Runs of homozygosity for autozygosity estimation and genomic analysis in production animals

Abstract: Runs of homozygosity (ROHs) are long stretches of homozygous genomic segments, identifiable by molecular markers, which can provide genomic information for accurate estimates to characterize populations, determine evolutionary history and demographic information, estimate levels of consanguinity, and identify selection signatures in production animals. This review paper aims to perform a survey of the works on the efficiency of ROHs for these purposes. Factors such as genetic drift, natural or artificial selection, founder effect, and effective population size directly influence the size and distribution of ROHs along the genome. Individually, genome estimates of consanguinity based on ROHs can be obtained using the FROH index, which is generally considered more accurate than indexes based on other types of genomic or genealogical information. High frequencies of specific ROHs in a population can be used to identify selection signatures. The results of recent studies with ROHs in domestic animals have shown the efficiency of their use to characterize herds in a reliable and accessible way, using genomic information.

Download Full-text

Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

Genes ◽

10.3390/genes10110938 ◽

2019 ◽

Vol 10 (11) ◽

pp. 938 ◽

Cited By ~ 4

Author(s):

Islam ◽

Li ◽

Liu ◽

Berihulay ◽

Abied ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Positive Selection ◽

Candidate Genes ◽

Runs Of Homozygosity ◽

Selection Signatures ◽

Effective Population ◽

Signature Of Selection ◽

Genomic Regions ◽

Insight Into

: Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

Download Full-text

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Animals ◽

10.3390/ani11020321 ◽

2021 ◽

Vol 11 (2) ◽

pp. 321

Author(s):

Jorge Hidalgo ◽

Alberto Cesarani ◽

Andre Garcia ◽

Pattarapol Sumreddee ◽

Neon Larios ◽

...

Keyword(s):

Genetic Variability ◽

Population Size ◽

Effective Population Size ◽

Genetic Background ◽

Cattle Breed ◽

Pedigree Information ◽

Runs Of Homozygosity ◽

Genomic Information ◽

Effective Population ◽

Genetic Progress

The ultimate goal of genetic selection is to improve genetic progress by increasing favorable alleles in the population. However, with selection, homozygosity, and potentially harmful recessive alleles can accumulate, deteriorating genetic variability and hampering continued genetic progress. Such potential adverse side effects of selection are of particular interest in populations with a small effective population size like the Romosinuano beef cattle in Mexico. The objective of this study was to evaluate the genetic background and inbreeding depression in Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The reduction in effective population size implies the existence of genetic bottlenecks and the decline of genetic diversity due to the intensive use of few individuals as parents of the next generations. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The shortest and longest segments were 1.0 and 36.0 Mb long, respectively, reflecting ancient and recent inbreeding. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. The correlation between FPED and FGRM was −0.25, and the correlations among FPED and FROH of different length classes were low (from 0.16 to 0.31). The correlations between FGRM and FROH of different length classes were moderate (from 0.44 to 0.58), indicating better agreement. A 1% increase in population inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to more sustainable breeding programs for the Mexican Romosinuano beef cattle breed.

Download Full-text

Population Genomic Analysis of ALMS1 in Humans Reveals a Surprisingly Complex Evolutionary History

Molecular Biology and Evolution ◽

10.1093/molbev/msp045 ◽

2009 ◽

Vol 26 (6) ◽

pp. 1357-1367 ◽

Cited By ~ 18

Author(s):

Laura B. Scheinfeldt ◽

Shameek Biswas ◽

Jennifer Madeoy ◽

Caitlin F. Connelly ◽

Eric E. Schadt ◽

...

Keyword(s):

Evolutionary History ◽

Genomic Analysis ◽

Population Genomic ◽

Complex Evolutionary History

Download Full-text

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

Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis ◽

10.11118/actaun201967061457 ◽

2019 ◽

Vol 67 (6) ◽

pp. 1457-1463 ◽

Cited By ~ 2

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.

Download Full-text

Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽

10.3390/ani9060361 ◽

2019 ◽

Vol 9 (6) ◽

pp. 361 ◽

Cited By ~ 3

Author(s):

Shuqi Diao ◽

Shuwen Huang ◽

Zhiting Xu ◽

Shaopan Ye ◽

Xiaolong Yuan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Conservation Status ◽

Snp Array ◽

Size Analysis ◽

Selection Signatures ◽

Effective Population ◽

Low Genetic Diversity ◽

Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

Download Full-text

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

Animals ◽

10.3390/ani10030498 ◽

2020 ◽

Vol 10 (3) ◽

pp. 498 ◽

Cited By ~ 1

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.

Download Full-text

Comparative genomic analysis of Klebsiella pneumoniae subsp. pneumoniae KP617 and PittNDM01, NUHL24835, and ATCC BAA-2146 reveals unique evolutionary history of this strain

Gut Pathogens ◽

10.1186/s13099-016-0117-1 ◽

2016 ◽

Vol 8 (1) ◽

Cited By ~ 9

Author(s):

Taesoo Kwon ◽

Young-Hee Jung ◽

Sanghyun Lee ◽

Mi-ran Yun ◽

Won Kim ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Evolutionary History ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

History Of

Download Full-text

Whole-Genome Sequencing of Mexican Strains of Anaplasma marginale: An Approach to the Causal Agent of Bovine Anaplasmosis

International Journal of Genomics ◽

10.1155/2020/5902029 ◽

2020 ◽

Vol 2020 ◽

pp. 1-7

Author(s):

Fernando Martínez-Ocampo ◽

Rosa Estela Quiroz-Castañeda ◽

Itzel Amaro-Estrada ◽

Edgar Dantán-González ◽

Jesús Francisco Preciado de la Torre ◽

...

Keyword(s):

Gc Content ◽

Genomic Analysis ◽

Anaplasma Marginale ◽

Etiologic Agent ◽

Genomic Information ◽

Genomic Comparison ◽

Bovine Anaplasmosis ◽

Molecular Landscape ◽

Average Size ◽

Mexican Strains

Anaplasma marginale is the main etiologic agent of bovine anaplasmosis, and it is extensively distributed worldwide. We have previously reported the first genome sequence of a Mexican strain of A. marginale (Mex-01-001-01). In this work, we report the genomic analysis of one strain from Hidalgo (MEX-14-010-01), one from Morelos (MEX-17-017-01), and two strains from Veracruz (MEX-30-184-02 and MEX-30-193-01). We found that the genome average size is 1.16-1.17 Mbp with a GC content close to 49.80%. The genomic comparison reveals that most of the A. marginale genomes are highly conserved and the phylogeny showed that Mexican strains cluster with Brazilian strains. The genomic information contained in the four draft genomes of A. marginale from Mexico will contribute to understanding the molecular landscape of this pathogen.

Download Full-text

Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage

mSystems ◽

10.1128/msystems.00867-20 ◽

2020 ◽

Vol 5 (6) ◽

Author(s):

Liangzhi Li ◽

Zhenghua Liu ◽

Min Zhang ◽

Delong Meng ◽

Xueduan Liu ◽

...

Keyword(s):

Acid Mine Drainage ◽

Evolutionary History ◽

Mine Drainage ◽

Extreme Environments ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Metabolic Potential ◽

Ecological Functions ◽

History Of

ABSTRACT Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium. In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium. Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions. IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.

Download Full-text