Genetic structure and inbreeding in Romney Marsh sheep in Brazil / Estrutura genética e consanguinidade de ovinos Romney Marsh no Brasil

According to the last livestock census, Brazil has 17,976,367 head of sheep. Approximately 23.69% of this herd is located in the south region, where wool or wool and meat-producing breeds are predominately farmed. Inbreeding, or consanguinity, is defined as the mating of related individuals, which tends to occur when herds are small or originate from few parents. This study proposes to investigate the genetic structure and diversity of the Romney Marsh sheep herd in Brazil. The pedigree data used were obtained from the Brazilian Association of Sheep Breeders (ARCO), which keeps the sheep register database. For a more complete analysis, data from the Purebred Register Books were used. The population herein referred to as "total" comprised 22,833 individuals, whereas the population termed "reference" consisted of 17,053 records. Individual and average inbreeding coefficients, as well as overall frequencies, were calculated using SAS software. Demographic indicators were determined using ENDOG software. The average inbreeding coefficient found was 2.90% in the total population and 3.55% in the reference population. The minimum inbreeding value found in the studied population was 0.01% and the maximum was 43.47%. Inbred animals in the complete reference population were 10.31%. In 2018, inbred animals represented 82.55% of the registered population. The average generation interval was 4.0488 years. Due to the intensive use of few breeding lines and the high degree of genetic uniformity in the population, the Romney Marsh breed has narrow pedigree bottlenecks. The current population of the Romney Marsh breed has only two genetic origins, warranting the introduction of new genes to avoid genetic erosion and severe losses due to inbreeding.(AU)

O último censo pecuário informa que o Brasil possui 17.976.367 cabeças de ovinos. Aproximadamente 23,69% desse efetivo está localizado na região sul do país, onde predomina a criação de raças produtoras de lã, ou lã e carne. Endogamia ou consanguinidade é definida como o acasalamento de indivíduos relacionados, e tende a ocorrer quando os rebanhos são pequenos ou provenientes de poucos genitores. Este estudo teve como objetivo estudar a estrutura e a diversidade genética do rebanho ovino da raça Romney Marsh no Brasil. Os dados de pedigree utilizados foram obtidos na Associação Brasileira de Criadores de Ovinos (ARCO), que é a mantenedora do banco de dados de registro de ovinos. Para uma análise mais completa foram utilizados dados dos Livros de Registro Puro de Origem (PO). A população referida como "total" foi composta por 22.833 indivíduos, e a população referida como "referência" composta por 17.053 registros. Os coeficientes de consanguinidade individual e médio, bem como as frequências gerais, foram calculados usando o software SAS. Os indicadores demográficos foram determinados a partir do software ENDOG. O coeficiente de consanguinidade médio encontrado na população total foi de 2,90%, e na população de referência foi de 3,55%. O valor mínimo de consanguinidade encontrado na população estudada foi de 0,01% e o máximo, foi de 43,47%. Animais consanguíneos na população de referência completa foi de 10,31%. Em 2018 os animais consanguíneos representavam 82,55% da população cadastrada. Intervalo médio de gerações 4,0488 anos. Devido ao uso intensivo de poucas linhas de reprodutores e ao alto grau de uniformidade genética da população, a raça Romney Marsh apresenta estreitos gargalos nos pedigrees. A população atual da raça Romney Marsh provém de apenas duas origens genéticas, sendo necessário introduzir genes novos para evitar a erosão genética e perdas por consanguinidade acentuada.(AU)

Efeitos da consanguinidade em rebanho de bubalinos no pantanal Mato-Grossense / Effects of inbreeding in bubaline herds in the pantanal Mato-Grossense / Efectos de la consanguinidad en rebaño de búfalos en el pantanal Mato-Grossense

A consanguinidade é uma realidade na criação de bubalinos no Brasil, devido ao número pequeno de animais no rebanho, e principalmente a falta de escrituração zootécnica e seleção genética da espécie. Isso faz com que exista muita endogamia e como consequência aparecem as anomalias congênitas, que associadas às condições ambientais resultam em animais com problemas de pele, baixo desenvolvimento, baixa produção e sanidade deficitária. O presente estudo demonstrou os efeitos de um manejo cuja persistência de um touro por período de 8 anos gerou progênie com despigmentação, culminando com alterações dermatológicas e baixo desenvolvimento em alguns animais de um rebanho, sendo estas: albinismo acentuado, albinismo parcial -cabeça e peitoral e fotossensibilização, na qual todos eram menos desenvolvidos se comparados aos pais não consanguíneos. A alta incidência de raios solares na região do Pantanal Mato-Grossense potencializou queimaduras cutâneas e desgaste desses animais. Com objetivo de eliminar os genes defeituosos, os animais foram descartados e um novo touro foi introduzido.(AU)

