Demographic structure and genetic diversity of the endangered Bísaro pig: Evolution and current status

Abstract

Bísaro pig, a local endangered swine breed, has gained popularity in the recent years. A complete pedigree was used to evaluate the population structure and investigate the current breed’s genetic variability in two reference populations (AlivePop and AliveBpop). Since the breed’s foundation, the number of registered animals, producers, and farrowing records has increased. The mean progeny size for sires was 116.17 ± 210.81, and 3.24% of the breeding boars originated 26.54% of all registered births showing a marked unbalanced use of certain sires. The mean calculated equivalent generations was 4.54, and 98.1% of all the animals had known parents, indicating a good degree of pedigree completion and depth. Approximately half of the individuals were inbred, with average inbreeding values of 10.41, 9.02, and 8.58% for the whole and reference populations, respectively. Considering both reference populations, a low effective founder/ancestor ratio was obtained (1.12), showing a well-balanced founder/ancestor contribution, and subsequent genetic transfer. However, the effective founder/founder ratio was particularly low (0.06 and 0.12) compared with other native breeds. The founder genome/effective founder ratios were 0.37 and 0.41 for AlivePop and AliveBpop. Contrarily to the whole population, the random genetic drift weighted significantly more than the drift due to unequal founder contribution in the reference populations. The effective population size based on the increase in coancestry ranged from 62.39 and 54.66, and 16.74 and 24.84 based on the increase of individual inbreeding, for the whole and reference populations. The genetic conservation index steadily grew over the years with a mean value of 6.53 for the whole pedigree. Genetic variability losses and diffuse structuring might have occurred in the Bísaro population. Notwithstanding, the recent genetic variability indicators seem positive, yet supported by an open herdbook policy. These characteristics must be taken into account to define future mating policies and selection programs.

Genetic parameters for reproductive, longevity and lifetime production traits in Bísaro pigs

“…In the recent years, the Bísaro population and producers have been thriving, contradicting the endangered condition of this indigenous Portuguese breed, characterized by excellent meat quality and well known by its smoked cured products. Despite the growing tendency, the BP population is characterized by high inbreeding levels and low effective population size (Paixão et al, 2018a). Reproductive management is often neglected; heat detection is not commonly used, and only a few producers make use of artificial insemination as breeding method (Paixão et al, 2018b).…”

Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds

“…Traditionally, BI production is based on small-scale family farms with a low number of sows, fed with domestic food scraps and horticultural by-products [17,18]. Nowadays, the number of sows per farm has increased, while reared by smallholders and in medium-sized farms based on free-ranged systems, most of them allowing access to pasture [19].The old perception of adipocytes as a mere energy storage tissue is nowadays incomplete due to its extensive autocrine, paracrine and endocrine activities via liberation of various specific cytokines that modulate gene expression and nutrient flow to balance current metabolic needs [20]. Identification of these mechanisms and how they interact can help understand and treat associated metabolic diseases such as obesity and type-2 diabetes.…”

“…Traditionally, BI production is based on small-scale family farms with a low number of sows, fed with domestic food scraps and horticultural by-products [17,18]. Nowadays, the number of sows per farm has increased, while reared by smallholders and in medium-sized farms based on free-ranged systems, most of them allowing access to pasture [19].…”

Genetic Variability and Management in Nero di Parma Swine Breed to Preserve Local Diversity

“…It is known that most losses of genetic variability occur just straight after the setting up of a conservation program as likely a substantial number of founders do not give progeny to the following generations [30][31][32]. The effective number of founders and ancestors were similar to Gochu Asturcelta pig breed [32], but lower if compared to Bísaro Pig [12] and to commercial breeds used in China [25], in Czech Republic [26] or Canada [27].…”

“…To evaluate whether the population had a well-balanced founder/ancestor contribution, the ratio between f a and f e was calculated. The ratio between f e and f was computed to evaluate the presence of bottlenecks after breed foundation [12]. Founder genome equivalents (f g ) was also computed which is defined as the number of founders that would be expected to produce the same genetic diversity if the founders were equally represented and no loss of alleles occurred [10].…”