Mapping QTL for porcine muscle fibre traits in a White Duroc × Erhualian F<sub>2</sub> resource population

Li, W.B.; Ren, Jun; Zhu, Weiping; Guo, Binhui; Yang, Bin; Liu, L.T.; Ding, Nengshui; Ma, Junwu; Li, L.; Huang, Lusheng

doi:10.1111/j.1439-0388.2009.00805.x

Cited by 6 publications

(5 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In our previous study, the following QTLs were identified within the same sample population: 3 QTLs associated with IIB_A on SSC7, SSC8, and SSC15; 3 QTLs associated with IIA_A on SS7 and SSC11; 1 QTL associated with FN on SSC7; and 1 QTL associated with I_NP on SSCX. The confidence interval for these QTLs ranged between 11 and 127 cM [10]. Interestingly, fewer QTLs and no consistent QTLs were detected in the present GWAS study compared with previous studies.…”

Section: Discussioncontrasting

confidence: 79%

“…These 11 traits included area (A), relative area (RA), and numerical percentage (NP) of the three types of myofibers (I, IIA, and IIB) and FN and FTN. This approach was based on previous study that measured muscle fiber traits [1,10].…”

Section: Methodsmentioning

confidence: 99%

“…One hundred and twenty F 2 individuals were measured for muscle fiber traits, of which 100 individuals were genotyped and analyzed and detailed descriptive statistics of the traits were presented in our previous study [10]. The relative area of fiber type IIB (IIB_RA) and the numerical percentage of fiber type IIB (IIB_NP) were highly negatively correlated with the relative area of fiber type IIA (IIA_RA), the numerical percentage of fiber type IIA (II A_NP), the relative area of fiber type I (I_RA) and the numerical percentage of fiber type I (I_NP; Figure 1).…”

Section: Phenotype Statisticsmentioning

confidence: 99%

“…Estellé et al [9] detected 20 significant genome regions associated with muscle fiber traits in an Iberian× Landrace F 2 pig population. We have previously evidenced 8 genome-wide significant QTLs for muscle fiber traits in a Chinese Erhualian×White Duroc F 2 resource population [10]. The confidence intervals of most QTLs were more than 10 centimorgan (cM) and massive numbers of genes were present in these regions, which hampered the further fine mapping and characterization of potential candidate genes.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

View full text Add to dashboard Cite

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.

show abstract

Section: Discussioncontrasting

confidence: 79%

Section: Methodsmentioning

confidence: 99%

Section: Phenotype Statisticsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

View full text Add to dashboard Cite

show abstract

“…The classical approach to dissecting the genetic architecture is linkage analysis. Quantitative trait locus mapping for traits related to loin muscle and muscle fiber composition via microsatellites markers has been reported in Japanese Wild Boar × Large White (Nii et al, 2005), Duroc × Berlin Miniature Pig (Wimmers et al, 2006(Wimmers et al, , 2007, Iberian × Landrace (Estellé et al, 2008) and White Duroc × Erhualian (Li et al, 2009). Although microsatellite-based genetic linkage mapping is valuable to discuss the common genetic loci across breeds or within breeds, it is limited by the low resolution.…”

Section: Den T I F Icat Ion Of Gen Et Ic Loc I a S Soc I At Ed W I T ...mentioning

confidence: 99%

Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig

Zeng,

2023

Animal Genetics

View full text Add to dashboard Cite

As a major source of protein in human diets, pig meat plays a crucial role in ensuring global food security. Key determinants of meat production refer to the chemical and physical compositions or characteristics of muscle fibers, such as the number, hypertrophy potential, fiber‐type conversion and intramuscular fat deposition. However, the growth and formation of muscle fibers comprises a complex process under spatio‐temporal regulation, that is, the intermingled and concomitant proliferation, differentiation, migration and fusion of myoblasts. Recently, with the fast and continuous development of next‐generation sequencing technology, the integration of quantitative trait loci mapping with genome‐wide association studies (GWAS) has greatly helped animal geneticists to discover and explore thousands of functional or causal genetic elements underlying muscle growth and development. However, owing to the underlying complex molecular mechanisms, challenges to in‐depth understanding and utilization remain, and the cost of large‐scale sequencing, which requires integrated analyses of high‐throughput omics data, is high. In this review, we mainly elaborate on research advances in integrative analyses (e.g. GWAS, omics) for identifying functional genes or genomic elements for longissimus dorsi muscle growth and development for different pig breeds, describing several successful transcriptome analyses and functional genomics cases, in an attempt to provide some perspective on the future functional annotation of genetic elements for muscle growth and development in pigs.

show abstract

Genomic variants associated with the number and diameter of muscle fibers in pigs as revealed by a genome-wide association study

Zhang

Guo

Wang

et al. 2020

Animal

View full text Add to dashboard Cite

Muscle fiber characteristics comprise a set of complex traits that influence the meat quality and lean meat production of livestock. However, the genetic and biological mechanisms regulating muscle fiber characteristics are largely unknown in pigs. Based on a genome-wide association study (GWAS) performed on 421 Large White × Min pig F2 individuals presenting well-characterized phenotypes, this work aimed to detect genome variations and candidate genes for five muscle fiber characteristics: percentage of type I fibers (FIB1P), percentage of type IIA fibers (FIB2AP), percentage of type IIB fibers (FIB2BP), diameter of muscle fibers (DIAMF) and number of muscle fibers per unit area (NUMMF). The GWAS used the Illumina Porcine SNP60K genotypic data, which were analyzed by a mixed model. Seven and 10 single nucleotide polymorphisms (SNPs) were significantly associated with DIAMF and NUMMF, respectively (P < 1.10E-06); no SNP was significantly associated with FIB1P, FIB2AP or FIB2B. For DIAMF, the significant SNPs on chromosome 4 were located in the previously reported quantitative trait loci (QTL) interval. Because the significant SNPs on chromosome 6 were not mapped in the previously reported QTL interval, a putative novel QTL was suggested for this locus. None of the previously reported QTL intervals on chromosomes 6 and 14 harbored significant SNPs for NUMMF; thus, new potential QTLs on these two chromosomes are suggested in the present work. The most significant SNPs associated with DIAMF (ALGA0025682) and NUMMF (MARC0046984) explained 12.02% and 11.59% of the phenotypic variation of these traits, respectively. In addition, both SNPs were validated as associated with DIAMF and NUMMF in Beijing Black pigs (P < 0.01). Some candidate genes or non-coding RNAs, such as solute carrier family 44 member 5 and miR-124a-1 for DIAMF, and coiled-coil serine rich protein 2 for NUMMF, were identified based on their close location to the significant SNPs. This study revealed some genome-wide association variants for muscle fiber characteristics, and it provides valuable information to discover the genetic mechanisms controlling these traits in pigs.

show abstract

Mapping QTL for porcine muscle fibre traits in a White Duroc × Erhualian F₂ resource population

Cited by 6 publications

References 21 publications

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

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

Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig

Genomic variants associated with the number and diameter of muscle fibers in pigs as revealed by a genome-wide association study

Contact Info

Product

Resources

About

Mapping QTL for porcine muscle fibre traits in a White Duroc × Erhualian F2 resource population

Cited by 6 publications

References 21 publications

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

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

Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig

Genomic variants associated with the number and diameter of muscle fibers in pigs as revealed by a genome-wide association study

Contact Info

Product

Resources

About

Mapping QTL for porcine muscle fibre traits in a White Duroc × Erhualian F₂ resource population