Identification of candidate genes associated with slaughter traits in F2 chicken population using genome‐wide association study

Liu, J.; Zhou, Jun; Li, J; Bao, Haigang

doi:10.1111/age.13079

Cited by 9 publications

(6 citation statements)

References 22 publications

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“…LCORL has been associated with height in humans (Horikoshi et al., 2013; Soranzo et al., 2009). Meanwhile, the NCAPG / LCORL region has been associated with the height and size of dogs (Vaysse et al., 2011), cows (Niu et al., 2021), horses (Tetens et al., 2013), donkeys (Liu et al., 2022), pigs (Rubin et al., 2012), sheep (Posbergh & Huson, 2021) and chickens (Liu et al., 2021). NCAPG is a subunit of the condensed protein I complex, which is crucial for maintenance of chromosome structure (Kimura et al., 2001).…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons

Hou,

Wang,

et al. 2023

Animal Genetics

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Selective breeding of meat pigeons is primarily based on growth traits, especially muscle mass (MM). Identification of functional genes and molecular markers of growth and slaughter traits through a genome‐wide association study (GWAS) will help to elucidate the underlying molecular mechanisms and provide a theoretical basis for the selective breeding of meat pigeons. The phenotypic data of body weight (BW) and body size (BS) of 556 meat pigeons at 52 and 80 weeks of age were collected. In total, 160 434 high‐quality single nucleotide polymorphism sites were obtained by restriction site‐associated DNA sequencing. The GWAS analysis revealed that MSTN, IGF2BP3 and NCAPG/LCORL were important candidate genes affecting the growth traits of meat pigeons. IGF2BP3 and NCAPG/LCORL were highly correlated to BW and BS, which are related to overall growth and development, while MSTN was associated with pectoral thickness and BW. Phenotypic association validation with the use of two meat pigeon populations found that the MSTN mutation c.C861T determines the MM. These results provide new insights into the genetic mechanisms underlying phenotypic variations of growth traits and MM in commercial meat pigeons. The identified markers and genes provide a theoretical basis for the selective breeding of meat pigeons.

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Section: Discussionmentioning

confidence: 99%

Genome‐wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons

Hou,

Wang,

et al. 2023

Animal Genetics

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“…In particular, the QTL on ECA3 close to the LCORL (ligand dependent nuclear receptor corepressor like) and NCAPG (non-SMC condensin I complex subunit G) genes has been confirmed in several studies for diverse horse breeds [31,32,[35][36][37][38]. This locus is also known to influence body size in numerous other species, including humans [39,40], cattle [41,42], sheep [43], pigs [44], rabbits [45], donkeys [46], chicken [47], and dogs [48]. To date, no causal variants underlying this QTL for withers height in horses have been identified, but there is growing evidence that LCORL retrocopies contributed to morphological changes during equid evolution and possibly also influence body size in present horses [49,50].…”

Section: Introductionmentioning

confidence: 93%

Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes

Reich,

Möller,

Stock

et al. 2024

Genet Sel Evol

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Background Body conformation, including withers height, is a major selection criterion in horse breeding and is associated with other important traits, such as health and performance. However, little is known about the genomic background of equine conformation. Therefore, the aim of this study was to use imputed sequence-level genotypes from up to 4891 German Warmblood horses to identify genomic regions associated with withers height and linear conformation traits. Furthermore, the traits were genetically characterised and putative causal variants for withers height were detected. Results A genome-wide association study (GWAS) for withers height confirmed the presence of a previously known quantitative trait locus (QTL) on Equus caballus (ECA) chromosome 3 close to the LCORL/NCAPG locus, which explained 16% of the phenotypic variance for withers height. An additional significant association signal was detected on ECA1. Further investigations of the region on ECA3 identified a few promising candidate causal variants for withers height, including a nonsense mutation in the coding sequence of the LCORL gene. The estimated heritability for withers height was 0.53 and ranged from 0 to 0.34 for the conformation traits. GWAS identified significantly associated variants for more than half of the investigated conformation traits, among which 13 showed a peak on ECA3 in the same region as withers height. Genetic parameter estimation revealed high genetic correlations between these traits and withers height for the QTL on ECA3. Conclusions The use of imputed sequence-level genotypes from a large study cohort led to the discovery of novel QTL associated with conformation traits in German Warmblood horses. The results indicate the high relevance of the QTL on ECA3 for various conformation traits, including withers height, and contribute to deciphering causal mutations for body size in horses.

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“…LCORL (ligand dependent nuclear receptor corepressor like) is a candidate gene associated with slaughter traits, being positionally associated with internal organ traits in chickens and located within a QTL for intestine length and gizzard weight. It is also a possible candidate responsible for growth and body weight and a reported candidate gene for carcass and eviscerated weight and egg quality traits [57,158,[160][161][162][163]. Its human homolog is involved in spermatogenesis, skeletal frame size, and adult height, with a ubiquitous expression in different tissues and the most upregulation in the testis [149].…”

Section: Gga4mentioning

confidence: 99%

“…The NCAPG (non-SMC condensin I complex subunit G) gene is involved in mitotic chromosome condensation and may regulate chicken bone growth and development. It is known as a candidate gene for bone size/mass and slaughter traits, with its SNP being also associated with egg albumen quality and other egg traits [160,[163][164][165][166]. NCAPG has a broad expression in bone marrow, lymph node, testis, and other human tissues [149].…”

Section: Gga4mentioning

confidence: 99%

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

Romanov,

Shakhin,

Abdelmanova

et al. 2024

Genes

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Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.

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Identification of candidate genes associated with slaughter traits in F2 chicken population using genome‐wide association study

Cited by 9 publications

References 22 publications

Genome‐wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons

Genome‐wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons

Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

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