scholarly journals Harmful mutation load in the mitochondrial genomes of cattle breeds

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Artificial Selection ◽  
Deleterious Mutation ◽  
Genetic Diseases ◽  
Mitochondrial Genomes ◽  
Deleterious Mutations ◽  
Founder Population ◽  
Mutation Load ◽  
Effective Population ◽  
Cattle Breeds

Abstract Objective Domestication of wild animals results in a reduction in the effective population size, and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to the accumulation of deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 364 animals belonging to 18 cattle breeds of the world. Results Our analysis revealed more than a fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the breed age and the proportion of deleterious amino acid-changing polymorphisms. This suggests a proportionally higher deleterious SNPs in young breeds compared to older breeds. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

scholarly journals Harmful Mutation Load in the Mitochondrial Genomes of Cattle Breeds 

2021 ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Amino Acid ◽  
Population Size ◽  
Artificial Selection ◽  
Deleterious Mutation ◽  
Mitochondrial Genomes ◽  
Deleterious Mutations ◽  
Founder Population ◽  
Mutation Load ◽  
Effective Population ◽  
Cattle Breeds

Abstract ObjectiveDomestication of wild animals results in a reduction in the effective population size and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to accumulation deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 252 animals belonging to 15 cattle breeds of the world. ResultsOur analysis revealed more than fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the neutral heterozygosity and the ratio of amino acid changing diversity to silent diversity. This suggests a proportionally higher amino acid changing variants in breeds with low diversity. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

scholarly journals Deleterious mutation load in diverse cattle breeds of the world

2021 ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Artificial Selection ◽  
High Frequency ◽  
Deleterious Mutation ◽  
East Asian ◽  
Low Frequency ◽  
Mutation Load ◽  
Cattle Breeds ◽  
The World ◽  
Low Diversity

Abstract Domestication of wild animals results in a reduction in the effective population size and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to accumulation deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using the whole genome data from 432 animals belonging to 54 cattle breeds of the world. Our analysis revealed a negative correlation between the genomic heterozygosity and the ratio of amino acid changing diversity to silent diversity. This suggests a proportionally higher amino acid changing Single Nucleotide variants (SNVs) in breeds with low diversity. Our results also showed that breeds with low diversity had more high-frequency (DAF > 0.51) deleterious SNVs than those with high diversity. A reverse trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, taurine cattle breeds had more high-frequency deleterious SNVs than indicine (or taurine-indicine hybrid) breeds. However, within taurine breeds European or Northeast Asian taurines had more high-frequency deleterious SNVs than East Asian or African taurine breeds. Similarly, within indicine breeds South Asian indicines had more high-frequency deleterious SNVs than East Asian indicine breeds. All the above observed patterns were reversed for low frequency deleterious SNVs. Some of the variation in the deleterious mutation load observed between different breeds could be attributed to the population sizes of the wild progenitors before domestication. However, the variations observed withing taurine and within indicine breeds could be due to the difference in the extent of inbreeding, strength of artificial selection and/or founding population size. The findings of this study imply that the rate of incidence of genetic diseases might vary between cattle breeds.

scholarly journals Deleterious protein-coding variants in diverse cattle breeds of the world

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Artificial Selection ◽  
High Frequency ◽  
Deleterious Mutation ◽  
Low Frequency ◽  
Mutation Load ◽  
Single Nucleotide Variants ◽  
Cattle Breeds ◽  
Low Diversity ◽  
Population Sizes ◽  
Taurine Cattle

AbstractThe domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.

scholarly journals The mutation load under tetrasomic inheritance and its consequences for the evolution of the selfing rate in autotetraploid species

1999 ◽  
Vol 74 (1) ◽  
pp. 31-42 ◽  
Author(s):  
J. RONFORT
Keyword(s):  
Inbreeding Depression ◽  
Deleterious Mutation ◽  
Stable State ◽  
Approximate Solutions ◽  
Balance Model ◽  
Deleterious Mutations ◽  
Selfing Rate ◽  
Mutation Load ◽  
Mean Fitness ◽  
The Mean

