Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations

Abstract

Linkage disequilibrium (LD) is a useful parameter for guiding the accuracy and power of both genome-wide association studies (GWAS) and genomic selection (GS) among different livestock species. The present study evaluated the extent of LD, persistence of phase and effective population size (Ne) for the purebred (Mediterranean buffalo; n = 411) and crossbred [Mediterranean × Jianghan × Nili-Ravi buffalo, n = 9; Murrah × Nili-Ravi × local (Xilin or Fuzhong) buffalo, n = 36] buffalo populations using the 90K Buffalo SNP genotyping array. The results showed that the average square of correlation coefficient (r2) between adjacent SNP was 0.13 ± 0.19 across all autosomes for purebred and 0.09 ± 0.13 for crossbred, and the most rapid decline in LD was observed over the first 200 kb. Estimated r2 ≥ 0.2 extended up to ~50 kb in crossbred and 170 kb in purebred populations, while average r2 values ≥0.3 were respectively observed in the ~10 and 60 kb in the crossbred and purebred populations. The largest phase correlation (RP, C = 0.47) was observed at the distance of 100 kb, suggesting that this phase was not actively preserved between the two populations. Estimated Ne for the purebred and crossbred population at the current generation was 387 and 113 individuals, respectively. These findings may provide useful information to guide the GS and GWAS in buffaloes.

Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk traits in Chinese buffalo breeds

“…The average distance over which LD decay dropped to the value of 0.2 was approximately 15 Kb for swamp and 50 Kb for river group, respectively. This finding was also supported by previous studies [5]. Moreover, it is well known that the Chinese indigenous breeds underwent a longer time of domestication compared with the river breeds.…”

“…Analysis of the genome-wide LD decay plays a vital role in the GWAS mapping of loci associated with economically important traits in livestock animals. Our previous studies have demonstrated that the LD extent was different between purebred and crossbred buffalo populations, with purebred having highest levels of LD [5]. In this study, we estimated the LD extent between river and swamp groups, showing that the LD decay in swamp group had declined markedly compared with the river group.…”

“…The cross-breeding programs in China began in the 1950s by introducing the exotic river breeds such as Murrah and Nili-Ravi, which has resulted in the different crossbred breeds including the Murrah × local buffalo, Nili-Ravi × indigenous buffalo, and Murrah × Nili-Ravi × indigenous buffalo. These animals have higher milk production (~1,700 kg per lactation) than that of swamp buffalo (~500-800 kg per lactation) after multiple cross breeding for several decades, which is still lower than that of the river buffalo breeds (~2,200 kg/lactation) [5]. Therefore, it is of great interest to genetically dissect the molecular basis of buffalo complex traits such as milk and meat, which contribute to the development of dairy buffalo industry.…”

Asian water buffalo: domestication, history and genetics

“…Historical relationships between populations were also identified, confirming two independent domestication events, one for river and one for swamp buffaloes. Deng et al (2019b) used the Affymetrix 90K SNP chip data from purebred river and crossbred river 9 swamp buffalo populations to evaluate the extent of LD, persistence of phase and effective population size, and suggested that performing these analyses should be routine as a preliminary step in advance of genomic selection and GWASs. Regarding the possible utilisation of the array outside the Asian water buffalo species, Iamartino et al (2017) found the 90K chip to be heavily affected by ascertainment bias.…”

Conservation Status and Historical Relatedness of South African Communal Indigenous Goat Populations Using Genome-Wide Snp Marker

“…The presence of the extent of an effective population size (Ne), is an important population genetic parameter that has recently received a great deal of research attention [64], determining population demographic development [12] and demographic processes such as migration and admixture [45], and having profound implications for understanding the architecture of the animal genome [27,3]. In addition, Ne is widely regarded as one of the most critical population parameters because it measures the rates of genetic drift and inbreeding as well as affects the e cacy of systematic evolutionary forces such as mutation, selection, and migration [56].…”