Livestock Research for Rural Development 27 (8) 2015 Guide for preparation of papers LRRD Newsletter

Citation of this paper

Genetic characterization of different lines of meat type chicken by microsatellite markers

M B R Mollah, M Asaduzzaman, F B Islam, M G Azam and M A Ali

Department of Poultry Science, Faculty of Animal Husbandry, Bangladesh Agricultural University, Mymensingh-2202.
mbrmollah@gmail.com

Abstract

A set of chicken microsatellite markers covering different chromosomes were used to characterize four lines of meat type chicken namely Male Line White (MLW), Male Line Color (MLC), Female Line White (FLW) and Female Line Color (FLC). Among the 10 primers initially tested, six primers viz. MCW248, MCW295, MCW183, ADL0112, LEI094 and MCW104 produced high intensity amplification products with minimal smearing. These six primers were used to detect polymorphism among four lines of meat type chicken.

In total, 10 alleles were detected at the 6 microsatellite loci that are distributed on different autosomes.For all loci in four lines, significant deviation from Hardy-Weinberg equilibrium was found. Among the six loci, no line specific allele was found in all lines. The observed homozygosity value varied from 0.667 to 0.867. The highest observed homozygosity (0.867) was found in MLW. On the other hand, the highest observed heterozygosity (0.333) was found in MLC. The percentages of genetic homogeneity in all lines across all loci were 86.67, 76.67, 73.33 and 66.67 in MLW, FLC, FLW and MLC, respectively. The fixation coefficient (FST) of six loci varies from -0.008 to 0.238, with the mean being 0.102. The fixation indices (FIT) ranged from -0.303 to 1.000. Individual’s fixation indices (FIS) varied from -0.379 to 1. The findings of this study suggest that MLW, FLC and FLW lines reached more than 70% genetic homogeneity.

Key words: chicken line, DNA marker, genetic homogeneity, heterozygosity, polymorphism


Introduction

Inbred lines of chicken are indispensable for harnessing heterosis by two-way and/or three-way crossing, which is an established method for producing commercial broilers and layers. Development of inbred lines requires enormous efforts, huge capital investment and long time selection program. However, integration of recently developed molecular tools with conventional chicken breeding techniques that involves crossing of the best chicken possessing the most desirable traits (e.g., high meat yield or disease resistance, better feed efficiency) along with intensive selection has helped in achieving this target to a considerable extent. In addition, the role of inbred lines in biological research has fundamental importance by providing genetic diversity between lines and constancy over time and place within each individual line (Abplanalp1992, Crooijmans et al 1996, Ponsuksiliet al 1996, Vanhala et al 1998, Hassen et al 2009). Inbred lines, after genetic characterization within and among the lines, can be used as resource populations in genome mapping and linkage analysis between DNA markers and qualitative or quantitative traits. With a view to develop inbred lines of meat type chicken, a long term selection program is continuing at the Department of Poultry Science, Bangladesh Agricultural University (BAU), Mymensingh. In this selection program, phenotypic index selection is practiced; therefore, molecular information related to within and between lines homozygosity, rate of allele fixing and rate of inbreeding is unavailable.

Recently, an increasing number of studies have focused on the genetic characterization of chicken lines by molecular genetic markers. In poultry, different genetic marker systems have been used for estimation of genetic variability and relatedness successfully. They are DNA fingerprints (Lynch 1991), RAPD (Mollah et al 2009; Rahimi et al 2005) and microsatellites (Olowofeso et al 2005a, b; Kaiser et al 2000; Rikimaru et al 2007; Dávila et al 2009 and Tautz 1989). Molecular typing methods provide a powerful and reproducible approach of estimating genetic relatedness within and among chicken lines based on DNA variation. Many studies have been conducted to determine intra- and inter-lines characteristics in chickens. Comprehensive surveys of relatedness, including jungle fowl, layer and broiler strains and white leghorn, based on DNA fingerprints, have been described (Hillel et al 1989, Siegel et al 1992, Kuhnlein et al 1989 and Ponsuksili et al 1998; Kaiser et al 2000). Chen and Lamont (1992) and Plotsky et al (1995) characterized genetic variation in many highly inbred chicken lines by restriction fragment length polymorphism (RFLP), DNA minisatellite fingerprinting and randomly amplified polymorphic DNA (RAPD). Microsatellite polymorphism in commercial broiler and layer lines has been estimated (Crooijmans et al 1996; Kaiser et al 2000). Currently, the determination of heterozygosity and genetic distances based on microsatellite analysis is regarded as most convenient tool because many microsatellite loci are available and distributed throughout in the chicken genome. In addition, it shows a higher degree of polymorphisms, ease of identification and reproducibility than other markers, such as allozyme assay or random amplified polymorphic DNA analysis (Takahashi 1998; Zhang et al 2002a, b). The microsatellite markers are extensively used for estimating genetic structure, diversity and relationships because of many advantages: they are numerous and ubiquitous throughout the genome, show a higher degree of polymorphisms, and have a co-dominant inheritance (Zhou and Lamont 1999, Tautz and Renz 1989). Microsatellite markers are more accurate and efficient method for estimating genetic diversity and relationships among populations (Takezaki and Nei 1996; Romanov and Weigend 2001; Zhang et al 2002a; Hillel et al 2003, Nakamura et al 2006; Kamara et al 2007; Boruszewska et al 2009; Dávila et al 2009 and Tadano et al 2014). Therefore, the objective of this study was to estimate within and between genetic variability and relatedness among the selected lines of chicken using microsatellite markers.