IInbreeding is a reality in buffalo breeding in Brazil, due to the small number of animals in the herd, and mainly the lack of zootechnical bookkeeping and genetic selection of the species. This means that there is a lot of inbreeding and, as a consequence, congenital anomalies appear, which, associated with environmental conditions, result in animals with skin problems, poor development, low production and poor health. The present study demonstrated the effects of a management whose persistence of a bull for a period of 8 years generated progeny with depigmentation, culminating with dermatological alterations and low development in some animals of a herd, namely: accentuated albinism, partial albinism -head and pectoral and photosensitization, in which all were less developed compared to non-consanguineous parents. The high incidence of solar rays in the Pantanal Mato-Grossense region potentiated skin burns and wear of these animals. In order to eliminate the defective genes, the animals were discarded anda new bull was introduced.(AU)

La consanguinidad es una realidad en la cría de búfalos en Brasil,debido al pequeño número de animales en el rebaño, y principalmente la falta de contabilidad zootécnica y de selección de genética de la especie. Esto provoca la existencia de mucha endogamia y como consecuencia aparecen las anomalías congénitas, que asociadas a las condiciones ambientales resultan en animales con problemas de piel, bajo desarrollo, baja producción y salud. El presente estudio demostró los efectos de un manejo donde la persistencia de un toro por un periodo de 8 años generó progenie con despigmentación, culminando en alteraciones dermatológicas en un rebaño de 35 animales, siendo de los afectados: despigmentación severa, albinismo parcial -cabeza y pecho y fotosensibilización, en los que todos fueron menos desarrollados si se comparan con los padres no consanguíneos. La alta incidencia de los rayos solares en la región del Pantanal Mato-Grossense colaboró con las quemaduras y el desgaste de estos animales. Con el objetivo de eliminar los genes defectuosos, los animales fueron descartados y se introdujo un nuevo toro.(AU)

Increased rate of close-kin unions in the central Andes in the half millennium before European contact.

Analyzing ancient DNA of the central Andes, Ringbauer and colleagues identify a markedly elevated rate of unions of closely related parents after ca. 1000 CE. This change of mating preferences sheds new light on a unique system of social organization based on ancestry ("ayllu") whereby within-group unions were preferred to facilitate sharing of resources.

Population structure and inbreeding of Holstein cattle in southern Brazil

The present investigation aimed to evaluate the population structure and inbreeding of Holstein herds in southern Brazil. To carry out the analysis, the Associação Paranaense de Criadores de Bovinos da Raça Holandesa (APCBRH) in Brazil provided the data, which consisted of a pedigree file of 206,796 animals born between 1970 and 2014. Results regarding the following parameters were determined: pedigree integrity, effective number of founders, effective number of ancestors, generation interval, inbreeding coefficient, realized effective population size, and average relatedness coefficient. POPREP and ENDOG v.4.5 software packages were employed to estimate these parameters. Based on the data set, the mean generation interval was found to be 6.3 years, and the average inbreeding coefficient, related to inbred animals, was 4.99%. Furthermore, the realized effective population size varied throughout the time period, ranging from 22 to 114, whereas the rate of inbreeding in this same period showed a decreasing trend towards the later years in the period until 2014. Upon evaluation, average relatedness coefficient was estimated to be 0.71%. Moreover, the effective number of founders and ancestors were estimated as 418 and 400 animals, respectively. According to the level of inbreeding observed, it could be noticed that genetic diversity remains elevated, which will be important to the genetic progress in the Holstein breeding program in Southern Brazil.(AU)

Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.

Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.

