scholarly journals Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment

2015 ◽  
Author(s):  
Zheya Sheng ◽  
Mats E Pettersson ◽  
Christa F Honaker ◽  
Paul B Siegel ◽  
Örjan Carlborg
Keyword(s):  
Body Weight ◽  
Genetic Variation ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Selection Response ◽  
Selective Sweeps ◽  
Base Population ◽  
A Genome ◽  
Wide Scale ◽  
Genomic Regions

Artificial selection has, for decades, provided a powerful approach to study the genetics of adaptation. Using selective-sweep mapping, it is possible to identify genomic regions in populations where the allele-frequencies have diverged during selection. To avoid misleading signatures of selection, it is necessary to show that a sweep has an effect on the selected trait before it can be considered adaptive. Here, we confirm candidate selective-sweeps on a genome-wide scale in one of the longest, on-going bi-directional selection experiments in vertebrates, the Virginia high and low body-weight selected chicken lines. The candidate selective-sweeps represent standing genetic variants originating from the common base-population. Using a deep-intercross between the selected lines, 16 of 99 evaluated regions were confirmed to contain adaptive selective-sweeps based on their association with the selected trait, 56-day body-weight. Although individual additive effects were small, the fixation for alternative alleles in the high and low body-weight lines across these loci contributed at least 40% of the divergence between them and about half of the additive genetic variance present within and between the lines after 40 generations of selection. The genetic variance contributed by the sweeps corresponds to about 85% of the additive genetic variance of the base-population, illustrating that these loci were major contributors to the realised selection-response. Thus, the gradual, continued, long- term selection response in the Virginia lines was likely due to a considerable standing genetic variation in a highly polygenic genetic architecture in the base-population with contributions from a steady release of selectable genetic variation from new mutations and epistasis throughout the course of selection.

scholarly journals Accumulation of mutations affecting body weight in inbred mouse lines

1995 ◽  
Vol 65 (2) ◽  
pp. 145-149 ◽  
Author(s):  
Armando Caballero ◽  
Peter D. Keightley ◽  
William G. Hill
Keyword(s):  
Body Weight ◽  
Maximum Likelihood ◽  
Genetic Variance ◽  
Inbred Mouse ◽  
Additive Genetic Variance ◽  
Selection Response ◽  
Spontaneous Mutations ◽  
Line Selection ◽  
Divergence Estimates ◽  
Mouse Lines

SummaryThe variation from spontaneous mutations for 6-week body weight in the mouse was estimated by selection from a cross of two inbred sublines, C57BL/6 and C57BL/10, separated about 50 years previously from the same inbred line. Selection was practised high and low for 12 generations from theF2, followed by one generation of relaxation. The lines diverged by approximately 1·7 g or 0·7 sd. The additive genetic variance was estimated in theF2by restricted maximum likelihood and from the selection response, and from this variance the mutational heritabilityhM2was estimated using the number of generations since divergence. Estimates ofhM2range from 0·08 to 0·10% depending on the method of analysis. These estimates are similar to those found for other species, but lower than other estimates for the mouse. It is concluded that substantial natural and, perhaps, artificial selection operated during the maintenance of the sublines.

scholarly journals Genetic variation in varying environments

1981 ◽  
Vol 37 (1) ◽  
pp. 79-93 ◽  
Author(s):  
Trudy F. C. Mackay
Keyword(s):  
Body Weight ◽  
Genetic Variation ◽  
Spatial Heterogeneity ◽  
Temporal Variation ◽  
Genetic Variance ◽  
Environmental Variability ◽  
Additive Genetic Variance ◽  
Environmental Variation ◽  
Heterogeneous Environments ◽  
Varying Environments

SUMMARYIn order to assess the relationship between genetic and environmental variability, a large natural population of Drosophila melanogaster was replicated as eight subpopulations, which were subjected to four different patterns of environmental variation. The environmental variable imposed was presence of 15% ethanol in the culture medium. Experimental treatments of the populations were intended to simulate constant environmental conditions, spatial heterogeneity in the environment, and two patterns of temporal environmental variation with different periodicity (long- and short-term temporal variation). Additive genetic and phenotypic variation in sternopleural and abdominal chaeta number, and body weight, were estimated in two successive years, and measurements were taken of the genotype–environment correlation of body weight and sternopleural bristle score with medium type.Additive genetic variance of sternopleural chaeta number and of body weight was significantly greater in the three populations experiencing environmental heterogeneity than in the control population, but additive genetic variance of abdominal bristle score was not clearly affected by exposing populations to varying environments. Temporal environmental variation was equally, if not more, efficient in promoting the maintenance of genetic variation than spatial heterogeneity, but the cycle length of the temporal variation was of no consequence. Specific genotype–environment interactions were not present, therefore adaptation to heterogeneous environments is by selection of heterozygosity per se, rather than by differential survival of genotypes in the alternate niches.

