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Genetic blueprinting of novel and performance traits-related SNPs in Indian Gir cattle using latest reference assembly : ddRAD analysis of Gir cattle for SNP discovery

Indian Agricultural Research Journals

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Title Genetic blueprinting of novel and performance traits-related SNPs in Indian Gir cattle using latest reference assembly : ddRAD analysis of Gir cattle for SNP discovery
 
Creator Nidhi Sukhija
Anjali Choudhary
Kanaka KK
Jaglan, Komal
M Joel Devadasan
Jayakumar Sivalingam
Archana Verma
 
Description Among the indicine breeds of cattle, Gir breed thrives in challenging arid habitats, produce more milk with less feed intake and are resistant to tropical diseases. Identification of novel and bias free SNPs are important to include in genetic studies and breeding programs. The current study aimed to explore SNPs in Gir cattle genome followed by annotation of the SNPs to different performance traits. Double-digest restriction site associated DNA sequencing (ddRAD-seq) was done and different bioinformatic tools and software used to mine SNPs and subsequent annotation to different performance traits. A total of 53,243 high quality SNPs were identified using the latest ARS-UCD 1.3 reference genome (GCF_002263795.2). In all, 2,931 SNPs were annotated to 452 candidate genes related to nine different traits of interest such as, milk production, reproduction, adaptation, disease-resistance, growth, carcass, coat thickness, coat colour, and domestication traits. ddRAD-seq offers mining of ascertainment free SNPs in a cost-effective way and hence the SNPs obtained in this studied population can be successfully used for population genetic studies and in breeding programs. The information mined in this study will aid in genetic improvement, designing appropriate breed improvement programmes and leveraging conservation efforts.
 
Publisher Indian Dairy Association, New Delhi, India
 
Date 2024-02-23
 
Type info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
 
Format application/pdf
 
Identifier https://epubs.icar.org.in/index.php/IJDS/article/view/141986
 
Source Indian Journal of Dairy Science; Vol. 77 No. 1 (2024): Jan Feb 2024
2454-2172
0019-5146
 
Language eng
 
Relation https://epubs.icar.org.in/index.php/IJDS/article/view/141986/54028