Genetic diversity of local Yunnan chicken breeds and their relationships with Red Junglefowl

Huo, Jinlong; Wu, Guo-Zhang; Chen, T.; Huo, Hailong; Yuan, Feng; Liu, L.X.; Ge, Chutian; Miao, Yongwang

doi:10.4238/2014.april.29.16

Cited by 17 publications

(17 citation statements)

References 26 publications

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“…The highest value of PIC (0.87) was that of LEI0234 and the mean PIC was 0.6451. The PIC values found in this study exceeded those (0.29-080) of Cameroon’s IC [21], and (0.31-0.49) of Chinese IC [21,22], but lower than those obtained by Tang for black-bone IC breeds (0.67) [24]. The mean frequency of alleles per marker found in this study (10.89) exceeded those recorded in previous reports in Cameroon (9.04) [21], in Ghana (7.8) [25], in Iran (5.4) [26], in China (3.8) [27], in Egypt (7.3) [28], in Pakistan (9.1) [29] and in Vietnam (6.41) [30].…”

Section: Discussioncontrasting

confidence: 44%

“…Among Rwanda IC, all populations showed a significantly high degree of inbreeding, which could have an impact on trait fixation in the populations. This degree of inbreeding exceeded that observed for Yunnan IC breeds (0.25) [22] and Turkish IC (0.301) with 10 SSR loci [35].…”

Section: Discussionmentioning

confidence: 59%

“…The IC populations in Rwanda had a similar level of diversity as their Ethiopian [36], Egyptian [28] and Cameroonian [22] counterparts, but had lower and higher diversity than those observed in southern China [23] and European and Asian IC breeds [25], respectively.…”

Section: Discussionmentioning

confidence: 99%

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Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Habimana

Okeno

Ngeno

et al. 2019

Preprint

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AbstractRwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chicken were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. 186 distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.

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Section: Discussioncontrasting

confidence: 44%

Section: Discussionmentioning

confidence: 59%

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Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Habimana

Okeno

Ngeno

et al. 2019

Preprint

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“…In various parts of the world, the genetic diversity of IC has been assessed using molecular markers including microsatellites [6][7][8][9][10][11][12][13][14][15][16][17][18][19]. Microsatellites are short, tandemly repeated simple sequences with one to six base pairs in length [20].…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Habimana¹,

Okeno²,

Ngeno³

et al. 2020

PLoS ONE

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Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chickens were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. One hundred eighty-six (186) distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant (p<0.05) in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.

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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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Genetic diversity of local Yunnan chicken breeds and their relationships with Red Junglefowl

Cited by 17 publications

References 26 publications

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

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

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