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Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei
Penaeus vannamei is the most important economic shrimp in the world. Many selective breeding programs are carried out to improve its production and performance traits. Although significant differences in the reproductive ability of female P. vannamei under artificial breeding conditions have been re...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9465174/ https://www.ncbi.nlm.nih.gov/pubmed/36105098 http://dx.doi.org/10.3389/fgene.2022.929889 |
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author | Sui, Juan Luan, Sheng Cao, Jiawang Dai, Ping Meng, Xianhong Luo, Kun Chen, Baolong Tan, Jian Fu, Qiang Kong, Jie |
author_facet | Sui, Juan Luan, Sheng Cao, Jiawang Dai, Ping Meng, Xianhong Luo, Kun Chen, Baolong Tan, Jian Fu, Qiang Kong, Jie |
author_sort | Sui, Juan |
collection | PubMed |
description | Penaeus vannamei is the most important economic shrimp in the world. Many selective breeding programs are carried out to improve its production and performance traits. Although significant differences in the reproductive ability of female P. vannamei under artificial breeding conditions have been reported, the genome-wide adaption of the reproductive ability of domesticated female P. vannamei is less investigated. In this study, whole-genome analysis was performed along with pooled DNA sequencing on two fecundity separated bulks, high fecundity bulk (HB), and low fecundity bulk (LB). Each bulk contained 30 individuals from 3 commercial populations. A sequencing depth of >30× was achieved for each bulk, leading to the identification of 625,181 and 629,748 single nucleotide polymorphisms (SNPs) in HB and LB, respectively. Fixation index (Fst) combined with p ratio allowed for the identification of 145 selective sweep regions, with a sequence length of 14.5 Mb, accounting for 0.59% of the genome. Among the 145 selective sweep regions, a total of 64,046 SNPs were identified, and further verification was performed by genotyping 50 candidate SNPs on 60 samples from the offspring of the three populations. Furthermore, 121 genes were screened from the sweep regions. GO annotation and KEGG enrichment analyses showed that partial genes were essential for fecundity regulation. This study provides important information for in-depth investigation of genomic characteristics for long-term selective breeding on the fecundity of female P. vannamei and will also be important for genome-assisted breeding of P. vannamei in the future. |
format | Online Article Text |
id | pubmed-9465174 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-94651742022-09-13 Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei Sui, Juan Luan, Sheng Cao, Jiawang Dai, Ping Meng, Xianhong Luo, Kun Chen, Baolong Tan, Jian Fu, Qiang Kong, Jie Front Genet Genetics Penaeus vannamei is the most important economic shrimp in the world. Many selective breeding programs are carried out to improve its production and performance traits. Although significant differences in the reproductive ability of female P. vannamei under artificial breeding conditions have been reported, the genome-wide adaption of the reproductive ability of domesticated female P. vannamei is less investigated. In this study, whole-genome analysis was performed along with pooled DNA sequencing on two fecundity separated bulks, high fecundity bulk (HB), and low fecundity bulk (LB). Each bulk contained 30 individuals from 3 commercial populations. A sequencing depth of >30× was achieved for each bulk, leading to the identification of 625,181 and 629,748 single nucleotide polymorphisms (SNPs) in HB and LB, respectively. Fixation index (Fst) combined with p ratio allowed for the identification of 145 selective sweep regions, with a sequence length of 14.5 Mb, accounting for 0.59% of the genome. Among the 145 selective sweep regions, a total of 64,046 SNPs were identified, and further verification was performed by genotyping 50 candidate SNPs on 60 samples from the offspring of the three populations. Furthermore, 121 genes were screened from the sweep regions. GO annotation and KEGG enrichment analyses showed that partial genes were essential for fecundity regulation. This study provides important information for in-depth investigation of genomic characteristics for long-term selective breeding on the fecundity of female P. vannamei and will also be important for genome-assisted breeding of P. vannamei in the future. Frontiers Media S.A. 2022-08-29 /pmc/articles/PMC9465174/ /pubmed/36105098 http://dx.doi.org/10.3389/fgene.2022.929889 Text en Copyright © 2022 Sui, Luan, Cao, Dai, Meng, Luo, Chen, Tan, Fu and Kong. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Sui, Juan Luan, Sheng Cao, Jiawang Dai, Ping Meng, Xianhong Luo, Kun Chen, Baolong Tan, Jian Fu, Qiang Kong, Jie Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei |
title | Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei
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title_full | Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei
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title_fullStr | Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei
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title_full_unstemmed | Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei
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title_short | Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei
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title_sort | genomic signatures of artificial selection in fecundity of pacific white shrimp, penaeus vannamei |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9465174/ https://www.ncbi.nlm.nih.gov/pubmed/36105098 http://dx.doi.org/10.3389/fgene.2022.929889 |
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