Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

Ünal, Emel Özkan; Işık, Raziye; Şen, Ayşe; Kuş, Elif Geyik; Soysal, M. I.

doi:10.3390/ani11041067

Cited by 6 publications

(7 citation statements)

References 58 publications

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“…Highly variable SSR markers extracted in the present study could be utilized to find genetic diversity ( Barker et al, 1997 ; Zhang et al, 2020 ). The SSR markers from different breeds could be used to find polymorphic SSRs ( Moore et al, 1995 ) and their utilization in the study of genetic diversity of respective breeds ( Moioli et al, 2001 ; Merdan et al, 2019 ; Vohra et al, 2021 ; Ünal et al, 2021 ). We also extracted ∼270000 polymorphic SSRs in the Mediterranean buffalo breed with respect to Murrah, Bangladesh, Jaffrabadi, and Egyptian breeds.…”

Section: Resultsmentioning

confidence: 99%

Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

et al. 2022

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Water buffalo (Bubalus bubalis), belonging to the Bovidae family, is an economically important animal as it is the major source of milk, meat, and drought in numerous countries. It is mainly distributed in tropical and subtropical regions with a global population of approximately 202 million. The advent of low cost and rapid sequencing technologies has opened a new vista for global buffalo researchers. In this study, we utilized the genomic data of five commercially important buffalo breeds, distributed globally, namely, Mediterranean, Egyptian, Bangladesh, Jaffrarabadi, and Murrah. Since there is no whole-genome sequence analysis of these five distinct buffalo breeds, which represent a highly diverse ecosystem, we made an attempt for the same. We report the first comprehensive, holistic, and user-friendly web genomic resource of buffalo (BuffGR) accessible at http://backlin.cabgrid.res.in/buffgr/, that catalogues 6028881 SNPs and 613403 InDels extracted from a set of 31 buffalo tissues. We found a total of 7727122 SNPs and 634124 InDels distributed in four breeds of buffalo (Murrah, Bangladesh, Jaffarabadi, and Egyptian) with reference to the Mediterranean breed. It also houses 4504691 SSR markers from all the breeds along with 1458 unique circRNAs, 37712 lncRNAs, and 938 miRNAs. This comprehensive web resource can be widely used by buffalo researchers across the globe for use of markers in marker trait association, genetic diversity among the different breeds of buffalo, use of ncRNAs as regulatory molecules, post-transcriptional regulations, and role in various diseases/stresses. These SNPs and InDelscan also be used as biomarkers to address adulteration and traceability. This resource can also be useful in buffalo improvement programs and disease/breed management.

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Section: Resultsmentioning

confidence: 99%

Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

et al. 2022

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“…We found a high level of genetic diversity in Thai swamp buffaloes based on a relatively high mean Fst (0.23) using TLR2 gene SNP data from 29 loci. Diversity declines have been reported in 17 populations of Turkey’s river buffaloes, with an estimated low Fst of 0.032 based on a study using 20 microsatellite markers [ 1 ]. An Fst of 0.13 has been reported in African buffaloes, a level of difference between buffalo populations that need to be controlled [ 36 ].…”

Section: Discussionmentioning

confidence: 99%

“…Genetically diverse populations are easy to select and improve through breeding. Improvement through breeding is essential to clearly understand the diversity of genetic resources to formulate breeding plans and for genetic conservation [ 1 ]. Generally, Thai swamp buffaloes are raised in rural areas of Thailand.…”

Section: Introductionmentioning

confidence: 99%

An Analysis of DNA Sequence Polymorphism in the Swamp Buffalo Toll-like Receptor (TLR2) Gene

Kenchaiwong

Pongthaisong

Kananit

et al. 2023

Animals

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Toll-like receptors (TLRs) are transmembrane proteins important for directing immune responses. Their primary role is to recognize pathogens based on single-nucleotide polymorphism (SNP) characteristics. TLR2 is categorized as a pattern recognition receptor (PRR) that is important for the recognition of pathogens. Nucleotide variation in the coding region determines the conformation of the TLR protein, affecting its protein domain efficiency. This study aimed to identify SNPs in the coding region of TLR2 to enhance available genetic tools for improving health and production in swamp buffalo. A total of 50 buffaloes were randomly sampled from the northeastern part of Thailand for genomic DNA extraction and sequencing. Nucleotide sequences were aligned and compared with cattle and river buffalo based on the database. The results showed, there were 29 SNP locations in swamp buffalo and 14 different locations in both cattle and buffaloes. Haplotype analysis revealed that 27 haplotypes occurred. Swamp buffalo were identified from 13 SNPs based on biallelic analysis, which found eight synonymous and five nonsynonymous SNPs. Nucleotide diversity (π) was 0.16, indicating genetic diversity. Genetic diversity (haplotype diversity; HD) was high at 0.99 ± 0.04. This indicates a high probability that the two sample haplotypes are different. The π and HD values are important indicators of the genetic diversity of the swamp buffalo population. In summary, the Thai swamp buffalo population detected a polymorphism of the coding region of the TRL2 gene. Therefore, further, in-depth study of the relationship between these genes in the immune system and disease resistance should be recommended.

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“…Observed heterozygosity in Kuantan cattle was lower than expected heterozygosity. Several factors can affect this condition, such as a higher rate of inbreeding due to the limited number of bulls (Unal et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity Analysis and Determination of Specific Alleles of Kuantan Cattle Using Microsatellite Markers

Misrianti

Wijaya

Sumantri

et al. 2022

Trop. Anim. Sci. J.

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Kuantan cattle have an important role in Riau Province, Indonesia. Identification of the genetic diversity of these cattle is important to get the basic information for breeding and conservation strategies. The aim of this research was to identify the genetic diversity of Kuantan cattle using microsatellite markers. A total of thirty-nine DNA samples from three breeds were used in this study. The polymerase chain reaction was conducted using four labeled primers of microsatellite (INRA035, ILSTS06, HEL9 and ETH225). The data were analyzed using GenAlEx 6.41, Cervus 3.0, POPTREE, and STRUCTURE Software. A total of thirty-two alleles were found from microsatellite loci. Two alleles in INRA035 locus 112 and 118 occurred as specific allele candidates for Kuantan cattle. The mean of observed heterozygosity value of the Kuantan-2 population (0.602) was higher than Kuantan-1 (0.471) but lower than Madura (0.688) and Pesisir cattle (0.625). PIC value was higher in HEL9 loci. The dendrogram showed that Kuantan cattle existed at different clusters with Pesisir and Madura cattle. This finding indicated that microsatellite markers successfully distinguished clusters of the cattle and could serve as information for conducting conservation and breeding program.

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Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

Cited by 6 publications

References 58 publications

Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

An Analysis of DNA Sequence Polymorphism in the Swamp Buffalo Toll-like Receptor (TLR2) Gene

Genetic Diversity Analysis and Determination of Specific Alleles of Kuantan Cattle Using Microsatellite Markers

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