一种快速挖掘鸡品种特征性SNP标记集合的方法

doi:10.11843/j.issn.0366-6964.2023.08.012

Abstract

Abstract: The purpose of this study was to establish a method to rapidly mine a few SNPs markers that can distinguish the target breeds or strains from other breeds or strains. The goal is to develop a technique for quickly mining the characteristic SNP markers set of chicken breeds or strains. The study used whole genome resequencing data of 19 breeds or strains, including Beijing yellow chicken, Jingxing yellow chicken, 7 Shandong local breeds, 5 Yunnan local breeds, Tibetan chicken, and the fast-growing white feather broiler terminal. After fixation indices analysis,SNP markers with MEAN_FAST ≥ 0.65 were extracted. The SNP markers set was further reduced by extracting independent SNP through linkage disequilibrium analysis. Six breeds or strains were chosen randomly to test this method. The results showed that, after loci screening by once fixation indices analysis and linkage disequilibrium analysis, the fast growing white feather broiler, Jingxing yellow chicken selective line H and Jingxing yellow chicken selective line D2 could be separated from other 18 representative breeds by 114, 220 and 226 SNPs, respectively; Wuding chicken and Piao chicken, which were clustered in one branch by principal component analysis and Neighbour Joining tree, could be separated from other representative breeds by 204 and 178 SNPs, respectively. Obtained the set of 114-226 SNPs markers, and that the target breeds or strains could be distinguished from other representative varieties by principal component analysis. The procedure is straightforward, and the quantity of SNP markers obtained is quite low, which helps for manage detection costs. It can be applied to construct the "molecular identity cards" of local variaties or commercial strairns to assist the protection and identification of germplasm resources.

Key words: chicken, principal component analysis, fixation indices analysis, linkage disequilibrium, characteristic SNP markers set

CLC Number:

S831.2

BAI Lu, WANG Mengjie, MA Xiaochun, HE Zhengxiao, TAN Xiaodong, LIU Jie, ZHAO Guiping, WEN Jie, LIU Ranran. A Method for Quickly Mining the Characteristic SNP Markers Set of Chicken[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3252-3261.

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A Method for Quickly Mining the Characteristic SNP Markers Set of Chicken

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