Materials and methods

Experimental populations

Female chickens from four lines namely Male Line White (MLW), Female Line White (FLW), Male Line Color (MLC) and Female Line Color (FLC) as described previously (Ali et al 2013) were used in this study. These lines of chicken were developed at BAU Poultry farm by index selection for rapid early growth and better egg production. The major characteristics these chickens are shown in Table 1.

Table 1.  Major phenotypic characteristics of different lines of chicken used in this study

Parameters

Lines

Male Line White
(MLW)

Female Line White
(FLW)

Male Line Color
(MLC)

Female Line Color
(FLC)

Base population

Commercial white broiler

Dual purpose white breed

Commercial color broiler

Dual purpose color breed (female) and Aseel (male)

Comb type

Single

Single

Single

Single, pea, rose

Plumagecolor

White

White

Brown, barred, black

Mixed color

Shank color

Yellow/White

Yellow

Yellow/white/Black

Yellow/White/Black

Beak color

White

White

Light yellowish/Black

Yellowish

Egg color

Brown

Brown

Brown

Brown

Selection criteria

3, 5 and 6 week body weight

3, 5 and 6 week body weight, egg size, egg number at 35 weeks of age

3, 5 and 6 week body weight

3, 5 and 6 week body weight, egg size, egg number at 35 weeks of age

Collection of blood samples and isolation of DNA

Blood was collected from five to seven female chickens of each line and prepared for DNA isolation by using the procedure suggested by Hoelzel (1992) with little modifications. Approximately 1-1.25ml blood was collected by 5ml disposable syringe from wing vein. The collected blood was immediately transferred into the 1.5ml microfuge tube. The blood containing tubes were kept in ice box, transported to the laboratory and centrifuged at 5000 rpm for 10 minutes and the serum was discarded. Genomic DNA was extracted from clotted blood cell using the standard Phenol: Chloroform: Isoamyl alcohol method with slight modifications. The isolated DNA samples were diluted with DNAase free water in a new tube and the concentration was measured by using UV-spectrophotometer (Spectronic® GENESISTM 5). Finally, the diluted DNA samples were kept at -20°C until further use.

Selection of primers, PCR, electrophoresis and visualization of amplified products

Initially highly polymorphic microsatellite markers were screened from chicken microsatellite primer set (http://poultry.mph.msu.edu/) and published articles based on the allele size, chromosomal location and annealing temperature. The details of the primers that were initially selected are shown in Table 2. These primers were screened on three sub samples from each population to test their suitability for amplifying DNA sequence. These primers were evaluated on the basis of polymorphism and potential for population discrimination. Finally, a subset of six primers, out of ten was retained for further analysis. Each PCR amplification was conducted in a 14μl reaction mixture, which included 10 pmol of each primer, 100μM deoxynucleoside triphosphate, 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl2, 0.001% gelatin, 0.5 U of AmpliTaq Gold (Applied Biosystems, Foster City, CA), and approximately 20 ng of genomic DNA as a template. The PCR procedure, using the GeneAmp PCR System 2700 (Applied Biosystems) was as follows: first denaturation step at 95°C for 10 min, 43 cycles of denaturation at 95°C for 1 min, annealing at primer-specific temperature (58 or 60°C) for 1 min, extension at 72°C for 1 min, followed by final extension at 72°C for 10 min. Then the samples were cooled at 4°C. The amplified DNA was placed into a submarine electrophoresis system (Mupid®-2X, Japan). A 100bp DNA ladder was also run along the amplified fragments. Electrophoresis was carried out at 100V for 45 minutes. Then the gel was stained with ethidium bromide for 15 minutes. The amplified fragments were visualized on UV Transilluminator and photographed by using Bimetra Gel Documentation System (Germany).

