Plymorphism of partial d loop mitochondrial dna region and phylogenetics in five duck breeds in vietnam

VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE
FACULTY OF BIOTECHNOLOGY
-------oOo-------

GRADUATION THESIS
TOPIC:
“POLYMORPHISM OF PARTIAL D-LOOP MITOCHONDRIAL
DNA REGION AND PHYLOGENETICS IN FIVE DUCK BREEDS
IN VIETNAM”

HA NOI - 2023


VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE
FACULTY OF BIOTECHNOLOGY
-------oOo-------

GRADUATION THESIS
TOPIC:
“POLYMORPHISM OF PARTIAL D-LOOP MITOCHONDRIAL
DNA REGION AND PHYLOGENETICS IN FIVE DUCK BREEDS
IN VIETNAM”

Student

: Bui Binh An

Code

: 637401

Class

: K63CNSHE

Instructor

: MSc. Nguyen Quoc Trung

HA NOI - 2023


COMMITMENT
The work contained in this thesis has not been previously submitted for a degree
or diploma at any other undergraduate education institution. I hereby declare
that all results of the thesis were done by me. To the best of my knowledge and
belief, the thesis contains no material previously published or written by another
person except where reference is made.

Hanoi, February 10th, 2023

Bui Binh An

i


ACKNOWLEDGEMENT
First of all, I would like to express my gratitude to the Board of Directors of
Vietnam National University of Agriculture, the Dean of the Faculty and all the
teachers in the Faculty of Biotechnology for creating a great learning environment and
provided me the valuable knowledge throughout four and a half academic years.

Additionally, I would like to thank Dr. Nguyen Hoang Thinh, Faculty of Animal
Science. Dr. Nguyen Thi Thuy Hanh, Dr. Dinh Truong Son, Faculty of Biotechnology
supported my thesis.
I also express my heartfelt respect, gratitude and sincere appreciation to Msc.
Nguyen Quoc Trung, Department of Molecular Biology and Applied Biotechnology,
Vietnam National University of Agriculture for his scholastic guidance, constructive
criticisms and constant inspiration during the entire period of the study as well as the
research, for your time to help me in writing and for provide me the opportunity to
carry out my thesis in the laboratory of Department of Molecular Biology and Applied
Biotechnology.
I would like to thank all professors from Department of Molecular Biology and
Applied Biotechnology, who encouraged me to enhance my knowledge and help me
get the orientation of thesis.
Along with my supervisor, I would like to thank Cao Thi Thu Thuy and Nguyen
Duc Hoang, two of my lab-mates, for all of their assistance throughout the experiment.
I appreciated their enthusiastic guidance as I conducted my research and wrote this
thesis.
Last but not least, I want to express my thanks to my dear parents, family members,
and friends for their support, blessings, inspiration, and unwavering sacrifice during
the entirety of my academic career.
With warm and regards!
Hanoi, February 10th, 2023

Bui Binh An

ii


TABLE OF CONTENTS
COMMITMENT ............................................................................................................ i

ACKNOWLEDGEMENT ........................................................................................... iv
LIST OF TABLE ........................................................................................................... v
LIST OF FIGURE ........................................................................................................ vi
LIST OF ABBREVIATIONS ................................................................................... viii
ABTRACT ..................................................................................................................... ix
CHAPTER I. INTRODUCTION ................................................................................. 1
1.1.

Introduction ........................................................................................................... 1

1.2.

Objective ............................................................................................................... 2

1.2.1.

Objective............................................................................................................. 2

1.2.2.

Specific objectives .............................................................................................. 2

CHAPTER II. LITERATURE REVIEWS ................................................................. 3
2.1. Duck status in the world. .......................................................................................... 3
2.2. The importance of duck in Vietnam. ........................................................................ 5
2.3. Diversity of Vietnamese duck .................................................................................. 6
2.4. Mitochondrial DNA as a tool for assessing the genetic diversity. ........................... 9
2.5. General information of the five duck breeds in this study ..................................... 12
2.5.1. General characteristics......................................................................................... 12
2.5.2. Co duck ................................................................................................................ 12

