High-throughput genotype-based population structure analysis of selected buffalo breeds
| Autor: | Dharamshibhai N. Rank, Dhruv Bhatia, A Sudhakar, Prakash B Thakor, Ankit T. Hinsu, Tejas M. Shah, Chaitanya G. Joshi, Nilesh Nayee |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Veterinary medicine Linkage disequilibrium Single-nucleotide polymorphism Quantitative trait locus Biology 03 medical and health sciences Indian buffalo Genetic variability General Veterinary affymetrix 0402 animal and dairy science Animal Genetics and Genomics 04 agricultural and veterinary sciences single-nucleotide polymorphism 040201 dairy & animal science Breed SNP genotyping 030104 developmental biology Genetic distance Genetic structure quantitative trait loci AcademicSubjects/SCI00960 admixture Animal Science and Zoology linkage disequilibrium |
| Zdroj: | Translational Animal Science |
| ISSN: | 2573-2102 |
| Popis: | India is considered as the home tract of some of the best buffalo breeds. However, the genetic structure of the Indian river buffalo is poorly understood. Hence, there is a need to characterize the populations and understand the genetic structure of various buffalo breeds for selection and to design breeding strategies. In this study, we have analyzed genetic variability and population structure of seven buffalo breeds from their respective geographical regions using Axiom Buffalo Genotyping Array. Diversity, as measured by expected heterozygosity, ranged from 0.364 in Surti to 0.384 in Murrah breed, and pair-wise FST values revealed the lowest genetic distance between Murrah and Nili-Ravi (0.0022), while the highest between Surti and Pandharpuri (0.030). Principal component analysis and structure analysis unveiled the differentiation of Surti, Pandharpuri, and Jaffarabadi in first two principal components and at K = 4, respectively, while remaining breeds were grouped together as a separate single cluster and admixed. Murrah and Mehsana showed early linkage disequilibrium (LD) decay, while Surti breed showed late decay. In LD blocks to quantitative trait locis (QTLs) concordance analysis, 4.65% of concordance was observed with 873 LD blocks overlapped with 2,330 QTLs. Overall, total 4,090 markers were identified from all LD blocks for six types of traits. Results of this study indicated that these single-nucleotide polymorphism (SNP) markers could differentiate phenotypically distinct breeds like Surti, Pandharpuri, and Jaffarabadi but not others. So, there is a need to develop SNP chip based on SNP markers identified by sequence information of local breeds. |
| Databáze: | OpenAIRE |
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