基于8个鸡品种的全基因组SNP解析品种特征形成的遗传基础

doi:10.1016/j.jia.2022.11.007

摘要/Abstract

摘要：

世界范围内有各种品种、类型的鸡，它们的品种特征各不相同，是宝贵的遗传资源。目前，对影响这些鸡品种的特异性表型的遗传决定因素的研究还有待进一步加深。深入了解品种特异性表型变异的潜在遗传机制可以帮助育种者培育和改良鸡品种。本研究对7个来自山东省的本地品种共140只鸡和20只引进的隐性白羽鸡的全基因组进行了重测序。基于常染色体单核苷酸多态性(SNPs)的群体基因组比较结果揭示了鸡群基于地理距离的聚类模式。通过全基因组范围内的选择性清除分析，本研究确定了甲状腺刺激激素受体(TSHR，繁殖性状，生理节律)，红细胞膜蛋白带4.1 样 1 (EPB41L1，体型大小)和烷基甘油单加氧酶(AGMO，攻击行为)是主要候选的鸡品种特异性决定基因。此外，本研究利用机器学习分类模型，基于与品种特征显著相关的SNPs对鸡的品种进行判别，预测准确率为92%，可有效实现莱芜黑鸡的品种鉴定。本研究首次提供了山东地方鸡种的完整基因组数据，相关的分析揭示了山东地方鸡种的地理模式和鸡的品种特异性性状相关的潜在的候选基因。此外，本研究开发了一个基于机器学习的预测模型，使用SNPs数据进行品种判别，该部分内容为利用机器学习方法开发品种分子身份证提供了参考。本研究揭示的地方鸡品种遗传基础有助于更好地理解鸡资源特性的内在机制。

Abstract: Many different chicken breeds are found around the world, their features vary among them, and they are valuable resources. Currently, there is a huge lack of knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these breeds of chickens. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved chicken breeds. The whole-genomes of 140 chickens from 7 Shandong native breeds and 20 introduced recessive white chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed geographically based clusters among the chickens. Through genome-wide scans for selective sweeps, we identified thyroid stimulating hormone receptor (TSHR, reproductive traits, circadian rhythm), erythrocyte membrane protein band 4.1 like 1 (EPB41L1, body size), and alkylglycerol monooxygenase (AGMO, aggressive behavior), as major candidate breed-specific determining genes in chickens. In addition, we used a machine learning classification model to predict chicken breeds based on the SNPs significantly associated with recourse characteristics, and the prediction accuracy was 92%, which can effectively achieve the breed identification of Laiwu Black chickens. We provide the first comprehensive genomic data of the Shandong indigenous chickens. Our analyses revealed phylogeographic patterns among the Shandong indigenous chickens and candidate genes that potentially contribute to breed-specific traits of the chickens. In addition, we developed a machine learning-based prediction model using SNP data to identify chicken breeds. The genetic basis of indigenous chicken breeds revealed in this study is useful to better understand the mechanisms underlying the resource characteristics of chicken.

Key words: chicken , genome , genetic diversity , support vector machine

WANG Jie, LEI Qiu-xia, CAO Ding-guo, ZHOU Yan, HAN Hai-xia, LIU Wei, LI Da-peng, LI Fu-wei, LIU Jie. 基于8个鸡品种的全基因组SNP解析品种特征形成的遗传基础 [J]. Journal of Integrative Agriculture, 2023, 22(7): 2200-2212.

WANG Jie, LEI Qiu-xia, CAO Ding-guo, ZHOU Yan, HAN Hai-xia, LIU Wei, LI Da-peng, LI Fu-wei, LIU Jie. Whole genome SNPs among 8 chicken breeds enable identification of genetic signatures that underlie breed features[J]. Journal of Integrative Agriculture, 2023, 22(7): 2200-2212.

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