A Study about the Piggery Sector Sustainability, Pig Breed Diversity and Its Ecological Implications in Urban Districts of Uttarakhand

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Citation: Sahu, K. A Study about the
Piggery Sector Sustainability, Pig
Breed Diversity and Its Ecological
Implications in Urban Districts of
Uttarakhand. Biol. Life Sci. Forum
2022,15, 19. https://doi.org/
10.3390/IECD2022-12410
Academic Editor: Matthieu
Chauvat
Published: 15 March 2022
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Proceeding Paper
A Study about the Piggery Sector Sustainability, Pig Breed
Diversity and Its Ecological Implications in Urban Districts
of Uttarakhand †
Khusbu Sahu
Department of Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun 248001, India;
khusbu.sahu@gmail.com
† Presented at the 2nd International Electronic Conference on Diversity (IECD 2022)—New Insights into the
Biodiversity of Plants, Animals and Microbes, 15–31 March 2022; Available online:
https://sciforum.net/event/IECD2022.
Abstract:
Uttarakhand is situated on the southern slope of the world’s youngest (geo-dynamically
sensitive) mountain system, “the Himalayas”. Owing to rapid deforestation in the planar districts due
to an increase in infrastructural growth, the wildlife–livestock–human interface has blurred. This has
increased the chances of contact exposure of wild boars to humans and domestic animals. The study
identifies the location of pig rearers and their pig rearing practices, with its ecological effects, and also
studies the mitochondrial DNA diversity using a control region from the 68 samples collected from
the surveyed household. Analysis showed that 60.7%, 10.7% and 21.4% of the households raised
pig near seasonal streams (slum settlements), the residential areas and near the forest, respectively.
Furthermore, 28.6% maintained breeding boar of feral origin and 96.94% followed semi-intensive pig
rearing practices; hence human settlements have stayed in close association with pigs (domestic and
wild) and other domestic animals. The possibility of the emergence of zoonotic and non-zoonotic
disease and its easy transmission to humans has become more prominent in the urban setting. A
total of 18 haplotypes were observed with 34 segregating sites in 68 analyzed sequences. The high
level of haplotype diversity and nucleotide diversity suggested an increase in crossbreeding among
the species.
Keywords: pig husbandry; urbanization; socio-economic; mitochondrial DNA; diversity
1. Introduction
Unlike other domesticated animal species, the abundance of domestic pigs in a partic-
ular region is influenced by the religion, culture, and traditions of people within the region
and their respective association with pork consumption. The worship and significance of
wild boar in India have been seen since time immemorial [1], however, on the question of
pig rearing, the scenario depends on the other aspect of Hinduism called the caste system,
which is the oldest form of surviving social stratification and its effect cannot be ignored
in modern society. According to the traditional caste system, the lower caste prefers pig
rearing. Hence, in India, pigs are raised mostly by scheduled caste and tribes to maintain
their social identity and traditional culture [
2
]. The present study aims to: (1) identify the
location of pig rearers and their pig rearing practices in urban districts of Uttarakhand
and analyze its ecological implications to the urban landscape and human settlement, and;
(2) investigate the mtDNA diversity among the domestic pig of the study area.
2. Methods
Household Survey and Rapid appraisals approach was adopted as “survey and
monitoring tools” to identify more geographical locations in Uttarakhand, where pig
rearers were localized [
3
]. In total, 28 households (HH) (25 in Dehradun, 2 in Haridwar, and
Biol. Life Sci. Forum 2022,15, 19. https://doi.org/10.3390/IECD2022-12410 https://www.mdpi.com/journal/blsf

Biol. Life Sci. Forum 2022,15, 19 2 of 5
1 in Nainital), were interviewed by preparing a semi-structured questionnaire from March
2019–December 2019 in the urban districts of Uttarakhand. The geographical position of
each participating family was recorded using the Android based software, Google Maps.
2.1. Sample Collection, DNA Extraction, Amplification and Sequencing
Non-invasive biological samples (hairs and tissues) were collected from 68 un-relatable
pigs from the surveyed household for mtDNA studies. Genomic DNA was extracted using
DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany) protocol and the amplification of
approximately 419 bp mtDNA hypervariable control region was recorded using control
region-specific primer pair [4].