scholarly journals The limits to artificial selection for body weight in the mouse II. The Genetic Nature of the Limits

1966 ◽  
Vol 8 (3) ◽  
pp. 361-375 ◽  
Author(s):  
R. C. Roberts
Keyword(s):  
Body Weight ◽  
Natural Selection ◽  
Artificial Selection ◽  
Sharp Increase ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Base Population ◽  
Relaxed Selection ◽  
Genetic Nature ◽  
Selection For

1. The effects of long-continued selection for body weight in two lines of mice, one large and one small, are described.2. The large line showed a sharp increase in weight after remaining at an apparent limit for twenty generations. A rare combinational event is suggested as the most likely explanation.3. Reversed and relaxed selection from the large line at the limit failed to yield any response. This indicates that effectively, the additive genetic variance in this line had been exhausted.4. In contrast, the small line at the limit regressed slightly towards the base population when selection was relaxed. Reversed selection yielded a ready response until a new limit was apparently reached. Loci affecting body weight in this line had therefore not been fixed by selection.5. Natural selection, operating on viability between conception and the time when the selection was made, appears to explain best the lack of fixation in the small line.6. Attention is drawn to the necessity of more experimental work to elucidate the genetic nature of the limits to artificial selection.

scholarly journals A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 500
Author(s):  
Hadi Atashi ◽  
Mazdak Salavati ◽  
Jenne De Koster ◽  
Mark Crowe ◽  
Geert Opsomer ◽  
...  
Keyword(s):  
Genetic Variance ◽  
Genome Wide Association Study ◽  
Additive Genetic Variance ◽  
Genomic Region ◽  
Single Step ◽  
Calving Interval ◽  
Alanine Transport ◽  
A Genome ◽  
Estimated Breeding Values ◽  
Genomic Regions

The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including ARHGAP29, SEC24D, METTL14, SLC36A2, and SLC36A3 inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows.

ESTIMASI NILAI HERITABILITAS BOBOT IKAN MAS VARIETAS PUNTEN DALAM PROGRAM SELEKSI INDIVIDU

2016 ◽  
Vol 11 (3) ◽  
pp. 217
Author(s):  
Estu Nugroho ◽  
Budi Setyono ◽  
Mochammad Su’eb ◽  
Tri Heru Prihadi
Keyword(s):  
Body Weight ◽  
Selection Response ◽  
Base Population ◽  
Breeding Programs ◽  
Male And Female ◽  
Body Weight Trait ◽  
Population Selection ◽  
Selection For ◽  
Weight Trait ◽  
Selection Of

Program pemuliaan ikan mas varietas Punten dilakukan dengan seleksi individu terhadap karakter bobot ikan. Pembentukan populasi dasar untuk kegiatan seleksi dilakukan dengan memijahkan secara massal induk ikan mas yang terdiri atas 20 induk betina dan 21 induk jantan yang dikoleksi dari daerah Punten, Kepanjen (delapan betina dan enam jantan), Kediri (tujuh betina dan 12 jantan), Sragen (27 betina dan 10 jantan), dan Blitar (15 betina dan 11 jantan). Larva umur 10 hari dipelihara selama empat bulan. Selanjutnya dilakukan penjarangan sebesar 50% dan benih dipelihara selama 14 bulan untuk dilakukan seleksi dengan panduan hasil sampling 250 ekor individu setiap populasi. Seleksi terhadap calon induk dilakukan saat umur 18 bulan pada populasi jantan dan betina secara terpisah dengan memilih berdasarkan 10% bobot ikan yang terbaik. Calon induk yang terseleksi kemudian dipelihara hingga matang gonad, kemudian dipilih sebanyak 150 pasang dan dipijahkan secara massal. Didapatkan respons positif dari hasil seleksi berdasarkan bobot ikan, yaitu 49,89 g atau 3,66% (populasi ikan jantan) dan 168,47 g atau 11,43% (populasi ikan betina). Nilai heritabilitas untuk bobot ikan adalah 0,238 (jantan) dan 0,505 (betina).Punten carp breeding programs were carried out by individual selection for body weight trait. The base population for selection activities were conducted by mass breeding of parent consisted of 20 female and 21 male collected from area Punten, eight female and six male (Kepanjen), seven female and 12 male (Kediri), 27 female and 10 male (Sragen), 15 female and 11 male (Blitar). Larvae 10 days old reared for four moths. Then after spacing out 50% of total harvest, the offspring reared for 14 months for selection activity based on the sampling of 250 individual each population. Selection of broodstock candidates performed since 18 months age on male and female populations separately by selecting based on 10% of fish with best body weight. Candidates selected broodstocks were then maintained until mature. In oder to produce the next generation 150 pairs were sets and held for mass spawning. The results revealed that selection response were positive, 49.89 g (3.66%) for male and 168.47 (11.43%) for female. Heritability for body weight is 0.238 (male) and 0.505 (female).

