PSI-B-23 Assessment of genomic inbreeding in Russian local and commercial dairy breeds of cattle

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 227-228
Author(s):  
Arina I Mishina ◽  
Alexandra S Abdelmanova ◽  
Arsen V Dotsev ◽  
Alexander A Sermyagin ◽  
Gottfried Brem ◽  
...  
Keyword(s):  
Higher Education ◽  
Genetic Diversity ◽  
Quality Control ◽  
Population Size ◽  
Milk Production ◽  
Artificial Insemination ◽  
Inbreeding Coefficient ◽  
Autosomal Snps ◽  
Cattle Breeds ◽  
Genomic Inbreeding

Abstract Drastic decline of population size of Russian local cattle breeds observed during last three decades has led to the decrease of genetic diversity. Due to the limited number of bulls used for artificial insemination, inbreeding in herds can be increased, which can lead to the decrease of reproduction capacity and adaptability of animals. Our aim was to assess genomic inbreeding in two Russian local cattle breeds, including Kholmogor (n = 26) and Istoben (n = 21). Two transboundary cattle breeds used for milk production in Russia including Holstein (n = 49) and Simmental (n = 38) were chosen for comparison. SNP genotyping was performed using the Bovine GGP 150K BeadArray (Illumina, CA, USA). After the quality control, 117591 autosomal SNPs were selected for analyzes. The degree of genomic inbreeding was assessed by calculations of inbreeding coefficient based on run of homozygosity (F(ROH)) and multilocus heterozygosity (sMLH). We found the strong negative correlations between the F(ROH) and sMLH values in animals of all of studied breeds (r2 = -0.805). The average F(ROH) values were 0.065 < mo >±< /mo >< /math >“>±± 0.003 for Kholmogor, 0.048 < mo >±< /mo >< /math >“>±± 0.006 for Istoben, 0.129 < mo >±< /mo >< /math >“>±± 0.007 for Holstein, and 0.102 < mo >±< /mo >< /math >“>±± 0.007 for Simmental breed. The sMLH values in Kholmogor, Istoben, Holstein and Simmental breeds varied from 0,99 to 1,076, from 0,829 to 1,102, from 0,890 to 1,069 and from 0,866 to 1,041, and averaged to 1.030, 1.013, 1.000, and 0.974, respectively. According to our research results, two studied Russian cattle breeds are characterized by lower levels of genomic inbreeding compared to transboundary cattle breeds. Our results will be helpful for developing the conservation programs for Russian Kholmogor and Istoben cattle breeds. The study was funded by the Russian Ministry of Science and Higher Education within theme No. 0445-2019-0024 and RFBR within project 19-316-90017 (the study of Kholmogor cattle).

scholarly journals Genomics Confirm an Alarming Status of the Genetic Diversity of Belgian Red and Belgian White Red Cattle

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3574
Author(s):  
Roel Meyermans ◽  
Wim Gorssen ◽  
Nadine Buys ◽  
Steven Janssens
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Size Estimation ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Genetic Management ◽  
Cattle Breeds ◽  
Signature Of Selection ◽  
Genomic Inbreeding

Genetic diversity is increasingly important for researchers and society. Small and local populations deserve more attention especially, as they may harbor important characteristics. Moreover, small populations are at greater risk and their genetic management is often more challenging. Likewise, European red cattle populations are threatened, as they are outcompeted by more specialized cattle breeds. In this study, we investigate the genetic diversity of two local Belgian red cattle breeds: Belgian Red and Belgian White Red cattle. A total of 270 animals were genotyped via medium density SNP arrays. Genetic diversity was assessed using runs of homozygosity screening, effective population size estimation and Fst analyses. Genomic inbreeding coefficients based on runs of homozygosity were estimated at 7.0% for Belgian Red and 6.1% for Belgian White Red cattle, and both populations had a low effective population size (68 and 86, respectively). PCA, Fst and admixture analyses revealed the relationship to 52 other international breeds, where they were closest related to some Belgian, French, Scandinavian and Dutch breeds. Moreover, Fst analyses revealed for Belgian Red cattle a signature of selection on BTA6, adjacent to the KIT gene. This study gains important knowledge on the genetic diversity of these two small local red cattle breeds, and will aid in their (genetic) management.

scholarly journals Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

2019 ◽  
Vol 67 (6) ◽  
pp. 1457-1463 ◽  
Author(s):  
Radovan Kasarda ◽  
Nina Moravčíková ◽  
Ondrej Kadlečík ◽  
Anna Trakovická ◽  
Marko Halo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quality Control ◽  
Genomic Analysis ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Snp Markers ◽  
Runs Of Homozygosity ◽  
Current Generation ◽  
Genomic Inbreeding

