Construction of a Single Nucleotide Polymorphism Linkage Map for the Silkworm, Bombyx mori, Based on Bacterial Artificial Chromosome End Sequences

Abstract

We have developed a linkage map for the silkworm Bombyx mori based on single nucleotide polymorphisms (SNPs) between strains p50T and C108T initially found on regions corresponding to the end sequences of bacterial artificial chromosome (BAC) clones. Using 190 segregants from a backcross of a p50T female 3 an F 1 (p50T 3 C108T) male, we analyzed segregation patterns of 534 SNPs between p50T and C108T, detected among 3840 PCR amplicons, each associated with a p50T BAC end sequence. This enabled us to construct a linkage map composed of 534 SNP markers spanning 1305 cM in total length distributed over the expected 28 linkage groups. Of the 534 BACs whose ends harbored the SNPs used to construct the linkage map, 89 were associated with 107 different ESTs. Since each of the SNP markers is directly linked to a specific genomic BAC clone and to whole-genome sequence data, and some of them are also linked to EST data, the SNP linkage map will be a powerful tool for investigating silkworm genome properties, mutation mapping, and map-based cloning of genes of industrial and agricultural interest.

Repression of tyrosine hydroxylase is responsible for the sex-linked chocolate mutation of the silkworm, Bombyx mori

“…The sch linkage map construction. To construct the sch linkage map, SNP markers on chromosome 1 and newly developed markers from BAC end sequences (25,26) were used to survey the segregation patterns in 4,501 BC1 individuals from the cross sch female × F1 male (sch female × p50T male). The primers for the SNP markers used in the linkage analysis are listed in Table S1.…”

“…B. mori has therefore been regarded as the major lepidopteran model for the study of color mutants, particularly because of the publication of its complete genome sequence (22)(23)(24) and a high-density linkage map (25,26). Mutations in the sepiapterin reductase (SPR) gene (BmSpr) are responsible for the yellow body coloration of the lemon and lemon lethal mutations during the larval developmental stages (20).…”

A comparison of recombination frequencies in intraspecific versus interspecific mapping populations of Nasonia

“…However, high-density maps are still restricted to species whose genomes have been sequenced: fruit flies of the genus Drosophila (Chen et al, 2009), the yellow fever mosquito Aedes aegypti (Fulton et al, 2001), the red flour beetle Tribolium castaneum (Lorenzen et al, 2005), the silkworm Bombyx mori (Yamamoto et al, 2006), and the honey bee Apis mellifera (Solignac et al, 2007). Here, we are concerned with the parasitoid (jewel) wasp Nasonia vitripennis, whose complete genome sequence has recently been published together with that of its closely related congeners N. giraulti and N. longicornis (Werren et al, 2010).…”

Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements

“…The insights gained from comparative genomic analyses using a reference genome from a model species such as the silkworm would greatly facilitate research on all Lepidoptera, and in particular on selective targets for innovative pest management at a time when competition for food between humans and insects is becoming a critical challenge for a rapidly growing human population. The 432 Mb genome of B. mori is the first fully sequenced lepidopteran genome (1), and detailed SNP and BAC-based chromosomal maps are available (6,7). We wished to compare the silkworm genome at a finer scale with that of major lepidopteran pests from the family Noctuidae, Helicoverpa armigera and Spodoptera frugiperda.…”