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Dynamics of adaptive alleles in divergently selected body weight lines of chickens.

Pettersson ME, Johansson AM, Siegel PB, Carlborg O - G3 (Bethesda) (2013)

Bottom Line: Overall, there were small changes in allele frequencies at individual loci over the studied time period; but, on average, the changes were greater in lines with larger phenotypic changes.This locus likely contains a novel, beneficial mutation that appeared between generations 40 and 45 and was driven to fixation in 5 to 10 generations.This result illustrates the dependence of continued long-term selection response on standing genetic variation at many loci as well as strong, novel, beneficial mutations.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden.

ABSTRACT
By studying genomic changes over time in populations subjected to strong artificial directional selection, we can gain insights to the dynamics of beneficial alleles originating from the founder population or emerging as novel mutations undergoing ongoing selection. The Virginia lines are a chicken resource population generated by long-term bi-directional, single-trait selection for juvenile body weight. We studied genome-wide allele frequency changes from generation 40 to 53 using genome-wide genotypes from directional and relaxed selection lines. Overall, there were small changes in allele frequencies at individual loci over the studied time period; but, on average, the changes were greater in lines with larger phenotypic changes. This is consistent with previous findings that much of the response to selection over the first 40 years of selection was attributable to utilization of standing genetic variation at many loci in the genome, indicating a mostly polygenic architecture for body weight. Over the course of the selection experiment, the largest phenotypic response to selection was observed in the high-weight selected line, and in this line we detected a single locus where the allele frequency changed rapidly during a late stage of the experiment. This locus likely contains a novel, beneficial mutation that appeared between generations 40 and 45 and was driven to fixation in 5 to 10 generations. This result illustrates the dependence of continued long-term selection response on standing genetic variation at many loci as well as strong, novel, beneficial mutations.

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Related in: MedlinePlus

Distribution of large haplotype blocks across the genome of the Virginia chicken lines. The figure shows the location of exceptionally large (>5 Mb) haplotype blocks in the HWS (purple) and LWS (green) lines together with previously identified QTL (blue; 18,19) (Wahlberg et al., 2009; Pettersson et al., 2011).
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fig5: Distribution of large haplotype blocks across the genome of the Virginia chicken lines. The figure shows the location of exceptionally large (>5 Mb) haplotype blocks in the HWS (purple) and LWS (green) lines together with previously identified QTL (blue; 18,19) (Wahlberg et al., 2009; Pettersson et al., 2011).

Mentions: A number of exceptionally large (>5 Mb) LD blocks were identified in both the HWS and LWS lines using Haploview (Barrett et al. 2005). Haplotype blocks larger than 5 Mb were identified in HWS40 (seven blocks), LWS40 (three blocks), and HWS50 (eight blocks), whereas no blocks were found in LWS50, probably because of the limited size of that group. The positions of all blocks are listed in Table 2, and the blocks from generation 40 are graphically displayed in Figure 5. The identified regions largely overlap with previously identified QTL in an intercross between HWS40 and LWS40 (Figure 5). There are three regions with haplotype blocks larger than 5 Mb that occur in both the high line and the low line. These three regions are located on GGA1, GGA7, and GGA8.


Dynamics of adaptive alleles in divergently selected body weight lines of chickens.

Pettersson ME, Johansson AM, Siegel PB, Carlborg O - G3 (Bethesda) (2013)

Distribution of large haplotype blocks across the genome of the Virginia chicken lines. The figure shows the location of exceptionally large (>5 Mb) haplotype blocks in the HWS (purple) and LWS (green) lines together with previously identified QTL (blue; 18,19) (Wahlberg et al., 2009; Pettersson et al., 2011).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852392&req=5

fig5: Distribution of large haplotype blocks across the genome of the Virginia chicken lines. The figure shows the location of exceptionally large (>5 Mb) haplotype blocks in the HWS (purple) and LWS (green) lines together with previously identified QTL (blue; 18,19) (Wahlberg et al., 2009; Pettersson et al., 2011).
Mentions: A number of exceptionally large (>5 Mb) LD blocks were identified in both the HWS and LWS lines using Haploview (Barrett et al. 2005). Haplotype blocks larger than 5 Mb were identified in HWS40 (seven blocks), LWS40 (three blocks), and HWS50 (eight blocks), whereas no blocks were found in LWS50, probably because of the limited size of that group. The positions of all blocks are listed in Table 2, and the blocks from generation 40 are graphically displayed in Figure 5. The identified regions largely overlap with previously identified QTL in an intercross between HWS40 and LWS40 (Figure 5). There are three regions with haplotype blocks larger than 5 Mb that occur in both the high line and the low line. These three regions are located on GGA1, GGA7, and GGA8.

Bottom Line: Overall, there were small changes in allele frequencies at individual loci over the studied time period; but, on average, the changes were greater in lines with larger phenotypic changes.This locus likely contains a novel, beneficial mutation that appeared between generations 40 and 45 and was driven to fixation in 5 to 10 generations.This result illustrates the dependence of continued long-term selection response on standing genetic variation at many loci as well as strong, novel, beneficial mutations.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden.

ABSTRACT
By studying genomic changes over time in populations subjected to strong artificial directional selection, we can gain insights to the dynamics of beneficial alleles originating from the founder population or emerging as novel mutations undergoing ongoing selection. The Virginia lines are a chicken resource population generated by long-term bi-directional, single-trait selection for juvenile body weight. We studied genome-wide allele frequency changes from generation 40 to 53 using genome-wide genotypes from directional and relaxed selection lines. Overall, there were small changes in allele frequencies at individual loci over the studied time period; but, on average, the changes were greater in lines with larger phenotypic changes. This is consistent with previous findings that much of the response to selection over the first 40 years of selection was attributable to utilization of standing genetic variation at many loci in the genome, indicating a mostly polygenic architecture for body weight. Over the course of the selection experiment, the largest phenotypic response to selection was observed in the high-weight selected line, and in this line we detected a single locus where the allele frequency changed rapidly during a late stage of the experiment. This locus likely contains a novel, beneficial mutation that appeared between generations 40 and 45 and was driven to fixation in 5 to 10 generations. This result illustrates the dependence of continued long-term selection response on standing genetic variation at many loci as well as strong, novel, beneficial mutations.

Show MeSH
Related in: MedlinePlus