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

Pedigree-based analysis of genetic variability in the registered Normande cattle breed in Colombia

2017 ◽  
Vol 57 (3) ◽  
pp. 422
Author(s):  
Derly Rodríguez Sarmiento ◽  
Emanuela Tullo ◽  
Rita Rizzi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Population Size ◽  
Cattle Breed ◽  
Inbreeding Coefficient ◽  
Mating Strategies ◽  
Effective Population ◽  
Significant Difference ◽  
Genealogical Information ◽  
Over Time

Genetic variability and structure of the population were studied in 7949 registered Normande cattle in Colombia. The pedigree was deep with 18 traced generations, but there were some incomplete genealogical information for the cattle born in the more distant past. The average number of complete and equivalent complete generations was 2.42 and 5.21, respectively. The average pedigree completeness index for five generations was 0.62, which increased over time, and a significant difference between sexes was found (males: 0.82 ± 0.11; females: 0.62 ± 0.38). The average generation interval was 7.57 years. The number of founders, effective founders, ancestors, and founder genomes were 575, 115, 47, and 22.22, respectively, which suggests that an unequal use of founders and a random loss of alleles from founders occurred over time. The level of inbreeding was 0.019 and increased to 0.023, when the inbreeding coefficient was calculated by assigning inbreeding of contemporaries to founders. These levels of inbreeding lead to an effective population size of 138.5 and 117.9 and to a 0.36% and 0.42% rate of inbreeding, respectively. Out of 267 herds with more than five registered breeding animals, only one nucleus herd was present, whereas 117 and 119 were classified as multiplier and commercial herds, respectively. About 92% of calves were sired by French bulls; but the use of Colombian bulls for breeding is increasing. The Colombian Normande breed is at an acceptable level of genetic variability, although some losses of founder alleles have occurred. As the level of inbreeding has been increasing, inbreeding and mating strategies should be monitored in order to maintain the genetic diversity of the breed.

scholarly journals Genetic characteristics and diversity of Korean Jeju Black cattle by whole genome SNP markers

2020 ◽  
Author(s):  
Mohammad Zahangir Alam ◽  
Hyo Jung Son ◽  
Yun Mi Lee ◽  
Lauren Hulsman Hanna ◽  
David Riley ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Improvement ◽  
Effective Population ◽  
Model Based Clustering ◽  
Cattle Breeds ◽  
Model Based ◽  
Jeju Black Cattle

Abstract Background Conservation and genetic improvement of cattle breeds requires to know the information about genetic diversity and population structure of animals. This study investigated the genetic diversity and population structure among the three breeds raised in Korean peninsula. Three popular breed found in Korea , i.e. Jeju Black, Hanwoo, Holstein with other six breeds such as Angus, Hereford, Brown Wagyu, Black Wagyu, Brahman and Nellore was examined in this study. Genetic diversity within the cattle breeds was analyzed using the popular measures of genetic diversity namely minor allele frequency (MAF), observed and expected heterozygosity (H O and H E ), inbreeding coefficient (F IS ) and past effective population size (N E ). Molecular variance and population structure were performed among the nine cattle breeds using model-based clustering (ADMIXTURE) analysis. Genetic distances between breed pairs were evaluated using Nei’s genetic distance (D A ) and with Weir and Cockerham’s F ST . Results This study revealed that Jeju Black cattle had lowest level of heterozygocity (HE = 0.21) among the studied taurine cattle breeds ranging from 0.25 to 0.30, and low MAF of 0.16, while other breeds have MAF ranging 0.11~0.21. The level of inbreeding was -0.076 in case of Jeju Black as compared to other breed (-0.018 ~ -0.118). PCA analysis and neighbor-joining (NJ) tree showed a clear separation of Jeju Black cattle from other local and exotic cattle breeds. Model-based clustering also revealed a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The F ST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The N E of Jeju Black cattle was 38, whereas Hanwoo was 209 in the most recent 13 generation ago. Conclusion This study indicates an alarming trend of reducing effective population size in Jeju Black cattle. Thus, a sustainable breeding policy should be implemented to increase the population of Jeju Black cattle for the genetic improvement and future conservation.

scholarly journals Monitoring of genetic diversity in autochthonous Czech poultry breeds assessed by genealogical data

2020 ◽  
Vol 65 (No. 6) ◽  
pp. 224-231
Author(s):  
Luboš Vostrý ◽  
Hana Vostrá-Vydrová ◽  
Nina Moravčíková ◽  
Barbora Hofmanová ◽  
Jana Rychtářová ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Inbreeding Coefficient ◽  
Pedigree Data ◽  
Allele Loss ◽  
Loss Of Genetic Diversity