2.2. Sequence Data Analysis
Sequences were confirmed using the BLAST tool on NCBI (http://ncbi.nlm.nih.gov/
accessed on 1 December 2021) and were clean and edited with SEQUENCHER
®
version 4.9
(Gene Codes Corporation, Ann Arbor, MI, USA). We obtained 2826 cleaned and aligned
global control region sequences (404 bp) representing Sus scrofa from GenBank. The global
control region sequences were aligned with 68 samples of Uttarakhand using the CLUSTAL
W algorithm [
5
] in program MEGA X [
6
]. Haplotype (Hd) and nucleotide diversities (Pi)
were calculated using program DnaSP v.5.10 [
7
]. Haplotypes were derived by removing
non-informative sites, and gaps were considered. The haplotypes sharing with global
sequences were reconstructed using the median-joining network in PopART v.1.7 [8].
3. Results and Discussion
3.1. Map Plotting Analysis
A total of 60.7% of households raised pigs near slum settlements (Figure 1) that had
inadequate sanitation, and these unhygienic environments pose a risk to animal health
and human health. Of the households interviewed, 21.4% raised pigs near forest areas,
increasing the chances of contact exposure of wild boars, which itself harbors several
viruses, bacteria, and parasites diseases. Thus, the transmission of pathogens between
wild boars and humans becomes more conspicuous in highly populated districts, either
by consumption of wild boar meat (which has been reported in Uttarakhand) or through
cross-breeding of the domestic population with the wild population.
Biol. Life Sci. Forum 2022, 2, x 3 of 6
Figure 1. Map showing the location of surveyed household in the study area of Uttarakhand.
3.2. Pig Husbandry Practices in Uttarakhand
Households kept 2–4 adult sows and 1–3 hybrid boars with their piglets in their herd
(Figure 2a–c). They identified the breeds as indigenous and mixed parentage of
indigenous crossed with the exotic breed and putative crossed with a wild pig. A total of
28.6% pig rearers maintained probable breeding boar of feral origin in secrecy due to its
easy availability and high sale value (Figure 2d). The combination of farrow to finish and
piglet production systems are observed in 85.7% of the households surveyed. Only 14.3%
of the households practiced fattener production. The major rearing pattern observed in
the study area was a semi-intensive system (96.94%) (Figure 2e), followed by an extensive
system (3.57%) (Figure 2f). These systems need less capital investment, but disease
incidences and parasite infestations are high.
Figure 2. (a) Pig herd in Ramnagar (Nainital district of Uttarakhand) (b) Pig herd of mixed parental
origin observed in Chandrabani (Dehradun district of Uttarakhand) (c) Pig herd in Jwalapur
(Haridwar district of Uttarakhand) (d) Possible hybridized feral origin or boar piglet for sale or
mating purpose (e) Semi-intensive system of pig management with housing facility (all the pen is
made of brick with tin as a roof within the house premises) (f) Extensive system of pig management
with no housing facility.
Figure 1. Map showing the location of surveyed household in the study area of Uttarakhand.

Biol. Life Sci. Forum 2022,15, 19 3 of 5
3.2. Pig Husbandry Practices in Uttarakhand
Households kept 2–4 adult sows and 1–3 hybrid boars with their piglets in their herd
(Figure 2a–c). They identified the breeds as indigenous and mixed parentage of indigenous
crossed with the exotic breed and putative crossed with a wild pig. A total of 28.6%
pig rearers maintained probable breeding boar of feral origin in secrecy due to its easy
availability and high sale value (Figure 2d). The combination of farrow to finish and piglet
production systems are observed in 85.7% of the households surveyed. Only 14.3% of the
households practiced fattener production. The major rearing pattern observed in the study
area was a semi-intensive system (96.94%) (Figure 2e), followed by an extensive system
(3.57%) (Figure 2f). These systems need less capital investment, but disease incidences and
parasite infestations are high.
Biol. Life Sci. Forum 2022, 2, x 3 of 6
Figure 1. Map showing the location of surveyed household in the study area of Uttarakhand.
