scholarly journals A complex multi-locus, multi-allelic genetic architecture underlying the long-term selection-response in the Virginia body weight line of chickens

2017 ◽  
Author(s):  
Yanjun Zan ◽  
Zheya Sheng ◽  
Lars Rönnegård ◽  
Christa F. Honaker ◽  
Paul B. Siegel ◽  
...  
Keyword(s):  
Body Weight ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Selection Response ◽  
Multiple Alleles ◽  
Term Selection ◽  
Selection Responses ◽  
Genome Wide ◽  
Genetic Mechanisms

AbstractThe ability of a population to adapt to changes in their living conditions, whether in nature or captivity, often depends on polymorphisms in multiple genes across the genome. In-depth studies of such polygenic adaptations are difficult in natural populations, but can be approached using the resources provided by artificial selection experiments. Here, we dissect the genetic mechanisms involved in long-term selection responses of the Virginia chicken lines, populations that after 40 generations of divergent selection for 56-day body weight display a nine-fold difference in the selected trait. In the F15 generation of an intercross between the divergent lines, 20 loci explained more than 60% of the additive genetic variance for the selected trait. We focused particularly on seven major QTL and found that only two fine-mapped to single, bi-allelic loci; the other five contained linked loci, multiple alleles or were epistatic. This detailed dissection of the polygenic adaptations in the Virginia lines provides a deeper understanding of genome-wide mechanisms involved in the long-term selection responses. The results illustrate that long-term selection responses, even from populations with a limited genetic diversity, can be polygenic and influenced by a range of genetic mechanisms.

scholarly journals LONG-TERM SELECTION RESPONSE FOR 12-DAY LITTER WEIGHT IN MICE

Genetics ◽  
1972 ◽  
Vol 72 (1) ◽  
pp. 129-142
Author(s):  
E J Eisen
Keyword(s):  
Body Weight ◽  
Genetic Correlation ◽  
Half Life ◽  
Selection Process ◽  
Selection Response ◽  
Exponential Model ◽  
Correlated Response ◽  
Term Selection ◽  
Litter Weight

ABSTRACT Long-term selection for increased 12-day litter weight in two replicate lines (W2, W3) of mice resulted in an apparent selection limit at about 17 generations. Quadratic polynomial and exponential models were fitted to the data in order to estimate the plateaued response and half-life of the selection process. Using the polynomial results, the half-life estimates were 4.5 and 8.6 generations for W2 and W3, respectively. The plateaued responses were 5.1 and 5.8 g which, when expressed in phenotypic standard deviation units, became 1.1 and 1.3. The exponential model provides similar estimates. A negative association between 12-day litter weight and fitness was not considered to be an adequate explanation for the plateau since there was no decrease in fertility of the selected lines. Evidence that exhaustion of genetic variability was not the cause of the plateau came from the immediate response to reverse selection. It was proposed that the plateau may be due to a negative genetic correlation between direct and maternal genetic effects, which would be expected to occur after many generations of selection. There were positive correlated responses in both replicates for adult body weight, which was in agreement with the positive genetic correlation between preweaning and postweaning body weight. The expected positive correlated response for number born was realized in only one of the replicates.

scholarly journals Low-coverage sequencing in a deep intercross of the Virginia body weight lines provides insight to the polygenic genetic architecture of growth: novel loci revealed by increased power and improved genome-coverage

2021 ◽  
Author(s):  
Tilman Rönneburg ◽  
Yanjun Zan ◽  
Christa F Honaker ◽  
Paul B Siegel ◽  
Örjan Carlborg
Keyword(s):  
Body Weight ◽  
Complex Traits ◽  
Low Cost ◽  
Minor Effect ◽  
Genome Coverage ◽  
Selection Responses ◽  
Genome Wide ◽  
Low Coverage ◽  
Experimental Crosses

Genetic dissection of highly polygenic traits is a challenge, in part due to the power necessary to confidently identify loci with minor effects. Experimental crosses are valuable resources for mapping such traits. Traditionally, genome-wide analyses of experimental crosses have targeted major loci using data from a single generation, often the F2, with additional, later generation individuals being generated for replication and fine-mapping. Here, we aim to confidently identify minor-effect loci contributing to the highly polygenic basis of the long-term, divergent bi-directional selection responses for 56-day body weight in the Virginia chicken lines. To achieve this, a powerful strategy was developed to make use of data from all generations (F2-F18) of an advanced intercross line, developed by crossing the low and high selected lines after 40 generations of selection. A cost-efficient low-coverage sequencing based approach was used to obtain high-confidence genotypes in 1Mb bins across 99.3% of the chicken genome for >3,300 intercross individuals. In total, 12 genome-wide significant and 10 additional suggestive QTL for 56-day body weight were mapped, with only two of these QTL reaching genome-wide, and one suggestive, significance in analyses of the F2 generation. Five of the significant, and four of the suggestive, QTL were among the 20 loci reaching a 20% FDR-threshold in previous analyses of data from generation F15. The novel, minor-effect QTL mapped here were generally mapped due to an overall increase in power by integrating data across generations, with minor contributions from increased genome-coverage and improved marker information content. Significant and suggestive QTL now explain >60% of the difference between the parental lines, three times more than the previously reported significant QTL. Making integrated use of all available samples from multiple generations in experimental crosses is now economically feasible using the low-cost, sequencing-based genotyping strategies outlined here. Our empirical results illustrate the value of this strategy for mapping novel minor-effect loci contributing to complex traits to provide a more confident, comprehensive view of the individual loci that form the genetic basis of the highly polygenic, long-term selection responses for 56-day body weight in the Virginia chicken lines.