Table 2.  List of microsatellite markers initially selected for population screening

Marker name

Chromosome (GCA)

Annealing temp (°C)

Allele size (bp)

Sequence (5’— 3’)

MCW0020

1

60

179-185

F: TCTTCTTTGACATGAATTGGCA

R: GCAAGGAAGATTTTGTACAAAATC

MCW0078

5

60

135-147

F: CCACACGGAGAGGAGAAGGTCT

R: TAGCATATGAGTGTACTGAGCTTC

MCW0104*

13

60

190-234

F: TAGCACAACTCAAGCTGTGAG

R: AGACTTGCACAGCTGTGTACC

MCW0183*

7

58

296-326

F: ATCCCAGTGTCGAGTATCCGA

R: TGAGATTTACTGGAGCCTGCC

MCW0248*

1

60

205-225

F: GTTGTTCAAAAGAAGATGCATG

R: TTGCATTAACTGGGCACTTTC

MCW0295*

4

60

88-106

F: ATCACTACAGAACACCCTCTC

R: TATGTATGCACGCAGATATCC

ADL0112*

10

58

120-134

F: GGCTTAAGCTGACCCATTAT

R: ATCTCAAATGTAATGCGTGC

ADL0268

1

60

102-116

F: CTCCACCCCTCTCAGAACTA

R: CAACTTCCCATCTACCTACT

LEI0094*

4

60

247-287

F: GATCTCACCAGTATGAGCTGC

R: TCTCACACTGTAACACAGTGC

LEI0234

2

60

216-364

F: ATGCATCAGATTGGTATTCAA

R: CGTGGCTGTGAACAAATATG

*Finally retained for analysis

Data analysis

The genetic diversity of each line was assessed by calculating the number of alleles per locus and its mean, observed heterozygosity, unbiased expected heterozygosity (Nei 1987). Additionally, F-statistics [fixation coefficient of an individual within a subpopulation (FIS), fixation coefficient of an individual within the total population (FIT), and fixation coefficient of a subpopulation within the total population (FST)] per locus across four lines were calculated. Nei’s (1972) genetic distance and construction of a UPGMA (Unweighted Pair Group Method of Arithmetic Means) dendrogram among lines with 1000 simulated samples which were carried out by using POPGENE (Version 1.31) (Yeh et al., 1999) computer program.


Results and discussion

The quality of isolated DNA is the major determinant in successful and reproducible Polymerase Chain Reaction (PCR), thus, the DNA samples were examined for its integrity through 1% agarose gel electrophoresis and absorption (OD) by spectrophotometer at 260nm and 280nm. The OD ratio (260/280nm) of all DNA samples was in between 1.68 to 1.75, whereas the concentration of extracted genomic DNA of all samples was in between 0.98 and 2.5 mg/ml. The value 1.68–1.75 of 260/280nm OD ratio indicated high quality DNA that was free from dissolved protein (Sambrook et al 1989). The PCR condition reported in the previous study (Cheng, 1997 and Croojimans et al 1996) did not work well with the lines of chicken used in this study. Thus, PCR condition was optimized by the examination of varying annealing temperatures and primer concentrations. Among the 10 primers initially tested, six primers namely MCW248, MCW295, MCW183, ADL0112, LEI094 and MCW104 produced high intensity amplification products with minimal smearing. These six primers were used to detect polymorphism among four lines (MLW, MLC, FLW and FLC). A representative microsatellite profiles generated by primer MCW0183 among the four lines of chickens are shown in Figure 1.

Figure 1.  A representative microsatellite profile generated by primer MCW0183 from four lines of chicken

The allele frequencies of six microsatellite markers across different lines of chicken are shown in Table 3. In total, 10 alleles were detected at six microsatellite loci distributed on different autosomes in the four lines of chicken. The summary of the observed number of alleles, effective number of alleles and Shannon’s information index are shown in Table 4. For all loci in four lines, significant deviation from Hardy-Weinberg equilibrium was found. Among the six loci, no monomorphic locus was found. As shown in Table 4, there was no line specific alleles were detected in this study.

