Genomic Heterogeneity of Chicken Populations in India

Rajkumar, U.; Gupta, Bhavna; Reddy, Anuradha

doi:10.5713/ajas.2008.80299

Cited by 22 publications

(9 citation statements)

References 31 publications

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“…This order encompasses domestic species such as Poephila cincta and Serinus canaria as well as to the globally distributed Passer domesticus (2.40 %). The most predominant species in the literature was Gallus gallus (7.80 %), which has a large number of lineages distributed across the globe and has been widely used as a model organism in biochemical, molecular (e.g., Piekarski et al, 2015;Guizard et al, 2016) and genetic studies such as those describing the genetic diversity of populations based on variations at microsatellite loci (Rajkumar et al, 2008;Zanetti et al, 2011;Babar et al, 2012). The large number of studies in Gallus gallus with its wide distribution obviates the obvious influence of its economic interest on the studies.…”

Section: Scientometricsmentioning

confidence: 99%

Towards inclusion of genetic diversity measures into IUCN assessments: a case study on birds

Vitorino¹,

Souza²,

Jardim³

et al. 2019

Anim. Biodiv. Conserv.

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The IUCN Red List categorizes species based on their geographical distribution and population size. However, attributes such as genetic information are not yet considered. We compiled information on genetic diversity (HE, HO) and inbreeding coefficient (f) along with their ecological attributes (IUCN category, migratory habit, forest dependence and habitat type) from a literature survey to assess whether bird species categorized as being of highest conservation concern display the lowest genetic diversity. We used generalized linear mixed models (GLMM) to test whether avian species with less inclusive characteristics (e.g., taxa with small geographical distributions or low dispersal capability) display lower genetic diversity than those classified as Least Concern (LC). We used hylogenetic generalized least squares (pGLS) to account for phylogenetic independence of predictor variables and to verify robustness of GLMMs (generalized linear mixed models). In general, GLMM revealed more significant relationships among ecological attributes and genetic diversity patterns. After accounting for phylogenetic independence, the highest average heterozygosity values were observed in species falling under the LC category; non–migratory birds showed lower HO and HE average values than migratory birds, while non–forest birds showed lower heterozygosity than forest birds. Hence, we corroborate our hypothesis that genetic diversity of birds is lower in species of high conservation concern. We hope our results promote further studies on genetic diversity of bird populations. Lastly, we propose the incorporation of genetic data as metrics in the assessment of bird conservation status.

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Section: Scientometricsmentioning

confidence: 99%

Towards inclusion of genetic diversity measures into IUCN assessments: a case study on birds

Vitorino¹,

Souza²,

Jardim³

et al. 2019

Anim. Biodiv. Conserv.

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“…; Rajkumar et al . ), whereas non‐commercial chicken breeds in Europe are of a smaller population size and bred for standardized traits (Granevitze et al . ; Siwek et al .…”

Section: Introductionmentioning

confidence: 99%

Global diversity and genetic contributions of chicken populations from African, Asian and European regions

et al. 2014

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Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (FST ) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour-Net genetic clustering and structure analysis revealed two main groups of Asian and north-west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north-west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds.

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“…The pairwise F ST values among 19 quail populations including three wild quail populations were remarkably higher than those of domestic chicken populations in India ( F ST = 0.06−0.14, 0.094 on average, in eight domestic populations) [60], China ( F ST = 0.176−0.302, 0.231 on average, in seven indigenous populations) [61], and Italy ( F ST = 0.03−0.32, 0.180, on average, in six local breeds and four commercial lines) [62]. The high F ST values in the quail populations used in this study seem to be attributed to their breeding history and the characteristics of microsatellite markers used in this study.…”

Section: Discussionmentioning

confidence: 99%

Genetic Divergence in Domestic Japanese Quail Inferred from Mitochondrial DNA D-Loop and Microsatellite Markers

et al. 2017

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To assess the genetic diversity of domestic Japanese quail (Coturnix japonica) populations, and their genetic relationships, we examined mitochondrial DNA (mtDNA) D-loop sequences and microsatellite markers for 19 Japanese quail populations. The populations included nine laboratory lines established in Japan (LWC, Quv, RWN, WE, AWE, AMRP, rb-TKP, NIES-L, and W), six meat-type quail lines reimported from Western countries (JD, JW, Estonia, NIES-Br, NIES-Fr, and NIES-Hn), one commercial population in Japan, and three wild quail populations collected from three Asian areas. The phylogenetic tree of mtDNA D-loop sequences revealed two distinct haplotype groups, Dloop-Group1 and Dloop-Group2. Dloop-Group1 included a dominant haplotype representing most of the quail populations, including wild quail. Dloop-Group2 was composed of minor haplotypes found in several laboratory lines, two meat-type lines, and a few individuals in commercial and wild quail populations. Taking the breeding histories of domestic populations into consideration, these results suggest that domestic quail populations may have derived from two sources, i.e., domestic populations established before and after World War II in Japan. A discriminant analysis of principal components and a Bayesian clustering analysis with microsatellite markers indicated that the domestic populations are clustered into four genetic groups. The two major groups were Microsat-Group1, which contained WE, and four WE-derived laboratory lines (LWC, Quv, RWN, and AWE), and Microsat-Group2 consisting of NIES-L, JD, JW, Estonia, NIES-Br, NIES-Fr, NIES-Hn, W, and commercial and wild populations. The remaining two lines (AMRP and rb-TKP) were each clustered into a separate clade. This hierarchical genetic difference between domestic quail populations is attributed to the genetic background derived from two different genetic sources—the pre-war and post-war populations—which is well supported by their breeding histories.

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Genomic Heterogeneity of Chicken Populations in India

Cited by 22 publications

References 31 publications

Towards inclusion of genetic diversity measures into IUCN assessments: a case study on birds

Towards inclusion of genetic diversity measures into IUCN assessments: a case study on birds

Global diversity and genetic contributions of chicken populations from African, Asian and European regions

Genetic Divergence in Domestic Japanese Quail Inferred from Mitochondrial DNA D-Loop and Microsatellite Markers

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