Strategies to control inbreeding in a pig breeding program: a simulation study / Estratégias para controle de endogamia em um programa de melhoramento genético de suínos: um estudo de simulação

The objective of this study was to evaluate, through data simulation, the impact of restrictions on the maximum number of full- and half-sibs selected for males and females on the level of inbreeding and genetic gain of the herd. Data came from real populations A and B, composed of Pietrain and Landrace breed pigs, respectively. To generate the simulated populations, a Fortran-language simulator was developed using the (co)variances of the breeding values and the productive and reproductive rates obtained from populations A and B. Two data files were created. The first contained the pedigree of the previous 10 years, with 21,906 and 251,343 animals in populations A and B, respectively. The second included breeding values for age to reach 110 Kg body weight, backfat thickness, and feed conversion, for both populations; longissimus dorsi muscle depth, for population A only; and number of live piglets at the 5th day of life per farrowing, for population B only. Three scenarios were simulated with ten generations by varying the restrictions on the number of full- and half-sibs selected for males and females, with 30 replicates per generation and scenario. Regardless of the mating strategy used in a closed production unit, there is an increase in inbreeding levels. Inbreeding increases are larger in populations of smaller effective size. Restrictions on the number of full- and half-sibs selected are effective in reducing increments in inbreeding. Restriction to a maximum of two full-sibs and three half-sibs for males and three full sisters for females provided the highest genetic gains.(AU)

O objetivo deste estudo foi avaliar, por meio de simulação de dados, o impacto das restrições no número máximo de irmãos completos e meios-irmãos selecionados para machos e fêmeas no nível de endogamia e ganho genético do rebanho. Os dados originais são provenientes das populações reais A e B, compostas por suínos da raça Pietrain e Landrace, respectivamente. Para gerar as populações simuladas, foi desenvolvido um simulador em linguagem Fortran utilizando as (co)variâncias dos valores genéticos e as taxas produtivas e reprodutivas obtidas das populações A e B. Dois arquivos de dados foram criados. O primeiro continha o pedigree dos 10 anos anteriores, com 21.906 e 251.343 animais nas populações A e B, respectivamente. O segundo incluiu os valores genéticos para idade para atingir 110 Kg de peso vivo, espessura de toucinho e conversão alimentar, para ambas as populações; profundidade do músculo longissimus dorsi, apenas para a população A; e número de leitões vivos no 5º dia de vida por parto, apenas para a população B. Três cenários foram simulados com dez gerações, variando as restrições quanto ao número de irmãos completos e meios-irmãos selecionados para machos e fêmeas, com 30 repetições por geração e cenário. Independentemente da estratégia de acasalamento utilizada em um núcleo de produção fechada, há aumento nos níveis de endogamia. Aumentos de endogamia são maiores em populações de menor tamanho efetivo. Restrições ao número de irmãos completos e meios-irmãos selecionados são eficazes na redução de incrementos na endogamia. A restrição de no máximo dois irmãos completos, três meios-irmãos para machos e três irmãs completas para fêmeas fornece os maiores ganhos genéticos.(AU)

Genetic diversity assessment of the Mexican Simmental population through pedigree analysis

The purpose of this study was to examine the genetic variability of the Mexican Simmental. Inbreeding was calculated by year for animals born from 1985 to 2014. Proportion of ancestors known, average equivalent complete generations, generation interval, and effective size, as well as the effective numbers of founders, ancestors, and founder genomes were calculated for animals born in six periods (1985-1989, 1990-1994, 1995-1999, 2000-2004, 2005-2009, and 2010-2014). The year 1985 was selected as the initial year to form the subpopulations since the registration of the first Simmental cattle born in Mexico began in this year. Gene contributions of ancestors with the highest genetic influence were also calculated, using data of animals born in the latter period. Coefficients of inbreeding were low, ranging from 0.0068 to 0.0165. The average number of equivalent complete generations increased from 3.71, for the 1985-1989 subpopulation, to 5.83, for the 2010-2014 subpopulation. The population showed an effective population size of 186.6 animals in the last period. The numbers of founders, ancestors, and founder genomes increased from 1985 to 2004, but decreased from 2005 to 2014. The ratio of effective number of ancestors to effective number of founders and the ratio of effective number of founder genomes to effective number of ancestors were 0.31 and 0.66 and 0.27 and 0.63 for animals born in the 2005-2009 and 2010-2014 periods, respectively, revealing loss of diversity due to bottlenecks and genetic drift in the last decade. One ancestor explained 3.4% of the total genetic variability of the progeny born from 2010 to 2014, whereas the first fifteen ancestors explained 20% of such variability. The pedigree analysis showed Mexican Simmental cattle are not currently endangered.(AU)

Production of interspecific hybrids between commercial cultivars of the eggplant (Solanum melongena L.) and its wild relative S. torvum.

