Nucleotide diversity and selection signature in the domesticated silkworm, Bombyx mori, and wild silkworm, Bombyx mandarina

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 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.

Figure 1.

The bottleneck model of coalescent simulation in this study. High quality figures are available online.

Figure 2.

Likelihood curves of 9 loci using the number of segregating sites (S) as fit standard with d=1000. High quality figures are available online.

Figure 3.

Joint likelihood surfaces of 8 neutral loci using the number of segregating sites (S) as fit standard with d=1000. High quality figures are available online.

Figure 4.

Decay of intralocus linkage disequilibrium against pairwise distance for 9 loci in domesticated silkworm (A) and wild silkworm (B). The solid and dotted lines represent logarithmic curves fitting to the data for B. mori and B. mandarina, respectively. High quality figures are available online.

Figure 5.

Decay of intralocus linkage disequilibrium against pairwise distance for DefA in wild silkworm. The dotted line represents logarithmic curve fitting to the data for B. mandarina only. High quality figures are available online.

Supplementary Figure S1:

Likelihood curves of 9 loci using Tajima's D (D) as fit standard with d = 1000. High quality figures are available online.

Supplementary Figure S2:

Joint likelihood curves of 8 neutral loci using S as fit standard without duration of bottleneck. High quality figures are available online.