QTL analysis to identify genes involved in the trade-off between silk protein synthesis and larva-pupa transition in silkworms

IF 3.6 1区农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE

Genetics Selection Evolution Pub Date : 2024-09-30 DOI:10.1186/s12711-024-00937-z

Rui Gao, Chunlin Li, Ang Zhou, Xiachao Wang, Kupeng Lu, Weidong Zuo, Hai Hu, Minjin Han, Xiaoling Tong, Fangyin Dai

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引用次数: 0

Abstract

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.

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通过 QTL 分析确定参与家蚕丝蛋白合成和幼虫-蛹过渡之间权衡的基因

以昆虫为基础的食品和饲料越来越受到人们的关注。作为一种驯化昆虫，蚕（Bombyx mori）的蛹营养价值很高，可以通过规模化养殖轻松实现大量饲养，是一种极具潜力的食物来源。蚕蛹与蚕茧的比率（RPC）指的是蚕蛹占蚕茧重量的比例，对食用利用具有重要价值，因为 RPC 越高，意味着桑叶转化为蚕蛹的比率越高。在家蚕生产中，RPC 与茧壳率（CSR）之间存在权衡，后者指的是蚕丝蛋白在整个蚕茧中的比例。了解这种平衡的遗传基础对于培育高RPC的可食用品系以及进一步推动其作为饲料的应用至关重要。通过 QTL-seq，我们确定了一个 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，包含十个非重叠的基因组选择区域，这些区域参与了驯化和遗传育种过程。这些区域包括 17 个基因，其中 9 个基因在丝腺中高度表达，而丝腺是 RPC 和 CSR 之间权衡的重要组成部分。我们在 KWMTBOMO06541 和 KWMTBOMO06485 基因的外显子中发现了一个和两个单核苷酸多态性（SNPs），它们会导致蛋白质结构域的氨基酸发生变化。在驯化过程中，这些 SNPs 被强烈选择。KWMTBOMO06485 基因编码 Bombyx mori（Bm）的 tRNA 甲基转移酶（BmDnmt2），敲除该基因会导致雌雄雌虫在 CSR 和 RPC 之间的权衡发生显著变化。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。已鉴定的影响 RPC 的 QTL 和基因可用于标记辅助和基因组选育高 RPC 的蚕品系。这将进一步提高家蚕以及与家蚕密切相关的食用和饲料昆虫的生产效率。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genetics Selection Evolution 生物-奶制品与动物科学

CiteScore

6.50

自引率

9.80%

发文量

审稿时长

1 months

期刊介绍： Genetics Selection Evolution invites basic, applied and methodological content that will aid the current understanding and the utilization of genetic variability in domestic animal species. Although the focus is on domestic animal species, research on other species is invited if it contributes to the understanding of the use of genetic variability in domestic animals. Genetics Selection Evolution publishes results from all levels of study, from the gene to the quantitative trait, from the individual to the population, the breed or the species. Contributions concerning both the biological approach, from molecular genetics to quantitative genetics, as well as the mathematical approach, from population genetics to statistics, are welcome. Specific areas of interest include but are not limited to: gene and QTL identification, mapping and characterization, analysis of new phenotypes, high-throughput SNP data analysis, functional genomics, cytogenetics, genetic diversity of populations and breeds, genetic evaluation, applied and experimental selection, genomic selection, selection efficiency, and statistical methodology for the genetic analysis of phenotypes with quantitative and mixed inheritance.