Table 3.  Frequencies of polymorphic loci

 

Allele

Locus

MCW248

MCW295

MCW183

ADL0112

LEI094

MCW104

MLW

Allele A

0.600

0.000

0.000

0.800

0.100

0.500

Allele B

0.400

1.000

1.000

0.200

0.900

0.500

MLC

Allele A

0.800

0.600

0.300

0.800

0.200

0.500

Allele B

0.200

0.400

0.700

0.200

0.800

0.500

FLW

Allele A

0.800

0.200

0.300

0.400

0.500

0.600

Allele B

0.200

0.800

0.700

0.600

0.500

0.400

FLC

 

Allele A

0.600

0.400

0.200

0.600

0.200

0.500

Allele B

0.400

0.600

0.800

0.400

0.800

0.500

Overall

Allele A

0.700 

0.300   

0.200   

0.650   

0.250   

0.525   

Allele B

0.300   

0.700   

0.800   

0.350   

0.750   

0.475   

The result using six microsatellite primers indicated that these lines of chicken show relatively low variation and allele distribution. The low distribution of the number of allele per population may be due to, firstly, the primer selected for this experiment have low polymorphism or use of agarose gel to resolve polymorphisms because agarose gel have low resolution power than acrylamide gel. Further use of acrylamide gel might provide an explanation in this regard. Secondly, the low distribution may be due the developmental strategies of these lines as they were first initiated from a very small base population.

Table 4.  Summary statistics of overall loci in all lines.

Lines

No1

Ne2

I3

MLW

1.667±0.516

1.436±0.444

0.365±0.313

MLC

2.000±0.000

1.677±0.243

0.580±0.091

 

FLW

2.000±0.000

1.752±0.236

0.609±0.088

FLC

2.000±0.000

1.785±0.245

0.619±0.092

No1 = Observed number of alleles; Ne2 = Effective number of alleles (Kimura and Crow, 1964); I3 = Shannon's Information index (Lewontin, 1972)

The summary of the observed homo- and heterozygosity value of four lines of chicken are shown in Table 5. The observed homozygosity value varied from 0.667 to 0.867. All values of observed homozygosity were higher than observed heterozygosity. The highest observed homozygosity (0.867) was found in MLW. On the other hand, the highest observed heterozygosity (0.333) was found in MLC.

Table 5.  Summary of homo- and heterozygosity statistics for all loci

Lines

Observed
homozygosity

Observed heterozygosity

Expected homozygosity1

Expected heterozygosity2

Nei3

MLW

0.867±0.242

0.133±0.242

0.726±0.249

0.274±0.249

0.247±0.224

MLC

0.667±0.413

0.333±0.413

0.563±0.094

0.437±0.094

0.393±0.085

FLW

0.733±0.301

0.267±0.301

0.533±0.091

0.467±0.091

0.420±0.082

FLC

0.767±0.266

0.233±0.266

0.522±0.095

0.478±0.095

0.430±0.086

1Expected homozygosity and 2heterozygosity were computed using Levene (1949); 3Nei's (1973) expected heterozygosity

The estimated genetic homogeneity in all lines across all loci are shown in Table 6. The homozygosity percentages were 86.67, 76.67, 73.33 and 66.67 in MLW, FLC, FLW and MLC, respectively. From the Table 6, it is evident that MLW lines are more homozygous (86.67%) than other lines of chicken. This result seems to reflect the present breeding state of MLW, in which intense selective breeding is carried out among closely related birds in small population to improve growth and reproductive traits. In contrast, relative high heterozygosity was observed in MLC (33.33%). This might be due to the fact that FLC line was introduced later and thus they are undergone for few generation of selection compared to other lines.

