Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India

AbstractSheep farming has been fundamental to many civilizations in the world and is practiced in India since antiquity. Several thousand years of adaptation to local environmental conditions and selective breeding have evolved 44 sheep breeds in India. They are paramount in terms of economic, scientific, and cultural heritage. Genetic characterization information is imperative for sustainable utilization and conservation of ovine heritage. In this study, the genetic diversity, differentiation, and structure of 11 indigenous sheep breeds from three different agro-ecological zones of India were explored with genomic microsatellite loci and mitochondrial DNA (D loop). The estimated diversity parameters indicated that populations retained high levels of genetic diversity (Na = 8.27 ± 0.17; Ho = 0.65 ± 0.01), which provides an optimistic viewpoint for their survival. However, significant inbreeding was also observed in the nine populations. Moderate genetic differentiation existed among the groups (FST = 0.129 ± 0.012), and most likely clusters existing in the dataset are seven. Phylogenetic clustering was in line with the geographical locations of sheep populations. Mitochondrial sequences revealed high haplotype diversity with the existence of maternal haplogroups A, B, and C, and signals of population expansion. Decreased genetic diversity and unique maternal lineage (C) in endangered Tibetan and Bonpala sheep breed, warrant their immediate scientific management. Overall, the quantitative data reported here on the extant variability, and genetic relationships among the Indian sheep breeds, provide critically important inputs that will be valuable for the decision-making process on their management, both for the conservation of endangered breeds, and formulation of breeding programs to check genetic erosion.

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Mitochondrial DNA D-loop sequence variability reveals high haplotype diversity and multiple maternal origins in twelve indigenous goat populations from Tanzania.

10.22541/au.161478201.16689055/v1 ◽

2021 ◽

Author(s):

Athumani Nguluma

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Haplotype Diversity ◽

Capra Hircus ◽

Maternal Origin ◽

High Genetic Diversity ◽

Ecological Zones ◽

Goat Population ◽

D Loop ◽

Indigenous Goats

The Small East African (SEA) goat (Capra hircus) breeds are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goats populations, namely Fipa (n = 44), Songwe (n = 34), Tanga (n = 33), Pwani (n = 40), Newala (n = 49), Lindi (n = 46), Gogo (n = 73), Pare (n = 67), Maasai (n = 72), Sukuma (n = 67), and Ujiji (n = 67), based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (Hd = 0.9619-0.9945) and nucleotide (π = 0.0120-0.0162) diversities were revealed from a total of 389 haplotypes. The majority of the haplotypes (h = 334) drawn from all the goat populations belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country.

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The genetic profiles and maternal origin of local sheep breeds on Java Island (Indonesia) based on complete mitochondrial DNA D-loop sequences

Veterinary World ◽

10.14202/vetworld.2020.2625-2634 ◽

2020 ◽

Vol 13 (12) ◽

pp. 2625-2634

Author(s):

Alek Ibrahim ◽

I Gede Suparta Budisatria ◽

Rini Widayanti ◽

Wayan Tunas Artama

Keyword(s):

Mitochondrial Dna ◽

Genetic Relationships ◽

Haplotype Diversity ◽

Maternal Origin ◽

Loop Analysis ◽

High Genetic Diversity ◽

Sheep Breeds ◽

Loop Region ◽

D Loop ◽

Genetic Profiles

Background and Aim: Java Island is one of the islands in Indonesia which has local sheep breeds with specific characteristics and native development geography in certain regions. This study aimed to determine the genetic profiles and maternal origin of six local sheep breeds on Java Island. Materials and Methods: This study was conducted by identifying the profiles of complete mitochondrial DNA (mtDNA) displacement loop (D-loop) region sequences on a total of 22 individual in six local sheep breeds on Java Island, including Javanese thin-tailed (JTT), Javanese Fat-Tailed (JFT), Batur (BTR), Wonosobo (WSB), Garut (GRT), and Priangan (PRG) sheep. The D-loop region was amplified using specific primers, and the polymerase chain reaction (PCR) was performed. The PCR products were purified and sequenced. Results: The mtDNA D-loop analysis identified 21 haplotypes in the analyzed 22 animals with 123 polymorphic sites (V) consisting of 60 singleton variable sites (S) and 63 parsimony informative sites (P). Within all breeds tested, the haplotype diversity, the average number of pairwise differences (K), and nucleotide diversity (Pi) were 0.99567, 25.36364, and 0.02153, respectively. The genetic distance (D) within groups and between groups was 0.001-0.006 and 0.004-0.036, respectively. The phylogeny resulted in the presence of two haplogroups (Hap), which are 5 Hap A and 16 Hap B. All JTT, JFT, BTR, and WSB breeds were in the same cluster in Hap B, whereas GRT and PRG breeds were in clusters in both Hap A and Hap B. Conclusion: The high genetic diversity in six local sheep breeds on Java Island suggests that they originated from different genetic sources. JTT sheep have closer genetic relationships to JFT, BTR, and WSB sheep, and they are close to European sheep, whereas GRT sheep have closer genetic relationships to PRG sheep. Both are closer to Asian sheep than to European sheep.