Czech local poultry breeds face high risks of extinction. Because these populations are closed, they are more likely to lose genetic diversity. The aim of this analysis was to determine the loss of genetic diversity in three Czech autochthonous poultry breeds. Pedigree data from a total of 1 932 Czech Gold Speckled Hens, 325 Czech White Geese and 111 Czech Crested Geese registered in studbooks between 2000 and 2018 were evaluated. Data were analysed to determine the major factors that affect the genetic variability of these breeds. The average numbers of equivalent complete generations ranged from 2.53 to 4.82. The effective numbers of founders were from 29 to 59, representing from 43% to 62% of the total number of founders. The effective number of ancestors was estimated in the range of 21 to 41. The average inbreeding coefficient and relatedness coefficient (in parentheses) for the reference populations were 2.0% (6.5%), 1.9% (4.9%) and 2.1% (9.3%), respectively. The results showed that the effective population size derived from the rate of inbreeding ranged from 46 to 108 and if derived from the rate of coancestry it ranged from 35 to 74. With regard to these results, the analysed breeds showed a high probability of allele loss and consequent loss of genetic diversity.

Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size

2009 ◽  
Vol 18 (16) ◽  
pp. 3394-3410 ◽  
Author(s):  
IVICA MEDUGORAC ◽  
ANA MEDUGORAC ◽  
INGOLF RUSS ◽  
CLAUDIA E. VEIT-KENSCH ◽  
PIERRE TABERLET ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Conservation Value ◽  
Effective Population ◽  
Cattle Breeds ◽  
European Cattle

scholarly journals Biodiversity of Russian Local Sheep Breeds Based on Pattern of Runs of Homozygosity

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 360
Author(s):  
Tatiana Deniskova ◽  
Arsen Dotsev ◽  
Marina Selionova ◽  
Gottfried Brem ◽  
Natalia Zinovieva
Keyword(s):  
Genetic Diversity ◽  
Biodiversity Loss ◽  
Inbreeding Coefficient ◽  
Loss Estimation ◽  
Runs Of Homozygosity ◽  
Sheep Breeds ◽  
Snp Data ◽  
Population Sizes ◽  
The Mean ◽  
Genomic Inbreeding

Russian sheep breeds traditionally raised in specific environments are valuable parts of sociocultural heritage and economic component of the regions. However, the import of commercial breeds negatively influences the population sizes of local sheep populations and might lead to biodiversity loss. Estimation of the runs of homozygosity (ROH) in local sheep genomes is an informative tool to address their current genetic state. In this work, we aimed to address the ROH distribution and to estimate genome inbreeding based on SNP data to evaluate genetic diversity in Russian local sheep breeds. Materials for this study included SNP-genotypes from twenty-seven Russian local sheep breeds which were generated using the Illumina OvineSNP50 BeadChip (n = 391) or the Illumina Ovine Infinium HD BeadChip (n = 315). A consecutive runs method was used to calculate ROH which were estimated for each animal and then categorized in the ROH length classes. The ROH were found in all breeds. The mean ROH length varied from 86 to 280 Mb, while the ROH number ranged from 37 to 123. The genomic inbreeding coefficient varied from 0.033 to 0.106. Our findings provide evidence of low to moderate genomic inbreeding in major local sheep populations.

scholarly journals Genetic Diversity, Inbreeding Level, and Genetic Load in Endangered Snub-Nosed Monkeys (Rhinopithecus)

2020 ◽  
Vol 11 ◽  
Author(s):  
Weimin Kuang ◽  
Jingyang Hu ◽  
Hong Wu ◽  
Xiaotian Fen ◽  
Qingyan Dai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Large Population ◽  
Population Decline ◽  
Genetic Load ◽  
Term Survival ◽  
Population Sizes ◽  
Genomic Inbreeding ◽  
Inbreeding Level