Interspecific hybrids between cultivars of eggplant (Solanum melongena L.) and its wild relative S. torvum, which has disease resistance and desirable traits for crop improvement, were obtained by cross-hybridization and embryo rescue. Twenty-one hybrid progenies were obtained and examined based on morphological traits, RAPD and ISSR markers. Five of them were confirmed to be true interspecific hybrids. Eighteen and 14 bands from 7 RAPD and 14 ISSR primers, respectively, were polymorphic and present in all five hybrid seedlings and their parents. The morphological characteristics of leaf margin, inflorescence type and spine positions of the five seedlings were intermediate to the parents. These interspecific hybrids had low pollen viability, probably due to abnormal meiosis.

Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes.

We have studied the nucleotide diversity of common bean, Phaseolus vulgaris, which is characterized by two independent domestications in two geographically distinct areas: Mesoamerica and the Andes. This provides an important model, as domestication can be studied as a replicate experiment. We used nucleotide data from five gene fragments characterized by large introns to analyse 214 accessions (102 wild and 112 domesticated). The wild accessions represent a cross-section of the entire geographical distribution of P. vulgaris. A reduction in genetic diversity in both of these gene pools was found, which was three-fold greater in Mesoamerica compared with the Andes. This appears to be a result of a bottleneck that occurred before domestication in the Andes, which strongly impoverished this wild germplasm, leading to the minor effect of the subsequent domestication bottleneck (i.e. sequential bottleneck). These findings show the importance of considering the evolutionary history of crop species as a major factor that influences their current level and structure of genetic diversity. Furthermore, these data highlight a single domestication event within each gene pool. Although the findings should be interpreted with caution, this evidence indicates the Oaxaca valley in Mesoamerica, and southern Bolivia and northern Argentina in South America, as the origins of common bean domestication.

Decision making in animal breeding programs and their consequences for animal production / Tomadas de decisão em programas de melhoramento animal e suas consequências para produção animal

Animal breeding technologies have advanced radically over the last 40 years and changed the way in which animals are farmed worldwide. While advances have been made, these methods have not always lived up to their promise or have led to the appearance of other unpredicted results. This has been caused by various factors such as ignorance of the correlated effects of selection or superestimation of the value of the technology. Also a dependence on technological advances often ignores important factors such as genotype x environment interaction, avoidance of inbreeding or maintenance of variation. This paper looks at some of these advances and their impact on farming practices.

As tecnologias de melhoramento animal têm avançado radicalmente nos últimos 40 anos e mudaram a maneira com que os animais são criados no mundo inteiro. Enquanto avanços têm sido realizados, os métodos nem sempre corresponderam a sua promessa ou levaram ao aparecimento de resultados inesperados. Isto se deve a vários fatores tais como ignorância dos efeitos correlacionados da seleção ou superestimação do valor da tecnologia. Além disso, uma dependência nos avanços tecnológicos frequentemente ignora fatores importantes como a interação genótipo-ambiente, impedição da endogamia ou manutenção da variação. Este artigo estuda alguns desses avanços e seu impacto nas práticas de criação dos animais.

Decision making in animal breeding programs and their consequences for animal production / Tomadas de decisão em programas de melhoramento animal e suas consequências para produção animal

Animal breeding technologies have advanced radically over the last 40 years and changed the way in which animals are farmed worldwide. While advances have been made, these methods have not always lived up to their promise or have led to the appearance of other unpredicted results. This has been caused by various factors such as ignorance of the correlated effects of selection or superestimation of the value of the technology. Also a dependence on technological advances often ignores important factors such as genotype x environment interaction, avoidance of inbreeding or maintenance of variation. This paper looks at some of these advances and their impact on farming practices.(AU)

As tecnologias de melhoramento animal têm avançado radicalmente nos últimos 40 anos e mudaram a maneira com que os animais são criados no mundo inteiro. Enquanto avanços têm sido realizados, os métodos nem sempre corresponderam a sua promessa ou levaram ao aparecimento de resultados inesperados. Isto se deve a vários fatores tais como ignorância dos efeitos correlacionados da seleção ou superestimação do valor da tecnologia. Além disso, uma dependência nos avanços tecnológicos frequentemente ignora fatores importantes como a interação genótipo-ambiente, impedição da endogamia ou manutenção da variação. Este artigo estuda alguns desses avanços e seu impacto nas práticas de criação dos animais.(AU)