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Impacts of habitat fragmentation on genetic diversity in a tropical forest butterfly on Borneo

Journal of Tropical Ecology ◽

10.1017/s0266467407004543 ◽

2007 ◽

Vol 23 (6) ◽

pp. 623-634 ◽

Cited By ~ 21

Author(s):

Suzan Benedick ◽

Thomas A. White ◽

Jeremy B. Searle ◽

Keith C. Hamer ◽

Nazirah Mustaffa ◽

...

Keyword(s):

Genetic Diversity ◽

Time Delay ◽

Habitat Fragmentation ◽

Forest Fragmentation ◽

Haplotype Diversity ◽

Genetic Erosion ◽

Forest Sites ◽

Increased Risk ◽

Forest Remnants ◽

Mtdna Diversity

Many areas of rain forest now exist as habitat fragments, and understanding the impacts of fragmentation is important for determining the viability of populations within forest remnants. We investigated impacts of forest fragmentation on genetic diversity in the butterfly Mycalesis orseis (Satyrinae) in Sabah (Malaysian Borneo). We investigated mtDNA diversity in 90 individuals from ten forest sites typical of the sizes of forest remnants that currently exist in the region. Nucleotide diversity declined with increasing isolation of remnants, but there was no effect of remnant size or population size, and haplotype diversity was similar among sites. Thus, approximately 50 y after forest fragmentation, few changes in genetic diversity were apparent and remnants apparently supported genetically viable populations of this butterfly. Many studies have shown that responses of species to habitat fragmentation usually follow a time delay, and so we developed a Monte Carlo simulation model to investigate changes in genetic diversity over time in small remnants. Model output indicated a substantial time delay (> 100 y) between fragmentation and genetic erosion, suggesting that, in the smallest study remnants, an increased risk of extinction from reduced genetic diversity is likely in the longer term.

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Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

Archives of Polish Fisheries ◽

10.1515/aopf-2016-0010 ◽

2016 ◽

Vol 24 (2) ◽

pp. 85-97 ◽

Cited By ~ 2

Author(s):

Sylvanus A. Nwafili ◽

Tian-Xiang Gao

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Control Region ◽

Haplotype Diversity ◽

Population Expansion ◽

Mitochondrial Control Region ◽

Recent Population Expansion ◽

Base Pair Fragment ◽

Population Structures ◽

High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

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STUDY OF GENETIC DIVERSITY USING MICROSATELLITE MARKERS IN IRAQI SHEEP BREEDS

IRAQI JOURNAL OF AGRICULTURAL SCIENCES ◽

10.36103/ijas.v51i5.1146 ◽

2020 ◽

Vol 51 (5) ◽

pp. 1367-1374

Author(s):

Hadi & et al.

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Allele Frequency ◽

Genetic Relationships ◽

Allelic Frequency ◽

Dominant Allele ◽

Sheep Breeds ◽

Biotechnology Research ◽

Pcr Technology ◽

Awassi Breed

Genotypes and allele frequency values were studied to determine the genetic diversity of three microsatellite markers (BM1329, BM134 and CSSM66) in two local Iraqi sheep breeds (50 Awasi ewes (AW) and 50 Naimi ewes (NA)) and breed in one Agricultural Stations in middle of Al-Furut Iraq (Karbala Governorate). The Genetic analyses for the study were carried out at the Biotechnology Research Center / Al-Nahrain University using PCR technology to obtain alleles for the studied microsatellites. The results of this study indicate that there is a multiplicity of genotypes and alleles resulting from these markers among the members of the single breed and between the studied breeds. It was revealed that the allele frequency values showed the presence of alleles dominant on the rest of alleles produce in this sample studied, the BM1329 microsatellite of the Awassi breed produced the dominant allele frequency in 195(0.25) and 320 (0.25), While in the Naimi breed were the values of the dominant allele frequency of the195(0.22), 220(0.21) and 230(0.24), and the dominant allelic frequency of (BM134) marker in the Awassi breed was 118 and 135 and repeated (0.21 and 0.26, respectively). For CSSM66 microsatellite, the dominant allelic results and their allelic frequency values were (195 (0.20), 205 (0.23) and 220 (0.25)) for Awasi breed, whereas it was 180 (0.24), 195 (0.28) and 220 (0.22) for Nuaimi breed. These results enable us to use these markers as a means of determining the diversity and genetic relationships between individuals of a single breed as well as between breeds.