2.5.3. Co Lung duck ..................................................................................................... 12
2.5.4. Na Tau duck......................................................................................................... 13
2.5.5. Troi duck.............................................................................................................. 14
2.5.6. Dom duck ............................................................................................................ 15
CHAPTER III. MATERIALS AND METHODS .................................................... 16
3.1. Material ................................................................................................................... 16
3.2. Place and time of study........................................................................................... 17
3.2.1. Place of study ...................................................................................................... 17
3.2.2. Time of study ....................................................................................................... 17
3.3. Method .................................................................................................................... 18
3.3.1. Sample collection ................................................................................................ 18

iii


3.3.2. DNA isolation ...................................................................................................... 18
3.3.3. PCR amplification and sequencing ..................................................................... 20
3.3.4. Data Analysis ....................................................................................................... 21
CHAPTER IV. RESULTS AND DISCUSSION ....................................................... 23
4.1. Results of DNA extraction ..................................................................................... 23
4.2. Amplification of D-loop region and sequencing .................................................... 23
4.2.1. PCR results .......................................................................................................... 23
4.2.2. Sequence identification ....................................................................................... 24
4.3. Phylogenetic analysis and distribution of haplotypes of all 5 duck breeds in
Vietnam ............................................................................................................ 25
4.3.1. Polymorphism and genetic diversity ................................................................... 25
4.3.2. Distribution of haplotypes of 84 samples belonging to 5 duck breeds ............... 27
4.3.3. Phylogenetic analysis of 84 samples belonging to 5 duck breeds....................... 29
4.4. Phylogenetic analysis and distribution of haplotypes of each breed ...................... 30
4.4.1. Phylogenetic analysis and distribution of haplotypes of Co breed ..................... 30

4.4.2. Phylogenetic analysis and distribution of haplotypes of Co Lung breed ............ 32
4.4.3. Phylogenetic analysis and distribution of haplotypes of Na Tau breed .............. 34
4.4.4. Phylogenetic analysis and distribution of haplotypes of Troi breed ................... 35
4.4.5. Phylogenetic analysis and distribution of haplotypes of Dom breed .................. 37
4.5. Discussion ............................................................................................................... 39
CHAPTER V. REFERENCES ................................................................................... 42
APPENDIX................................................................................................................... 44

iv


LIST OF TABLE
Table 2.1. Price of duck products in Vietnam on 06/09/2022 .........................................6
Table 3.1. Sample condition and total number of samples ...........................................16
Table 3.2. Primers used for PCR amplification ............................................................. 21
Table 4.1. Diversity indices and neutrality test results based on the genetic
analysis of mtDNA D-loop sequence fragments for the five duck
populations studied* .....................................................................................25
Table 4.2. Haplotype distribution table in all 5 duck breeds in Vietnam ......................27
Table 4.3. Polymorphic analysis from partial sequencing of the mitochondrial Dloop gene segment of 5 duck breeds in Vietnam .........................................28
Table 4.4. Haplotype distribution table in Co duck ......................................................30
Table 4.5. Polymorphic analysis from partial sequencing of the mitochondrial Dloop gene segment of Co breed ....................................................................31
Table 4.6. Haplotype distribution table in Co Lung duck .............................................32
Table 4.7. Polymorphic analysis from partial sequencing of the mitochondrial Dloop gene segment of Co Lung breed ..........................................................33
Table 4.8. Haplotype distribution table in Na Tau duck ...............................................34
Table 4.9. Polymorphic analysis from partial sequencing of the mitochondrial Dloop gene segment of Na Tau breed ............................................................ 34
Table 4.10. Haplotype distribution table in Troi duck ..................................................36
Table 4.11. Polymorphic analysis from partial sequencing of the mitochondrial Dloop gene segment of Troi breed..................................................................36
Table 4.12. Haplotype distribution table in Dom duck .................................................37
Table 4.13. Polymorphic analysis from partial sequencing of the mitochondrial Dloop gene segment of Dom breed ................................................................ 38