3.2. Pig Husbandry Practices in Uttarakhand
Households kept 2–4 adult sows and 1–3 hybrid boars with their piglets in their herd
(Figure 2a–c). They identified the breeds as indigenous and mixed parentage of
indigenous crossed with the exotic breed and putative crossed with a wild pig. A total of
28.6% pig rearers maintained probable breeding boar of feral origin in secrecy due to its
easy availability and high sale value (Figure 2d). The combination of farrow to finish and
piglet production systems are observed in 85.7% of the households surveyed. Only 14.3%
of the households practiced fattener production. The major rearing pattern observed in
the study area was a semi-intensive system (96.94%) (Figure 2e), followed by an extensive
system (3.57%) (Figure 2f). These systems need less capital investment, but disease
incidences and parasite infestations are high.
Figure 2. (a) Pig herd in Ramnagar (Nainital district of Uttarakhand) (b) Pig herd of mixed parental
origin observed in Chandrabani (Dehradun district of Uttarakhand) (c) Pig herd in Jwalapur
(Haridwar district of Uttarakhand) (d) Possible hybridized feral origin or boar piglet for sale or
mating purpose (e) Semi-intensive system of pig management with housing facility (all the pen is
made of brick with tin as a roof within the house premises) (f) Extensive system of pig management
with no housing facility.
Figure 2.
(
a
) Pig herd in Ramnagar (Nainital district of Uttarakhand) (
b
) Pig herd of mixed parental
origin observed in Chandrabani (Dehradun district of Uttarakhand) (
c
) Pig herd in Jwalapur (Harid-
war district of Uttarakhand) (
d
) Possible hybridized feral origin or boar piglet for sale or mating
purpose (
e
) Semi-intensive system of pig management with housing facility (all the pen is made of
brick with tin as a roof within the house premises) (
f
) Extensive system of pig management with no
housing facility.
3.3. Haplotype Analysis and Sequence Variability
A total of 18 mtDNA haplotypes with 34 segregating sites in 68 analyzed sequences
were observed. The haplotype (gene) diversity for the analyzed sequence were Hd = 0.749
(0.0024) and nucleotide diversity was Pi = 0.0132 (0.002). Eighteen haplotype obtained from
the Uttarakhand sample shared the haplotype with n = 998 sequences from the GenBank.
Figure 3shows the region-wise haplotype sharing with the global sequences.
The Hap_1 consists of 32 modern sequences of Uttarakhand that share its haplotype
with the domestic breed (Richengang) of Bhutan [
9
] and the Indian wild population [
10
]
from GenBank. Hap_1 has multiple connections, and by forming a star-like pattern,
suggests that this haplotype is older and is widely distributed among the domestic pigs
of Bhutan and Northern/Central India. Moreover it also shares the haplotype with the
museum sample of the Indian wild population of Kashmir and the wild and domestic
population of West Bengal [
10
]. This Haplotype is widely found in samples of Dehradun
and Nainital districts of Uttarakhand.
Hap_11 has only one sample from Uttarakhand share its haplotype with domestic pigs
from Nepal [
9
]. Hap_12 have 10 sequences, which include a sequence from the Haridwar
District of Uttarakhand and Hap_2, Hap_14, Hap_13, Hap_17 have only one sequence each
of a single area of Dehradun near river Song, and shows that these are a recently evolved
population and their carriers are still localized in its evolved areas.

Biol. Life Sci. Forum 2022,15, 19 4 of 5
Biol. Life Sci. Forum 2022, 2, x 4 of 6
3.3. Haplotype Analysis and Sequence Variability
A total of 18 mtDNA haplotypes with 34 segregating sites in 68 analyzed sequences
were observed. The haplotype (gene) diversity for the analyzed sequence were Hd = 0.749
(0.0024) and nucleotide diversity was Pi = 0.0132 (0.002). Eighteen haplotype obtained
from the Uttarakhand sample shared the haplotype with n = 998 sequences from the
GenBank. Figure 3 shows the region-wise haplotype sharing with the global sequences.
The Hap_1 consists of 32 modern sequences of Uttarakhand that share its haplotype
with the domestic breed (Richengang) of Bhutan [9] and the Indian wild population [10]
from GenBank. Hap_1 has multiple connections, and by forming a star-like pattern,
suggests that this haplotype is older and is widely distributed among the domestic pigs
of Bhutan and Northern/Central India. Moreover it also shares the haplotype with the
museum sample of the Indian wild population of Kashmir and the wild and domestic
population of West Bengal [10]. This Haplotype is widely found in samples of Dehradun
and Nainital districts of Uttarakhand.
