Insect-based food and feed are increasingly attracting attention. As a domesticated insect, the silkworm (Bombyx mori) has a highly nutritious pupa that can be easily raised in large quantities through large-scale farming, making it a highly promising source of food. The ratio of pupa to cocoon (RPC) refers to the proportion of the weight of the cocoon that is attributed to pupae, and is of significant value for edible utilization, as a higher RPC means a higher ratio of conversion of mulberry leaves to pupa. In silkworm production, there is a trade-off between RPC and cocoon shell ratiao(CSR), which refers the ratio of silk protein to the entire cocoon, during metamorphosis process. Understanding the genetic basis of this balance is crucial for breeding edible strains with a high RPC and further advancing its use as feed. Using QTL-seq, we identified a quantitative trait locus (QTL) for the balance between RPC and CSR that is located on chromosome 11 and covers a 9,773,115-bp region. This locus is an artificial selection hot spot that contains ten non-overlapping genomic regions under selection that were involved in the domestication and genetic breeding processes. These regions include 17 genes, nine of which are highly expressed in the silk gland, which is a vital component in the trade-off between RPC and CSR. These genes are annotate with function related with epigenetic modifications and the regulation of DNA replication et al. We identified one and two single nucleotide polymorphisms (SNPs) in the exons of teh KWMTBOMO06541 and KWMTBOMO06485 genes that result in amino acid changes in the protein domains. These SNPs have been strongly selected for during the domestication process. The KWMTBOMO06485 gene encodes the Bombyx mori (Bm) tRNA methyltransferase (BmDnmt2) and its knockout results in a significant change in the trade-off between CSR and RPC in both sexes. Taken together, our results contribute to a better understanding of the genetic basis of RPC and CSR. The identified QTL and genes that affect RPC can be used for marker-assisted and genomic selection of silkworm strains with a high RPC. This will further enhance the production efficiency of silkworms and of closely-related insects for edible and feed purposes.

中文翻译：

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QTL 分析以确定参与蚕丝蛋白合成和幼虫-蛹转变之间权衡的基因


以昆虫为基础的食品和饲料越来越受到人们的关注。作为一种家养昆虫，蚕（Bombyx mori）的蛹营养丰富，可以通过大规模养殖轻松大量饲养，使其成为极具前景的食物来源。蛹茧比（RPC）是指蚕茧重量所占的比例，对于食用利用具有重要价值，RPC越高意味着桑叶转化为蛹的比例越高。蚕生产中，变态过程中，RPC与茧壳率（CSR）之间存在着权衡，CSR是指丝蛋白与整个茧的比例。了解这种平衡的遗传基础对于培育具有高 RPC 的食用菌株并进一步推进其作为饲料的用途至关重要。使用 QTL-seq，我们确定了一个用于 RPC 和 CSR 之间平衡的数量性状位点 (QTL)，该位点位于 11 号染色体上，覆盖 9,773,115 bp 的区域。该基因座是一个人工选择热点，包含十个正在选择的不重叠的基因组区域，这些区域涉及驯化和遗传育种过程。这些区域包括 17 个基因，其中 9 个在丝腺中高表达，丝腺是 RPC 和 CSR 之间权衡的重要组成部分。这些基因注释有与表观遗传修饰和DNA复制调控等相关的功能。我们在 KWMTBOMO06541 和 KWMTBOMO06485 基因的外显子中鉴定出 1 个和 2 个单核苷酸多态性 (SNP)，这些多态性导致蛋白质结构域中的氨基酸变化。这些 SNP 在驯化过程中经过严格筛选。 KWMTBOMO06485 基因编码家蚕 (Bm) tRNA 甲基转移酶 (BmDnmt2)，其敲除会导致两性 CSR 和 RPC 之间的权衡发生显着变化。总而言之，我们的结果有助于更好地理解 RPC 和 CSR 的遗传基础。所鉴定的影响RPC的QTL和基因可用于具有高RPC的家蚕品系的标记辅助和基因组选择。这将进一步提高蚕及其近缘昆虫食用和饲料的生产效率。