Table 6. Homo and heterozygosity of alleles across different lines of chicken

Chicken
lines

Alleles

Microsatellite loci

All loci

MCW248

MCW295

MCW183

ADL0112

LEI094

MCW104

MLW

AA (%)

60.00

0.00

0.00

80.00

0.00

20.00

26.67

BB (%)

40.00

100.00

100.00

20.00

100.00

40.00

60.00

AB (%)

0.00

0.00

0.00

0.00

0.00

40.00

13.33

Homozygous (%)

100.00

100.00

100.00

100.00

100.00

60.00

86.67

MLC

AA (%)

80.00

60.00

0.00

80.00

0.00

0.00

36.67

BB (%)

20.00

40.00

40.00

20.00

60.00

0.00

30.00

AB (%)

0.00

0.00

60.00

0.00

40.00

100.00

33.33

Homozygous (%)

100.00

100.00

40.00

100.00

60.00

0.00

66.67

FLW

AA (%)

80.00

20.00

0.00

40.00

20.00

40.00

33.33

BB (%)

20.00

80.00

40.00

60.00

20.00

20.00

40.00

AB (%)

0.00

0.00

60.00

0.00

60.00

40.00

26.67

Homozygous (%)

100.00

100.00

40.00

100.00

40.00

60.00

73.33

FLC

AA (%)

60.00

40.00

0.00

60.00

20.00

20.00

33.33

BB (%)

40.00

60.00

60.00

40.00

40.00

20.00

43.33

AB (%)

0.00

0.00

40.00

0.00

40.00

60.00

23.33

Homozygous (%)

100.00

100.00

60.00

100.00

60.00

40.00

76.67

The summary of F-statistics and gene flow for all six loci are shown in Table 7. For the genetic divergence of the lines, the fixation coefficient (F ST) of six loci varies from 0.008 to 0.238, with the mean being 0.102. The fixation indices (FIT) ranged from -0.303 to 1.000. Individual’s fixation indices (FIS) varied from -0.379 to 1.

Table 7 Summary of F-Statistics and gene flow for all loci

Locus

FIS

FIT

FST

MCW248

1.000

1.000

0.048

MCW295

1.000

1.000

0.238

MCW183

-0.379

-0.250

0.094

ADL0112

1.000

1.000

0.121

LEI094

-0.212

-0.067

0.120

MCW104

-0.313

-0.303

0.008

Mean

0.351

0.417

0.102

The FST represent a degree of nonrandom mating (deviation from Hardy-Weinberg equilibrium). A positive number for FST means deviation from Hardy-Weinberg equilibrium. As expected, all loci showed a positive FST number, which indicated that nonrandom mating was practised in these lines of chicken. From the breeding strategies of these lines (Ali et al 2013), it is evident that that these lines were produced through inbreeding with selection to improve growth or egg production. The mean FST value of 0.102 indicates that approximately 89.80% of the total genetic variation is caused by line differences, whereas the remaining 10.20% is due to differences among individuals within lines. Tadano et al (2007) reported the mean FST value of 0.383 from long tailed Japanese breeds, whereas Vanhala et al (1998) reported the mean FST value of 0.303 from 8 Finnish chicken lines using 9 microsatellite markers. As compared to other domestic animals, the mean FST value in this study was relatively low. For instance, Kim et al (2001, 2005) reported the mean FST value of 0.261 and 0.154 for pig breeds and East Asian native dog breeds, respectively. This fact might suggest that the chicken lines used in the present study are genetically subdivided to a higher extent than other chicken breeds/lines because of inbreeding between related individuals or more intensive selection to fix desirable traits.

Table 8 shows the Nei’s original measure of genetic identity and distance between each pair of all four chicken lines, based on 6 microsatellite loci. The genetic identity was ranged from 0.882 (between MLC and FLW lines) to 0.964 (between FLW and FLC lines).

Table 8. Nei's original measures of genetic identity and distance

Lines

MLW

MLC

FLW

FLC

MLW

****

0.883

0.883

0.946

MLC

0.125

****

0.882

0.964

FLW

0.125

0.125

****

0.933

FLC

0.055

0.037

0.069

****

Nei's genetic identity (above diagonal) and genetic distance (below diagonal)


Figure 2. Dendrogram based on Nei’s genetic distance

A phylogenetic relationship of four lines of chicken based on Nei (1972) using UPGMA method with 1000 simulated data is shown in Figure 2. With the limited information we found that the lines were relatively distinct in which FLC and MLC were clustered in one group, whereas MLW and FLW were in separate group.

The findings of this study may suggest that the level of genetic homogeneity is relatively high among these lines of chicken and the lines may be relatively distinct.


Acknowledgment

The research is partly supported by the SPGR NATP: Phase -1 research grant of Bangladesh Agricultural Research Council (BARC), Bangladesh.


