Evaluation of genetic diversity and population structure of west-central Indian cattle breeds

Shah, Tejas; PATEL, None J. S.; Bhong, C. D.; Doiphode, Aakash; Umrikar, U. D.; Parmar, Shivnandan Singh; Rank, D. N.; Solanki, J. V.; Joshi, Chaitanya G.

doi:10.1111/age.12013

Cited by 13 publications

(11 citation statements)

References 9 publications

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“…The moderate F ST value noted between African and Bangladeshi zebu breeds was related to their common genetic background, as the paternal origin of Ethiopian zebu is traced to the Indian subcontinent (Dadi et al, 2009). The F ST value observed here for Red Chittangong and non-descript Deshi was far lower than that reported between Ongole and Deoni zebu from India (0.117) (Metta et al, 2004) and 0.26667 for the Khillar-Kenkatha breeds of west-central India, although closer to the value (0.0126) reported for Kankrej-Malvi (Shah et al, 2012). Within populations, the genetic variability estimated for Bangladeshi zebu was higher than the reported average for Indian zebu (Shah et al, 2012).…”

Section: Discussionsupporting

confidence: 58%

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

Edea

Bhuiyan

Dessie³

et al. 2015

Animal

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Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.

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Section: Discussionsupporting

confidence: 58%

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

Edea

Bhuiyan

Dessie³

et al. 2015

Animal

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“…In the present study, a total of 13932 genotypes were generated across 27 microsatellite loci in 516 cattle belonging to 10 draught type zebu breeds, 2 commercial taurine breeds and 2 crossbred populations. and comparable to that of West-Central, North and East Indian cattle (Shah et al 2012;Sharma et al 2013Sharma et al , 2015. As expected, the crossbred cattle (Jersey crossbreds and Holstein-Friesian crossbreds) exhibited a higher level of allelic diversity and heterozygosity than indigenous zebu cattle.…”

Section: Basic Diversity Measures and Hardy-weinberg Equilibriumsupporting

confidence: 72%

“…The mean F IS estimates observed in most South Indian cattle breeds were higher than those reported for East Indian (Sharma et al 2013) and most North Indian cattle with the exception of Mewati and Gaolao (Sharma et al 2015). However, the mean F IS estimates reported for West-Central Indian cattle were much higher than that of South Indian cattle (Shah et al 2012). Similarly, the mean F IS for Vechur and Ongole cattle observed in the present study was significantly lower than reported previously by Radhika et al (2018) and Sharma et al (2015) Figure SF1).…”

Section: Basic Diversity Measures and Hardy-weinberg Equilibriummentioning

confidence: 58%

“…The global F ST among South Indian zebu cattle observed in the present study was comparable to that of East Indian zebu (Sharma et al 2013) cattle. However, much higher genetic differentiation had been reported among West-Central (Shah et al 2012) and North Indian (Sharma et al 2015) The radial tree and dendrogram constructed following UPGMA algorithm based on pairwise Nei's genetic distance is presented in Figure 1. Broadly, the taurine, zebu and their crossbred cattle clustered separately as expected.…”

Section: Genetic Differentiation and Phylogenymentioning

confidence: 93%

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Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

Manomohan

Saravanan

Pichler

et al. 2021

Preprint

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The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately higher. A significantly strong negative correlation coefficient of −0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The phylogeny and genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

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“…Worldwide, cattle (Bos taurus) have been economically and culturally important farm animal species since their domestication. Many studies have assessed the diversity of cattle in Asia (Sharma et al, 2016;Nishimaki et al, 2013;Shah et al, 2013), Europe (Mateus et al, 2004;Maudet et al, 2002;Di et al, 2018), Africa (Dadi et al, 2008;Edea et al, 2015), and South America (Acosta et al, 2013;Brasil et al, 2013;Piccoli et al, 2014) and in cattle native to Korea (Suh et al, 2014). In recent years, several microsatellite studies on diversity in Chinese cattle have been published (Yang et al, 2016;Wang et al, 2015;Lou et al, 2006;Han et al, 2006;Li et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Microsatellite marker-based estimation of the genetic diversity of cattle in Chongqing

Jiang

Zhang

et al. 2018

IJAR

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Cattle are the main source of meat in Chongqing. This study investigated the genetic diversity of cattle native to Chongqing and 4 introduced breeds. A total of 96 individuals from 5 breeds were genotyped using six microsatellite markers. Five markers were highly polymorphic within the breed populations, and one marker had moderate levels of polymorphism. Heterozygosity ranged from 0.5379±0.0434 in Simmental to 0.6667±0.0559 in Charolais. The heterozygosity deficit was significant in all populations analyzed compared with the expected level of heterozygosity. In addition, two microsatellite markers (TGLA53 and OarFCB20) deviated from Hardy-Weinberg equilibrium across populations (except in cattle native to Chongqing). The mean number of alleles ranged from 6.00±2.37 in Angus to 7.17±2.14 in Droughtmaster across six markers. The coefficient of inbreeding ranged from 0.0017 in Simmental and Droughtmaster to 0.0367 in Angus. Pairwise difference analyses revealed that Simmental and Droughtmaster were the most differentiated (FST= 0.06861) from each other, whereas cattle native to Chongqing and Charolais were the least differentiated (FST= 0.00557). In summary, this study showed that cattle native to Chongqing and 4 introduced breeds were genetically well protected in Chongqing, and information from this study would be helpful for guiding hybridization and genetic improvements in the future.

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Evaluation of genetic diversity and population structure of west-central Indian cattle breeds

Cited by 13 publications

References 9 publications

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

Microsatellite marker-based estimation of the genetic diversity of cattle in Chongqing

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