Single-locus equilibrium frequencies of a partially recessive deleterious mutation under the mutation–selection balance model are derived for partially selfing autotetraploid populations. Assuming multiplicative fitness interactions among loci, approximate solutions for the mean fitness and inbreeding depression values are also derived for the multiple locus case and compared with expectations for the diploid model. As in diploids, purging of deleterious mutations through consanguineous matings occurs in autotetraploid populations, i.e. the equilibrium mutation load is a decreasing function of the selfing rate. However, the variation of inbreeding depression with the selfing rate depends strongly on the dominance coefficients associated with the three heterozygous genotypes. Inbreeding depression can either increase or decrease with the selfing rate, and does not always vary monotonically. Expected issues for the evolution of the selfing rate consequently differ depending on the dominance coefficients. In some cases, expectations for the evolution of the selfing rate resemble expectations in diploids; but particular sets of dominance coefficients can be found that lead to either complete selfing or intermediate selfing rates as unique evolutionary stable state.

scholarly journals Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0246497
Author(s):  
Vandana Manomohan ◽  
Ramasamy Saravanan ◽  
Rudolf Pichler ◽  
Nagarajan Murali ◽  
Karuppusamy Sivakumar ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
South India ◽  
Genetic Admixture ◽  
Zebu Cattle ◽  
Effective Population ◽  
Cattle Breeds ◽  
South Indian ◽  
Indian Cattle

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

scholarly journals Lethals in subdivided populations

2005 ◽  
Vol 86 (1) ◽  
pp. 41-51 ◽  
Author(s):  
SYLVAIN GLÉMIN
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Inbreeding Depression ◽  
Deleterious Mutations ◽  
Mutation Load ◽  
General Picture ◽  
Analytical Approximations ◽  
Size Population ◽  
Subdivided Populations ◽  
Numerical Approaches

The fate of lethal alleles in populations is of interest in evolutionary and conservation biology for several reasons. For instance, lethals may contribute substantially to inbreeding depression. The frequency of lethal alleles depends on population size, but it is not clear how it is affected by population structure. By analysing the case of the infinite island model by numerical approaches and analytical approximations it is shown that, like population size, population structure affects the fate of lethal alleles if dominance levels are low. Inbreeding depression caused by such alleles is also affected by the population structure, whereas the mutation load is only weakly affected. Heterosis also depends on population structure, but it always remains low, of the order of the mutation rate or less. These patterns are compared with those caused by mildly deleterious mutations to give a general picture of the effect of population structure on inbreeding depression, heterosis, and the mutation load.

scholarly journals Inbreeding depression due to mildly deleterious mutations in finite populations: size does matter

2000 ◽  
Vol 75 (1) ◽  
pp. 75-81 ◽  
Author(s):  
THOMAS BATAILLON ◽  
MARK KIRKPATRICK
Keyword(s):  
Population Size ◽  
Inbreeding Depression ◽  
Deleterious Mutation ◽  
Large Population ◽  
Genetic Load ◽  
Breeding Systems ◽  
Deleterious Mutations ◽  
Single Locus Analysis ◽  
Population Sizes ◽  
Inbreeding Rate

We studied the effects of population size on the inbreeding depression and genetic load caused by deleterious mutations at a single locus. Analysis shows how the inbreeding depression decreases as population size becomes smaller and/or the rate of inbreeding increases. This pattern contrasts with that for the load, which increases as population size becomes smaller but decreases as inbreeding rate goes up. The depression and load both approach asymptotic limits when the population size becomes very large or very small. Numerical results show that the transition between the small and the large population regimes is quite rapid, and occurs largely over a range of population sizes that vary by a factor of 10. The effects of drift on inbreeding depression may bias some estimates of the genomic rate of deleterious mutation. These effects could also be important in the evolution of breeding systems in hermaphroditic organisms and in the conservation of endangered populations.

