Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle (<i>Bos indicus</i>) breeds

Pramod, R Kumar; Velayutham, Dinesh; Sajesh, P. K.; Beena, P.; Zachariah, Anil; Zachariah, Arun; Chandramohan, B; Sujith, S S; Ganapathi, P; Kumar, Bangarusamy Dhinoth; Iype, S.; Gupta, Ravi; Santhosh, Sam; Thomas, George

doi:10.1080/10495398.2018.1476376

Cited by 13 publications

(10 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The number of registered cattle breeds in India has increased steadily over time, with Sukhatme [ 13 ] reporting 26 cattle breeds in 1968 and the National Bureau of Animal Genetic Resources ( http://www.nbagr.res.in/nbagr.html ) listing 50 registered Indian cattle breeds to date. Five of these registered breeds—Sahiwal, Gir, Red Sindhi, Tharparkar, and Deoni—are pure milking breeds, whereas the others are dual purpose or pure draught animals [ 14 , 15 ]. Only a small percentage of the Indian indigenous breeds are raised as pure breeds and the large majority of cattle used by smallholder farmers are of non-descript breeds [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

“…Detailed studies on the genetic diversity of Bos indicus cattle are still lacking. Among the studies reported in the literature, some have used limited numbers of mitochondrial DNA markers [ 14 , 16 , 17 ], or a few selected autosomal microsatellite or single nucleotide polymorphisms (SNPs) [ 16 , 18 – 20 ], and others have analyzed a limited number of breeds from India [ 21 ], or indicine breeds from other countries [ 17 , 22 ]. Thus, relatively little is known about the genetic diversity of Indian cattle.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genetic diversity and effective population sizes of thirteen Indian cattle breeds

et al. 2021

View full text Add to dashboard Cite

Background The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds. Results Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds. Conclusions The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic diversity and effective population sizes of thirteen Indian cattle breeds

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Recent estimates, based on genome-wide sequence data, place the evolutionary divergence time between the two cattle subspecies at 150 to 500 kya (Chen et al 2018;Wang et al 2018;Wu et al 2018), although some analyses of complete mitogenomes have suggested a deeper split (Hiendleder et al 2008;Bibi 2013;Pramod et al 2019).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide local ancestry and direct evidence for mitonuclear coadaptation in African hybrid cattle populations (Bos taurus/indicus)

Ward

McHugo

Dover

et al. 2021

Preprint

View full text Add to dashboard Cite

Domestic cattle have a key economic role in African societies, providing an important source of mobile wealth through supply of meat, milk, cowhide, fuel, transport, and traction. The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which share a common ancestor 150-500 thousand years ago. Human migration and trade from Asia have left a peak of zebu nuclear ancestry in East Africa and most cattle populations across the continent have a hybrid genetic composition. Notwithstanding this, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu nuclear ancestry. In this regard, the efficient functioning of the mitochondrion relies on a network of biochemical interactions between the products of 37 mitochondrial genes and more than one thousand nuclear genes; therefore, admixed African cattle represent ideal populations for evaluating mitonuclear interactions and mismatch between the nuclear and mitochondrial genomes. Using high-density SNP array data from 18 different cattle populations, including ten African admixed breeds, we find strong evidence for mitonuclear coevolution in hybrid African cattle with significant retention of Bos taurus alleles at mitochondrially-targeted nuclear genes, particularly those genes with products that directly interact with mtDNA-encoded protein subunits in OXPHOS and ribosomal complexes, or that have functions in mtDNA replication. We also show that subspecific local ancestry varies substantially across the genomes of admixed populations, with a marked signal of taurine ancestry at the major histocompatibility (MHC) gene cluster, which likely reflects adaptation to infectious disease challenges facing African livestock. Our results demonstrate that African admixed cattle represent an excellent comparative model for studying the phenotypic consequences of mitonuclear mismatch and genomic introgression in humans and other large mammals.

show abstract

“…Recent sequencing and analysis of the complete mitochondrial genome of seven Indian cattle breeds indicates that in addition to the previously known domestication of a sub-species of Aurochs within the Indus Valley around 6500 BCE, another domestication location in Southern India also gave rise to the humped zebu cattle: B. indicus [42]. A earlier assumption that B. taurus arose from a point source domestication of Aurochs around 8500 BCE within the Fertile Crescent—the region of the Tigris and Euphrates Rivers within Iran and Iraq extending east across from the Persian Gulf towards and southwards along the eastern border of the Mediterranean Sea—has been disproven in recent studies [43,44,45,46,47,48].…”

Section: Cattle Domestication and Early Religious Symbolismmentioning

confidence: 99%

The Alpha Hypothesis: Did Lateralized Cattle–Human Interactions Change the Script for Western Culture?

Robins

2019

Animals

View full text Add to dashboard Cite

Simple SummaryThe domestication of cattle was a key innovation early in the development of Western civilization. Cattle provided the main tractor force to enable broad-scale agriculture and the land transportation of goods. Their initial significance was religiously celebrated as the bull-like creator god ’El, in Canaan (modern day Lebanon and Syria), and for over 6000 years in Ancient Egypt as the sky-goddess Hathor, often depicted as a sacred cow. In addition, the Ancient Egyptian hieroglyphic logogram of a horned ox head profile viewed from either the left or right side was used to signify the concept of “wisdom”. Stylizations of the ox head logogram seen from the left, and not right side have recently been found used in Egyptian graffito dating from around 1900 BCE (Before the Common Era). The strings of symbols have provided the earliest known examples of writing using phonemes such as used in the modern Western alphabet. The use of the directionally-asymmetrical left side ox-head symbol to represent a specific phoneme subsequently migrated around the Eastern basin of the Mediterranean Sea variously as ’al, ’el, alep, allup, eleph and alif in Ancient Semitic cultures, including Phoenician, Hebrew and Arabic, before becoming “alpha” in Ancient Greece by 700 BCE. For reasons that have not been fully understood, the ox-head symbol has always been positioned as the first letter in the lexicographical order of the respective Western languages. This review outlines the etymology of the strongly conserved position and directional asymmetry of the alpha symbol, and of its religious connection. In the light of recent behavioural studies, the hypothesis was presented to argue that the directional asymmetry of alpha represents early recognition and critical importance of behavioural lateralization in domesticated cattle when interacting with their human handlers.AbstractDomestic cattle possess lateralized cognitive processing of human handlers. This has been recently demonstrated in the preference for large groups of cattle to view a human closely within the predominantly left visual field. By contrast, the same stimulus viewed predominantly within the right visual field promotes a significantly greater frequency of dispersal from a standing position, including flight responses. The respective sets of behaviours correspond with the traditional terms of “near side” for the left side of cattle and horses, and the “off” or “far side” for the right side. These traditional terms of over 300 years usage in the literature communicate functional practicalities for handling livestock and the recognition of lateralized cognitive processing. In this review, the possibility of even earlier recognition and the significance of laterality in cattle-human interaction was argued, from the earliest representations of the letter "A", originally illustrated from nearly 4000 years before the present time as the head of an ox as viewed not from the front or from the right, but from the left (near) side. By extension, this knowledge of latera...

show abstract

Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle (Bos indicus) breeds

Cited by 13 publications

References 60 publications

Genetic diversity and effective population sizes of thirteen Indian cattle breeds

Genetic diversity and effective population sizes of thirteen Indian cattle breeds

Genome-wide local ancestry and direct evidence for mitonuclear coadaptation in African hybrid cattle populations (Bos taurus/indicus)

The Alpha Hypothesis: Did Lateralized Cattle–Human Interactions Change the Script for Western Culture?

Contact Info

Product

Resources

About