v


LIST OF FIGURE
Figures 2.1. Duck distribution map (FAO, 2010) ...........................................................3
Figure 2.2. Population genetics of the duck populations (Jiang et al., 2021) .................4
Figure 2.3. Spot-billed ducks (Anas zonorhyncha) .........................................................7
Figure 2.4. Cairina moschata ..........................................................................................7
Figure 2.5. Domestic Cairina moschata..........................................................................7
Figure 2.6. Distribution of duck in Vietnam ...................................................................8
Figure 2.7. Distribution of ducks by region in Vietnam .................................................9
Figure 2.8. Co duck has heterogeneous feathers ........................................................... 12
Figure 2.9. Co Lung duck in Ba Thuoc district, Thanh Hoa province ..........................13
Figure 2.10. Na Tau duck, also known as short-necked gourd duck ............................ 13
Figure 2.11. There are many varieties of Troi duck that have been introduced into
Vietnam ........................................................................................................14
Figure 2.12. Dom duck (Pất Lài duck) ..........................................................................15
Figure 3.1. Sample blood............................................................................................... 18
Figure 3.2. Sample bloodfeathers ..................................................................................18
Figure 4.1. Total DNA of 11 Na Tau samples was separated from blood (left) and
11 male Co Lung samples were separated from wing feathers (right). .......23
Figure 4.2. Selected samples were compared with 100ng/nL Lamda DNA giving
expected results from 600 to 700bp ............................................................. 23
Figure 4.3. Some partial D-loop region sequences .......................................................25
Figure 4.4. Unrooted Maximum Likelihood phylogenetic tree constructed using
the D-loop sequences obtained for the domestic duck breeds in
Vietnam considered in the present study .....................................................29
Figure 4.5. A phylogenetic tree showing D-loop mtDNA related evolutionary
relationships in Co ducks .............................................................................32

Figure 4.6. A phylogenetic tree showing D-loop mtDNA related evolutionary
relationships in Co Lung ducks ....................................................................33
Figure 4.7. A phylogenetic tree showing D-loop mtDNA related evolutionary
relationships in Na Tau ducks ......................................................................35

vi


Figure 4.8. A phylogenetic tree showing D-loop mtDNA related evolutionary
relationships in Troi ducks ...........................................................................37
Figure 4.9. A phylogenetic tree showing D-loop mtDNA related evolutionary
relationships in Dom ducks ..........................................................................38

vii


LIST OF ABBREVIATIONS
Abbreviation

Meaning

bp

base pair

DNA

Axit deoxyribonucleic

MEGA

Molecular Evolutionary Genetics Analysis

EDTA

Axit ethylen diamine tetra acetic

PCR

Polymerase Chain Reaction

rpm

revolutions per minute

SDS

Sodium dodecyl sulfate

SNPs

Single-nucleotide polymorphisms

TE

Tris-EDTA

UV

Ultraviolet

µL

microlit

viii


ABTRACT
In this study, partial mitochondrial DNA (mtDNA) D-loop sequences of five
duck breeds in Vietnam, including Na Tau, Co, Dom, Troi and Co Lung, were
analyzed to determine sequence polymorphism and phylogeny among breeds.
The D-loop regions of 84 duck individuals were amplified by PCR using
primers L78-H774 and sequenced by Sanger method. Sequence alignments of
658 nucleotides at the 5' end were carried out and compared with other Anas
spp. using ClustalW of MEGA11 software. Phylogenetic investigation shows
that the Vietnamese ducks have a relatively close genetic relationship with Anas
zonorhyncha (GU246018.1) and Cairina moschata (GQ922096.1). SNPs
detection among 5 breeds resulted in 41 nucleotides within D-loop region. This
high diversity could be explained by the tendency of farmers to graze and breed
freely for a long time. In the phylogenetic analysis, it suggested that five
Vietnamese duck breeds have common maternal lineages with Anas
zonorhyncha and Cairina moschata.

Keywords: D-loop sequence, maternal lineages, phylogenetic, sequence
polymorphism, Vietnamese duck breeds.

ix

CHAPTER I. INTRODUCTION
1.1.

Introduction

Duck is one of the most common domestic poultry in the world, along
with chicken, guinea fowl, geese and turkeys. Compare to chicken, duck are
more resistant to diseases, have longer egg-production life, eggs are heavier and
fetch a better price. Duck meat is also well known for their delicacy and are
consummed worldwide. For many Asia contries, duck production plays an
important part in the agricultural economy. The continent alone accounts for
82.6% of the total duck meat produced worldwide (Adzitey and Adzitey, 2011).
In Vietnam, duck rearing and farming has been a consistant way for farmers to
increase income and reduce poverty, needless to say, duck is essential to
Vietnam agriculture.
Come from the realization of the importance of duck, 5 Vietnamese duck
breeds were selected: Co duck, Co Lung duck, Na Tau duck, Troi duck, Dom
duck, to conduct the study: “ Polymorphism of partial D-Loop Mitochondrial
DNA Region and Phylogenetics in five duck breeds in Vietnam” with the aim
to find origin of the selected duck breeds, opening up a better understanding in
genetic diferrences between breeds for serving breeding selection, genetic
selection and conservation of rare duck breeds.
One of the main theories about the origin of domestic ducks is to be from
the Mallard (Anas platyrhynchos) and Spot-billed Duck (Anas zonorynchos).
They are both migratory birds, but may settle in areas with good food and
habitat. They also have characteristics that allow them to be easily domesticated.
In addition, Mallards may cross with Spot-billed Duck, and the hybrids appear
in natural habitats (Jin et al., 2014). In addition, there are also some studies
showing that the Muscovy duck (Cairina moschata) is native to Mexico and
South America (HM, 1994). They were domesticated and introduced to Asia by

