Genome-wide association study identified genes associated with ammonia nitrogen tolerance in Litopenaeus vannamei

Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei . To identify the genes associated with ammonia nitrogen tolerance, we performed an extreme phenotype genome-wide association study method (XP-GWAS) on a population of 200 individuals. The...

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Published inFrontiers in genetics Vol. 13; p. 961009
Main Authors Fu, Shuo, Liu, Jianyong
Format Journal Article
LanguageEnglish
Published Frontiers Media S.A 22.08.2022
Subjects
ammonia nitrogen tolerance
breeding
candidate genes
Genetics
Litopenaeus vannamei
XP-GWAS
Online AccessGet full text
ISSN1664-8021
1664-8021
DOI10.3389/fgene.2022.961009

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Abstract Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei . To identify the genes associated with ammonia nitrogen tolerance, we performed an extreme phenotype genome-wide association study method (XP-GWAS) on a population of 200 individuals. The single nucleotide polymorphism (SNP) genotyping array method was used to construct the libraries and 36,048 SNPs were genotyped. Using the MLM, FarmCPU and Blink models, six different SNPs, located on SEQ3, SEQ4, SEQ5, SEQ7 and SEQ8, were determined to be significantly associated with ammonia nitrogen tolerance. By integrating the results of the GWAS and the biological functions of the genes, seven candidate genes (PDI, OZF, UPF2, VPS16, TMEM19, MYCBP2, and HOX7) were found to be associated with ammonia nitrogen tolerance in L . vannamei . These genes are involved in cell transcription, cell division, metabolism, and immunity, providing the basis for further study of the genetic mechanisms of ammonia nitrogen tolerance in L . vannamei . Further candidate gene association analysis in the offspring population revealed that the SNPs in the genes zinc finger protein OZF-like (OZF) and homeobox protein Hox-B7-like (HOX7) were significantly associated with ammonia nitrogen tolerance trait of L. vannamei . Our results provide fundamental genetic information that will be useful for further investigation of the molecular mechanisms of ammonia nitrogen tolerance. These associated SNPs may also be promising candidates for improving ammonia nitrogen tolerance in L. vannamei .
AbstractList Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei. To identify the genes associated with ammonia nitrogen tolerance, we performed an extreme phenotype genome-wide association study method (XP-GWAS) on a population of 200 individuals. The single nucleotide polymorphism (SNP) genotyping array method was used to construct the libraries and 36,048 SNPs were genotyped. Using the MLM, FarmCPU and Blink models, six different SNPs, located on SEQ3, SEQ4, SEQ5, SEQ7 and SEQ8, were determined to be significantly associated with ammonia nitrogen tolerance. By integrating the results of the GWAS and the biological functions of the genes, seven candidate genes (PDI, OZF, UPF2, VPS16, TMEM19, MYCBP2, and HOX7) were found to be associated with ammonia nitrogen tolerance in L. vannamei. These genes are involved in cell transcription, cell division, metabolism, and immunity, providing the basis for further study of the genetic mechanisms of ammonia nitrogen tolerance in L. vannamei. Further candidate gene association analysis in the offspring population revealed that the SNPs in the genes zinc finger protein OZF-like (OZF) and homeobox protein Hox-B7-like (HOX7) were significantly associated with ammonia nitrogen tolerance trait of L. vannamei. Our results provide fundamental genetic information that will be useful for further investigation of the molecular mechanisms of ammonia nitrogen tolerance. These associated SNPs may also be promising candidates for improving ammonia nitrogen tolerance in L. vannamei.Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei. To identify the genes associated with ammonia nitrogen tolerance, we performed an extreme phenotype genome-wide association study method (XP-GWAS) on a population of 200 individuals. The single nucleotide polymorphism (SNP) genotyping array method was used to construct the libraries and 36,048 SNPs were genotyped. Using the MLM, FarmCPU and Blink models, six different SNPs, located on SEQ3, SEQ4, SEQ5, SEQ7 and SEQ8, were determined to be significantly associated with ammonia nitrogen tolerance. By integrating the results of the GWAS and the biological functions of the genes, seven candidate genes (PDI, OZF, UPF2, VPS16, TMEM19, MYCBP2, and HOX7) were found to be associated with ammonia nitrogen tolerance in L. vannamei. These genes are involved in cell transcription, cell division, metabolism, and immunity, providing the basis for further study of the genetic mechanisms of ammonia nitrogen tolerance in L. vannamei. Further candidate gene association analysis in the offspring population revealed that the SNPs in the genes zinc finger protein OZF-like (OZF) and homeobox protein Hox-B7-like (HOX7) were significantly associated with ammonia nitrogen tolerance trait of L. vannamei. Our results provide fundamental genetic information that will be useful for further investigation of the molecular mechanisms of ammonia nitrogen tolerance. These associated SNPs may also be promising candidates for improving ammonia nitrogen tolerance in L. vannamei.
Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei . To identify the genes associated with ammonia nitrogen tolerance, we performed an extreme phenotype genome-wide association study method (XP-GWAS) on a population of 200 individuals. The single nucleotide polymorphism (SNP) genotyping array method was used to construct the libraries and 36,048 SNPs were genotyped. Using the MLM, FarmCPU and Blink models, six different SNPs, located on SEQ3, SEQ4, SEQ5, SEQ7 and SEQ8, were determined to be significantly associated with ammonia nitrogen tolerance. By integrating the results of the GWAS and the biological functions of the genes, seven candidate genes (PDI, OZF, UPF2, VPS16, TMEM19, MYCBP2, and HOX7) were found to be associated with ammonia nitrogen tolerance in L . vannamei . These genes are involved in cell transcription, cell division, metabolism, and immunity, providing the basis for further study of the genetic mechanisms of ammonia nitrogen tolerance in L . vannamei . Further candidate gene association analysis in the offspring population revealed that the SNPs in the genes zinc finger protein OZF-like (OZF) and homeobox protein Hox-B7-like (HOX7) were significantly associated with ammonia nitrogen tolerance trait of L. vannamei . Our results provide fundamental genetic information that will be useful for further investigation of the molecular mechanisms of ammonia nitrogen tolerance. These associated SNPs may also be promising candidates for improving ammonia nitrogen tolerance in L. vannamei .
Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei. To identify the genes associated with ammonia nitrogen tolerance, we performed an extreme phenotype genome-wide association study method (XP-GWAS) on a population of 200 individuals. The single nucleotide polymorphism (SNP) genotyping array method was used to construct the libraries and 36,048 SNPs were genotyped. Using the MLM, FarmCPU and Blink models, six different SNPs, located on SEQ3, SEQ4, SEQ5, SEQ7 and SEQ8, were determined to be significantly associated with ammonia nitrogen tolerance. By integrating the results of the GWAS and the biological functions of the genes, seven candidate genes (PDI, OZF, UPF2, VPS16, TMEM19, MYCBP2, and HOX7) were found to be associated with ammonia nitrogen tolerance in L. vannamei. These genes are involved in cell transcription, cell division, metabolism, and immunity, providing the basis for further study of the genetic mechanisms of ammonia nitrogen tolerance in L. vannamei. Further candidate gene association analysis in the offspring population revealed that the SNPs in the genes zinc finger protein OZF-like (OZF) and homeobox protein Hox-B7-like (HOX7) were significantly associated with ammonia nitrogen tolerance trait of L. vannamei. Our results provide fundamental genetic information that will be useful for further investigation of the molecular mechanisms of ammonia nitrogen tolerance. These associated SNPs may also be promising candidates for improving ammonia nitrogen tolerance in L. vannamei.
Author Liu, Jianyong
Fu, Shuo
AuthorAffiliation 2 Guangdong Provincial Shrimp Breeding and Culture Laboratory , Guangdong Ocean University , Zhanjiang , China
1 College of Fisheries, Guangdong Ocean University , Zhanjiang , China
AuthorAffiliation_xml – name: 1 College of Fisheries, Guangdong Ocean University , Zhanjiang , China
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crossref_primary_10_3390_biology13090731
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Reviewed by: Sheng Luan, Yellow Sea Fisheries Research Institute (CAFS), China
This article was submitted to Livestock Genomics, a section of the journal Frontiers in Genetics
Baohua Chen, Xiamen University, China
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Snippet Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei . To identify the genes associated with ammonia...
Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei. To identify the genes associated with ammonia...
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SubjectTerms ammonia nitrogen tolerance
breeding
candidate genes
Genetics
Litopenaeus vannamei
XP-GWAS
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Title Genome-wide association study identified genes associated with ammonia nitrogen tolerance in Litopenaeus vannamei
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