References

Abplanalp H 1992 Inbred lines as genetic resource of chickens. Poultry Science, 4: 29-38

Ali, M A, Mollah, M B R, Haque M A, and Azam M G 2013 Selection in sire and dam line parents for meat chicken production. In: 8th International Poultry Show & Seminar, 2013, 101-108. Dhaka, Bangladesh

Boruszewska K, Łukaszewicz M, Zięba G, Witkowski A, Horbańczuk J and Jaszczak K 2009 Microsatellite markers may be ineffective in selection of laying hens for polygenic production traits. Poultry Science, 88: 932-937

Chen Y, and Lamont S J 1992 Major histocompatibility complex class I restriction fragment length polymorphism analysis in highly inbred chicken lines and lines selected for MHC and Immunoglobulin production. Poultry Science, 71: 999-1006

Cheng H H 1997 Mapping the chicken genome. Poultry Science, 76: 1101-1107

Crooijmans R P M A, Groen A F, Van Kampen A J A, Van der Beek S, Van der Poel JJ and Groenen M A M 1996 Microsatellite polymorphism in commercial broiler and layer lines estimated using pooled blood samples. Poultry Science, 75: 904-909

Dávila S G, Gil M G, Resino-Talaván P and Campo J L 2009 Evaluation of diversity between different Spanish chicken breeds, a tester line, and a White Leghorn population based on microsatellite markers. Poultry Science, 88: 2518-2525

Hassen H, Neser F W C, Kock A and Marle-Köster E 2009 Study on the genetic diversity of native chickens in northwest Ethiopia using microsatellite markers. African Journal of Biotechnology, 8: 1347-1353

Hillel J, Groenen M A M, Tixier-Boichard M, Korol A B, David L, Kirzhner V M, Burke T, Barre-Dirie A, Crooijmans R P, Elo K, Feldman M W, Freidlin P J, Mäki-Tanila A, Oortwijn M, Thomson P, Vignal A, Wimmers K and Weigend S 2003 Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genetic Selection and Evolution, 35: 533–557

Hillel J, Plotsky Y, Haberfeld A, Lavi U, Cahaner A and Jeffreys A J 1989 DNA fingerprints of poultry. Animal Genetics, 20: 145-55

Hoelzel A R 1992 Molecular genetic analysis of populations: A practical approach. Oxford University Press, New York, 55-58

Kaiser M G, Yonash N, Cahaner A and Lamont S J 2000 Microsatellite polymorphism between and within broilers populations. Poultry science, 79: 626-628

Kamara D, Gyenai K B, Geng T, Hammade H and Smith E J 2007 Microsatellite Marker-Based Genetic Analysis of Relatedness Between Commercial and Heritage Turkeys (Meleagris gallopavo). Poultry Science, 86: 46-49

Kim K S, Tanabe Y, Park C K and Ha J H 2001 Genetic variability in East Asian dogs using microsatellite loci analysis. Journal of Heredity, 92: 398-403

Kim T H, Kim K S, Choi B H, Yoon D H, Jang G W, Lee K T, Chung H Y, Lee H Y, Park H S and Lee J W 2005 Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. Journal of Animal Science, 83: 2255-2263

Kimura M and Crow J F 1964 The number of alleles than can be maintained in a finite population. Genetics, 49: 725-738

Kuhnlein U, Dawe D, Zadworny D and Gavora J S 1989 DNA fingerprinting: a tool for determining genetic distances between strains of poultry. Theoretical and Applied Genetics 77: 669-672

Levene H 1949 On a matching problem arising in genetics. The annals of mathematical statistics, 91-94

Lewontin R C 1972The apportionment of human diversity. Evolutionary Biology, 6: 381-398

Lynch M 1991 Analysis of population genetic structure by DNA fingerprint. In: Burke T., Dolf G., Jeffeys A. J. and Wolf R. (Eds.) DNA fingerprinting approaches and applications. Basel, Switzerland, 113-126

Mollah M B R, Alam M S, Islam F B and Ali M A 2005 Effectiveness of RAPD marker in generating polymorphism in different chicken populations. Biotechnology, 4: 73-75

Mollah M B R, Islam F B, Islam M S, Ali M A and Alam M S 2009 Analysis of genetic diversity in Bangladeshi chicken using RAPD markers. Biotechnology, 8: 462-467

Nakamura A, Kino K, Minezawa M, Noda K and Takahashi H 2006 A method for discriminating a Japanese chicken, the nagoya breed, using microsatellite markers. Poultry Science, 85: 2124-2129

