Genetic Diversity of 17 Autochthonous Italian Chicken Breeds and Their Extinction Risk Status.

Francesco Perini,Margherita Profiti,Dominga Soglia,Sandra Maione,Cesare Castellini,Filippo Cendron,Chiara Bianchi,Emiliano Lasagna,Sihem Dabbou,Nicolaia Iaffaldano,Stefano Sartore,Margherita Marzoni,Arianna Buccioni,Annelisse Castillo,Martino Cassandro,Silvia Cerolini,Achille Schiavone,Paola Sacchi

doi:10.3389/fgene.2021.715656

Abstract

The preservation of genetic variability of autochthonous poultry breeds is crucial in global biodiversity. A recent report revealed small breed size and potential risk of extinction of all native Italian poultry breeds; therefore, a correct assessment of their genetic diversity is necessary for a suitable management of their preservation. In this work, we provided an overview of the contribution to poultry biodiversity of some Italian autochthonous breeds reared in conservation centers devoted to local biodiversity preservation. The level of genetic diversity, molecular kinship, inbreeding, contribution to overall genetic diversity, and rate of extinction of each breed were analyzed with a set of 14 microsatellite loci in 17 autochthonous chicken breeds. To evaluate genetic variability, total number (Na), and effective number (Ne) of alleles, observed (Ho) and expected (He) heterozygosity, and F (Wright’s inbreeding coefficient) index were surveyed. The contribution of each analyzed breed to genetic diversity of the whole dataset was assessed using MolKin3.0; global genetic diversity and allelic richness contributions were evaluated. All the investigated loci were polymorphic; 209 alleles were identified (94 of which private alleles). The average number of alleles per locus was 3.62, and the effective number of alleles was 2.27. The Ne resulted lower in all breeds due to the presence of low-frequency alleles that can be easily lost by genetic drift, thus reducing the genetic variability of the breeds, and increasing their risk of extinction. The global molecular kinship was 27%, the average breed molecular kinship was 53%, and the mean inbreeding rate 43%, with a self-coancestry of 78%. Wright’s statistical analysis showed a 41% excess of homozygous due to breed genetic differences (34%) and to inbreeding within the breed (9%). Genetic variability analysis showed that 11 breeds were in endangered status. The contribution to Italian poultry genetic diversity, estimated as global genetic diversity, and ranged from 30.2 to 98.5%. In conclusion, the investigated breeds maintain a unique genetic pattern and play an important role in global Italian poultry biodiversity, providing a remarkable contribution to genetic variability.

Highlights

In the last decade, many developed countries recorded a raising interest toward local breeds and traditional products (Franzoni et al, 2021); the most likely explanation of this new tendency may be due to the fact that the farming system of local breeds, extensive and more sustainable, is perceived to be more respectful of animal welfare and environment compared to intensive industrial farming (Soglia et al, 2017, 2020)
We investigated the level of genetic diversity, molecular kinship, inbreeding, contribution to overall genetic diversity, and rate of extinction of each breed
Our investigation provides a current picture of the genetic diversity and of the potential risk status of 17 local chicken breeds reared in North, Central, and South of Italy

Summary

Introduction

Many developed countries recorded a raising interest toward local breeds and traditional products (Franzoni et al, 2021); the most likely explanation of this new tendency may be due to the fact that the farming system of local breeds, extensive and more sustainable, is perceived to be more respectful of animal welfare and environment compared to intensive industrial farming (Soglia et al, 2017, 2020). Most of the genetic investigations were focused on commercial lines so far [Food and Agriculture Organization (FAO), 2011]; because of their low commercial performances, local chicken breeds are hardly matter of interest, and far less attention was given to genetic conservation of these resources compared to other livestock species such as cattle and sheep so far (Blackburn, 2006; Wilkinson et al, 2011). In this regard, a main interest is represented by the assessment of the genetic variability of native breeds to start adequate and reliable conservation programs. It is paramount to take into account that conservation priorities may significantly differ according to the weight given to within- and between-breeds genetic diversity (Ginja et al, 2013)

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