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Short Communication: Genetic diversity of scalloped hammerhead sharks (Sphyrna lewini) landed in Muncar Fishing Port, Banyuwangi

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d200430 ◽

2019 ◽

Vol 20 (4) ◽

pp. 1154-1159 ◽

Cited By ~ 1

Author(s):

FAQIH AKBAR ALGHOZALI ◽

DIAH PERMATA WIJAYANTI ◽

AGUS SABDONO

Keyword(s):

Genetic Diversity ◽

Short Communication ◽

Polymerase Chain Reaction Amplification ◽

Haplotype Diversity ◽

Population Expansion ◽

Fishing Ground ◽

Sphyrna Lewini ◽

Scalloped Hammerhead ◽

Hammerhead Sharks ◽

Longline Fisheries

Abstract. Alghozali FA, Wijayanti DP, Sabdono A. 2019. Short Communication: Genetic diversity of scalloped hammerhead sharks (Sphyrna lewini) landed in Muncar Fishing Port, Banyuwangi. Biodiversitas 20: 1154-1159. The majority of sharks caught in Indonesian fisheries were bycatch products from the tuna longline fisheries, but some regions in Indonesia fish the sharks as their main target. One of these regions is located in Muncar, Banyuwangi, which fishes the endangered Scalloped Hammerhead sharks (Sphyrna lewini) as target species. This research aimed to study the genetic diversity of the endangered Scalloped Hammerhead sharks landed in Muncar Fishing Port, Banyuwangi. Genetic analysis was done through PCR (Polymerase Chain Reaction) amplification and sequencing of the mitochondrial DNA COI (Cytochrome Oxidase subunit I) gene. Out of the 37 samples collected, 30 were successfully amplified and sequenced.The results showed moderate haplotype diversity (Hd: 0,582 ± 0,079) and low nucleotide diversity (π: 0,00392± 0,0024) with five haplotypes (h) and 26 polymorphic sites (S). Tajima’s D neutrality model values indicated a population expansion event. Two different clades were determined through phylogenetic analysis and by GenBank sequences comparison. These results provided basic information and present status of the Scalloped Hammerhead sharks population genetically within the fishing ground (Makassar Strait-Kangean Islands).

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Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta

Jurnal Biologi Indonesia ◽

10.47349/jbi/17022021/105 ◽

2021 ◽

Vol 17 (2) ◽

pp. 105-114

Author(s):

Anik Budhi Dharmayanthi ◽

Achmad Muchsinin ◽

Afriana Pulungan ◽

Moch Syamsul Arifin Zein

Keyword(s):

Genetic Diversity ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Population Expansion ◽

Bird Populations ◽

Low Genetic Diversity ◽

In Captivity ◽

D Loop ◽

Haplotype 1

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

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Molecular genetic diversity and relationship of indigenous sheep breeds of Pakistan based on nuclear microsatellite loci

Revista Veterinaria ◽

10.30972/vet.3013906 ◽

2019 ◽

Vol 30 (1) ◽

pp. 54

Author(s):

T Hussain ◽

M M. Musthafa ◽

M E. Babar ◽

M Shaheen ◽

F M. Marikar

Keyword(s):

Genetic Diversity ◽

Microsatellite Loci ◽

Molecular Genetic ◽

Sheep Breeds ◽

Indigenous Sheep ◽

Molecular Genetic Diversity ◽

Nuclear Microsatellite ◽

Relationship Of

<p>En Pakistán los recursos genéticos ovinos son abundantes, disponiéndose de varias diferentes castas extendidas en todo el país. No obstante, la diversidad molecular de las razas de ovejas es poco conocida en la región. Por ello, en el presente estudio se investigaron 16 marcadores microsatelitales de las razas indígenas Buchi y Hashtnagri, en las provincias de Pendjab y Balochistan respectivamente. Para indagar la diversidad genética se obtuvieron muestras de sangre de 25 animales de cada raza. El promedio del número de alelos en Buchi y Hashtnagri fue de 3,375±1,455 y 3,50±1,591 respectivamente. Los promedios de heterocigosis registradas fueron de 0,878±0,204 para la raza Buchi y 0,885±0,218 para Hashtnagri. Los índices de Shannon fueron 1,032±0,371 para Buchi y 1,070±0,412 para Hashtnagri, respectivamente. La estimación de los coeficientes de endogamia (FIS y FIT) mostró valores negativos, en tanto que el flujo genético (migración) fue de 10,09 y el promedio de la diferencia poblacional (FST) resultó de 2,4%. En ambas razas, el índice de información polimórfica fue 0,56, indicando el valor del marcador del tablero. Entre las ovejas Buchi y Hashtnagri, la distancia genética estándar de Nei (Ds) fue 0,0218. Según estos resultados, ambas razas mostraron considerable diversidad genética. Los datos obtenidos permiten vislumbrar una promisoria mejoría en el área de la conservación y en el diseño de las estrategias para la cría de ovejas en el futuro cercano.</p>

