State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Yibin Academy of Southwest University, Southwest University, Chongqing, 400715, China.
Genet Sel Evol. 2024 Sep 30;56(1):68. doi: 10.1186/s12711-024-00937-z.
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.
昆虫类食物和饲料越来越受到关注。家蚕作为一种驯化昆虫，其幼虫具有极高的营养价值，并且可以通过大规模养殖大量繁殖，因此是一种很有前途的食物来源。蛹重比（RPC）是指茧重中属于蛹的比例，对于可食用的利用具有重要价值，因为 RPC 越高，桑叶转化为蛹的比例就越高。在蚕的生产中，RPC 与茧层率（CSR）之间存在权衡，CSR 是指丝蛋白与整个茧的比例，这一比例在变态过程中发生变化。了解这种平衡的遗传基础对于培育具有高 RPC 的可食用品种以及进一步推进其作为饲料的使用至关重要。
利用 QTL-seq，我们鉴定出一个位于第 11 号染色体上的、控制 RPC 与 CSR 平衡的数量性状位点（QTL），该 QTL 包含一个 9773115bp 的区域。该位点是一个人工选择的热点，包含 10 个非重叠的基因组选择区域，这些区域参与了家蚕的驯化和遗传选育过程。这些区域包含 17 个基因，其中 9 个在丝腺中高度表达，丝腺是 RPC 与 CSR 权衡的关键部分。这些基因注释的功能与表观遗传修饰和 DNA 复制调控等有关。我们在 KWMTBOMO06541 和 KWMTBOMO06485 基因的外显子中鉴定出一个和两个导致蛋白质结构域中氨基酸变化的单核苷酸多态性（SNP）。这些 SNP 在驯化过程中受到强烈选择。KWMTBOMO06485 基因编码的是家蚕 tRNA 甲基转移酶（BmDnmt2），其敲除会导致 CSR 和 RPC 在雌雄两性中都发生显著变化。
总之，我们的研究结果有助于更好地理解 RPC 和 CSR 的遗传基础。鉴定出的影响 RPC 的 QTL 和基因可用于高 RPC 家蚕品种的标记辅助和基因组选择。这将进一步提高蚕和相关昆虫的生产效率，使其更适用于食用和饲料用途。
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