Genetic diversity of Brazilian Brahman cattle by pedigree analysis

Cavani, Lígia; Silva, Rafael Medeiros de Oliveira; Carreño, Luis; Ono, Rafael Keith; Bertipaglia, Tássia Souza; Farah, Michel Marques; Millen, D. D.; Fonseca, Ricardo da

doi:10.1590/s0100-204x2018000100008

Cited by 11 publications

(11 citation statements)

References 17 publications

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“…Also, the effective number of founders ( fe ) [22], and the effective number of ancestors ( fa ) [25] were considered. The fe / fa ratio and the number of ancestors explaining 50% [22,24] of the genetic contribution (ANC_50), expressed as a percentage on reference population [25], were also calculated. Ratio fe / fa = 1 shows the absence of bottleneck in the population under study, and low ANC_50 is an indicator of the founder effect [30].…”

Section: Methodsmentioning

confidence: 99%

“…Indeed, demographic analyses can also help to understand factors regarding genetic history, conservation status of a population, and relationships within and between breeds [21]. Although several studies have been carried out on the population structure and genetic diversity of cattle [22,23,24], only a few were focused on small populations.…”

Section: Introductionmentioning

confidence: 99%

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Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies

Fabbri

Rezende²,

Dadousis

et al. 2019

Animals

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Simple SummaryThe recent alarming reports on global climate change and the challenges facing the agricultural sector to meet the increase in meat consumption, impose research in biodiversity. An important genetic pool of local breeds might play a crucial role in the near future to address these challenges. Although Italy is considered as one of the richest countries in biodiversity, there are autochthonous cattle breeds under extinction. To safeguard biodiversity and increase genetic diversity within breeds, appropriate management tools must be developed. To achieve this, precise knowledge of the population structure and genetic diversity per breed are required. This study analyzed pedigree data of six local beef breeds: Calvana, Mucca Pisana, and Pontremolese (from the region of Tuscany), all under extinction, and Sarda, Sardo Bruna, and Sardo Modicana, from the island of Sardinia, that are larger in number but of lower productivity. In addition, the study investigated the population structure of the cosmopolitan beef breeds, Charolais and Limousine, reared in the same regions and undergoing selection. The high mating percentage between relatives for Mucca Pisana and Calvana is an alarming situation for these breeds. The population structure of the Sardinian breeds suggests the application of breeding programs.AbstractThe aim was to investigate the population structure of eight beef breeds: three local Tuscan breeds under extinction, Calvana (CAL), Mucca Pisana (MUP), and Pontremolese (PON); three local unselected breeds reared in Sardinia, Sarda (SAR), Sardo Bruna (SAB), and Sardo Modicana (SAM); and two cosmopolitan breeds, Charolais (CHA) and Limousine (LIM), reared in the same regions. An effective population size ranges between 14.62 (PON) to 39.79 (SAM) in local breeds, 90.29 for CHA, and 135.65 for LIM. The average inbreeding coefficients were higher in Tuscan breeds (7.25%, 5.10%, and 3.64% for MUP, CAL, and PON, respectively) compared to the Sardinian breeds (1.23%, 1.66%, and 1.90% in SAB, SAM, and SAR, respectively), while for CHA and LIM they were <1%. The highest rates of mating between half-siblings were observed for CAL and MUP (~9% and 6.5%, respectively), while the highest rate of parent–offspring mating was ~8% for MUP. Our findings describe the urgent situation of the three Tuscan breeds and support the application of conservation measures and/or the development of breeding programs. Development of breeding strategies is suggested for the Sardinian breeds.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies

Fabbri

Rezende²,

Dadousis

et al. 2019

Animals

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“…However, the accuracy of these comparisons depends on the degree of connectedness among MU: the higher the connectedness, the more reliable the comparison. Genetic connectedness has traditionally been calculated through pedigree-based methods ( Lewis et al, 1999b ; Kuehn et al, 2007a ); however, these methods may underestimate connectedness in production systems such as the beef cattle industry, where commercial herds are poorly registered and multi-sire mating is practiced ( Caires et al, 2012 ; Barbosa et al, 2013 ; Tonussi et al., 2017 ; Cavani et al, 2018 ). A lack of connectedness occurs: when the MU are genetically isolated (or semi-isolated) or there is limited sharing of genetic material; with the use of an incomplete numerator relationship matrix based on poor pedigree data ( Carneiro et al, 2001 ); and with poor use of artificial insemination (AI).…”

