Genetic diversity of Brazilian Brahman cattle by pedigree analysis

The objective of this work was to evaluate the genetic diversity of Brahman cattle in Brazil with pedigree analysis. Genealogical records of a subpopulation were used considering all pedigree information (Pt) and the pedigree information divided into two periods (P1, from 1994 to 2004; and P2, from 2005 to 2012) or according to the raising system (Ppt, animals on pasture; or Pst, on stable). Estimates were obtained for average inbreeding coefficients, generation intervals (GI), number of equivalent known generation (CGE), number of founders (Nf), effective number of founders (fe), effective number of ancestors (fa), and founder genome equivalents (fg). The average inbreeding coefficients were 11.97, 7.79, 11.95, 11.74, and 11.31% for Pt, P1, P2, Ppt, and Pst, respectively. Average GI was 4.4 years, whereas CGE was 3.18. The fe values were similar to those of fa, which were greater than those of fg. The fe/fa and fg/fe ratios were close to 1, which indicates no genetic bottleneck and small losses by genetic drift. The genetic diversity in the Brazilian population of Brahman breed is not significantly reduced.

Index terms:
beef cattle; founders; genetic bottleneck; inbreeding

Authorship

Ligia Cavani

Universidade Estadual Paulista (Unesp), Rodovia Comandante João Ribeiro de Barros, Km 651, CEP 17900-000 Dracena, SP, Brazil. E-mail: ligiacavani@hotmail.com, danilomillen@dracena.unesp.br, ricardo@dracena.unesp.brUniversidade Estadual PaulistaBrazilDracena, SP, BrazilUniversidade Estadual Paulista (Unesp), Rodovia Comandante João Ribeiro de Barros, Km 651, CEP 17900-000 Dracena, SP, Brazil. E-mail: ligiacavani@hotmail.com, danilomillen@dracena.unesp.br, ricardo@dracena.unesp.br

Rafael Medeiros de Oliveira Silva

Unesp, Via de Acesso Professor Paulo Donato Castellane, s/no, CEP 14884-900 Jaboticabal, SP, Brazil. E-mail: rafael.zte@gmail.com, lorlando82@hotmail.com, keith@zootecnista.com.br, tassia_bertipaglia@hotmail.com, michelmfarah@gmail.comUnespBrazilJaboticabal, SP, BrazilUnesp, Via de Acesso Professor Paulo Donato Castellane, s/no, CEP 14884-900 Jaboticabal, SP, Brazil. E-mail: rafael.zte@gmail.com, lorlando82@hotmail.com, keith@zootecnista.com.br, tassia_bertipaglia@hotmail.com, michelmfarah@gmail.com

Luis Orlando Duitama Carreño

Rafael Keith Ono

Tássia Souza Bertipaglia

Michel Marques Farah

Danilo Domingues Millen

Ricardo da Fonseca

SCIMAGO INSTITUTIONS RANKINGS

Figures | Tables | Formulas

Figures (1)
Tables (4)
Formulas (3)

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Figure 1.
Comparison between average inbreeding coefficients of the whole population (inbred and noninbred animals), expressed as percentage, and number of inbred animals between 1994 and 2012 in the Brazilian Brahman breed population.

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Table 1.
Number of pedigree records (n), number of sires and dams, and number of males and females, considering all pedigree information (Pt) and the pedigree information for the periods from 1994 to 2004 (P1) and from 2005 to 2012 (P2), as well as for cattle raised on pasture (Ppt) or stabled (Pst), in a Brazilian Brahman breed population.

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Table 2.
Estimates of average inbreeding coefficients considering all pedigree information and only inbred animals, as well as the number of complete generation equivalents (CGE), for the whole population (Pt), for cattle born between 1994 and 2004 (P1), for cattle born between 2005 and 2012 (P2), and for animals raised either on pasture (Ppt) or stabled (Pst), in a Brazilian Brahman breed population.

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Table 3.
Generation intervals for four gametic pathways and average generation interval in years, considering the whole population (Pt), cattle born between 1994 and 2004 (P1), cattle born between 2005 and 2012 (P2), and animals raised either on pasture (Ppt) or stabled (Pst), in a Brazilian Brahman breed population.

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Table 4.
Parameters based on the probability of gene origin considering the whole population (Pt), cattle born between 1994 and 2004 (P1), cattle born between 2005 and 2012 (P2), and animals raised either on pasture (Ppt) or stabled (Pst) in a Brazilian Brahman breed population.

