, Zhu, et al., 2019). Creole populations had an accelerated decline and presented lower values, consisting of a few individuals compared with dozens of animals for worldwide distributed breeds (Sargolzaei et al., 2008; Biegelmeyer et al., 2016; Campos et al., 2022; present work).…”

“…The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction (FAO, 2007). Several countries, such as Argentina, Bolivia and Brazil, have established conservation plans to preserve Creole populations (da Silva Mariante, 1990a, 1990bMichiels et al, 2023). These plans are fundamental because endangered native populations are naturally adapted to the local environment and contribute a high proportion of the species genetic diversity.…”

Genomic Regions Associated with Wool, Growth and Reproduction Traits in Uruguayan Merino Sheep

“…Other genes that were found to be associated with the ewe LWM in the present study have been reported as candidate genes for LW-related traits in different species. For example, A1CF, ZNF830, CCT6B and MYO10 were associated with residual feed intake in cattle [47][48][49], while the genes CTBP2 and AP2B1 have been linked to meat quality and lipid metabolism in pigs [50,51].…”

Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review

“…It is noteworthy that signatures of selection spanning melanophilin ( MLPH ), melanocyte stimulating hormone receptor ( MC1R ), membrane‐associated transporter ( SLC45A2 ) and Ras oncogene family genes ( RAB17 , RAB37 ) were detected in African cattle breeds. These genes play a direct role in melanogenesis (Cieslak et al, 2011; Dlamini et al, 2022; Taye et al, 2018; Taye, Lee, Caetano‐Anolles, et al, 2017; Taye, Lee, Jeon, et al, 2017). A mutation in the MLPH gene in dogs, cats and rabbits is thought to disrupt the transportation of melanosomes to the outer edges of melanocytes (Philipp et al, 2005); it prevents the transfer of melanosomes into the keratinocytes, thus resulting in hairs of lighter colour (Demars et al, 2018; Ishida et al, 2006).…”