Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds

Abstract

The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = 100) were used. All cattle were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. The genotype quality control for each breed was conducted separately, and SNPs with call rate < 0.95 and minor allele frequency (MAF) > 1% were used for the analysis. LD extent was estimated in PLINK v1.9 using the squared correlation between pairs of loci (r2) across autosomes. Moreover, r2 values were used to calculate historical and contemporary effective population size (Ne) in each breed. Average r2 was similar in Calvana and Mucca Pisana (~0.14) and higher in Pontremolese (0.17); Limousin presented the lowest LD extent (0.07). LD up to 0.11–0.15 was persistent in the local breeds up to 0.75 Mbp, while in Limousin, it showed a more rapid decay. Variation of different LD levels across autosomes was observed in all the breeds. The results demonstrated a rapid decrease in Ne across generations for local breeds, and the contemporary population size observed in the local breeds, ranging from 41.7 in Calvana to 17 in Pontremolese, underlined the demographic alarming situation.

Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity

“…In particular, in both analyses Sardinian and cosmopolitan breeds were more similar to each other than Tuscan populations, except for PON, which clustered together with Sardinian and cosmopolitan breeds in MDS but not in PCA. This might be because sampled animals of PON were few due to the little size of population (only 49 living animals are reported [ 34 ]), and this could affect PCA results but it does not influence MDS analysis, solely based on genetic distances clustering. Plotting of the eight breeds was therefore a description of the breeds sample size.…”

Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity

“…In particular, in both analyses Sardinian and cosmopolitan breeds were more similar to each other than Tuscan populations, except for PON, which clustered together with Sardinian and cosmopolitan breeds in MDS but not in PCA. This might be because sampled animals of PON were few due to the little size of population (only 49 living animals are reported [35]), and this could affect PCA results but it does not influence MDS analysis, solely based on genetic distances clustering. Plotting of the eight breeds was therefore a description of the breeds sample size.…”

“…MUP and PON presented consecutive genomic regions on BTA5, sharing the CACNG2 gene. Interestingly, this gene was found to be associated with milk protein percentage QTL (https://www.animalgenome.org), which is probably because these two breeds originate from several past crossbreeding events including with Holstein and Schwyz (MUP) [35] and Reggiana (PON) (http://www.anacli.it).…”

Cattle Conservation in the 21st Century: A Mini Review

“…LD is population-specific and is difficult between populations depending on the demographic history of the populations [61] [62] [63]. Also, the LD of genome markers is related to various evolutionary forces such as inbreeding, nonrandom mating, population bottleneck, drift, recombination, and mutation [64].…”

“…Moreover, the validity of genetic association studies depends considerably on the use of appropriate controls such as HWE [72]. In recent decades, there has been a greater interest in retrieving and conserving local breeds, especially their capacity to adapt in marginal areas and for their importance as a reservoir of genetic diversity [64].…”