Estimating breed composition for pigs: A case study focused on Mangalitsa pigs and two methods

Chinchilla-Vargas, Josue; Bertolini, Francesca; Stalder, Kenneth J.; Steibel, Juan P.; Rothschild, Max F.

doi:10.1016/j.livsci.2021.104398

Cited by 3 publications

(3 citation statements)

References 25 publications

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“…Native breeds are animal populations originating from local primitive breeds in a specific region or country. Breeders and their associations maintain the purity of the breed by enforcing the maintenance of certain conformational and performance traits, including the pedigree of each registered animal [48].…”

Section: Characteristics Of Selected European Native Pig Breedsmentioning

confidence: 99%

Native Pig Breeds as a Source of Biodiversity—Breeding and Economic Aspects

Kasprzyk

Walenia

2023

Agriculture

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The purpose of this paper is to summarize the available important information on local pig breeds maintained in Europe. Genetic erosion has prompted national and international bodies to take organized action aimed at the minimization of further losses of biodiversity. Since the genetic resources of livestock ensure both food security and the sustainable development of rural areas, genetic diversity is indispensable for sufficient flexibility of future animal husbandry to adapt to changing consumer demands and climatic conditions. Therefore, the problem of biodiversity has recently become an essential part of the comprehensive international program of the World Conservation Strategy and the global idea of the so-called sustainable development. The issue of biodiversity protection occupies an important place in the provisions of the EU Common Agricultural Policy. The successive financial perspectives assume an increase in relevant expenditure from the EU and national budgets. With regard to the protection of native pig breeds, a particularly large increase in funding was recorded in 2014–2020.

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Section: Characteristics Of Selected European Native Pig Breedsmentioning

confidence: 99%

Native Pig Breeds as a Source of Biodiversity—Breeding and Economic Aspects

Kasprzyk

Walenia

2023

Agriculture

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“…The three above-mentioned methods (F ST , PCA and RF) have already been applied to the selection of the most informative SNPs in several animal species such as cattle (Barbato et al, 2020;Bertolini et al, 2015Bertolini et al, , 2018Hulsegge et al, 2013Hulsegge et al, , 2019Wilkinson et al, 2011), sheep (Mastrangelo et al, 2014;Somenzi et al, 2020;Sottile et al, 2018), pig (Chinchilla-Vargas et al, 2021;Schiavo et al, 2020;Zhang et al, 2018), and chicken (Seo et al, 2021;Zhang et al, 2019). However, there are few studies on the application of RF and different variable importance criteria to the identification of the most informative SNPs in dairy and beef cattle breeds and comparison of its predictive performance with more traditional approaches such as the F ST and PCA.…”

Section: Introductionmentioning

confidence: 99%

Classification of cattle breeds based on the random forest approach

et al. 2023

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“…An approach has been developed to assign alleles in three-way CB pigs to their PB of origin; the approach has high accuracy, but as it infers local ancestry, it is highly computationally demanding ( Sevillano et al, 2016 ; Vandenplas et al, 2016 ). Another study tried using random forest for this purpose in pigs; however, the method did not accurately estimate breed composition for the breeds in question with the available markers ( Chinchilla-Vargas et al, 2021 ). Recently, an interesting study was published showing the advantage of partial least squares regression (PLSR) and partial least square–discriminant analysis (PLS-DA) for global ancestry identification of pig breeds ( Miao et al, 2023 ).…”

Section: Introductionmentioning

confidence: 99%

Classification of breed combinations for slaughter pigs based on genotypes—modeling DNA samples of crossbreeds as fuzzy sets from purebred founders

Vinje,

Brustad,

Heggli

et al. 2023

Front. Genet.

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In pig production, the production animals are generally three- or four-way crossbreeds. Reliable information regarding the breed of origin of slaughtered pigs is useful, even a prerequisite, for a number of purposes, e.g., evaluating potential breed effects on carcass grading. Genetic data from slaughtered pigs can easily be extracted and used for crossbreed classification. In the current study, four classification methods, namely, random forest (RF), ADMIXTURE, partial least squares regression (PLSR), and partial least squares together with quadratic discriminant analysis (PLS-QDA) were evaluated on simulated (n = 7,500) genomic data of crossbreeds. The derivation of the theory behind PLS-QDA is a major part of the current study, whereas RF and ADMIXTURE are known and well-described in the literature. Classification success (CS) rate, square loss (SL), and Kullback–Leibler (KL) divergence loss for the simulated data were used to compare methods. Overall, PLS-QDA performed best with 99%/0.0018/0.002 (CS/SL/KL) vs. 97%/0.0084/0.051, 97%/0.0087/0.0623, and 17%/0.068/0.39 for PLSR, ADMIXTURE, and RF, respectively. PLS-QDA and ADMIXTURE, as the most relevant methods, were used on a real dataset (n = 1,013) from Norway where the two largest classes contained 532 and 192 (PLS-QDA), and 531 and 193 (ADMIXTURE) individuals, respectively. These two classes were expected to be dominating a priori. The Bayesian nature of PLS-QDA enables inclusion of desirable features such as a separate class “unknown breed combination” and informative priors for crossbreeds, making this a preferable method for the classification of breed combination in the industry.

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Estimating breed composition for pigs: A case study focused on Mangalitsa pigs and two methods

Cited by 3 publications

References 25 publications

Native Pig Breeds as a Source of Biodiversity—Breeding and Economic Aspects

Native Pig Breeds as a Source of Biodiversity—Breeding and Economic Aspects

Classification of cattle breeds based on the random forest approach

Classification of breed combinations for slaughter pigs based on genotypes—modeling DNA samples of crossbreeds as fuzzy sets from purebred founders

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