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Figure 1. Comparison between average inbreeding coefficients of the whole population (inbred and noninbred animals), expressed as percentage, and number of inbred animals between 1994 and 2012 in the Brazilian Brahman breed population.

Table 1. Number of pedigree records (n), number of sires and dams, and number of males and females, considering all pedigree information (Pt) and the pedigree information for the periods from 1994 to 2004 (P1) and from 2005 to 2012 (P2), as well as for cattle raised on pasture (Ppt) or stabled (Pst), in a Brazilian Brahman breed population.

Pedigree	n	Sires	Dams	Males	Females
Pt	94,369	2,320	32,253	37,286	57,083
P1	16,312	553	4,502	4,064	12,248
P2	91,606	2,303	31,962	35,365	56,241
Ppt	51,343	1,600	19,029	17,961	33,382
Pst	20,766	980	7,085	6,982	13,787

Table 2. Estimates of average inbreeding coefficients considering all pedigree information and only inbred animals, as well as the number of complete generation equivalents (CGE), for the whole population (Pt), for cattle born between 1994 and 2004 (P1), for cattle born between 2005 and 2012 (P2), and for animals raised either on pasture (Ppt) or stabled (Pst), in a Brazilian Brahman breed population.

Item	Pt	P1	P2	Ppt	Pst
All animals
Number of records (n)	94,369	16,312	91,606	51,343	20,766
Inbreeding coefficient (%)	11.97	7.79	11.95	11.74	11.31
Inbred animals
Number of records (n)	86,801	10,044	84,098	46,614	18,432
Inbreeding coefficient (%)	13.02	12.655	13.02	12.94	12.75
CGE	3.18	2.65	3.18	3.15	3.04

Table 3. Generation intervals for four gametic pathways and average generation interval in years, considering the whole population (Pt), cattle born between 1994 and 2004 (P1), cattle born between 2005 and 2012 (P2), and animals raised either on pasture (Ppt) or stabled (Pst), in a Brazilian Brahman breed population.

Population	Gametic pathways				Mean
Population	Sire-son	Sire-daughter	Dam-son	Dam-daughter	Mean
Pt	4.6	4.0	4.7	4.1	4.4
P1	3.1	3.4	3.3	3.3	3.3
P2	4.1	4.0	4.7	4.1	4.2
Ppt	4.3	4.0	4.7	4.1	4.3
Pst	4.5	4.0	5.0	4.2	4.4

Table 4. Parameters based on the probability of gene origin considering the whole population (Pt), cattle born between 1994 and 2004 (P1), cattle born between 2005 and 2012 (P2), and animals raised either on pasture (Ppt) or stabled (Pst) in a Brazilian Brahman breed population.

Parameter⁽¹⁾	Pt	P1	P2	Ppt	Pst
RP	51,585	7,540	50,783	30,509	12,907
fe	5.40	4.50	5.40	5.10	4.6
fa	5.40	4.50	5.40	5.10	4.56
fg	3.84	3.84	3.85	3.84	3.83
Na 50%	5	3	5	5	3
fe/fa	1	1	1	1	1.01
fg/fe	0.71	0.85	0.71	0.75	0.83
1-GD*	0.09	0.11	0.09	0.10	0.11
GD*-GD	0.04	0.02	0.04	0.03	0.02

⁽¹⁾RP, size of the reference population (known parents); fe, effective number of founders; fa, effective number of ancestors, fg, founder genome equivalents; Na 50%, number of ancestors that explain 50% of genetic diversity; 1-GD*, loss of genetic diversity due to the unequal contributions of founders; and GD*-GD, loss of diversity by genetic drift accumulated over nonfounder generations.

f e = 1 / \sum_{k = 1}^{f} q_{k}^{2}

f a = 1 / \sum_{j = 1}^{a} q_{j}^{k}

f g = 1 / \sum_{j = 1}^{N f} (\frac{p_{j}^{2}}{r_{j}})

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Genetic diversity of Brazilian Brahman cattle by pedigree analysis

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[TFN1] ⁽¹⁾RP, size of the reference population (known parents); fe, effective number of founders; fa, effective number of ancestors, fg, founder genome equivalents; Na 50%, number of ancestors that explain 50% of genetic diversity; 1-GD*, loss of genetic diversity due to the unequal contributions of founders; and GD*-GD, loss of diversity by genetic drift accumulated over nonfounder generations.