scholarly journals Inbreeding in artificial selection programmes

1961 ◽  
Vol 2 (2) ◽  
pp. 189-194 ◽  
Author(s):  
Alan Robertson
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Artificial Selection ◽  
Actual Number ◽  
Effective Population

In a population under artificial selection, the effective population size may be less than the actual number of parents selected because there will be variation between families in the character under selection and consequently in the probability of selection. Expressions are developed for the magnitude of the effect, which will be greater the more intense the selection and the higher the heritability of the selected character. The inbreeding due to outstanding individuals may rise for several generations after their use.

scholarly journals The effects of X-rays on quantitative characters

1964 ◽  
Vol 5 (3) ◽  
pp. 410-422 ◽  
Author(s):  
G. A. Clayton ◽  
Alan Robertson
Keyword(s):  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Artificial Selection ◽  
Inbred Lines ◽  
X Rays ◽  
Effective Population ◽  
Outbred Population ◽  
Culture Bottle ◽  
Quantitative Characters

1. The rate of production by X-rays of new genetic variation in two quantitative characters in Drosophila melanogaster (sternital and sternopleural bristles) has been investigated, using ‘plateaued’ populations which had reached the limit under artificial selection and, for sternital bristles only, populations which had been made genetically invariant by inbreeding. The genetic variation was always measured by the response of the population to selection. The X-rays dose given in any generation was always 1800 r. to adults.2. Seven plateaued lines had eight cycles of alternate irradiation and selection, each with its non-irradiated control. All the responses were small but in three lines they were significantly greater after irradiation.3. Selection was applied to three different inbred lines, genetically marked to detect contamination, after varying periods of irradiation. At the same time, the inbred lines and lines derived from them which had been mass mated in bottles were selected. The irradiated populations showed a greater response. The new genetic variance produced by the irradiation was approximately 10−5 units/r. The estimate of the dose required to introduce new variation equal to that in a standard outbred population was 500,000 r.4. The effective population size was an important factor in the interpretation of some of these results on the long-term effects of radiation. By observing the variation between replicate lines in the frequency of a gene with a visible effect under these culture conditions (i.e. in a single culture bottle) the effective population size was estimated at sixty. Outbred populations kept under these conditions for many generations showed a reduction of genetic variability in agreement with this value.5. To investigate the possibility that the deleterious genes produced by irradiation would interfere with the response to artificial selection, a standard outbred population was irradiated and selected. In spite of the observed high frequency of recessive lethals produced, the response to selection was very similar to that of the standard population.

scholarly journals Time for spreading of compensatory mutations under gene duplication.

Genetics ◽  
1989 ◽  
Vol 123 (3) ◽  
pp. 579-584
Author(s):  
T Ohta
Keyword(s):  
Gene Duplication ◽  
Diffusion Equation ◽  
Population Size ◽  
Computer Simulations ◽  
Deleterious Mutation ◽  
Selective Constraint ◽  
Effective Population ◽  
Gene Redundancy ◽  
Tight Linkage ◽  
Compensatory Mutations

Abstract Evolution by compensatory mutations is accelerated by gene duplication because selective constraint is relaxed by gene redundancy. A mutation is called compensatory if it corrects the effect of an earlier deleterious mutation. Without duplication, Kimura has shown that the time for spreading of compensatory mutations is much reduced by tight linkage between the two chromosomal sites of mutations. In this report, the time for spreading with gene duplication was studied by using the diffusion equation method of Kimura, together with computer simulations. It was shown that, when 2Nv- is much less than unity, the time for spreading is greatly shortened by gene duplication as compared with the case of complete linkage between the two sites of mutations, where 2N is the effective population size (haploid) and v- is the rate of compensatory mutations. However, if 2Nv- greater than 1, gene duplication is not effective for accelerating the evolution by such mutations.

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