scholarly journals A Mix of Old British and Modern European Breeds: Genomic Prediction of Breed Composition of Smallholder Pigs in Uganda

2021 ◽  
Vol 12 ◽  
Author(s):  
Brian Martin Babigumira ◽  
Johann Sölkner ◽  
Gábor Mészáros ◽  
Christina Pfeiffer ◽  
Craig R. G. Lewis ◽  
...  
Keyword(s):  
Longitudinal Study ◽  
Genomic Prediction ◽  
Production Systems ◽  
Inbreeding Coefficient ◽  
Growing Pigs ◽  
Runs Of Homozygosity ◽  
Breeding Programs ◽  
Snp Data ◽  
Hair Samples ◽  
Genomic Inbreeding

Pig herds in Africa comprise genotypes ranging from local ecotypes to commercial breeds. Many animals are composites of these two types and the best levels of crossbreeding for particular production systems are largely unknown. These pigs are managed without structured breeding programs and inbreeding is potentially limiting. The objective of this study was to quantify ancestry contributions and inbreeding levels in a population of smallholder pigs in Uganda. The study was set in the districts of Hoima and Kamuli in Uganda and involved 422 pigs. Pig hair samples were taken from adult and growing pigs in the framework of a longitudinal study investigating productivity and profitability of smallholder pig production. The samples were genotyped using the porcine GeneSeek Genomic Profiler (GGP) 50K SNP Chip. The SNP data was analyzed to infer breed ancestry and autozygosity of the Uganda pigs. The results showed that exotic breeds (modern European and old British) contributed an average of 22.8% with a range of 2–50% while “local” blood contributed 69.2% (36.9–95.2%) to the ancestry of the pigs. Runs of homozygosity (ROH) greater than 2 megabase (Mb) quantified the average genomic inbreeding coefficient of the pigs as 0.043. The scarcity of long ROH indicated low recent inbreeding. We conclude that the genomic background of the pig population in the study is a mix of old British and modern pig ancestries. Best levels of admixture for smallholder pigs are yet to be determined, by linking genotypes and phenotypic records.

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 The German Shorthair Pointer Dog Breed (Canis lupus familiaris): Genomic Inbreeding and Variability

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 498 ◽  
Author(s):  
Antonio Boccardo ◽  
Stefano Paolo Marelli ◽  
Davide Pravettoni ◽  
Alessandro Bagnato ◽  
Giuseppe Achille Busca ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Inbreeding Coefficient ◽  
Nucleotide Polymorphisms ◽  
Canis Lupus Familiaris ◽  
Runs Of Homozygosity ◽  
Single Nucleotide ◽  
The Mean ◽  
Dog Breed ◽  
Genomic Inbreeding ◽  
Genealogical Information

The German Shorthaired Pointer (GSHP) is a breed worldwide known for its hunting versatility. Dogs of this breed are appreciated as valuable companions, effective trackers, field trailers and obedience athletes. The aim of the present work is to describe the genomic architecture of the GSHP breed and to analyze inbreeding levels under a genomic and a genealogic perspective. A total of 34 samples were collected (24 Italian, 10 USA), and the genomic and pedigree coefficients of inbreeding have been calculated. A total of 3183 runs of homozygosity (ROH) across all 34 dogs have been identified. The minimum and maximum number of Single Nucleotide Polymorphisms (SNPs) defining all ROH are 40 and 3060. The mean number of ROH for the sample was 93.6. ROH were found on all chromosomes. A total of 854 SNPs (TOP_SNPs) defined 11 ROH island regions (TOP_ROH), in which some gene already associated with behavioral and morphological canine traits was annotated. The proportion of averaged observed homozygotes estimated on total number of SNPs was 0.70. The genomic inbreeding coefficient based on ROH was 0.17. The mean inbreeding based on genealogical information resulted 0.023. The results describe a low inbred population with quite a good level of genetic variability.

