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

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Genetic Diversity in the Portuguese Mertolenga Cattle Breed Assessed by Pedigree Analysis animals Article Genetic Diversity in the Portuguese Mertolenga Cattle Breed Assessed by Pedigree Analysis Nuno Carolino 1,2,3,* , Andreia Vitorino 1 , Inês Carolino 1,2, José Pais 4, Nuno Henriques 4, Manuel Silveira 5 and António Vicente 3,6 1 Instituto Nacional de Investigação Agrária e Veterinária, Fonte Boa, 2005-048 Vale de Santarém, Portugal; [email protected] (A.V.); [email protected] (I.C.) 2 Escola Universitária Vasco da Gama, Lordemão 197, 3020-210 Coimbra, Portugal 3 Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária—Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal; [email protected] 4 Associação de Criadores de Bovinos Mertolengos, Rua Diana de Liz, Apartado 466, Horta do Bispo, 7006-806 Évora, Portugal; [email protected] (J.P.); [email protected] (N.H.) 5 Ruralbit Lda, Avenida Dr. Domingos Gonçalves Sá 132, 4435-213 Rio Tinto, Portugal; [email protected] 6 Escola Superior Agrária do Instituto Politécnico de Santarém, Apartado 310, 2001-904 Santarém, Portugal * Correspondence: [email protected] Received: 28 September 2020; Accepted: 18 October 2020; Published: 29 October 2020 Simple Summary: The conservation and maintenance of genetic diversity is one of the priorities of the Convention of Biological Diversity and is included in the United Nations (UN’s) Sustainable Development Goals. The evaluation of the genetic variability of a breed is fundamental for its future use in a sustainable way, being indispensable to outline a successful conservation or improvement strategy. Preserving genetic diversity in a population is one of the main objectives for a breed conservation program. Nevertheless, the correct management of genetic diversity is also essential for the adaptation of a population to a new environment, production system or genetic improvement. For the purpose of population monitoring, assessing changes in genetic variability and genetic erosion in animal populations, many methodologies based on pedigree analyses of inbreeding and relationships, and on the probability of genetic origin from different herds, founders and ancestors, have been used. This study presents several genetic diversity indicators in a Portuguese native cattle breed, Mertolenga, assessed by pedigree analysis, and demonstrates the usefulness of these indicators and how they can be used in the genetic management of a breed. Abstract: The Mertolenga beef cattle, currently with 27,000 breeding females in Portugal, is the largest Portuguese native breed, despite some variation in the breeding stock over the last years. The purpose of this study was to estimate parameters related to the population structure and genetic diversity and to investigate the major factors affecting genetic erosion in the breed, based on the pedigree herdbook information collected since the 1950s, including records on 221,567 animals from 425 herds. The mean generation intervals were 6.4 years for sires and 7.1 years for dams, respectively. The rate of inbreeding per year was 0.183% 0.020% and the correspondent effective population size was ± 38.83. In the reference population (35,017 calves born between 2015 and 2019), the average inbreeding and relatedness were 8.82% 10% and 2.05% 1.26%, respectively. The mean relationship among ± ± animals from the same and from different herds was 29.25% 9.36% and 1.87% 1.53%, respectively. ± ± The estimates for the effective number of founders, ancestors, founding herds and herds supplying sires were 87.9, 59.4, 21.4 and 73.5, respectively. Although the situation of the Mertolenga breed is not alarming, these results indicate the need to adopt measures to maintain the genetic variability of the population. Animals 2020, 10, 1990; doi:10.3390/ani10111990 www.mdpi.com/journal/animals Animals 2020, 10, 1990 2 of 23 Animals 2020, 10, x 2 of 23 Keywords: native cattle; inbreeding; founders; ancestors; population structure 1.1. Introduction Introduction TheThe Mertolenga Mertolenga beef beef cattle cattle breed,breed, currentlycurrently with 27,000 27,000 breeding breeding females, females, is isthe the largest largest of ofthe the fifteenfifteen Portuguese Portuguese native native breeds, breeds, althoughalthough only 8000 of of them them are are purebred purebred.. The The rest rest are are crossbred crossbred withwith international international exotic exotic breeds. breeds. Recently,Recently, thisthis breed experienced a aperiod period of of strong strong census census decline decline causedcaused by by drastic drastic changes changes in in thethe livestocklivestock sector and and unplanned unplanned crossbreeding crossbreeding with with exotic exotic breeds. breeds. WithWith three three quite quite di ffdifferenterent coat coat types types (red, (red, roan roan and and red red spotted; spotted; Figure Figure1 ),1), Mertolenga Mertolenga cows cows areare usedused in severalin several regions regions of Portugal of Portugal in morein more than than 700 700 farms, farms, 216 216 ofof whichwhich are are controlled controlled by by the the Mertolenga Mertolenga’s’s Herdbook (MHB), mainly in the southern area of Portugal, but are also bred in other regions of the Herdbook (MHB), mainly in the southern area of Portugal, but are also bred in other regions of the country, including the Azores Islands. country, including the Azores Islands. (a) (b) (c) FigureFigure 1. 