Section: Introductionmentioning

confidence: 99%

An assessment of genomic connectedness measures in Nellore cattle

Amorim

Hyeong-keun

Momen

et al. 2020

Journal of Animal Science

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An important criterion to consider in genetic evaluations is the extent of genetic connectedness across management units (MU), especially if they differ in their genetic mean. Reliable comparisons of genetic values across MU depend on the degree of connectedness; the higher the connectedness, the more reliable the comparison. Traditionally, genetic connectedness was calculated through pedigree-based methods; however, in the era of genomic selection, this can be better estimated utilizing new approaches based on genomics. Most procedures consider only additive genetic effects, which may not accurately reflect the underlying gene action of the evaluated trait, and little is known about the impact of non-additive gene action on connectedness measures. The objective of this study was to investigate the extent of genomic connectedness measures, for the first time, in Brazilian field data by applying additive and non-additive relationship matrices using a fatty acid profile dataset from seven farms located in the three regions of Brazil, which are part of the three breeding programs. Myristic acid (C14:0) was used due to its importance for human health, and reported presence of non-additive gene action. The pedigree included 427,740 animals and 925 of them were genotyped using the Bovine high-density genotyping chip. Six relationship matrices were constructed, parametrically and non-parametrically capturing additive and non-additive genetic effects from both pedigree and genomic data. We assessed genome-based connectedness across MU using the prediction error variance of difference (PEVD) and the coefficient of determination (CD). PEVD values ranged from 0.540 - 1.707, and CD from 0.146 - 0.456. Genomic information consistently enhanced the measures of connectedness compared to the numerator relationship matrix by at least 63%. Combining additive and non-additive genomic kernel relationship matrices or a non-parametric relationship matrix increased the capture of connectedness. Overall, the Gaussian kernel yielded the largest measure of connectedness. Our findings showed that connectedness metrics can be extended to incorporate genomic information and non-additive genetic variation using field data. We propose that different genomic relationship matrices can be designed to capture additive and non-additive genetic effects, increase the measures of connectedness, and to more accurately estimate the true state of connectedness in herds

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“…Previous studies on Brahman cattle have reported fa and fe values ranging from 5.4 to 50 and from 5.4 to 718, respectively. Additionally, average F values ranged from 0.69% to 11.9% (Faria et al, 2010;Santana et al, 2016;Cavani et al, 2018).…”

Section: Resultsmentioning

confidence: 99%

Pedigree Analysis and Population Structure of Brahman Cattle From Costa Rica

Vásquez-Loaiza¹,

Cruz-Méndez²,

Castro-Vásquez³

et al. 2021

Chil. j. agric. anim. sci.

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The objective of this study was to evaluate the population of Brahman cattle from Costa Rica. Pedigree analysis of 98,749 animals was used to estimate the following parameters: pedigree integrity, as a proportion of known ancestors; the number of complete generations, maximum generations traced, and equivalent complete generations; inbreeding coefficient (F); generation interval (GI) across four selection paths; additive genetic relationship (AGR); effective number of founders (fe) and ancestors (fa); and effective population size (Ne). The analysis was carried out using the ENDOG software. The maximum proportions of unknown parents, grandparents, and great-grandparents were 14.1%, 38.9%, and 61.2%, respectively. Average F for the whole population was 0.86, while 27.4% of the population was inbred, with an average F of 3.1%. The inbred population increased through the time, while F decreased. The average AGR was 0.64, with maximum values of 4.1 and positive trends. The fe and fa were 617.8 and 172.0, respectively. The Ne indicated increases of F, with values lower than 1%. The GI fluctuated from 6.4 to 7.4, with an average of 6.85 years. These results summarize previous breeding practices and represent useful information for designing breeding programs by anticipating the relationship between the selection response and increases of inbreeding.

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Genetic diversity of Brazilian Brahman cattle by pedigree analysis

Cited by 11 publications

References 17 publications

Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies

Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies

An assessment of genomic connectedness measures in Nellore cattle

Pedigree Analysis and Population Structure of Brahman Cattle From Costa Rica

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