Association of growth traits with a structural variation downstream of the KCNJ11 gene: a large population-based study in chickens

Wang, X; Wei, Changyong; Zhang, Z; Liu, D; Guo, Yaping; Sun, Guirong; Wang, Y; Li, H; Tian, Yadong; Kang, Xin; Han, Ruili; Li, Z

doi:10.1080/00071668.2020.1724878

Cited by 6 publications

(7 citation statements)

References 31 publications

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“…In fact, it was found to be highly expressed in the muscle tissue of one-week-old chicks [56], which supports our findings that this gene, closely located to a significantly associated CNV segment, can play a role in the regulation of birth weight. Our analysis of regulatory elements suggests that changes in the copy number in the KCNJ11 gene might be affecting gene transcription and could explain the effect on birth weight associated with these changes.…”

Section: Discussionsupporting

confidence: 90%

“…This hypothesis, however, needs to be addressed by RNA data on different tissues. Interestingly, a novel 163-bp indel in the downstream region of this gene was significantly associated with growth traits in chickens [56]. In the same study, synteny analyses found that KCNJ11 maintains a close connection with its neighboring genes.…”

Section: Discussionmentioning

confidence: 74%

“…The KCNJ11 gene, found to be 2217 base pairs upstream of the aforementioned significant CNV segment, is known to regulate insulin secretion [56]. A glucose metabolism disorder is usually linked as a cause of reduced development of chicken muscle tissue under stress, especially in broilers [57].…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide detection of CNVs and their association with performance traits in broilers

et al. 2021

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Background Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age. Results We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels. Conclusions Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 74%

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Genome-wide detection of CNVs and their association with performance traits in broilers

et al. 2021

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“…For this reason, this gene may promote early growth and muscle development in chickens. In fact, it was found to be highly expressed in the muscle tissue of one-week-old chicks [126], which supports our findings that this gene, closely located to a significantly associated CNV segment, can play a role in the regulation of birth weight. In addition, a novel 163-bp indel in the downstream region of this gene was significantly associated with growth traits in chickens [130].…”

Section: Discussionsupporting

confidence: 90%

“…The KCNJ11 gene, found to be 2,217 base pairs downstream of the significant CNV segment cited above, is known to regulate insulin secretion [126]. A glucose metabolism disorder is usually linked as a cause of reduced development of chicken muscle tissue under stress, especially in broilers [127].…”

Section: Discussionmentioning

confidence: 99%

CNV-based genome-wide association studies with performance traits in broilers

Fernandes¹

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First and foremost, thank you, God, for always being there for me. To my parents, Anna and Douglas, for your truly selfless and unconditional love. Thank you both for always giving me strength, for reminding me every day that I can do this and for being a constant source of support in my many many moments of crisis, during the challenges of graduate school and life. You are my world and my everything this life can bring. I could not have done it without you. My little brother André, aunt Kátia and uncle Luciano deserve my wholehearted thanks and appreciation as well. To my beloved grandpa Pasquale and great-aunts Lola and Beta. You are loved beyond words and missed beyond measures. I will always have this piece of my heart that smiles whenever I think about you. You were a priceless gift in my life and I will be forever grateful for the love, knowledge and values you instilled in me. I would like to sincerely express my gratitude and appreciation to my academic advisor, Dr. Luiz Coutinho, for his guidance, help and support, and especially for his confidence in me. You have set an example of excellence as a researcher and mentor. I would also like to thank my LBA team, in particular Dr. Gabriel and Dr. Vinicius, for guiding me throughout this study; your discussion, ideas, and feedback have been absolutely invaluable. To all my friends, in particular Pedro and Thais. You are the people who make me smile brighter, laugh louder and live better. True friendship isn't about being inseparable. It's being separated and nothing changes. Your friendship makes my life a better experience! Finally, I wish to express my deepest gratitude to University of São Paulo-"Luiz de Queiroz" College of Agriculture (USP/ESALQ) for the privilege granted and for aggregating so much knowledge in my academic history. You challenged me to be fearless in the pursuit of all opportunities and taught me that learning knows no boundaries. A special acknowledgment to CNPq for supporting me with a scholarship (process 134211/2019-7).

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Hundreds of independent midsize deletions mediate DNA loss in wild relatives of Red Jungle Fowl

2023

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Association of growth traits with a structural variation downstream of the KCNJ11 gene: a large population-based study in chickens

Cited by 6 publications

References 31 publications

Genome-wide detection of CNVs and their association with performance traits in broilers

Genome-wide detection of CNVs and their association with performance traits in broilers

CNV-based genome-wide association studies with performance traits in broilers

Hundreds of independent midsize deletions mediate DNA loss in wild relatives of Red Jungle Fowl

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