The snub-nosed monkey genus (Rhinopithecus) comprises five closely related species (R. avunculus, R. bieti, R. brelichi, R. roxellana, and R. strykeri). All are among the world's rarest and most endangered primates. However, the genomic impact associated with their population decline remains unknown. We analyzed population genomic data of all five snub-nosed monkey species to assess their genetic diversity, inbreeding level, and genetic load. For R. roxellana, R. bieti, and R. strykeri, population size is positively correlated with genetic diversity and negatively correlated with levels of inbreeding. Other species, however, which possess small population sizes, such as R. brelichi and R. avunculus, show high levels of genetic diversity and low levels of genomic inbreeding. Similarly, in the three populations of R. roxellana, the Shennongjia population, which possesses the lowest population size, displays a higher level of genetic diversity and lower level of genomic inbreeding. These findings suggest that although R. brelichi and R. avunculus and the Shennongjia population might be at risk, it possess significant genetic diversity and could thus help strengthen their long-term survival potential. Intriguingly, R. roxellana with large population size possess high genetic diversity and low level of genetic load, but they show the highest recent inbreeding level compared with the other snub-nosed monkeys. This suggests that, despite its large population size, R. roxellana has likely been experiencing recent inbreeding, which has not yet affected its mutational load and fitness. Analyses of homozygous-derived deleterious mutations identified in all snub-nosed monkey species indicate that these mutations are affecting immune, especially in smaller population sizes, indicating that the long-term consequences of inbreeding may be resulting in an overall reduction of immune capability in the snub-nosed monkeys, which could provide a dramatic effect on their long-term survival prospects. Altogether, our study provides valuable information concerning the genomic impact of population decline of the snub-nosed monkeys. We revealed multiple counterintuitive and unexpected patterns of genetic diversity in small and large population, which will be essential for conservation management of these endangered species.

scholarly journals Genomic Characterization of the Istrian Shorthaired Hound

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2013
Author(s):  
Ivona Djurkin Kušec ◽  
Ivica Bošković ◽  
Minja Zorc ◽  
Kristina Gvozdanović ◽  
Dubravko Škorput ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Size ◽  
Snp Array ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
Indigenous Breed ◽  
Hunting Dogs ◽  
Hunting Dog ◽  
Genealogical Data

Istrian shorthaired hound is an old indigenous Croatian dog breed with historical traces of its origin, which date back to the 14th century. Due to its intelligence and great hunting abilities, it is considered an excellent hunting dog. Despite its ancient origin, there is no data on genetic diversity, population structure, and degree of inbreeding that could be used for advanced management and conservation of this breed. Our study aimed to provide a high-resolution population structure of the Istrian shorthaired hound using a 220K HD SNP array, to compare the obtained data with the genealogical records and to place the breed in a broader context of world dog populations. Relatively high population size and low inbreeding coefficient estimated from genealogical data indicate a preserved genetic diversity in this breed. The principle component analysis, the NeighborNet network, and TreeMix were used to determine the genetic relationship between the Istrian shorthaired hound and other breeds. The Istrian shorthaired hound was found to be genetically related to Italian hunting dogs sharing the same branch with the Segugio Italiano a Pelo Raso and Segugio Italiano a Pelo Forte. The ADMIXTURE analysis indicated that the Istrian shorthaired hound could be involved in the development of some other hunting dog breeds. The estimated effective population size (Ne) based on SNP data was similar to Ne calculated from genealogical data indicating the absence of bottlenecks and well-balanced use of breeding animals. The low genomic inbreeding coefficient, together with the higher number of short runs of homozygosity, observed in the Istrian shorthaired hound, confirms the ancient origin of the breed based on historical documents. The analysis of selective sweeps identified genomic regions with the strongest selection signals in the vicinity of the genes associated with cognitive performance and behavior. Genome analysis proved to be a useful tool for estimating population parameters and can be implemented in the conservation plan for this indigenous breed.

Challenges and Opportunities of Artificial Insemination on Dairy Cattle in Ethiopia

2021 ◽  
Vol 1 (2) ◽  
pp. 47-54
Author(s):  
Mohammed Yousuf
Keyword(s):  
Dairy Cattle ◽  
Milk Production ◽  
Artificial Insemination ◽  
Genetic Improvement ◽  
Dairy Industry ◽  
Dairy Farmers ◽  
Local Breed ◽  
Cattle Breeds ◽  
Challenges And Opportunities

Artificial insemination is very important for genetic improvement, especially in dairy cattle breeds. It has problems in meeting the needs of some producers, not its opportunities. The objective of this study was the challenge and opportunity of artificial insemination on dairy cattle in the case of Sayo district, west Wollega Zone, Ethiopia. The problem of not using Artificial insemination is not limited to the region, and there are also dairy farmers in our district who have not practiced the service due to various challenges. In addition, most of the Artificial insemination services reported by the dairy industry have failed, rather than bull services. However, although there are few attempts to quantify opportunities, constraints, and why producers do not use artificial insemination services in other regions, researchers have not disclosed well-documented data on the challenges and opportunities of artificial insemination services in the Sayo region. The Result is Artificial insemination has played an important role in increasing milk production in the study area because the crossbreed that got good traits from exotic breeds gave high milk than local breed.

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