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...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 repeats,predominantly Long Inter-spersed Nuclear Elements(LINEs).Additionally,70.28%of BICIs are shared with other domesticated and wild species,highlighting their evolutionary significance.Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India.The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.展开更多
Rohtak is one of the eight priority towns (Regional Centres) of National Capital Region (NCR) Regional Plan 2001. It lies 70 kms north-west from Delhi, the National Capital of India. Located at 28?41'1'' N...Rohtak is one of the eight priority towns (Regional Centres) of National Capital Region (NCR) Regional Plan 2001. It lies 70 kms north-west from Delhi, the National Capital of India. Located at 28?41'1'' North latitude and 76?12'42'' East longitude in the NCR region of Haryana state on National Highway No. 10, it spreads over 100.57 km2. Its population was projected to grow to 500,000 by 2001. Despite its nearness to the national capital it did not attract investment and the rate of urbanization remained low. Rohtak city grew slower than the state of Haryana in the three decades ending in 2001. On being declared as Municipal Corporation in 2010 urban growth of Rohtak took place in the form of extension in territorial jurisdiction and inclusion of urbanized eight villages. The new economic environment demands sustainable land management. Spatial information of land use/land cover types and their change detection in time series are important means for city planning and undertaking development activities. The present work is undertaken in that spirit. It has analyzed the relationship between urban growth and land use changes and their impact on Rohtak city. The period of focus is from 1983 to 2010. Both primary and secondary sources of data have been used for the present study. Secondary sources of data—guide map, topographical sheet and high resolution satellite imageries have been used to detect land use/land cover changes from the study area whereas primary source of data include ground truth and photographs from the field.展开更多
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 ), Indiathe 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。
文摘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 repeats,predominantly Long Inter-spersed Nuclear Elements(LINEs).Additionally,70.28%of BICIs are shared with other domesticated and wild species,highlighting their evolutionary significance.Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India.The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.
文摘Rohtak is one of the eight priority towns (Regional Centres) of National Capital Region (NCR) Regional Plan 2001. It lies 70 kms north-west from Delhi, the National Capital of India. Located at 28?41'1'' North latitude and 76?12'42'' East longitude in the NCR region of Haryana state on National Highway No. 10, it spreads over 100.57 km2. Its population was projected to grow to 500,000 by 2001. Despite its nearness to the national capital it did not attract investment and the rate of urbanization remained low. Rohtak city grew slower than the state of Haryana in the three decades ending in 2001. On being declared as Municipal Corporation in 2010 urban growth of Rohtak took place in the form of extension in territorial jurisdiction and inclusion of urbanized eight villages. The new economic environment demands sustainable land management. Spatial information of land use/land cover types and their change detection in time series are important means for city planning and undertaking development activities. The present work is undertaken in that spirit. It has analyzed the relationship between urban growth and land use changes and their impact on Rohtak city. The period of focus is from 1983 to 2010. Both primary and secondary sources of data have been used for the present study. Secondary sources of data—guide map, topographical sheet and high resolution satellite imageries have been used to detect land use/land cover changes from the study area whereas primary source of data include ground truth and photographs from the field.
