Genome-wide identification of QTL for age at puberty in gilts using a large intercross F<sub>2</sub>population between White Duroc times Erhualian

Yang, Guoqiang; Ren, Jun; Li, Shijun; Mao, Huirong; Guo, Yuanmei; Zou, Zhengzhi; Ren, Dongren; Ma, Junwu; Huang, Lusheng

doi:10.1051/gse:2008019

Cited by 6 publications

(3 citation statements)

References 29 publications

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“…Likewise a QTL for weight of ovary was also described in a Meishan–White composite population between 116 and 137 cM on SSC8 (Rohrer et al, 1999). An age at puberty study using a White Duroc–Erhualian population detected a peak at 77 cM on SSC8 using a 5% chromosome-wide threshold, but a secondary peak just below the threshold was notable at approximately 125 cM within the region of HPSE (Yang et al, 2008). It is also worth noting that Buske et al (2006) compiled several fertility-related QTL studies and found a predominant clustering of QTL across SSC8 for reproductive traits in swine.…”

Section: Discussionmentioning

confidence: 99%

Association of Porcine Heparanase and Hyaluronidase 1 and 2 with Reproductive and Production Traits in a Landrace–Duroc–Yorkshire Population

Rempel¹,

Freking²,

Miles³

et al. 2011

Front. Gene.

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The ovary and placenta are dynamic structures requiring constant modification both structurally and through cell–cell communication capabilities. The extracellular matrix and basement membranes are primarily composed of a milieu of glycosaminoglycans, including heparan sulfate and hyaluronan. Heparanase (HPSE) and hyaluronidases (HYAL) are responsible for degrading heparan sulfate and hyaluronan, respectively. Therefore, the objective of this study was to evaluate the relationship of SNPs distinct to HPSE, HYAL1, and HYAL2 with measurements of reproduction and production traits in swine. Single trait associations were performed on a Landrace–Duroc–Yorkshire population using SNPs discovered and identified in HPSE, HYAL1, and HYAL2. Analyses were conducted on an extended pedigree and SNPs were found to be associated with reproductive and production traits. Prior to multiple-testing corrections, SNPs within HPSE were weakly associated (P < 0.03) having additive effects with age at puberty (−2.5 ± 1.08 days), ovulation rate (0.5 ± 0.24 corpora lutea), and number of piglets born alive (0.9 ± 0.44 piglets). A HYAL1 and two HYAL2 SNP were nominally associated (P ≤ 0.0063) with number of piglets born alive after multiple-testing corrections (effects between 1.02 and 1.44 piglets), while one of the same HYAL2 markers maintained a modest association (P = 0.0043) having a dominant effect with number of piglets weaned (1.2 ± 0.41 piglets) after multiple-testing correction. Functionally, HPSE and HYAL1 and 2 have been shown to participate in events related to ovarian and placental activity. SNPs from these studies could potentially assist with understanding genetic components underlying sow lifetime productivity as measured by piglet survivability based on number born alive and number weaned, thereby contributing to a greater number of pigs/sow/year.

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Section: Discussionmentioning

confidence: 99%

Association of Porcine Heparanase and Hyaluronidase 1 and 2 with Reproductive and Production Traits in a Landrace–Duroc–Yorkshire Population

Rempel¹,

Freking²,

Miles³

et al. 2011

Front. Gene.

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“…A three-generation White Duroc×Erhualian F 2 resource population was established as described previously [13]. In short, two White Duroc boars were mated to 17 Erhualian sows as founders.…”

Section: Methodsmentioning

confidence: 99%

“…Genomic DNA was extracted from swine ear tissues using a standard phenol-chloroform method. The DNA samples were then quantified using a Nanodrop 1,000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and diluted to a concentration of 50 ng/μL in a 96-well plate as previously described [13]. A total of 1,020 individuals (19 F 0 , 68 F 1 , and 933 F 2 ) were genotyped using the Illumina PorcineSNP60 BeadChip (62,163 SNPs) according to the manufacturer's protocols.…”

Section: Dna Collection and Genotypingmentioning

confidence: 99%

A whole genome sequence association study of muscle fiber traits in a White Duroc×Erhualian F2 resource population

