Structure of genomic DNA in chicken populations revealed by multilocus DNA probe

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Abstract

Molecular genetic technologies are taking an increasing place in breeding work to improve existing breeds and populations of chickens, as well as in programs to preserve a valuable gene pool. Small local breeds are a source of valuable genes that can be used in breeding. The aim of this work was to obtain new knowledge about the structure of genomic DNA of six chicken populations using multilocus analysis with a labeled molecular probe (GTG)5. Multilocus analysis using labeled DNA probes provides working simultaneously with a large number of genetic loci and calculating population genetic parameters both within populations and between them. The data on use of the multilocus probe (GTG)5 in molecular hybridization reaction in six breeds and populations of chickens were analyzed. The results revealed a large genetic distance between Black-and-White Australorp and the Bald-necked chickens (D = 0.155). Bald-necked chickens are bred in isolation from other breeds to maintain the unique trait of ‘naked necks’. According to the criterion of average heterozygosity, the population of Bald-necked chickens surpassed the Yurlov Crowers and Black-and-White Australorps. Obviously, this is due to the intensive breeding work carried out in the last two populations, which reduces genetic diversity. Marker DNA fragments specific for individual breeds were identified. The effectiveness of multilocus analysis as a tool for identifying the features of genome organization in chicken breeds and populations was confirmed.

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Fig. 1. Outline of main experimental stages of multilocus analysis

Table 1
Population and genetic parameters in 3 chicken populations (Yurlov Crowers, Black-and-White Australorp and Bald-necked chickens) generated by DNA fingerprinting

Chicken population

n

Bands per lane,
X ± m

P

BS1

BS2

D

Yurlov Crowers

Black-and- White Australorp

10

11

27.7 ± 0.9

27.4 ± 0.5

9.2 × 10–13

6.9 × 10–12

0.37

0.39

0.29

0.090

Yurlov Crowers

Bald-necked chickens

10

11

27.7 ± 0.9

22.7 ± 1.6

9.2 × 10–13

4.6 × 10–12

0.37

0.32

0.20

0.145

Black-and- White Australorp Bald-necked chickens

11

11

27.4 ± 0.5

22.7 ± 1.6

6.9 × 10–12

4.6 × x10–12

0.39

0.32

0.20

0.155

Note. P — the probability of occurrence of two individuals with an identical set of all DNA fragments; BS1 — coefficient of similarity within groups; BS2 — coefficient of similarity between groups; D — genetic distance.

Table 2
Specific DNA fragments and alleles with different frequency of occurrence in 3 chicken populations (Yurlov Crower, Black-and-White Australorp and Bald-necked chicken) calculated by DNA fingerprinting

DNA fragment

DNA fragment frequ

ency

Frequency of allele occurrence q = 1 — √1 — p

I

II

III

I

II

III

85

0.80

0.27

0.18

0.55

0.15

0.09

106

0.10

0.00

0.73

0.05

0.00

0.48

108

0.60

0.91

0.00

0.37

0.68

0.00

112

0.00

0.91

0.18

0.00

0.05

0.09

Note. I — Yurlov Crower; II — Black-and-W hite Australorp; III — Bald-necked chicken; p — frequency of DNA fragment in population.

Table 3
Heterozygosity (H) in three chicken populations: Yurlov Crower,  Black-and-White Australorp and Bald-necked chicken

Chicken population

n

Number of loci

Number  of alleles

Number  of polymorphic loci

H

Yurlov Crower

10

16.16

5.88

1.00

0.71

Black-and-White Australorp

11

16.05

5.48

1.00

0.71

Bald-necked chicken

11

12.91

6.50

1.00

0.76

 

Fig. 2. Phylogenetic tree showing genetic relationships in chicken breeds according to the Statistica 6.0™ program (Cluster analysis module): Var1 — Yurlov Crowers, Var2 — Black-and-White Australorp, Var3 — Bald-necked chicken. On the y-axis — conventional units of genetic distance

Table 4
Population and genetic parameters in 3 groups of Pavlov chickens (RRIFAGB, Moscow region, Barnaul), as revealed by DNA fingerprinting

Chiken group

n

Bands per lane,
X ± m

Р

BS1

BS2

D

Pavlov RRIFAGB

Pavlov Moscow region

15

12

10.6 ± 0.9

13.6 ± 0.9

4.7 × 10–5

5.5 × 10–4

0.39

0.58

0.43

0.055

Pavlov RRIFAGB Pavlov Barnaul

15

13

10.6 ± 0.9

15.0 ± 1.4

4.7 × 10–5

7.5 × 10–5

0.39

0.53

0.36

0.100

Pavlov Moscow region Pavlov Barnaul

12

13

13.6 ± 0.9

15.0 ± 1.4

5.5 × 10–4

7.5 × 10–5

0.58

0.53

0.45

0.105

×

About the authors

Valeriy P. Terletskiy

Russian Research Institute of Farm Animal Genetics and Breeding

Author for correspondence.
Email: valeriter@mail.ru
ORCID iD: 0000-0003-4043-3823
SPIN-code: 4512-5328

Doctor of Biological Sciences, Professor, Chief Researcher, Laboratory of Molecular Genetics, Russian Research Institute of Farm Animal Genetics and Breeding

55a Moskovskoe highway, Tyarlevo vil., Pushkin, St. Petersburg, 196625, Russian Federation

Valentina I. Tyshchenko

Russian Research Institute of Farm Animal Genetics and Breeding

Email: tinatvi@mail.ru
ORCID iD: 0000-0003-4964-9938
SPIN-code: 6294-2400

Candidate of Biological Sciences, Senior Researcher, Laboratory of Molecular Genetics, Russian Research Institute of Farm Animal Genetics and Breeding

55a Moskovskoe highway, Tyarlevo vil., Pushkin, St. Petersburg, 196625, Russian Federation

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1. Fig. 1. Outline of main experimental stages of multilocus analysis

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2. Fig. 2. Phylogenetic tree showing genetic relationships in chicken breeds according to the Statistica 6.0™ program (Cluster analysis module): Var1 — Yurlov Crowers, Var2 — Black-and-White Australorp, Var3 — Bald-necked chicken. On the y-axis — conventional units of genetic distance

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Copyright (c) 2023 Terletskiy V.P., Tyshchenko V.I.

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