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Nucleotide Diversity and Selection Signature in the Domesticated Silkworm, Bombyx mori, and Wild Silkworm, Bombyx mandarina

To investigate the patterns of nucleotide diversity in domesticated silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) and its wild relative, Chinese wild silkworm, Bombyx mandarina Moore, we sequenced nine nuclear genes. Neutrality test and coalescent simulation for these genes were performed to lo...

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Autores principales: Guo, Yi, Shen, Yi-Hong, Sun, Wei, Kishino, Hirohisa, Xiang, Zhong-Huai, Zhang, Ze
Formato: Online Artículo Texto
Lenguaje:English
Publicado: University of Wisconsin Library 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3391917/
https://www.ncbi.nlm.nih.gov/pubmed/22239062
http://dx.doi.org/10.1673/031.011.15501
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author Guo, Yi
Shen, Yi-Hong
Sun, Wei
Kishino, Hirohisa
Xiang, Zhong-Huai
Zhang, Ze
author_facet Guo, Yi
Shen, Yi-Hong
Sun, Wei
Kishino, Hirohisa
Xiang, Zhong-Huai
Zhang, Ze
author_sort Guo, Yi
collection PubMed
description To investigate the patterns of nucleotide diversity in domesticated silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) and its wild relative, Chinese wild silkworm, Bombyx mandarina Moore, we sequenced nine nuclear genes. Neutrality test and coalescent simulation for these genes were performed to look at bottleneck intensity and selection signature; linkage disequilibrium (LD) within and between loci was employed to investigate allele association. As a result, B. mori lost 33–49% of nucleotide diversity relative to wild silkworm, which is similar to the loss levels found in major cultivated crops. Diversity of B. mori is significantly lower than that of B. mandarina measured as π(total) (0.01166 vs. 0.1741) or θ(W)(0.01124 vs. 0.02206). Bottleneck intensity of domesticated silkworm is 1.5 (in terms of k = N(b)/d, N(b)-bottleneck population size; d-bottleneck duration) with different durations. Gene DefA showed signature of artificial selection by all analysis methods and might experience strong artificial selection in B. mori during domestication. For nine loci, both curves of LD decay rapidly within 200 bp and drop slowly when distance is > 200 bp, although that of B. mori decays slower than B. mandarina at loci investigated. However, LD could not be estimated at DefA in B. mori and at ER in both silkworms. Elevated LD observed in B. mori may be indicator of selection and demographic events.
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spelling pubmed-33919172012-07-09 Nucleotide Diversity and Selection Signature in the Domesticated Silkworm, Bombyx mori, and Wild Silkworm, Bombyx mandarina Guo, Yi Shen, Yi-Hong Sun, Wei Kishino, Hirohisa Xiang, Zhong-Huai Zhang, Ze J Insect Sci Article To investigate the patterns of nucleotide diversity in domesticated silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) and its wild relative, Chinese wild silkworm, Bombyx mandarina Moore, we sequenced nine nuclear genes. Neutrality test and coalescent simulation for these genes were performed to look at bottleneck intensity and selection signature; linkage disequilibrium (LD) within and between loci was employed to investigate allele association. As a result, B. mori lost 33–49% of nucleotide diversity relative to wild silkworm, which is similar to the loss levels found in major cultivated crops. Diversity of B. mori is significantly lower than that of B. mandarina measured as π(total) (0.01166 vs. 0.1741) or θ(W)(0.01124 vs. 0.02206). Bottleneck intensity of domesticated silkworm is 1.5 (in terms of k = N(b)/d, N(b)-bottleneck population size; d-bottleneck duration) with different durations. Gene DefA showed signature of artificial selection by all analysis methods and might experience strong artificial selection in B. mori during domestication. For nine loci, both curves of LD decay rapidly within 200 bp and drop slowly when distance is > 200 bp, although that of B. mori decays slower than B. mandarina at loci investigated. However, LD could not be estimated at DefA in B. mori and at ER in both silkworms. Elevated LD observed in B. mori may be indicator of selection and demographic events. University of Wisconsin Library 2011-11-14 /pmc/articles/PMC3391917/ /pubmed/22239062 http://dx.doi.org/10.1673/031.011.15501 Text en © 2011 http://creativecommons.org/licenses/by/2.5/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Article
Guo, Yi
Shen, Yi-Hong
Sun, Wei
Kishino, Hirohisa
Xiang, Zhong-Huai
Zhang, Ze
Nucleotide Diversity and Selection Signature in the Domesticated Silkworm, Bombyx mori, and Wild Silkworm, Bombyx mandarina
title Nucleotide Diversity and Selection Signature in the Domesticated Silkworm, Bombyx mori, and Wild Silkworm, Bombyx mandarina
title_full Nucleotide Diversity and Selection Signature in the Domesticated Silkworm, Bombyx mori, and Wild Silkworm, Bombyx mandarina
title_fullStr Nucleotide Diversity and Selection Signature in the Domesticated Silkworm, Bombyx mori, and Wild Silkworm, Bombyx mandarina
title_full_unstemmed Nucleotide Diversity and Selection Signature in the Domesticated Silkworm, Bombyx mori, and Wild Silkworm, Bombyx mandarina
title_short Nucleotide Diversity and Selection Signature in the Domesticated Silkworm, Bombyx mori, and Wild Silkworm, Bombyx mandarina
title_sort nucleotide diversity and selection signature in the domesticated silkworm, bombyx mori, and wild silkworm, bombyx mandarina
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3391917/
https://www.ncbi.nlm.nih.gov/pubmed/22239062
http://dx.doi.org/10.1673/031.011.15501
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