Guo

Gao

Yang

et al. 2020

Asian-Australas J Anim Sci

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Objective: Muscle fiber types, numbers and area are crucial aspects associated with meat production and quality. However, there are few studies of pig muscle fibre traits in terms of the detection power, false discovery rate and confidence interval precision of whole-genome quantitative trait loci (QTL). We had previously performed genome scanning for muscle fibre traits using 183 microsatellites and detected 8 significant QTLs in a White Duroc× Erhualian F2 population. The confidence intervals of these QTLs ranged between 11 and 127 centimorgan (cM), which contained hundreds of genes and hampered the identification of QTLs. A whole-genome sequence imputation of the population was used for fine mapping in this study.Methods: A whole-genome sequences association study was performed in the F2 population. Genotyping was performed for 1,020 individuals (19 F0, 68 F1, and 933 F2). The whole-genome variants were imputed and 21,624,800 single nucleotide polymorphisms (SNPs) were identified and examined for associations to 11 longissimus dorsi muscle fiber traits.Results: A total of 3,201 significant SNPs comprising 7 novel QTLs showing associations with the relative area of fiber type I (I_RA), the fiber number per square centimeter (FN) and the total fiber number (TFN). Moreover, one QTL on pig chromosome 14 was found to affect both FN and TFN. Furthermore, four plausible candidate genes associated with FN (kinase non-catalytic C-lobe domain containing [KNDC1]), TFN (KNDC1), and I_RA (solute carrier family 36 member 4, contactin associated protein like 5, and glutamate metabotropic receptor 8) were identified.Conclusion: An efficient and powerful imputation-based association approach was utilized to identify genes potentially associated with muscle fiber traits. These identified genes and SNPs could be explored to improve meat production and quality via marker-assisted selection in pigs.

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Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances

Yang

Dong

et al. 2017

Animal Genetics

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Selection affects the patterns of linkage disequilibrium (LD) around the site of a beneficial allele with an increase in LD among the hitchhiking alleles. Comparing the differences in regional LD between pig populations could help to identify putative genomic regions with potential adaptations for economic traits. In this study, using Illumina Porcine SNP60K BeadChip genotyping data from 207 Chinese indigenous, 117 South American village and 408 Large White pigs, we estimated the variation of genome-wide LD between populations using the varld program. The top 0.1% standardized VarLD scores were used as a criterion for all comparisons, and compared with LD blocks, a total of four selection signatures on Sus scrofa chromosome (SSC) 7, 9, 13 and 14 were identified in all populations. These signatures overlapped with quantitative trait loci for linoleic acid content, age at puberty, number of muscle fibers per unit area, hip structure and body weight traits in pigs. Among them, one of the signatures (56.5-56.6 Mb on SSC7) in Large White pigs harbored the ADAMTSL3 gene, which is known to affect body length. The findings of this study seem to point toward recent selection in different pig populations. Further investigations are encouraged to confirm the selection signatures detected by varld in the present study.

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Genome-wide identification of QTL for age at puberty in gilts using a large intercross F₂population between White Duroc times Erhualian

Cited by 6 publications

References 29 publications

Association of Porcine Heparanase and Hyaluronidase 1 and 2 with Reproductive and Production Traits in a Landrace–Duroc–Yorkshire Population

Association of Porcine Heparanase and Hyaluronidase 1 and 2 with Reproductive and Production Traits in a Landrace–Duroc–Yorkshire Population

A whole genome sequence association study of muscle fiber traits in a White Duroc×Erhualian F2 resource population

Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances

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Genome-wide identification of QTL for age at puberty in gilts using a large intercross F2population between White Duroc times Erhualian

Cited by 6 publications

References 29 publications

Association of Porcine Heparanase and Hyaluronidase 1 and 2 with Reproductive and Production Traits in a Landrace–Duroc–Yorkshire Population

Association of Porcine Heparanase and Hyaluronidase 1 and 2 with Reproductive and Production Traits in a Landrace–Duroc–Yorkshire Population

A whole genome sequence association study of muscle fiber traits in a White Duroc×Erhualian F2 resource population

Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances

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Product

Resources

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Genome-wide identification of QTL for age at puberty in gilts using a large intercross F₂population between White Duroc times Erhualian