scholarly journals Genetic variation in recombination rate in the pig

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Material ◽  
A Genome ◽  
Pig Genome ◽  
Genetic Length ◽  
Trait Locus ◽  
Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

Effects of Selection at Linked Sites on Patterns of Genetic Variability

2021 ◽  
Vol 52 (1) ◽  
pp. 177-197
Author(s):  
Brian Charlesworth ◽  
Jeffrey D. Jensen
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Frequency Distributions ◽  
A Genome ◽  
Demographic Processes ◽  
Dna Sequence Variants ◽  
Genomic Regions ◽  
Functional Components

Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.

scholarly journals Emerging Technologies for Genome-Wide Profiling of DNA Breakage

2021 ◽  
Vol 11 ◽  
Author(s):  
Matthew J. Rybin ◽  
Melina Ramic ◽  
Natalie R. Ricciardi ◽  
Philipp Kapranov ◽  
Claes Wahlestedt ◽  
...  
Keyword(s):  
Genome Instability ◽  
Dna Double Strand Breaks ◽  
Single Nucleotide ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Nucleotide Resolution ◽  
Genomic Regions

Genome instability is associated with myriad human diseases and is a well-known feature of both cancer and neurodegenerative disease. Until recently, the ability to assess DNA damage—the principal driver of genome instability—was limited to relatively imprecise methods or restricted to studying predefined genomic regions. Recently, new techniques for detecting DNA double strand breaks (DSBs) and single strand breaks (SSBs) with next-generation sequencing on a genome-wide scale with single nucleotide resolution have emerged. With these new tools, efforts are underway to define the “breakome” in normal aging and disease. Here, we compare the relative strengths and weaknesses of these technologies and their potential application to studying neurodegenerative diseases.

scholarly journals How does parental environment influence the potential for adaptation to global change?

2018 ◽  
Vol 285 (1886) ◽  
pp. 20181374 ◽  
Author(s):  
Evatt Chirgwin ◽  
Dustin J. Marshall ◽  
Carla M. Sgrò ◽  
Keyne Monro
Keyword(s):  
Genetic Variation ◽  
Global Change ◽  
Adaptive Capacity ◽  
Genetic Variance ◽  
Life Stage ◽  
Additive Genetic Variance ◽  
Parental Exposure ◽  
Future Warming ◽  
The Mean ◽  
Negative Impacts

Parental environments are regularly shown to alter the mean fitness of offspring, but their impacts on the genetic variation for fitness, which predicts adaptive capacity and is also measured on offspring, are unclear. Consequently, how parental environments mediate adaptation to environmental stressors, like those accompanying global change, is largely unknown. Here, using an ecologically important marine tubeworm in a quantitative-genetic breeding design, we tested how parental exposure to projected ocean warming alters the mean survival, and genetic variation for survival, of offspring during their most vulnerable life stage under current and projected temperatures. Offspring survival was higher when parent and offspring temperatures matched. Across offspring temperatures, parental exposure to warming altered the distribution of additive genetic variance for survival, making it covary across current and projected temperatures in a way that may aid adaptation to future warming. Parental exposure to warming also amplified nonadditive genetic variance for survival, suggesting that compatibilities between parental genomes may grow increasingly important under future warming. Our study shows that parental environments potentially have broader-ranging effects on adaptive capacity than currently appreciated, not only mitigating the negative impacts of global change but also reshaping the raw fuel for evolutionary responses to it.

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