Nei M 1972 Genetic distance between populations. The American Naturalist, 106:283-292

Nei M 1973 Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences.70: 3321-3323

Olowofeso O, Wang J Y, Dai G J, Yang Y, Mekki D M and Musa H H 2005a Measurement of genetic parameter within and between Haimen chicken populations using microsatellite markers. International Journal of Poultry Science, 4: 143-148

Olowofeso O, Wang J Y, Shen J C, Chen KW, Sheng H W, Zhang P and Wu R 2005b Estimation of the cumulative power of discrimination in Haimen chicken populations with ten microsatellite markers. Asian-Australia Journal of Animal Science, 18:1066-1070

Plotsky Y, Kaiser M G and Lamont S J 1995 Genetic characterization of highly inbred chicken lines by two DNA methods: DNA fingerprinting and polymerase chain reaction using arbitrary primers.Animal Genetics, 26: 163-70

Ponsuksili S, Wimmers K and Horst P 1996 Genetic variability in chickens using polymorphic microsatellite markers. Thailand Journal of Agricultural Science, 29: 571-580

Ponsuksili S, Wimmers K and Horst P 1998 Evaluation of genetic variation within and between different chicken lines by DNA fingerprinting. Journal of Heredity, 89: 17-23

Rahimi G, Khanahmadi A, Nejati-Javaremi A and Smailkhanian S 2005 Evaluation of genetic variability in a breeder flock of native chicken based on randomly amplified polymorphic DNA markers. Iranian Journal of Biotechnology, 3: 231-234

Rikimaru K and Takahashi H 2007 A method for discriminating a Japanese brand of chicken, the Hinai-jidori, using microsatellite markers. Poultry Science, 86: 1881-1886

Romanov M N and Weigend S 2001 Analysis of genetic relationships between various populations of domestic and jungle fowl using microsatellite markers. Poultry Science, 80: 1057-1063

Sambrook J, Fritsch E and Maniatis T 1989 Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. p. E.5

Siegel P B A H, Mukherjee T K, Stallard L C, Mark F L, Anthony N B and Dunnington E A 1992 Jungle fowl-domestic fowl relationships: a use of DNA fingerprinting. World's Poultry Science Journal, 48: 147-55

Tadano R, Kinoshita K, Mizutani M and Tsudzuki M 2014 Comparison of microsatellite variations between red jungle fowl and a commercial chicken gene pool. Poultry Science, 93: 318-325

Tadano R, Nishibori M, Nagasaka N and Tsudzuki M 2007 Assessing of genetic diversity and population structure for commercial chicken lines based on forty microsatellite analyses. Poultry Science, 86: 2301-2308

Takahashi H, Nirasawa K, Nagamine Y, Tsudzuki M and Yamamoto Y 1998 Genetic relationships among Japanese native breeds of chicken based on microsatellite DNA polymorphisms. Journal of Heredity, 89: 543-546

Takezaki N and Nei M 1996 Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics, 144: 389-399

Tautz D 1989 Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research, 17: 6463-6471

Tautz D and Renz M 1984 Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Research, 12: 4127-4138

Vanhala T, Tuiskula-Haavisto M, Elo K, Vilkki J and Maki-Tanila A 1998 Evaluation of genetic variability and genetic distances between eight chicken lines using microsatellite markers.Poultry Science, 77: 783-790

Yeh F C, Yang R C and Boyle T 1999 POPGENE VERSION 1.31: Microsoft Windows- based Free ware for population genetic Analysis. ftp://ftp. Microsoft.com/Softlib/HPGL.exe.

Zhang X, Leung F C, Chan D K O, Chen Y and Wu C 2002a Comparative analysis of allozyme, random amplified polymorphic DNA and microsatellite polymorphism on Chinese native chickens. Poultry Science, 81: 1093-1098

Zhang X, Leung F C, Chan D K O, Yang G and Wu C 2002b Genetic diversity of Chinese native chicken breeds based on protein polymorphism, randomly amplified polymorphic DNA and microsatellite polymorphism. Poultry Science, 81: 1463-1472

Zhou H and Lamont S J 1999 Genetic characterization of biodiversity in highly inbred chicken lines by microsatellite markers. Journal of Animal Genetics, 30: 256-264


Received 22 May 2015; Accepted 11 June 2015; Published 1 August 2015

Go to top