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A genome-wide linkage analysis for reproductive traits in F2 Large White × Meishan cross gilts.

ABSTRACT: Female reproductive performance traits in pigs have low heritabilities thus limiting improvement through traditional selective breeding programmes. However, there is substantial genetic variation found between pig breeds with the Chinese Meishan being one of the most prolific pig breeds known. In this study, three cohorts of Large White × Meishan F2 cross-bred pigs were analysed to identify quantitative trait loci (QTL) with effects on reproductive traits, including ovulation rate, teat number, litter size, total born alive and prenatal survival. A total of 307 individuals were genotyped for 174 genetic markers across the genome. The genome-wide analysis of the trait-recorded F2 gilts in their first parity/litter revealed one QTL for teat number significant at the genome level and a total of 12 QTL, which are significant at the chromosome-wide level, for: litter size (three QTL), total born alive (two QTL), ovulation rate (four QTL), prenatal survival (one QTL) and teat number (two QTL). Further support for eight of these QTL is provided by results from other studies. Four of these 12 QTL were mapped for the first time in this study: on SSC15 for ovulation rate and on SSC18 for teat number, ovulation rate and litter size.

SUBMITTER: Hernandez SC

PROVIDER: S-EPMC4282129 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

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A genome-wide linkage analysis for reproductive traits in F2 Large White × Meishan cross gilts.

Hernandez S C SC Finlayson H A HA Ashworth C J CJ Haley C S CS Archibald A L AL

Animal genetics 20140123 2

Female reproductive performance traits in pigs have low heritabilities thus limiting improvement through traditional selective breeding programmes. However, there is substantial genetic variation found between pig breeds with the Chinese Meishan being one of the most prolific pig breeds known. In this study, three cohorts of Large White × Meishan F2 cross-bred pigs were analysed to identify quantitative trait loci (QTL) with effects on reproductive traits, including ovulation rate, teat number, ...[more]

PMID: 24456574

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Project description:Within-litter uniformity in pigs is a major factor affecting piglet survival and growth performance. We know that Meishan (MS) gilts have higher piglet survival rate than Large White (LW) gilts because their foetal weight is less varied. To understand the molecular basis for placental nutritional transport during the late stages of gestation in LW and MS, we employed the isobaric tags for relative and absolute quantification (iTRAQ) method to investigate alterations in the placental proteomes of LW and MS gilts on gestational day 90. Investigation of foetal weight at different uterine positions revealed that the foetal and placental weights as well as the foetal concentration of glucose were significantly higher in LW gilts positioned towards the utero-tubal junction than in those positioned toward the cervix; however, no such differences were observed in MS gilts, and MS gilts had a greater uniformity in foetal weight on day 90 of gestation. Comparisons of the proteomes between placentas positioned toward the cervix and those positioned toward the utero-tubal junction identified 38 differentially expressed proteins in the two breeds. These proteins play a central role in nutrient transport and metabolism, as well as in transcriptional and translational regulation. Of particular interest is the finding that the placentas of LW gilts showed 14 differential expression of proteins mainly related to lipid transport and energy metabolism (including solute carrier family 27, mitochondrial trifunctional protein, and NADH dehydrogenase [ubiquinone] flavoprotein 2), but only 2 proteins in MS gilts. In contrast, the differentially expressed proteins in MS gilts were primarily involved in transcriptional and translational regulation (such as ribosome-sec61 and 40S ribosomal protein S23), with a few related to glucose and coenzyme transport and metabolism (including glucose transport protein and ferrochelatase). Our results revealed that placental lipid and energy metabolism might play a crucial role in the regulation of foetal weight, based on uterine position in two distinct pig breeds. These findings provide a deeper understanding of placental efficiency that can be utilized to provide a new method to enhance the efficiency of livestock production.