Assessment of genomic inbreeding in Polish Konik horses

2017 ◽  
Vol 20 (3) ◽  
pp. 603-605 ◽  
Author(s):  
S. Kamiński ◽  
D.M. Hering ◽  
Z. Jaworski ◽  
T. Zabolewicz ◽  
A. Ruść
Keyword(s):  
Statistical Analysis ◽  
Allele Frequency ◽  
Minor Allele Frequency ◽  
Snp Markers ◽  
Inbreeding Coefficient ◽  
Effective Management ◽  
Runs Of Homozygosity ◽  
Chromosome X ◽  
Genomic Inbreeding ◽  
A Minor

Abstract The aim of this study was to assess the inbreeding coefficient of Polish Konik horses based on runs of homozygosity (ROH). Ninety six horses kept in 6 herds located across Poland were genotyped with the use of EquineSNP60 BeadChip (Illumina). SNP markers with a Minor Allele Frequency lower than 0.01 and SNPs assigned to chromosome X or Y were excluded from the study. A total of 50 708 SNPs were included for statistical analysis (SVS software, Golden Helix). The analysis showed that the population is in genetic equilibrium, with He and Ho estimates both equal to 0.3086. Seven categories of Runs of Homozygozity (ROH) length were defined: >0.5, >1, >2, >4, >8, >16, >25 Mb. The genomic inbreeding coefficient derived from ROH (FROH) calculated for each ROH length ranged from 15.96% based on the shortest ROH (>0,5Mb) to 2.71% for the longest ROH (>25Mb). Among individual horses, the inbreeding coefficient ranged from 5.25% to 22.41% (for ROH >1Mb). Analysis of ROH in Polish Koniks allows for more effective management of their inbreeding in the future.

scholarly journals Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhong Xu ◽  
Shuqi Mei ◽  
Jiawei Zhou ◽  
Yu Zhang ◽  
Mu Qiao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genomic Selection ◽  
Artificial Selection ◽  
Sus Scrofa ◽  
Genome Structure ◽  
Inbreeding Coefficient ◽  
Runs Of Homozygosity ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Genomic Inbreeding

The primary purpose of the current study was to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore hotspot regions for traces of selection. First, we estimated the length, number, and frequency of ROH in 262 Xidu black pigs using the Porcine SNP50 BeadChip and compared the estimates of inbreeding coefficients, which were calculated based on ROHs (FROH) and homozygosity (FHOM). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In addition, Sus scrofa chromosome (SSC) 8 and SSC10, respectively, has the highest and lowest chromosome coverage by ROH. These results suggest that inbreeding estimation based on total ROH may be a useful method, especially for crossbreed or composite populations. We also calculated an inbreeding coefficient of 0.077 from the total ROH. Eight ROH islands were found in this study. These ROH islands harbored genes associated with fat deposition, muscular development, reproduction, ear shape, and adaptation, such as TRAF7, IGFBP7, XPO1, SLC26A8, PPARD, and OR1F1. These findings may help to understand the effects of environmental and artificial selection on the genome structure of composite pigs. Our results provide a basis for subsequent genomic selection (GS), and provides a reference for the hybrid utilization of other pig breeds.

scholarly journals Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3234
Author(s):  
José Cortes-Hernández ◽  
Adriana García-Ruiz ◽  
Carlos Gustavo Vásquez-Peláez ◽  
Felipe de Jesus Ruiz-Lopez
Keyword(s):  
Inbreeding Coefficient ◽  
Pedigree Information ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Genomic Relationship ◽  
Runs Of Homozygosity ◽  
Inbreeding Coefficients ◽  
Improvement Programs ◽  
Genomic Inbreeding ◽  
Holstein Population

