Nucleotide diversity and selection signature in the domesticated silkworm, Bombyx mori, and wild silkworm, Bombyx mandarina
1The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400715, China
2The Laboratory of Biometrics and Bioinformatics, Graduate School of Agriculture and Life Science, The University
of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
3The Institute of Agricultural and Life Sciences, Chongqing University, Chongqing 400044, China
Abstract
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 πtotal (0.01166 vs. 0.1741) or θw (0.01124 vs. 0.02206). Bottleneck intensity of domesticated silkworm is 1.5 (in terms of k = Nb/d, Nb-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.
Keywords: bottleneck, domestication, nucleotide diversity, selection
Abbreviations: LD, linkage disequilibrium
Correspondence:
a guo1983752@163.com,
b cs_shenyh@swu.edu.cn,
c sunwei077@163.com,
d kishino@lbm.ab.a.u-tokyo.ac.jp,
e xbxzh@swu.edu.cn,
f zezhang@swu.edu.cn, *Corresponding author
Editor: Zhijian Jake Tu was Editor of this paper.
Received: 16 September 2010 | Accepted: 22 December 2010 | Published: 14 November 2011
Copyright: This is an open access paper. We use the Creative Commons Attribution 3.0 license that permits unrestricted use, provided that the paper is properly attributed.
ISSN: 1536-2442 | Volume 11, Number 155
Guo Y, Shen Y-H, Sun W, Kishino H, Xiang Z-H, Zhang Z. 2011. Nucleotide diversity and selection signature in the domesticated silkworm, Bombyx mori, and wild silkworm, Bombyx mandarina. Journal of Insect Science 11:155 available online: insectscience.org/11.155
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