Project description:This experiment was designed to determine the effects of variations in dietary energy intake on reproductive performance and gene expression of luteal and endometrium tissues in Large White (LW) and Meishan (MS) gilts during early and middle pregnancy. After insemination, 32 LW gilts were assigned to high and low (HEL and LEL, 14.23 and 12.56 MJ DE/kg, respectively) diet treatment groups, while 32 MS gilts were allocated to HEM and LEM (12.56 and 10.88 MJ DE/kg) groups. Gilts were slaughtered on days 35, 55 and 90 of gestation. The fetal survival and luteal progesterone (P4) concentration in the HEL group were higher on day 35 but lower on day 90 of gestation compared with the LEL group (P < 0.05) for LW gilts. However, fetal survival and luteal P4 concentration on day 35 of gestation were greater (P < 0.05) in the LEM group than in the HEM group for MS gilts, but no significant difference in mid-gestation was showed. The fetal weights of both breeds were higher for the high energy diets compared with the respective control group on day 90 of gestation (P < 0.05). In addition, the mRNA levels of P4 synthesis-related proteins had correlated with luteal P4 concentration in both breeds. Further, endometrial levels of uteroferrin (ACP5), retinol-binding protein 4 (RBP4) and secreted phosphoprotein 1 (SPP1) mRNA were upregulated in the HEL group on day 35 of gestation but ACP5 and SPP1 were downregulated on day 55 of gestation compared with the LEL group (P < 0.05) for LW gilts. In MS gilts, diet only affected the expression of SPP1 (P < 0.05). Our results revealed the differential sensitivity of LW and MS breeds to variations in dietary energy intake. For LW gilts, the HEL group improved fetal survival on day 35 but a sustained high energy diet decreased fetal survival on day 90 of gestation. The differences in dietary energy intake did not influence fetal survival on day 90 of gestation but the higher energy diet did increase fetal weight in the MS breed compared with the lower energy intake diet. These results may be due to differential luteal secretion activity and endometrium gene expression in these two breeds.

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Project description:Efficient management of swine production systems requires understanding of complex reproductive physiological mechanisms. Our objective in this study was to investigate potential causal biological relationships between reproductive performance traits in high-producing gilts and sows. Data originated from a nutrition experiment and consisted of 200 sows and 440 gilts arranged in body weight blocks and randomly assigned to dietary treatments during late gestation at a commercial swine farm. Reproductive performance traits consisted of weight gain during late gestation, total number born and number born alive in a litter, born alive average birth weight, wean-to-estrous interval, and total litter size born in the subsequent farrowing. Structural equation models combined with the inductive causation algorithm, both adapted to a hierarchical Bayesian framework, were employed to search for, estimate, and infer upon causal links between the traits within each parity group. Results indicated potentially distinct reproductive networks for gilts and for sows. Sows showed sparse connectivity between reproductive traits, whereas the network learned for gilts was densely interconnected, suggesting closely linked physiological mechanisms in younger females, with a potential for ripple effects throughout their productive lifecycle in response to early implementation of tailored managerial interventions. Cross-validation analyses indicated substantial network stability both for the general structure and for individual links, though results about directionality of such links were unstable in this study and will need further investigation. An assessment of relative statistical power in sows and gilts indicated that the observed network discrepancies may be partially explained on a biological basis. In summary, our results suggest distinctly heterogeneous mechanistic networks of reproductive physiology for gilts and sows, consistent with physiological differences between the groups. These findings have potential practical implications for integrated understanding and differential management of gilts and sows to enhance efficiency of swine production systems.

Project description:With the broad application of genomic information, SNP-based measures of estimating inbreeding have been widely used in animal breeding, especially based on runs of homozygosity. Inbreeding depression is better estimated by SNP-based inbreeding coefficients than pedigree-based inbreeding in general. However, there are few comprehensive comparisons of multiple methods in pigs so far, to some extent limiting their application. In this study, to explore an appropriate strategy for estimating inbreeding depression on both growth traits and reproductive traits in a Large White pig population, we compared multiple methods for the inbreeding coefficient estimation based on both pedigree and genomic information. This pig population for analyzing the influence of inbreeding was from a pig breeding farm in the Inner Mongolia of China. There were 26,204 pigs with records of age at 100 kg (AGE) and back-fat thickness at 100 kg (BF), and 6,656 sows with reproductive records of the total number of piglets at birth (TNB), and the number of alive piglets at birth (NBA), and litter weight at birth. Inbreeding depression affected growth and reproductive traits. The results indicated that pedigree-based and SNP-based inbreeding coefficients had significant effects on AGE, TNB, and NBA, except for BF. However, only SNP-based inbreeding coefficients revealed a strong association with inbreeding depression on litter weight at birth. Runs of homozygosity-based methods showed a slight advantage over other methods in the correlation analysis of inbreeding coefficients and estimation of inbreeding depression. Furthermore, our results demonstrated that the model-based approach (RZooRoH) could avoid miscalculations of inbreeding and inbreeding depression caused by inappropriate parameters, which had a good performance on both AGE and reproductive traits. These findings might improve the extensive application of runs of homozygosity analysis in pig breeding and breed conservation.

Dataset Information

A genome-wide linkage analysis for reproductive traits in F2 Large White × Meishan cross gilts.

Publications

A genome-wide linkage analysis for reproductive traits in F2 Large White × Meishan cross gilts.

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