Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies

Abstract

Simple SummaryThe recent alarming reports on global climate change and the challenges facing the agricultural sector to meet the increase in meat consumption, impose research in biodiversity. An important genetic pool of local breeds might play a crucial role in the near future to address these challenges. Although Italy is considered as one of the richest countries in biodiversity, there are autochthonous cattle breeds under extinction. To safeguard biodiversity and increase genetic diversity within breeds, appropriate management tools must be developed. To achieve this, precise knowledge of the population structure and genetic diversity per breed are required. This study analyzed pedigree data of six local beef breeds: Calvana, Mucca Pisana, and Pontremolese (from the region of Tuscany), all under extinction, and Sarda, Sardo Bruna, and Sardo Modicana, from the island of Sardinia, that are larger in number but of lower productivity. In addition, the study investigated the population structure of the cosmopolitan beef breeds, Charolais and Limousine, reared in the same regions and undergoing selection. The high mating percentage between relatives for Mucca Pisana and Calvana is an alarming situation for these breeds. The population structure of the Sardinian breeds suggests the application of breeding programs.AbstractThe aim was to investigate the population structure of eight beef breeds: three local Tuscan breeds under extinction, Calvana (CAL), Mucca Pisana (MUP), and Pontremolese (PON); three local unselected breeds reared in Sardinia, Sarda (SAR), Sardo Bruna (SAB), and Sardo Modicana (SAM); and two cosmopolitan breeds, Charolais (CHA) and Limousine (LIM), reared in the same regions. An effective population size ranges between 14.62 (PON) to 39.79 (SAM) in local breeds, 90.29 for CHA, and 135.65 for LIM. The average inbreeding coefficients were higher in Tuscan breeds (7.25%, 5.10%, and 3.64% for MUP, CAL, and PON, respectively) compared to the Sardinian breeds (1.23%, 1.66%, and 1.90% in SAB, SAM, and SAR, respectively), while for CHA and LIM they were <1%. The highest rates of mating between half-siblings were observed for CAL and MUP (~9% and 6.5%, respectively), while the highest rate of parent–offspring mating was ~8% for MUP. Our findings describe the urgent situation of the three Tuscan breeds and support the application of conservation measures and/or the development of breeding programs. Development of breeding strategies is suggested for the Sardinian breeds.

Genetic Diversity in the Portuguese Mertolenga Cattle Breed Assessed by Pedigree Analysis

“…This value is higher than the one for some breeds whose herdbook started at the same time, and close to the values obtained in the Charolais and Limousine breed reported by Bouquet et al [51]. It is higher than that in several native Spanish breeds [48][49][50], but lower than some international breeds with a longer established herdbook (e.g., Charolais and Limousine) that have a n i above 15 [57].…”

“…The annual rate of inbreeding (∆F = 0.183%/year) estimated for the entire Mertolenga population enrolled in the MHB (209,503 animals born between 1978 and 2019) is lower than that obtained for the Alentejana breed for animals born between 1968 and 2003 (0.33%/year) [5], in animals born between 1968 and 2016 (0.23%/year) [38], and lower than the rates found in the Morucha, Asturiana de la Montaña and Alistana [48,49] Spanish breeds (Table 4). This estimate (∆F = 0.183%/year) is inferior to those obtained for the Portuguese breeds Arouquesa [43] and Preta [40] and in the Italian Sardo Bruna and Sardo Modicana [57]. The annual rate of inbreeding estimated for Charolais and Limousine (between 0% and 0.03%/year) is also lower than the ones for Mertolenga.…”

Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data

“…The evaluation of genetic diversity with traditional methods based on pedigree analyses have been widely used to manage animals’ genetic resources. In small livestock populations, where financial support is generally a limiting factor, pedigree-based methods are still commonly adopted due to their cost–effectiveness ratio [ 5 , 57 , 58 , 59 , 60 ]. However, with novel molecular and bioinformatics approaches, genetic variability can be more proficiently evaluated by using genomic information, and could lead to more precise and effective conservation programs.…”

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

“…The pedigree-based method requires an adequate completeness of data over several generations [7], and for local breeds, this is not an easy task for practical reasons related to breeding management. In a previous study [8], N e from pedigrees was calculated for the same Tuscan breeds, but generally, the low quality of pedigrees and the alarming demographic situation of these breeds have raised the necessity to estimate the effective population size with genomic data; the linkage disequilibrium (LD) method was chosen for this purpose.…”