Hap_11 has only one sample from Uttarakhand share its haplotype with domestic
pigs from Nepal [9]. Hap_12 have 10 sequences, which include a sequence from the
Haridwar District of Uttarakhand and Hap_2, Hap_14, Hap_13, Hap_17 have only one
sequence each of a single area of Dehradun near river Song , and shows that these are a
recently evolved population and their carriers are still localized in its evolved areas.
Figure 3. Median-joining haplotype network of 18 haplotypes identified in Uttarakhand sample and
its sharing with global sequences (n = 998). Circle size represents the frequency of individuals, and
color defines the region-wise populations. Small black circles represent median vectors. Mutational
steps are shown by bar on the respective branches.
Hap_9, which has two sequences from the Naintal Districts of Uttarakhand, shared
the haplotype with a museum specimen of wild pig from Nepal and India [10], and also
from wild pigs from Northern and Central India. Hap_15, which has also recently
evolved, does not share its haplotype with any sequence.
Hap_4 includes seven sequences of Uttarakhand that share its haplotype with
Bhutan’s domestic breed, Machay Madhuri, and Nepal’s domestic pig breed. Hap_3 and
Hap_6 contains only Uttarakhand sequences. Hap_7, 8, 10, 16, 18 each contain a single
sequence of Uttarakhand and are globally distributed.
Figure 3.
Median-joining haplotype network of 18 haplotypes identified in Uttarakhand sample and
its sharing with global sequences (n = 998). Circle size represents the frequency of individuals, and
color defines the region-wise populations. Small black circles represent median vectors. Mutational
steps are shown by bar on the respective branches.
Hap_9, which has two sequences from the Naintal Districts of Uttarakhand, shared
the haplotype with a museum specimen of wild pig from Nepal and India [
10
], and also
from wild pigs from Northern and Central India. Hap_15, which has also recently evolved,
does not share its haplotype with any sequence.
Hap_4 includes seven sequences of Uttarakhand that share its haplotype with Bhutan’s
domestic breed, Machay Madhuri, and Nepal’s domestic pig breed. Hap_3 and Hap_6
contains only Uttarakhand sequences. Hap_7, 8, 10, 16, 18 each contain a single sequence
of Uttarakhand and are globally distributed.
Hence the results show a possibility of maternal gene flow between India, Bhutan
and Nepal.
4. Conclusions
The findings from the small representation of pig rearers in Uttarakhand suggest that
the wild cross with domestic are included in the herd due to their easy availability, disease
resistance, meat preference, and medicinal values; hence, they come in close contact with
humans and other livestock species and these interactions create a potential threat for
disease spill over from wild pigs to humans and other livestock species. The intensity
of the risk of transmission becomes more profound with an increase in urbanization and
anthropogenic influence beyond the carrying capacity of the area’s ecological system. The
government often neglects public health policies while planning for urban development.
This neglect poses a higher risk for both zoonotic and non-zoonotic disease to the population
living near slums and informal settlements. Hence these settlements can become an
epicenter for the outbreak of infectious disease and, due to pigs roaming in these areas, the
chances of zoonotic disease will also increase. The location of the herd and its foraging
should be strictly monitored. A report of multiple outbreaks of ‘Human Trichinosis’ caused
by eating undercooked wild boar meat has been reported [
11
], hence sensitization of the
local community for avoiding the wild animal meat should be developed.
The mitochondrial diversity is high and eight haplotype are unique to Uttarakhand,
hence efforts should be made to conserve the haplotypes and classify the phenotypic
characteristics of the indigenous breed.

Biol. Life Sci. Forum 2022,15, 19 5 of 5
Funding:
This research was funded by the Department of Science and technology under the Women
Scientist Scheme-A (WOS-A) scheme with project number SR/WOS-A/LS-304/2018.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement:
Informed consent was obtained from all subjects involved in the study.
Data Availability Statement: Not applicable.
Acknowledgments:
The author thanks Director and Dean WII for their support. Surya Prakash
Sharma is thanked for helping in map preparation and field assistants Rakesh Kumar and Anil Kumar.
Conflicts of Interest: The author declares no conflict of interest.
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