SNP-based genetic signatures revealed breeding effects in indigenous Livni compared with Landrace and Large White breeds

IF 1.3 Q4 FOOD SCIENCE & TECHNOLOGY

Foods and Raw Materials Pub Date : 2023-11-17 DOI:10.21603/2308-4057-2024-2-609

I. Chernukha, E. Kotenkova, L. Fedulova

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引用次数: 0

Abstract

Livni is one of the Russian local pig breeds. We previously reported that this breed was more distinct from Duroc breed than from Landrace and the Large White breeds, which participated in the Livni breed creation. The aim of the study was to determine the SNP-based genetic signatures in fat-type Livni breed shared with commercial Landrace and the Large White breeds, and ones that are affected by putative selection. The genome-wide SNP genotyping was carried out using the Porcine GGP HD BeadChip, which contains ~ 80 000 SNPs. Obtained breed relationship and admixture results indicated the insignificant participation of the Landrace and the Large White breeds in the formation of the modern allelofund of Livni pigs. 238 candidate genes were found in the genomic regions with selection signatures, 182 genes with described functions were identified. In the Livni and Landrace breeds, 35 common genes were detected which formed one cluster with enrichment coefficient = 4.94 and predominant HOXD genes. In the Livni and Large White breeds, the largest amounts of common genes were detected (62 in average), which formed two clusters. Cluster 1, with enrichment coefficient = 2.11, was characterized with genes involved in glucose metabolism. Cluster 2, with enrichment coefficient = 1.60, demonstrated helicase genes. Annotated clusters were not determined for the Livni breed. However, 50 candidate genes were specific to Livni pigs and associated with various growth, carcass and reproductive traits, essential for thermoregulation. Results revealed common SNP-based genetic signatures and breeding effects in indigenous Livni compared with Landrace and Large White breeds.

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基于 SNP 的遗传特征揭示了本土利夫尼犬种与陆地犬种和大白犬种相比的育种效果

利夫尼是俄罗斯地方猪种之一。我们以前曾报道过，该猪种与杜洛克猪种的区别大于与兰德瑞斯和大白猪种的区别，而兰德瑞斯和大白猪种参与了利夫尼猪种的创建。本研究的目的是确定肥育型 Livni 品种与商业化陆地猪种和大白猪种共有的基于 SNP 的遗传特征，以及受假定选择影响的特征。全基因组 SNP 基因分型是利用包含约 80 000 个 SNP 的猪 GGP HD BeadChip 进行的。获得的品种关系和混杂结果表明，在现代里夫尼猪等位基因的形成过程中，陆地猪种和大白猪种的参与并不明显。在具有选择特征的基因组区域发现了 238 个候选基因，并确定了 182 个具有描述功能的基因。在利夫尼猪和兰德猪品种中，发现了 35 个共同基因，它们组成了一个富集系数为 4.94 的基因簇，其中主要是 HOXD 基因。在利夫尼和大白品种中，检测到的常见基因数量最多（平均 62 个），形成了两个聚类。聚类 1 的富集系数为 2.11，其特征是涉及葡萄糖代谢的基因。聚类 2 的富集系数为 1.60，展示了螺旋酶基因。利夫尼品种没有确定注释群。不过，有 50 个候选基因是利夫尼猪所特有的，与各种生长、胴体和繁殖性状有关，对体温调节至关重要。研究结果表明，基于 SNP 的遗传特征和育种效应在本土 Livni 猪种中与 Landrace 猪种和大白猪种相比较。

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来源期刊

Foods and Raw Materials FOOD SCIENCE & TECHNOLOGY-

CiteScore

3.70

自引率

20.00%

发文量

审稿时长

24 weeks

期刊介绍： The journal «Foods and Raw Materials» is published from 2013. It is published in the English and German languages with periodicity of two volumes a year. The main concern of the journal «Foods and Raw Materials» is informing the scientific community on the works by the researchers from Russia and the CIS, strengthening the world position of the science they represent, showing the results of perspective scientific researches in the food industry and related branches. The main tasks of the Journal consist the publication of scientific research results and theoretical and experimental studies, carried out in the Russian and foreign organizations, as well as on the authors'' personal initiative; bringing together different categories of researchers, university and scientific intelligentsia; to create and maintain a common space of scientific communication, bridging the gap between the publications of regional, federal and international level.