European colonists. And became the domestic duck for meat in many Asian
1


countries (Chen et al., 2009). Most domestic ducks are difficult to classify using
genetic makers because they share these wild duck ancestors (Seo et al., 2016).
Mitochondrial DNA (mtDNA) has been used to gain molecular information to
identify the origin of breeds. Proteins are not encoded in the D-loop region and
this region evolves much faster than other regions of the mtDNA genome.
Mitochondrial DNA and especially D-loop sequences have been used in
phylogenetic analysis for the past 20 years. Several studies using mtDNA Dloop control region genetic variation have been conducted to elucidate the gene
flow of domestic and wild ducks and their genetic relationships in several
geographical regions (Sultana et al., 2016).
1.2.

Objective

1.2.1. Objective
Evaluation on Polymorphism of D-Loop mitochondrial DNA region and
phylogenetics of some selected duck breeds. In order to breeding and
conservation of local animals genetic resources.
1.2.2. Specific objectives
In order to achieve the objective of the study, following requirements need to
be completed:
 Collecting blood and bloodfeathers for and extracting DNA from samples.
 Amplifying and sequencing the mtDNA D-Loop fragments.
 Detecting DNA polymorphism in the sequences and identifying
haplotypes in the sequences.
 Analyzing the phylogenetic and haplotype distribution of the five duck
breeds in Vietnam.

2


CHAPTER II. LITERATURE REVIEWS
2.1. Duck status in the world
Duck is the second largest poultry industry that provides income to farmers
through egg and meat production. They are particularly numerous in
Bangladesh, China and Southeast Asia but are also popular in Egypt, Nigeria
and much of Europe, particularly in western France. Breeds vary greatly
depending on location and whether they are specialized for meat, egg or feather
production or whether they are multipurpose (FAO). They are raised in a wide
range of production systems, from small flocks kept in mixed farms to enormous
flocks hauled in lorries to clear paddy fields after rice harvests.

Figures 2.1. Duck distribution map (FAO, 2010)
Wild Mallard (Anas boschas) are generally regarded as the ancestor of all
breeds of domestic ducks, but there are also another hypothesis stated that
domestic

ducks

orginated

from hybrid

between

the

mallard

(Anas

platyrhynchos) and the Eastern spot-billed duck (Anas p. zonorhyncha) (Cherry
and Morris, 2008). The domestication process start about 4000 years ago in
China and Southeast Asia, though the exact time is still unknown.

3


Figure 2.2. Population genetics of the duck populations (Jiang et al., 2021)
Nowadays duck has become a important farmed poultry in many country,
especially in developing countries thanks to high diseases resistent, high egg
production, tasty and nutritious meat, good feed conversion ratio (FCR) and
good finished product pricing. In 2021, total duck meat production is estimated
at 5 million tons. Due to the uncontrolled breeding, interbreeding, and
4


hybridization of domesticated and natural populations of closely related species
all over the world, duck species conservation is today an issue of great concern.
Seo et al., 2016 stated that native duck breeds need to be protected for
biodiversity conservation and development of economically important traits,
which would also be valuable ecologically and to breed survival.
2.2. The importance of duck in Vietnam
Poultry production, including waterfowl, plays an important role in
Vietnam's agricultural production, creating jobs, social security, and can get rich
from the development of the farm economy camps, businesses. Vietnam's
poultry industry in the past 10 years (2010-2019) has achieved encouraging

achievements. Total poultry flock increased from 100 million to nearly 467
million heads;

