High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis)

Anupama  Mukherjee; Sabyasachi  Mukherjee; Rajan Dhakal; Moonmoon  Mech; Imsusosang  Longkumer; Nazrul Haque; Kezhavituo Vupru; Kobu Khate; Yanger  Jamir; Pursenla  Pongen; Chandan  Rajkhowa; Abhijit  Mitra; Bernt Guldbrandtsen; Goutam  Sahana

High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis)

Anupama Mukherjee, Sabyasachi Mukherjee^*, Rajan Dhakal, Moonmoon Mech, Imsusosang Longkumer, Nazrul Haque, Kezhavituo Vupru, Kobu Khate, Yanger Jamir, Pursenla Pongen, Chandan Rajkhowa, Abhijit Mitra, Bernt Guldbrandtsen, Goutam Sahana

^*Corresponding author for this work

5 Citations (Scopus)

Abstract

The current study aimed at genomic characterization and improved understanding of genetic diversity of two Indian mithun populations (both farm, 48 animals and field, 24 animals) using genome wide genotype data generated with Illumina BovineHD BeadChip. Eight additional populations of taurine cattle (Holstein and NDama), indicine cattle (Gir) and other evolutionarily closely related species (Bali cattle, Yak, Bison, Gaur and wild buffalo) were also included in this analysis (N = 137) for comparative purposes. Our results show that the genetic background of mithun populations was uniform with few possible signs of indicine admixture. In general, observed and expected heterozygosities were quite similar in these two populations. We also observed increased frequencies of small-sized runs of homozygosity (ROH) in the farm population compared to field mithuns. On the other hand, longer ROH were more frequent in field mithuns, which suggests recent founder effects and subsequent genetic drift due to close breeding in farmer herds. This represents the first study providing genetic evidence about the population structure and genomic diversity of Indian mithun. The information generated will be utilized for devising suitable breeding and conservation programme for mithun, an endangered bovine species in India.

Original language	English
Journal	Scientific Reports
ISSN	2045-2322
Publication status	Published - 1 Dec 2018
Externally published	Yes

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Mukherjee, A., Mukherjee, S., Dhakal, R., Mech, M., Longkumer, I., Haque, N., Vupru, K., Khate, K., Jamir, Y., Pongen, P., Rajkhowa, C., Mitra, A., Guldbrandtsen, B., & Sahana, G. (2018). High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis). Scientific Reports. https://www.nature.com/articles/s41598-018-28718-x

Mukherjee, A, Mukherjee, S, Dhakal, R, Mech, M, Longkumer, I, Haque, N, Vupru, K, Khate, K, Jamir, Y, Pongen, P, Rajkhowa, C, Mitra, A, Guldbrandtsen, B & Sahana, G 2018, 'High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis)', Scientific Reports. <https://www.nature.com/articles/s41598-018-28718-x>

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title = "High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis)",

abstract = "The current study aimed at genomic characterization and improved understanding of genetic diversity of two Indian mithun populations (both farm, 48 animals and field, 24 animals) using genome wide genotype data generated with Illumina BovineHD BeadChip. Eight additional populations of taurine cattle (Holstein and NDama), indicine cattle (Gir) and other evolutionarily closely related species (Bali cattle, Yak, Bison, Gaur and wild buffalo) were also included in this analysis (N = 137) for comparative purposes. Our results show that the genetic background of mithun populations was uniform with few possible signs of indicine admixture. In general, observed and expected heterozygosities were quite similar in these two populations. We also observed increased frequencies of small-sized runs of homozygosity (ROH) in the farm population compared to field mithuns. On the other hand, longer ROH were more frequent in field mithuns, which suggests recent founder effects and subsequent genetic drift due to close breeding in farmer herds. This represents the first study providing genetic evidence about the population structure and genomic diversity of Indian mithun. The information generated will be utilized for devising suitable breeding and conservation programme for mithun, an endangered bovine species in India.",

author = "Anupama Mukherjee and Sabyasachi Mukherjee and Rajan Dhakal and Moonmoon Mech and Imsusosang Longkumer and Nazrul Haque and Kezhavituo Vupru and Kobu Khate and Yanger Jamir and Pursenla Pongen and Chandan Rajkhowa and Abhijit Mitra and Bernt Guldbrandtsen and Goutam Sahana",

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T1 - High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis)

AU - Mukherjee, Anupama

AU - Mukherjee, Sabyasachi

AU - Dhakal, Rajan

AU - Mech, Moonmoon

AU - Longkumer, Imsusosang

AU - Haque, Nazrul

AU - Vupru, Kezhavituo

AU - Khate, Kobu

AU - Jamir, Yanger

AU - Pongen, Pursenla

AU - Rajkhowa, Chandan

AU - Mitra, Abhijit

AU - Guldbrandtsen, Bernt

AU - Sahana, Goutam

PY - 2018/12/1

Y1 - 2018/12/1

N2 - The current study aimed at genomic characterization and improved understanding of genetic diversity of two Indian mithun populations (both farm, 48 animals and field, 24 animals) using genome wide genotype data generated with Illumina BovineHD BeadChip. Eight additional populations of taurine cattle (Holstein and NDama), indicine cattle (Gir) and other evolutionarily closely related species (Bali cattle, Yak, Bison, Gaur and wild buffalo) were also included in this analysis (N = 137) for comparative purposes. Our results show that the genetic background of mithun populations was uniform with few possible signs of indicine admixture. In general, observed and expected heterozygosities were quite similar in these two populations. We also observed increased frequencies of small-sized runs of homozygosity (ROH) in the farm population compared to field mithuns. On the other hand, longer ROH were more frequent in field mithuns, which suggests recent founder effects and subsequent genetic drift due to close breeding in farmer herds. This represents the first study providing genetic evidence about the population structure and genomic diversity of Indian mithun. The information generated will be utilized for devising suitable breeding and conservation programme for mithun, an endangered bovine species in India.

AB - The current study aimed at genomic characterization and improved understanding of genetic diversity of two Indian mithun populations (both farm, 48 animals and field, 24 animals) using genome wide genotype data generated with Illumina BovineHD BeadChip. Eight additional populations of taurine cattle (Holstein and NDama), indicine cattle (Gir) and other evolutionarily closely related species (Bali cattle, Yak, Bison, Gaur and wild buffalo) were also included in this analysis (N = 137) for comparative purposes. Our results show that the genetic background of mithun populations was uniform with few possible signs of indicine admixture. In general, observed and expected heterozygosities were quite similar in these two populations. We also observed increased frequencies of small-sized runs of homozygosity (ROH) in the farm population compared to field mithuns. On the other hand, longer ROH were more frequent in field mithuns, which suggests recent founder effects and subsequent genetic drift due to close breeding in farmer herds. This represents the first study providing genetic evidence about the population structure and genomic diversity of Indian mithun. The information generated will be utilized for devising suitable breeding and conservation programme for mithun, an endangered bovine species in India.

M3 - Journal article

SN - 2045-2322

JO - Scientific Reports

JF - Scientific Reports

ER -

High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis)

Abstract

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