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Novel Insights Into the Genetic Population Connectivity of Transient Whale Sharks (Rhincodon typus) in Pacific Panama Provide Crucial Data for Conservation Efforts

Frontiers in Marine Science ◽

10.3389/fmars.2021.744109 ◽

2021 ◽

Vol 8 ◽

Author(s):

Héctor M. Guzmán ◽

Caitlin E. Beaver ◽

Edgardo Díaz-Ferguson

Keyword(s):

Genetic Diversity ◽

Gulf Of California ◽

Haplotype Diversity ◽

Population Expansion ◽

Population Connectivity ◽

Region Gene ◽

Genetic Population ◽

Regional Patterns ◽

Rhincodon Typus ◽

Whale Sharks

The whale shark (Rhincodon typus) is an endangered and highly migratory species, of which solitary individuals or aggregations are observed in oceans worldwide and for which conservation efforts are hindered by a lack of comprehensive data on genetic population connectivity. Tissue samples were collected from wandering whale sharks in Pacific Panama to determine genetic diversity, phylogeographic origin, and possible global and local connectivity patterns using a 700–800 bp fragment of the mitochondrial control region gene. Genetic diversity among samples was high, with five new haplotypes and nine polymorphic sites identified among the 15 sequences. Haplotype diversity (Hd = 0.83) and nucleotide diversity (π = 0.00516) were similar to those reported in other studies. Our sequences, in particular haplotypes PTY1 and PTY2, were similar to those previously reported in the Arabian Gulf and the Western Indian Ocean populations (a novel occurrence in the latter case). Haplotypes PTY3, PTY4, and PTY5 were similar to populations in Mexico and the Gulf of California. In contrast, the only populations to which our Panamanian sequences were genetically dissimilar were those from the Atlantic Ocean. The absence of reference sequences in GenBank from southern sites in the Eastern Tropical Pacific, such as Galapagos (Ecuador), Gorgona and Malpelo Islands (Colombia), and Coco Island (Costa Rica), reduced our capacity to genetically define regional patterns. Genetic differentiation and connectivity were also assessed using an analysis of molecular variance (AMOVA), which showed a similar population structure (five groups) to the neighbor-joining tree. Other population features based on neutrality tests, such as Tajima’s D and Fu’s Fs statistics, showed positive values for Panama of 0.79 and 1.61, respectively. Positive values of these statistics indicate a lack of evidence for population expansion among the sampled individuals. Our results agree with previous reports suggesting that whale sharks can travel over long distances and that transboundary conservation measures may be effective for species protection.

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Post-Disturbance Genetic Changes: The Impact of the 2010 Mega-Earthquake and Tsunami on Chilean Sandy Beach Fauna

Scientific Reports ◽

10.1038/s41598-019-50525-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Antonio Brante ◽

Garen Guzmán-Rendón ◽

Erwin M. Barría ◽

Marie-Laure Guillemin ◽

Iván Vera-Escalona ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Haplotype Diversity ◽

Population Expansion ◽

Adult Survival ◽

Genetic Changes ◽

Species Response ◽

Emerita Analoga ◽

Mtdna Sequence ◽

The Impact

Abstract Earthquake/tsunamis can have profound impacts on species and their genetic patterns. It is expected that the magnitude of this impact might depend on the species and the time since the disturbance occurs, nevertheless these assumptions remain mostly unexplored. Here we studied the genetic responses of the crustacean species Emerita analoga, Excirolana hirsuticauda, and Orchestoidea tuberculata to the 27F mega-earthquake/tsunami that occurred in Chile in February 2010. mtDNA sequence analyses revealed a lower haplotype diversity for E. analoga and E. hirsuticauda in impacted areas one month after the 27F, and the opposite for O. tuberculata. Three years after the 27F we observed a recovery in the genetic diversity of E. analoga and E. hirsuticauda and decrease in the genetic diversity in O. tuberculata in 2/3 of sampled areas. Emerita analoga displayed decrease of genetic differentiation and increase in gene flow explained by long-range population expansion. The other two species revealed slight increase in the number of genetic groups, little change in gene flow and no signal of population expansion associated to adult survival, rapid colonization, and capacity to burrow in the sand. Our results reveal that species response to a same disturbance event could be extremely diverse and depending on life-history traits and the magnitude of the effect.

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