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1. Journal Information

2a. Identification BPMRC in the abstract

Acetyl-coenzyme A carboxylase (ACACA) catalyses the first committedstep in thebiosynthesis of long-chain fatty acids (FA) by converting acetyl-CoA intomalonyl-CoA. Inpigs, the ACACA gene maps to a chromosome 12 QTL with importanteffects on FA composition.

Journal

Journal

Author

Background

Principal activity (or purpose of thestudy)


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In the present study, we have sequenced the coding region of the pigACACA gene in 15 pigs, identifying 21 polymorphic sites that were either

synonymous or non-coding.

..we have sequenced the coding region of the pig ACACA gene in 15pigs, identifying 21 polymorphic sites that were either synonymous ornon-coding. Ten of these SNPs segregated in a Duroc commercialpopulation (n = 350) for which lipid metabolism and meat and carcassquality trait records were available.

Significant associations were found between two linked single nucleotidepolymorphisms (c.4899G>A and c.5196T>C) and percentages of carcasslean, intramuscular fat, monounsaturated, saturated (myristic, palmiticand stearic) and polyunsaturated (linoleic) FAs in the longissimus thoraciset lumborum muscle, along with serum HDL-cholesterol concentration.The most important allele substitution effects were observed for thepolyunsaturated/saturated FA ratio (1321% of the phenotypic mean) as

well as for the percentages of x-6 and polyunsaturated FAs, especiallylinoleic acid (716% of the phenotypic mean).

These results suggest the existence of a causal mutation, mapping to thechromosomal region containing the pig ACACA gene, with marked effectson FA composition of meat.

2b. Identification five stages in the introduction section

Methodology

Result

Conclusion or


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The acetyl-coenzyme A carboxylase a (ACACA) enzyme is involved in thebiosynthesis of long-chain fatty acids (FAs) by playing a key role in theconversion of acetyl-CoA to malonyl-CoA (Abu-Elheiga et al. 1995), the

precursor of palmitate. In addition, malonyl-CoA might act as an inhibitorof the import of FAs into the mitochondria for -oxidation (Barber et al.2005).

Comment: The general background explaned about the function ofACACA gene

The ACACA gene has been completely sequenced in human, as well as inother mammalianspecies, and is organized in 54 exons, which encode a protein of 2346amino acids (Barber et al. 2005). The pig ACACA gene has been mappedto chromosome 12 (SSC12) by Calvo et al. (2000) and most of its codingsequence has been characterized (Munoz et al. 2007). Interestingly, thegenomic location of this gene coincides with the confidence interval for aquantitative trait locus (QTL) for FA composition. The existence of thisSSC12 QTL has been independently confirmed in an Iberian Landraceresource population (Munoz et al. 2007) as well as in the Duroccommercial line employed in the current study (Quintanilla

et al. 2007). In addition, associations between the polymorphism of theACACA gene and FA composition have been recently reported (Munoz et

General Background

Literature review


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al. 2007).

Comment : This literature section review gave information about theACACA gene sequence condition in other species (human & other

mamalia), QTL position and association of the ACACA gene withphenotypic trait (fatty acid composition) based on previous study.

In the light of these positional and functional evidences, we haveselected ACACA as a candidate gene for the aforementioned SSC12 QTLsegregating in our Duroc commercial line. In this way, we havecharacterized the polymorphism of this gene by sequencing its completecoding region (approximately 7 kb) in 15 individuals. Moreover,

development of typing methods and performance of an associationanalysis with carcass quality, intramuscular fat (IMF) content andcomposition and serum lipid traits have been carried out

Comment : The author need more evidence to know exactly thepolymorphism of the gene, try a new method and investigate theassociation of the gene with phenotypic trait.

the aim of investigating if genetic variation at the pig ACACA gene has anyeffect on these phenotypes.

Comment : the main purpose of this study is to investigate the geneticvariation of the pig ACACA gene and their association with FA composition

2c. Identification of six elements in the discussion section

Investigationneeded

Purpose of study


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First informationelements


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In the discussion section of the journal, there are no subtitles exactly butimplicitly the discussion is divided by paragraph based on parameterstudy.

Paragraph 1

Growth, fatness, serum lipid concentrations and carcass andmeat quality traits have been recorded in a commercialDuroc line in order to perform an association analysis withgenetic variation at the pig ACACA locus (Tables 1 and 2).

Growth, fatness and carcass phenotypic means were similarto values reported by Edwards et al. (2003, 2006) andSchwab et al. (2007) in other Duroc commercial populations.Serum lipid levels were higher than values reportedby other authors (Hasler-Rapacz et al. 1995; Lu et al. 1995)and showed a considerable level of phenotypic variability.

These differences between studies might be because ofgenetic (e.g. breed), environmental (e.g. nutrition) andexperimental (e.g. sample size) factors. The analysis ofphenotypic correlations in our Duroc population showedthat heavier and fatter pigs have higher serum cholesteroland lipoprotein levels (Table 2). Similarly, in humans, thereis a significant correlation between obesity and plasma

lipids, with fatter individuals having higher cholesterolconcentrations (Hollister et al. 1967; McCarthy et al. 2008).Backfat thickness and lean percentage also showed a strongassociation with FA composition. In general, fatter pigs hada higher content of SFA and MUFA, while the percentage ofPUFA was lower. This is relevant from a technological pointof view because, in the pig industry, individuals are selectedfor augmenting lean percentage and decreasing backfatthickness. According to our data, this kind of selectionwould be expected to decrease the percentage of oleic FA,which would be a nutritionally unfavourable feature, and to

increase the percentage of PUFA, which is associated withincreased susceptibility to lipid oxidation (Wood et al.2008).