meat production reached over 1.2 million tons, of which

waterfowl reached nearly 260 thousand tons; egg production reached over 13
billion eggs (Department of Livestock Production, 2020).
Duck production systems have developed in Vietnam over a long period of
time and play an important role in providing income for small farmers, and meat
and eggs for the human population (Pingel and Germany, 2011).
Vietnam is ranked the second in the world in terms of farmed duck
production, and is located in the largest duck consumption market, Asia, after
China. The total duck population of the country in 2020 is 82.5 million, of
which mainly (over 60%) are concentrated in the two deltas of the Mekong and
Red rivers. Ducks in Vietnam currently account for only 7% of the poultry
population with about 72-75 million ducks, of which it is estimated that 35% are
raised for eggs and 65% for meat, it can be said that duck is a strategic product
of Vietnam's poultry industry if well-develop.
Currently, Vietnam has mastered the technology of producing domestic
waterfowl broodstock, and at the same time selectively created a number of
5


high-yield and high-quality lines. the world's largest waterfowl, so the waterfowl
breeds that thrive in production have become a great source of income for
breeders. Vietnam owns all the high-yielding duck breeds in the world.
GIÁ SẢN PHẨM CHĂN NUÔI (TẠI TRẠI) CẢ NƯỚC NGÀY 06/09/2022

Sản phẩm

Đơn vị tính

Giá ngày

Giá bình qn

So giá BQ

So giá BQ

06/09/2022

trong tháng

tháng trước

năm trước

(đồng)

(đồng)

(đồng)

(%)

(đồng)

(%)

Vịt giống Super-M (Miền Đông)

đ/con 1 ngày tuổi

16.000-17.000

17,100

-500 -2.8

10,800 171.4

Vịt giống Grimaud (Miền Đông)

đ/con 1 ngày tuổi

18.000-19.000

18,500

-1200 -6.1

11,200 153.4

Vịt giống Bố mẹ Super-M (Miền Đông) đ/trống 1 ngày tuổi

40,000

40,000

-

0.0

7,000 21.2

Vịt giống Bố mẹ Super-M (Miền Đông) đ/mái 1 ngày tuổi

35,000

35,000

-

0.0

5,000 16.7

Vịt giống Bố mẹ Grimaud (Miền Đông) đ/trống 1 ngày tuổi

55,000

55,000

-

0.0

2,000

3.8

Vịt giống Bố mẹ Grimaud (Miền Đông) đ/mái 1 ngày tuổi

50,000

50,000

-

0.0

0

0.0

Vịt thịt Super-M (Miền Đông)

đ/kg

40.000-41.000

41,700

-9000 -17.8

16,000 62.3

Vịt thịt Grimaud (Miền Đông)

đ/kg

41.000-42.000

43,100

-9600 -18.2

15,400 55.6

Trứng vịt (Miền Bắc)

đ/quả

2.700-3.000

2,880

80

2.9

410 16.6

Trứng vịt (Miền Trung)

đ/quả

2.700-3.000

2,870

60

2.1

400 16.2

Trứng vịt (Miền Đông)

đ/quả

2.700-2.800

2,750

-130 -4.5

380 16.0

Trứng vịt (Miền Tây)

đ/quả

2.500-2.600

2,550

-140 -5.2

380 17.5

Nguồn: Channuoivietnam.com

Table 2.1. Price of duck products in Vietnam on 06/09/2022
2.3. Diversity of Vietnamese duck
Vietnam is a country with a high level of biodiversity with many endemic
species, contains. The genetic resources of domestic ducks in Vietnam are quite
a lot, naming a few: Ky Lua, Indian spot-billed, Bach tuyet, Co, SinChéng,
Minh Huong, Bau Ben, Bau Quy, Co Lung, Moc, O Mon and Hoa Lan.
The Eastern spot-billed ducks (Anas zonorhyncha) are raised as backyard
duck in Vietnam. Improvement of the growth performance of this breed is
important for duck production in rural areas in Vietnam (Thinh et al., 2021).

6


Figure 2.3. Spot-billed ducks (Anas zonorhyncha)
Muscovy duck (swan) is native to South America, swan is different from all
duck breeds: The face is covered with a rough, bright red skin, the male geese
has a fleshy tumor at the base of the beak, both male and female have a narrow
head, however, due to duck-like characteristics in terms of meat production, it is
still considered a meat-oriented duck. In Vietnam, swans are called Siamese
ducks, which means that Vietnamese people also think of swans as a duck breed.
The British Waterfowl Association classifies geese as meat ducks (Tiệu, 2004).

