Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus  

作　　者：Sarwar Azam Abhisek Sahu Naveen Kumar Pandey Mahesh Neupane Curtis P Van Tassell Benjamin D Rosen Ravi Kumar Gandham Subha Narayan Rath Subeer S Majumdar 

机构地区：[1]National Institute of Animal Biotechnology,Hyderabad,India [2]Indian Institute of Technology Hyderabad,Sangareddy,India [3]Animal Genomics and Improvement Laboratory,USDA-ARS,Beltsville,MD 20705,USA [4]Animal Biotechnology,ICAR-NBAGR,Karnal,Haryana,India

出　　处：《Journal of Animal Science and Biotechnology》2025年第2期497-516,共20页畜牧与生物技术杂志(英文版)

基　　金：the project “Genomics for Conservation of Indigenous Cattle Breeds and for Enhancing Milk Yield, Phase-I” [BT/ PR26466/AAQ/1/704/2017], funded by the Department of Biotechnology (DBT ), India;the project “Identification of key molecular factors involved in resistance/susceptibility to paratuberculosis infection in indigenous breeds of cows” [BT/PR32758/AAQ/1/760/2019], which was also funded by Department of Biotechnology (DBT ), India。

摘　　要：Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle.To comprehensively characterize the genomic variation within Bos indicus and,specifically,dairy breeds,we aim to identify non-reference sequences and construct a comprehensive pangenome.Results Five representative genomes of prominent dairy breeds,including Gir,Kankrej,Tharparkar,Sahiwal,and Red Sindhi,were sequenced using 10X Genomics‘linked-read’technology.Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to the Bos indicus Brahman reference genome.A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods,revealing 8 Mb and 17.7 Mb of novel sequence respectively.A confident set of 6,844 Non-reference Unique Insertions(NUIs)spanning 7.57 Mb was identified through both methods,representing the pange-nome of Indian Bos indicus breeds.Comparative analysis with previously published pangenomes unveiled 2.8 Mb(37%)commonality with the Chinese indicine pangenome and only 1%commonality with the Bos taurus pange-nome.Among these,2,312 NUIs encompassing~2 Mb,were commonly found in 98 samples of the 5 breeds and des-ignated as Bos indicus Common Insertions(BICIs)in the population.Furthermore,926 BICIs were identified within 682 protein-coding genes,54 long non-coding RNAs(lncRNA),and 18 pseudogenes.These protein-coding genes were enriched for functions such as chemical synaptic transmission,cell junction organization,cell-cell adhesion,and cell morphogenesis.The protein-coding genes were found in various prominent quantitative trait locus(QTL)regions,suggesting potential roles of BICIs in traits related to milk production,reproduction,exterior,health,meat,and carcass.Notably,63.21%of the bases within the BICIs call set contained interspersed r

关 键 词：BICIs Bos indicus CATTLE Genome assembly Linked-reads NUIs Pangenome 

分 类 号：S823[农业科学—畜牧学]