Paragraph 2

Analysis of genetic variation at the pig ACACA geneshowed a moderate level of polymorphism, with 21 SNPs

Important finding

The most important finding

Comparison with other

Explanation or speculation


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distributed in 7.4 kb of the coding and 3-UTR regions.

This figure gives a rough estimate of one SNP every0.28 kb, which is similar to what has been found in a

recent survey of pig genome variation (Du et al. 2007).Notably, all of these coding region SNPs are synonymous.This contrasts markedly with the similar proportionsof non-synonymous and synonymous SNPs found inthe protein coding regions of the human genome(Crawford et al. 2005).

This high proportion of silentmutations in the ACACA gene is consistent with thenotable structural conservation of this enzyme throughout

evolution (BlastP amino acid identity between pig andfission yeast is 45%).

Paragraph 3

We were interested in finding out if polymorphisms in thepig ACACA gene were associated with traits related to lipidmetabolism and carcass and meat quality. Different statisticalapproaches (Tables S6 and S7) consistently showedthat c.4899G>A and c.5196T>C, which are in stronglinkage disequilibrium, are associated with meat lipid composition.

Our results showed that pigs inheriting theA4899C5196 haplotype via dam tended to be leaner, with alower backfat thickness and a higher lean percentage.Moreover, serum CT and HDL concentrations were lower inpigs inheriting this haplotype. Conversely, allele substitutioneffects via sire for these traits were in general nonsignificant.

This might be because of the fact that computingallele substitution effects within families involves a loss

of statistical power. Moreover, it is possible that linkagedisequilibrium between the c.4899G>A-c.5196T>C haplotypeand the causal mutation differs at the population andwithin-family levels. No significant effects on live or carcassweight were observed, a feature that makes sense from afunctional perspective, because to the best of our knowledge,ACACA is not involved in physiological processesregulating growth rate.

Paragraph 4

Intramuscular fat content and FA composition in the

Comparison with other study


The most Important finding

Important finding but nocomparison with other references


The most important finding


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longissimus thoracis et lumborum muscle showed the mostconsistent and significant associations with ACACA genotypes(Table 3), with relevant allele substitution effectsfrom both maternally and paternally inherited alleles.

It is worth mentioning that although allele substitution effectsobtained at the population level and within paternal familiesdiffered in their magnitude, they consistently followedthe same direction. In this way, haplotype A4899C5196 decreasedIMF percentage and increased SFA (myristic, palmiticand stearic) and MUFA (oleic) contents. Moreover,this haplotype was associated with a pronounced decreasein PUFA and x-6 FA (linoleic and arachidonic). Asc.4899G>A and c.5196T>C are not expected, in principle,

to have any functional effect (both are synonymous),we hypothesize that they must be in linkage disequilibriumwith the causal mutation explaining the associationsfound.

The associations with meat FA composition foundin our study do not coincide with the ones reported byMunoz et al. (2007) in backfat samples of an Iberian byLandrace divergent cross.

In this latter work, ACACApolymorphisms c.5634T>C and c.6681G>T were the onesto display the strongest associations with backfat FAcomposition. In this way, the c.5634C allele showed positiveassociations with the percentage of palmitoleic andoleic FA and negative associations with the percentage ofstearic FA, while the c.6681G allele had a positive effect onthe percentage of stearic FA. In contrast, in our Durocpopulation, polymorphisms c.5634T>C and c.6681G>Tshowed associations with the PUFA/MUFA ratio and myristic

FA content respectively.

These discrepancies amongstpopulations could be explained by three factors: (i) differencesin tissue sampling (IMF vs. backfat) (ii) differentgenetic backgrounds of the analysed populations (Durocvs. Iberian Landrace) and (iii) the much larger amountof linkage disequilibrium generated in a divergent crosswith regard to an outbred population

Other Important finding but nocomparison with other references

Comparison with other study

Explanation

Speculation

Later information elements


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In summary, haplotype A4899C5196 of the pig ACACA

gene is associated with leaner animals displaying lowerlevels of serum HDL and IMF content. Currently, there is anongoing debate about the impact of IMF content on meattenderness, juiciness and palatability (Rincker et al. 2008),so it is difficult to ascertain if this decrease in IMF is disadvantageousor not. Moreover, the A4899C5196 haplotype isassociated with a decrease in the PUFA and x-6 percentagesand the PUFA/MUFA ratio. This could be considered asfavourable, from a technological point of view, because increasesin PUFA content are associated with the occurrenceof a rancid odour and taste in meat (Wood et al. 2008).From a human health perspective, a high x-6/x-3 ratio hasbeen found to promote the pathogenesis of many chronicillnesses, including cardiovascular disease (Simopoulos2008). Moreover, a diet rich in SFA and with a low PUFAcontent augments LDL levels and increases susceptibility tocoronary disease and atherosclerosis (LaRosa et al. 1990).

These features highlight the importance of identifying SNPsthat can be used in gene-assisted selection, with the finalobjective of improving meat FA composition without adversely

affecting its technological and organoleptic properties

Implication of the study

Recommendation of the study

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