Fig 2.4. Cairina moschata

Fig 2.5. Domestic Cairina moschata

However, biodiversity in Vietnam in recent years is facing extremely
serious threats from human activities such as overexploitation, destruction and
degradation of the natural environment. Some duck breeds have disappeared or
are endangered such as Bach Tuyet , O Mon, Ky Lua duck (Ba et al.).
7


Figure 2.6. Distribution of duck in Vietnam
Vietnamese local ducks consist of different phenotypes kept in distinct
agroecological zones of Vietnam, which stretches 1600km from North to South.
Duck genetic resources comprise a wide range of breeds and populations
including native and fancy breeds, middle level food producers, industrial
stocks, and specializedlines. Both direct and indirect contacts between freegrazing duck flocks were frequent and diverse. The flocks were transported
extensively across district and province boundaries, mainly by boat but also by
truck or on foot (Meyer et al., 2017). Geographical isolation of the populations
could result in substructuring through drift, mutation and divergent selective
forces. However, it is not known to what degree Vietnamese local duck
populations differ. Thus, a method of assessing the genetic variation and genetic
diversity of duck is needed.
A number of high-meat-yielding duck breeds have been imported to meet
the rising demand for duck meat. It results in the replacement of native breeds
with superior performing exotic breeds or in crossbreeding between local and
exotic breeds, changing livestock production systems. However, this might
cause a large decline in the genetic variety of local breeds, which would result in
the loss of genetic resources (Pham et al., 2022).

8


Figure 2.7. Distribution of ducks by region in Vietnam (nguoichannuoi.vn)

Within Vietnam, local governments have issued a number of policies and
decisions to support conservation and to promote the development of local duck
breed. For instance, in 1995, Que Phong district (Nghe An province) started to
have a policy to restore the Phu Quy fat duck. In 2016, Ba Thuoc district (Thanh
Hoa province) started project restore and develop good quality Co Lung native
ducks. Also in Thanh Hoa province, Nhu Xuan district has been training farmers
on how to conserv the local Thanh Quan fat duck.
A recent studies based on microsatellite markers showed the level of
genetic diversity of Vietnamese ducks and provided evidence that Vietnamese
native duck breeds origin was from Anas platyrhynchos (Ba et al.).
2.4. Mitochondrial DNA as a tool for assessing the genetic diversity
Genetic diversity is the total number of genetic characteristics in the genetic
makeup of a species. It is distinguished from genetic variability, which describes
the tendency of genetic characteristics to vary. According to "National
Biological Information Infrastructure". Introduction to Genetic Diversity. U.S.
Geological Survey, 2011, genetic diversity serves as a way for populations to
adapt to changing environments. With more variation, it is more likely that some
individuals in a population will possess variations of alleles that are suited for
the environment. Those individuals are more likely to survive to produce
9


offspring bearing that allele. The population will continue for more generations
because of the success of these individuals.
Using molecular genetic markers to assess genetic diversity between breeds
and within livestock breeds themselves at the molecular level will help guide the
management, conservation and use of dynamic genetic resources pets in a useful
way. Mitochondrial DNA is one of the genetic markers widely used in the study
of population genetic diversity. An important tool for determining the
phylogeny, population structure, and maternal origin of domestic animals is

mitochondrial DNA (mtDNA) study. In mitochondrial DNA, especially in some
segments of the control region (D-loop), cytochrome b and 12S rRNA loci, they
evolve very rapidly and have been shown to be very effective in the study
structure and genetic diversity of mitochondrial DNA (Ba et al.). The control
region has often been the focus of the majority of mtDNA investigations to date.
However, studying the genetic makeup of animals using the whole
mitochondrial genome sequence can provide us more accurate phylogenies of
maternal lineages. The mitochondrial DNA molecule does not undergo any
recombination state. Furthermore, the mitochondrial genome is maternally
inherited in most species and thus each mitochondrial gene lineage has
independent inheritance. Therefore, mitochondrial genomes are very suitable for
the study of evolutionary ancestry (Ouithavon et al., 2009).
Microsatellites and mitochondrial DNA (mtDNA) sequences have already
proved to be useful for assessing genetic variability, while single nucleotide
polymorphisms (SNPs) are becoming more and more popular due to their very
high density and availability of high throughput genotyping techniques. Unlike
microsatellite markers, mtDNA is maternally inherited and sequencing a specific
fragment of mtDNA (e.g., D-loop) gives more accurate information on evolution
and genetic diversity (Fumihito et al., 1994). In addition, unlike the mtDNA
with the presence of only maternal encoding genetic sequences, the nuclear
10


genes represent the integrative genetic information derived from both parental
sides in every generation, which could hide the history of individuals due to
recombination. Tracking the history of particular nuclear DNA segment is
therefore difficult.
The mtDNA is a circular molecule of 16,785 bp in size (Desjardins and
Morais, 1990). The displacement loop (D-loop) region of the mtDNA contains
elements that control the replication of the molecule and is highly polymorphic.

