Molecular characterization and a duplicated 31-bp indel within the LDB2 gene and its associations with production performance in chickens

Wei, Changyong; Hou, Dan; Feng, Yi; Li, Tong; Jing, Zhenzhu; Li, Wenya; Han, Ruili; Li, Guoxi; Sun, Guirong; Tian, Yun; Liu, Xiaojun; Kang, Xiangtao; Li, Zhuanjian

doi:10.1016/j.gene.2020.145046

Cited by 13 publications

(8 citation statements)

References 41 publications

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“…In Wang's et al they performed a new GWAS using specific locus amplified fragment sequencing (SLAF-seq) technology to discover that the LDB2 gene in this region had a very strong association with body weight ( 34 ). Wei et al indicated that a 31-bp indel located in the second intron region of the LDB2 gene was significantly correlated with some growth traits and carcass traits of chickens ( 35 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study of Body Weight Traits in Inner Mongolia Cashmere Goats

et al. 2021

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Objective: Body weight is an important economic trait for a goat, which greatly affects animal growth and survival. The purpose of this study was to identify genes associated with birth weight (BW), weaning weight (WW), and yearling weight (YW).Materials and Methods: In this study, a genome-wide association study (GWAS) of BW, WW, and YW was determined using the GGP_Goat_70K single-nucleotide polymorphism (SNP) chip in 1,920 Inner Mongolia cashmere goats.Results: We discovered that 21 SNPs were significantly associated with BW on the genome-wide levels. These SNPs were located in 10 genes, e.g., Mitogen-Activated Protein Kinase 3 (MAPK3), LIM domain binding 2 (LDB2), and low-density lipoprotein receptor-related protein 1B (LRP1B), which may be related to muscle growth and development in Inner Mongolia Cashmere goats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these genes were significantly enriched in the regulation of actin cytoskeleton and phospholipase D signaling pathway etc.Conclusion: In summary, this study will improve the marker-assisted breeding of Inner Mongolia cashmere goats and the molecular mechanisms of important economic traits.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study of Body Weight Traits in Inner Mongolia Cashmere Goats

et al. 2021

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“…The polymorphisms of TAPT1 were significantly associated with carcass weight and eviscerated weight in broilers [ 27 ]. The 31-bp InDel of the LDB2 gene was significantly correlated with multiple growth and carcass traits in the F 2 resource population and affected the expression of LDB2 in muscle tissue [ 28 ]. The PRKCA gene was associated with intramuscular fat content in bovine muscle tissue [ 29 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association studies for growth traits in broilers

et al. 2022

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Background The identification of markers and genes for growth traits may not only benefit for marker assist selection /genomic selection but also provide important information for understanding the genetic foundation of growth traits in broilers. Results In the current study, we estimated the genetic parameters of eight growth traits in broilers and carried out the genome-wide association studies for these growth traits. A total of 113 QTNs discovered by multiple methods together, and some genes, including ACTA1, IGF2BP1, TAPT1, LDB2, PRKCA, TGFBR2, GLI3, SLC16A7, INHBA, BAMBI, APCDD1, GPR39, and GATA4, were identified as important candidate genes for rapid growth in broilers. Conclusions The results of this study will provide important information for understanding the genetic foundation of growth traits in broilers.

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“…To date the most common associations found between SVs and phenotypes in avian model systems underlie traits related to body size and weight (e.g. Han et al., 2019; Hirwa et al., 2010; Li et al., 2022; Li, Chen, et al., 2021; Lin et al., 2021; Qin et al., 2023; Ren et al., 2020; Sohrabi et al., 2018; Wang, Wang, et al., 2020; Wei et al., 2020; see remaining references in Table S1 under phenotype category ‘Bodyweight’) followed by plumage colouration and pigmentation (e.g. Bruders et al., 2020; Domyan et al., 2014; Han et al., 2011; Krishnan & Cryberg, 2019; Krishnan, 2019; Maclary et al., 2023; Shen et al., 2022; Vickrey et al., 2018; Wang et al., 2013; see remaining references in Table S1 under phenotype category ‘Plumage Colouration and Pigmentation’).…”

Section: Identifying Associations Between Svs and Phenotypic Traitsmentioning

confidence: 99%

How structural variants shape avian phenotypes: Lessons from model systems

Recuerda,

Campagna

2024

Molecular Ecology

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Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long‐read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short‐read sequencing and associated analytical methods. SVs most commonly involve non‐coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co‐occur with single‐nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long‐read technologies become commonly implemented in non‐model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.

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Molecular characterization and a duplicated 31-bp indel within the LDB2 gene and its associations with production performance in chickens

Cited by 13 publications

References 41 publications

Genome-Wide Association Study of Body Weight Traits in Inner Mongolia Cashmere Goats

Genome-Wide Association Study of Body Weight Traits in Inner Mongolia Cashmere Goats

Genome-wide association studies for growth traits in broilers

How structural variants shape avian phenotypes: Lessons from model systems

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