scholarly journals Effects of thyroid hormone deficiency on mice selected for increased and decreased body weight and fatness

1998 ◽  
Vol 72 (1) ◽  
pp. 39-53 ◽  
Author(s):  
LUTZ BÜNGER ◽  
HELEN WALLACE ◽  
JOHN O. BISHOP ◽  
IAN M. HASTINGS ◽  
WILLIAM G. HILL
Keyword(s):  
Body Weight ◽  
Genetic Background ◽  
Selection Response ◽  
Fat Content ◽  
Hormone Deficiency ◽  
Substantial Part ◽  
Growth Depression ◽  
Term Selection ◽  
Body Weights

A study was undertaken to test whether the elimination of metabolic pathways strongly involved in growth and fatness, comprising thyroid hormones (TH) and growth hormone (GH), is responsible for a substantial part of the genetic change produced by selection. Lines used in this study have been selected for about 50 generations for high (PH) and low (PL) body weight at 10 weeks and for high (F) and low fat content (L) at 14 weeks, producing a 3-fold difference in body weights and a 5-fold difference in fat content. Thyroid ablation was achieved by repeated backcrossing into the four selection lines of a transgene comprising the HSV1-tk gene coupled to the promoter of the thyroglobulin gene. Hemizygous pregnant dams were treated with ganciclovir leading to thyroid-ablated dams and offspring and therefore to a lack of TH and subsequently of GH. In the absence of TH and GH, lines still differ in body weight over the period studied (10 d to about 100 d; e.g. at the end PH=32·1 g vs PL=10·2 g) and in fat content (F=16·2% vs L=3·8%) ; the corresponding values for the wild-type controls were PH=49·9 g vs PL=17·4 g and F=27·5% vs L=4·8%. The effect of the transgene depended on the genetic background for body weights at most ages and for relative gonadal fat pad weights, but less for fat content. The L line showed the lowest growth depression. The lit gene, which causes GH but not TH deficiency, was also transferred by repeated backcrosses into three of these lines (PH, PL, F). The combined deficiency of TH and GH had bigger effects on body weights at earlier ages than did GH deprivation. The data show that changes in the TH- and GH-systems are not the only cause of line differences in growth and fatness resulting from long-term selection, but both are involved to a significant extent. The interactions between the effects of the transgene and of the lit gene and the genetic background were, nevertheless, relatively small and therefore these results support a polygenic model of selection response.

scholarly journals Long-term selection for protein amount over 70 generations in mice

1998 ◽  
Vol 72 (2) ◽  
pp. 93-109 ◽  
Author(s):  
LUTZ BÜNGER ◽  
ULLA RENNE ◽  
GERHARD DIETL ◽  
SIEGFRIED KUHLA
Keyword(s):  
Body Weight ◽  
Selection Response ◽  
Direct Selection ◽  
Control Line ◽  
Phenotypic Variance ◽  
Effective Population ◽  
Term Selection ◽  
General Importance ◽  
Selection For

Based on the outbred mouse strain Fzt: Du, which has been obtained by systematic crossing of four inbred and four outbred lines, a long-term selection experiment was carried out for total protein amount (PA) in the carcass, starting in 1975. An unselected control line (CO) was kept under the same management but without continuous protein analysis. The protein amount of male carcasses at 42 days of age (P42) increased from 2·9 g in generation 0 to 5·2 g at generation 70, representing 97% of a theoretical selection limit. The total selection response amounts to 2·3 g, which is about 80% above the initial value and corresponds to 9σp or 12σA . The estimated realized heritability of protein amount decreased from 0·56 to 0·03 at generation 70, which was due to an increase in phenotypic variance from 0·065 to 0·24 g2 and a reduction in genetic variance from 0·04 to 0·01 g2. Half the selection response was obtained after about 18 to 23 generations, a half-life of 0·25 to 0·3 Ne. The maximum selection response was 0·094 g/generation and the response was 0·01 g/generation at generation 70. The measurements of body weights at 0, 10, 21, 42 and 63 days throughout the experiment showed a strong correlated effect for all weights. The PA mice are one of the heaviest lines of mice ever reported, and do not differ significantly in their body composition from control mice at 42 days. The direct selection response was due primarily to increased general growth. Body weight and protein amount are phenotypically and genetically highly correlated (rp=0·82, rA≈1); however, selection for body weight led to fatter animals, whereas selection for protein opposed increased fatness (at least until selection age). This may be of general importance in animal breeding. The comparatively high selection response in this experiment seems due to the heterogeneity of the base population, the relatively high effective population size, and the duration of the experiment.

scholarly journals Spatio-temporal ecological and evolutionary dynamics in natural butterfly populations

2017 ◽  
Vol 40 ◽  
pp. 31-36
Author(s):  
Zachariah Gompert ◽  
Lauren Lucas
Keyword(s):  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Distance Sampling ◽  
Spatial And Temporal Variation ◽  
Insect Community ◽  
Long Term Study ◽  
Greater Yellowstone Area ◽  
Genome Wide ◽  
Spatio Temporal

Long term studies of wild populations indicate that natural selection can cause rapid and dramatic changes in traits, with spatial and temporal variation in the strength of selection a critical driver of genetic variation in natural populations. In 2012, we began a long term study of genome-wide molecular evolution in populations of the butterfly Lycaeides ideas in the Greater Yellowstone Area (GYA). We aimed to quantify the role of environment-dependent selection on evolution in these populations. Building on previous work, in 2017 we collected new samples, incorporated distance sampling, and surveyed the insect community at each site. We also defined the habitat boundary at anew, eleventh site. Our preliminary analyses suggest that both genetic drift and selection are important drivers in this system.   Featured photo from Figure 1 in report.

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.

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