The D-loop region does not encode protein and evolves much faster than other
region of the mtDNA genome. For the past 20 years, mtDNA and particularly
D-loop sequences have been used in phylogenetic analysis (Moore, 1995).
MtDNA is used to infer regions of domestication and to identify the number of
maternal lineages and their geographic origins

(FAO, 2007b). In additon,

mtDNA analysis can offer qualitative indicators of population changes through
comparative studies, enabling effective targeting of resource-intensive
ecological investigations. Therefore, there are a few relatively simple
applications of mtDNA that can significantly aid in the long-term planning and
short-term implementation of species recovery programs, preferably in
conjunction with tests of nuclear variation (Moritz, 1994).
A massive amount of research has focused on finding level of genetic
diversity and reconstructing the matrilineal history of domestic duck using
mitochondrial DNA (mtDNA) sequence data. Central Javanese duck is shown to
be closely related to Anas platyrhynchos and Anas zonorynchos (Susanti et al.,
2017). Another research reported that East Asian ducks shared more haplotypes
with commercial ducks than South Asian ducks, and they had more independent
haplotypes than others did (Seo et al., 2016).

11


2.5. General information of the five duck breeds in this study
2.5.1. General characteristics
The five duck varieties in Vietnam including Co, Co Lung, Na Tau, Troi,
Dom gained a rising popularity due to their exotic traits and their high quality
meat, eggs and their resistant to harsh climates.

2.5.2. Co duck
Co duck (Vietnamese: vịt Cỏ), also called field duck, is a breed of
domestic duck originating in Vietnam, this is one of the widely raised duck
breeds in rural Vietnam. They are derived from mallards, through the natural
domestication process to form grass ducks adapted to grazing life. Because there
is no selective effect, the breed is being heavily adulterated. Grass ducks have
the behavior of herds, move quite quickly, find good prey, endure hardship,
resist diseases well, and are convenient for grazing in the fields. They are also
one of the symbols of Vietnamese villages, especially a familiar animal in the
water areas.

Figure 2.8. Co duck has heterogeneous feathers
2.5.3. Co Lung duck
Co Lung duck (Vietnameses: vịt Cổ Lũng), also known as Mường
Khoòng duck, is an indigenous breed of duck originating in Cổ Lũng commune,
Bá Thước district, Thanh Hóa, Vietnam. Co Lung Duck is a rare breed of duck,
a long-standing genetic breed, preserved and developed by generations of Bá
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Thước people. They are specialty of Thanh Hoá. Co Lung Duck is recognized
by the Vietnamese government as a domestic animal breed that is allowed to be
produced, traded and circulated within the Vietnamese territory.

Figure 2.9. Co Lung duck in Ba Thuoc district, Thanh Hoa province
2.5.4. Na Tau duck

Figure 2.10. Na Tau duck, also known as short-necked gourd duck
The Na Tau duck (Vietnamese: vịt Nà Tấu), also known as the shortnecked gourd duck, is famous for its fragrant and delicious meat, which has
become a trademark product of Nà Tấu commune, Tủa Chùa district (Điện

Biên). However, for people to keep raising spontaneously, the quality of the
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seed is degraded. Tủa Chùa district has a project to develop safe, sustainable and
high economic efficiency commercial duck.
2.5.5. Troi duck
The Mallard (Anas platyrhynchos) (Vietnamese: vịt Trời) is the most
common widespread dabbling duck in Vietnam. The Mallards are resident in
Vietnam year-round and are found in virtually all kinds of wetlands and water
bodies, from large lakes to small streams and ponds. Mallards prefer shallow
water with plenty of vegetation, but are also found in deeper open water. They
have a wide range of foods, including aquatic insects, snails, small fish, and
aquatic plants. Mallards are also known to feed in agricultural fields and can
sometimes be found foraging in grassy areas. They are commonly seen in parks
and gardens and are often seen as pets. The Mallard is the ancestor of most
domestic duck breeds, and has a distinctive green head and chestnut brown
body.

Figure 2.11. There are many varieties of Troi duck that have been
introduced into Vietnam

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