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https://doi.org/10.5713/ab.22.0163    [Accepted] Published online November 14, 2022.
Discriminant Canonical Analysis as a tool to determine traces of endangered native hen breed introgression through egg hatchability phenomics
Antonio González Ariza1  , Francisco Javier Navas González1,2,*  , Ander Arando Arbulu1,3  , Jose Manuel León Jurado4  , Juan Vicente Delgado Bermejo1  , María Esperanza Camacho Vallejo2 
1Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain
2Institute of Agricultural Research and Training (IFAPA), 14004 Córdoba, Spain
3Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 01192 Arkaute, Spain
4Agropecuary Provincial Centre, Diputación Provincial de Córdoba, 14071 Córdoba, Spain
Correspondence:  Francisco Javier Navas González, Tel: +34-651679262, Fax: +34-957218706, Email: fjng87@hotmail.com
Received: 21 April 2022   • Revised: 20 June 2022   • Accepted: 30 October 2022
Abstract
Objective
The main objective of this study was to develop a pipeline to detect phenogenomic introgression across different multivariety breeds and to validate such classification focusing on external egg and hatchability-related traits using a discriminant canonical analysis approach.
Methods
For this, 1368 eggs belonging a flock of 94 endangered Spanish autochthonous breed breeding hens (Andalusian Tufted, Blue Andalusian, Spanish White-Faced, and Utrerana) and a control outgroup comprising 32 eggs belonging to 4 Araucana hens were considered. Multicollinearity analysis of hatchability-related traits revealed embryonic mortality, embryonic mortality in the second stage of incubation, viable hatching chick, major diameter, and minor diameter should be discarded from the analysis (VIF≤5) given they did not significantly contribute to variability explanation potential of the discriminant model.
Results
A stepwise discriminant canonical analysis was developed and egg weight, shape index, hatchability, and fertility variables reported the highest discriminant power (Wilks' Lambda values of 0.7861, 0.7871, 0.8076, and 0.9457, respectively). The first two functions explained 85.25% intergroup variability. Interbreed and varieties proximity was evaluated using Mahalanobis distances representation and data mining cross-validation allowed to detect genetic introgression between different genotypes.
Conclusion
Easily collectable traits as egg weight and shape index must be considered for the development of breeding programs as a measure to ensure breed protection. The model may be translatable to other endangered breeds to optimize avian breeds conservation plans worldwide.
Keywords: Data Mining; Egg Shape and Weight; External Traits; Genetic Resources; Incubation; Native Hen Breed
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