Limits...
A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL.

Noguera JL, Rodríguez C, Varona L, Tomàs A, Muñoz G, Ramírez O, Barragán C, Arqué M, Bidanel JP, Amills M, Ovilo C, Sánchez A - BMC Genomics (2009)

Bottom Line: This relative paucity of significant results contrasted very strongly with the wide array of highly significant epistatic QTL that emerged in the bi-dimensional genome-wide scan analysis.Different patterns of interactions (a x a, a x d, d x a and d x d) were found amongst the epistatic QTL pairs identified in the current work.Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genètica i Millora Animal, IRTA-Lleida, 25198 Lleida, Spain. joseluis.noguera@irta.es

ABSTRACT

Background: Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA) and total number of piglets born (TNB) in a three generation Iberian by Meishan F(2) intercross.

Results: The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P < 0.001) and SSC17 (P < 0.01) with effects on both traits. This relative paucity of significant results contrasted very strongly with the wide array of highly significant epistatic QTL that emerged in the bi-dimensional genome-wide scan analysis. As much as 18 epistatic QTL were found for NBA (four at P < 0.01 and five at P < 0.05) and TNB (three at P < 0.01 and six at P < 0.05), respectively. These epistatic QTL were distributed in multiple genomic regions, which covered 13 of the 18 pig autosomes, and they had small individual effects that ranged between 3 to 4% of the phenotypic variance. Different patterns of interactions (a x a, a x d, d x a and d x d) were found amongst the epistatic QTL pairs identified in the current work.

Conclusions: The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17), dominant and epistatic QTL in an Iberian x Meishan F(2) intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

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Network representation of the epistatic QTL interactions in thirteen pig chromosomes (SSC) for prolificacy traits NBA (red arrows) and TNB (black arrows).
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Figure 1: Network representation of the epistatic QTL interactions in thirteen pig chromosomes (SSC) for prolificacy traits NBA (red arrows) and TNB (black arrows).

Mentions: A graphical overview of the epistatic interactions for NBA (red arrows) is shown in Figure 1. As much as twelve of the 18 pig autosomes (1, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15 and 18) were involved in these interactions, forming a complex network with a non-radial geometry. This means that a specific region did not interact simultaneously with multiple loci, but with a very limited number of them (usually interactions were one to one). For example, the SSC12 region located at 11 cM, interacted significantly with another SSC12 region at 89 cM (Figure 1; Table 4). Similarly, two non-overlapping SSC6 QTL regions showed epistatic interactions, one of them with QTL on SSC1 and SSC7 (SSC6, 54-69 cM) and another one with SSC14 (SSC6, 1-10 cM). As shown in Figure 1, other pig chromosomes exhibiting more than one significant interacting QTL were SSC1 (at positions 76 and 153 cM respectively), and SSC7 (at positions 28 cM, and 107 cM). An interesting feature of our analysis was that the highly significant NBA QTL identified in the one-dimensional genome scan (SSC13 at 50 cM and SSC17 at 22 cM) did not show any significant epistatic interaction with other regions across the genome, meaning that its mode of action is purely additive. In contrast, a NBA QTL found on another region of SSC13 (73 cM) had significant epistatic interactions with a QTL located at position 4 cM of SSC9. Similarly, in mice, Peripato et al. [3] identified two significant QTL for litter size in a one-dimensional genome scan (chromosomes 7 and 12) that did not emerge in the bi-dimensional analysis (chromosomes 2, 4, 5, 11, 14, 15 and 18). In the light of these results and ours, we could conclude that there is a low concordance between the QTL identified in one- and bi-dimensional genome scans. This means that, in general, the additive and epistatic components of prolificacy traits encompass different sets of genes.


A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL.

Noguera JL, Rodríguez C, Varona L, Tomàs A, Muñoz G, Ramírez O, Barragán C, Arqué M, Bidanel JP, Amills M, Ovilo C, Sánchez A - BMC Genomics (2009)

Network representation of the epistatic QTL interactions in thirteen pig chromosomes (SSC) for prolificacy traits NBA (red arrows) and TNB (black arrows).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2812473&req=5

Figure 1: Network representation of the epistatic QTL interactions in thirteen pig chromosomes (SSC) for prolificacy traits NBA (red arrows) and TNB (black arrows).
Mentions: A graphical overview of the epistatic interactions for NBA (red arrows) is shown in Figure 1. As much as twelve of the 18 pig autosomes (1, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15 and 18) were involved in these interactions, forming a complex network with a non-radial geometry. This means that a specific region did not interact simultaneously with multiple loci, but with a very limited number of them (usually interactions were one to one). For example, the SSC12 region located at 11 cM, interacted significantly with another SSC12 region at 89 cM (Figure 1; Table 4). Similarly, two non-overlapping SSC6 QTL regions showed epistatic interactions, one of them with QTL on SSC1 and SSC7 (SSC6, 54-69 cM) and another one with SSC14 (SSC6, 1-10 cM). As shown in Figure 1, other pig chromosomes exhibiting more than one significant interacting QTL were SSC1 (at positions 76 and 153 cM respectively), and SSC7 (at positions 28 cM, and 107 cM). An interesting feature of our analysis was that the highly significant NBA QTL identified in the one-dimensional genome scan (SSC13 at 50 cM and SSC17 at 22 cM) did not show any significant epistatic interaction with other regions across the genome, meaning that its mode of action is purely additive. In contrast, a NBA QTL found on another region of SSC13 (73 cM) had significant epistatic interactions with a QTL located at position 4 cM of SSC9. Similarly, in mice, Peripato et al. [3] identified two significant QTL for litter size in a one-dimensional genome scan (chromosomes 7 and 12) that did not emerge in the bi-dimensional analysis (chromosomes 2, 4, 5, 11, 14, 15 and 18). In the light of these results and ours, we could conclude that there is a low concordance between the QTL identified in one- and bi-dimensional genome scans. This means that, in general, the additive and epistatic components of prolificacy traits encompass different sets of genes.

Bottom Line: This relative paucity of significant results contrasted very strongly with the wide array of highly significant epistatic QTL that emerged in the bi-dimensional genome-wide scan analysis.Different patterns of interactions (a x a, a x d, d x a and d x d) were found amongst the epistatic QTL pairs identified in the current work.Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genètica i Millora Animal, IRTA-Lleida, 25198 Lleida, Spain. joseluis.noguera@irta.es

ABSTRACT

Background: Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA) and total number of piglets born (TNB) in a three generation Iberian by Meishan F(2) intercross.

Results: The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P < 0.001) and SSC17 (P < 0.01) with effects on both traits. This relative paucity of significant results contrasted very strongly with the wide array of highly significant epistatic QTL that emerged in the bi-dimensional genome-wide scan analysis. As much as 18 epistatic QTL were found for NBA (four at P < 0.01 and five at P < 0.05) and TNB (three at P < 0.01 and six at P < 0.05), respectively. These epistatic QTL were distributed in multiple genomic regions, which covered 13 of the 18 pig autosomes, and they had small individual effects that ranged between 3 to 4% of the phenotypic variance. Different patterns of interactions (a x a, a x d, d x a and d x d) were found amongst the epistatic QTL pairs identified in the current work.

Conclusions: The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17), dominant and epistatic QTL in an Iberian x Meishan F(2) intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

Show MeSH