1.Di Differentfferent MertolengaMertolenga coat types types:: ( (aa)) red red spotted spotted,, (b (b) roan) roan,, (c ()c red.) red. ManagingManaging the the genetic genetic diversity diversity ofof aa breedbreed is fundamental for for its its future future use use in in a sustainable a sustainable manner manner inin order order to to outline outline a a balanced balanced and and e effectiveffective strategystrategy for conservation or or genetic genetic improvement improvement of ofthe the population,population, because because a a limited limited numbernumber of breeders breeders will will inevitably inevitably lead lead to toincreased increased inbreeding inbreeding with with a a reductionreduction in additive additive genetic genetic variance variance [1– [3]1– 3and] and possibly possibly to inbreeding to inbreeding depression depression [4]. To [4 keep]. To the keep thegenetic genetic variability variability of a population, of a population, it is essential it is essential to take in toto consideration take into consideration several indicators, several in additio indicators,n to breeding females’ total number, which allows to describe and take advantage of any genetic structure in addition to breeding females’ total number, which allows to describe and take advantage of any in a population [5]. genetic structure in a population [5]. Genetic characterization by pedigree analysis makes it possible to define the structure and dynamics Genetic characterization by pedigree analysis makes it possible to define the structure and of a population over time, considering it as a group of individuals in permanent renewal and taking into dynamics of a population over time, considering it as a group of individuals in permanent renewal and account its gene pool [6]. The use of pedigree analysis for measuring genetic diversity is referred by takingseveral into authors account and its in genemany pool species [6]. [7 The–10] useas a ofgreat pedigree methodology analysis to forstudy measuring populations, genetic as it describes diversity is referredthe genetic by several structure authors and its and evolution in many through species [generations7–10] as a great. It also methodology contributes to substantially study populations, to animal as it describesbreeding the and genetic conservation structure genetics and its research, evolution resulting through ingenerations. many applications It also [5 contributes–18]. substantially to animalThe breeding main goal and of this conservation study is to genetics describe research, genetic diversity resulting in in the many Mertolenga applications cattle breed [5–18]. based onThe pedigree main analysis, goal of thistaking study into is consideration to describe genetic their different diversity coat in types, the Mertolenga and identify cattleing factors breed that based onmay pedigree have affected analysis, the taking population, into consideration in order to establish their di ffconservationerent coat types, strategies and and identifying minimiz factorse further that maylosses have in atermsffected of thegenetic population, diversity. in order to establish conservation strategies and minimize further losses in terms of genetic diversity. 2. Materials and Methods 2. Materials and Methods 2.1. Ethics Statement 2.1. Ethics Statement The Animal Care and Use Committee’s approval was not obtained for this study because the dataThe was Animal gathered Care from and the Use Mertolenga Committee’s Breeders approval Association was not (ACBM) obtained digital for this herdbook study because database. the data was gathered from the Mertolenga Breeders Association (ACBM) digital herdbook database. 2.2. Animals The Mertolenga breed is a medium sized animal with a red or reddish coat with white patches and white hook-shaped horns. It is known for its remarkable maternal features and adaptability to poor Animals 2020, 10, 1990 3 of 23 2.2. Animals The Mertolenga breed is a medium sized animal with a red or reddish coat with white patches and white hook-shaped horns. It is known for its remarkable maternal features and adaptability
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