Genome analyses revealed genetic admixture and selection signatures in Bos indicus

Abstract The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having g...

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Autores principales:	S. P. Dixit, A. K. Bhatia, Indrajit Ganguly, Sanjeev Singh, Soumya Dash, Anurodh Sharma, N. Anandkumar, A. K. Dang, S. Jayakumar
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c906cffbe20e424bb3883d85e2c8ce4b
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spelling	oai:doaj.org-article:c906cffbe20e424bb3883d85e2c8ce4b2021-11-14T12:22:54ZGenome analyses revealed genetic admixture and selection signatures in Bos indicus10.1038/s41598-021-01144-22045-2322https://doaj.org/article/c906cffbe20e424bb3883d85e2c8ce4b2021-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-01144-2https://doaj.org/toc/2045-2322Abstract The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.S. P. DixitA. K. BhatiaIndrajit GangulySanjeev SinghSoumya DashAnurodh SharmaN. AnandkumarA. K. DangS. JayakumarNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q S. P. Dixit A. K. Bhatia Indrajit Ganguly Sanjeev Singh Soumya Dash Anurodh Sharma N. Anandkumar A. K. Dang S. Jayakumar Genome analyses revealed genetic admixture and selection signatures in Bos indicus
description	Abstract The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.
format	article
author	S. P. Dixit A. K. Bhatia Indrajit Ganguly Sanjeev Singh Soumya Dash Anurodh Sharma N. Anandkumar A. K. Dang S. Jayakumar
author_facet	S. P. Dixit A. K. Bhatia Indrajit Ganguly Sanjeev Singh Soumya Dash Anurodh Sharma N. Anandkumar A. K. Dang S. Jayakumar
author_sort	S. P. Dixit
title	Genome analyses revealed genetic admixture and selection signatures in Bos indicus
title_short	Genome analyses revealed genetic admixture and selection signatures in Bos indicus
title_full	Genome analyses revealed genetic admixture and selection signatures in Bos indicus
title_fullStr	Genome analyses revealed genetic admixture and selection signatures in Bos indicus
title_full_unstemmed	Genome analyses revealed genetic admixture and selection signatures in Bos indicus
title_sort	genome analyses revealed genetic admixture and selection signatures in bos indicus
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/c906cffbe20e424bb3883d85e2c8ce4b
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Genome analyses revealed genetic admixture and selection signatures in Bos indicus

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