Genomic characterisation of endangered Landim pigs suggests distinctive features and immune-related selection

Fábio Teixeira^1,2Pedro Sa³Dulce Santos⁴Carmen Garrine^5,6Rosa Zimba⁷Laurinda Augusto⁵Endika Varela Martinez⁸Hermenegildo Chiaia^10,2,9Kiala Sebastino^10,11,9José Moras Cordeiro²Alexandre Leitão^10,9Luis Telo Da Gama^10,9Andreia J. Amaral^1,10,12,9*

• ¹Universidade de Évora, MED (Mediterranean Institute for Agriculture, Environment and Development) & CHANGE (Global Change and Sustainability Institute), Pólo da Mitra, Ap. 94, 7002-554, Èvora, Portugal
• ²Faculty of Veterinary Medicine, Universidade José Eduardo dos Santos, Huambo, Huambo, Angola
• ³Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
• ⁴BE, Bioinsight & Ecoa, Odivelas, Portugal
• ⁵Faculty of Veterinary Medicine, Eduardo Mondlane University, Maputo, Mozambique
• ⁶Faculty of Veterinary Medicine, Lusofona University, Lisboa, Lisbon, Portugal
• ⁷Escola Superior de Desenvolvimento Rural de Vilankulo, University Eduardo Mondlane, Inhambane, Mozambique
• ⁸Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country, Leioa, Basque Country, Spain
• ⁹AL4AnimalS - Associate Laboratory for Animal and Veterinary Sciences, Lisbon, Portugal
• ¹⁰Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisboa, Lisboa, Portugal
• ¹¹IIV - Instituto de Investigação Veterinária, Huambo, Angola
• ¹²Department of Zootechny, School of Science and Technology, University of Evora, Évora, Portugal

The Landim pigs of Mozambique are an important local breed raised by small-scale farmers in extensive systems, predominantly sustained by leftover food. These pigs serve as a cornerstone for the economic stability of these communities. However, their existence is currently endangered by uncontrolled crossbreeding with commercial pig breeds. Preserving these local pigs is also crucial given their role as a source of genetic diversity. To this end, we have conducted whole genome resequencing on six Landim pigs, characterising their genetic makeup and establishing their relationship with other worldwide pig breeds. Our findings suggest that Landim pigs are more closely related to Angolan pigs, although recent introgression of European cosmopolitan breeds is shown to have occurred. Results show that Landim pigs display a unique genetic signature, with positive selection detected in variants of genes acting in the neuroimmune axis fundamental for survival and immune response.