This study aimed to identify inbreeding coefficient (F) estimators useful for improvement programs in a small Holstein population through the evaluation of different methodologies in the Mexican Holstein population. F was estimated as follows: (a) from pedigree information (Fped); (b) through runs of homozygosity (Froh); (c) from the number of observed and expected homozygotic SNP in the individuals (Fgeno); (d) through the genomic relationship matrix (Fmg). The study included information from 4277 animals with pedigree records and 100,806 SNP. The average and standard deviation values of F were 3.11 ± 2.30 for Fped, −0.02 ± 3.55 for Fgeno, 2.77 ± 0.71 for Froh and 3.03 ± 3.05 for Fmg. The correlations between coefficients varied from 0.30 between Fped and Froh, to 0.96 between Fgeno and Fmg. Differences in the level of inbreeding among the parent’s country of origin were found regardless of the method used. The correlations among genomic inbreeding coefficients were high; however, they were low with Fped, so further research on this topic is required.

The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations

Genomics ◽  
2021 ◽  
Author(s):  
Maryam Nosrati ◽  
Hojjat Asadollahpour Nanaei ◽  
Arash Javanmard ◽  
Ali Esmailizadeh
Keyword(s):  
World Wide ◽  
Runs Of Homozygosity ◽  
Genomic Inbreeding

scholarly journals Plant breeding in the semiarid region of Brazil: examples of success

2012 ◽  
Vol 12 (spe) ◽  
pp. 57-66 ◽  
Author(s):  
Manoel Abílio de Queiroz ◽  
Levi de Moura Barros ◽  
Luiz Paulo de Carvalho ◽  
Jonas de Araújo Candeia ◽  
Edinardo Ferraz
Keyword(s):  
Cotton Fiber ◽  
Production Systems ◽  
Rio Grande ◽  
Semiarid Region ◽  
Breeding Programs ◽  
Caatinga Biome ◽  
Colored Cotton ◽  
Nut Production ◽  
Production Area ◽  
Naturally Colored Cotton

The Northeastern region of Brazil comprises the Caatinga biome (900,000 km²) part of which is a semiarid region with rainfed and irrigated production systems. Among the successful breeding programs are cashew and cotton. The first led to a substantial increase in nut production in Ceará, Rio Grande do Norte and Piauí and the second bred a naturally colored cotton fiber, now processed in small clothing industries in Paraiba, exporting to 11 countries. In the lower-middle São Francisco valley, the previously grown onion was replaced by improved varieties, on 90% of the production area, and by industrial tomato, introduced by research in 1972, which came to be used on more than 80% of the area at the time. The participation of the private sector and continuity of breeding programs were crucial for the success. More examples of success are expected with the establishment of postgraduate courses in Agricultural Sciences in the Semiarid region.

scholarly journals Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0232436
Author(s):  
Christos Dadousis ◽  
Francesca Cecchi ◽  
Michela Ablondi ◽  
Maria Chiara Fabbri ◽  
Alessandra Stella ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cross Validation ◽  
Small Region ◽  
Economic Factors ◽  
Admixture Analysis ◽  
Goat Breed ◽  
Runs Of Homozygosity ◽  
Genomic Inbreeding ◽  
Assignment Success ◽  
Integrated Study

The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (~25 goats/breed), whose genotypes were available from the AdaptMap project [Argentata (ARG), Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of breed traceability via discriminant analysis on principal components (DAPC) based on cross-validation. ROH analyses was used to assess the genetic diversity of GRF, while admixture and DAPC to evaluate its relationship to the other breeds. For GRF, common ROH (more than 45% in GRF samples) was detected on CHR 12 at, roughly 50.25–50.94Mbp (ARS1 assembly), which spans the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area of common ROH was also present in DIT, while a broader region (~49.25–51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis revealed a small region of common ancestry from GRF shared by BIO, VSS, ARG and CCG breeds. The DAPC model yielded 100% assignment success for GRF. Overall, our results support the identification of GRF as a distinct native Italian goat breed. This work can contribute to planning conservation programmes to save GRF from extinction and will improve the understanding of the socio-agro-economic factors related with the farming of GRF.

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