Research Article: Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array

Date Published: May 31, 2019

Publisher: Public Library of Science

Author(s): Mahdi Mokhber, Mohammad Moradi Shahrbabak, Mostafa Sadeghi, Hossein Moradi Shahrbabak, Alessandra Stella, Ezequiel Nicolzzi, John L. Williams, Tzen-Yuh Chiang.


Accuracy of genome-wide association studies, and the successful implementation of genomic selection depends on the level of linkage disequilibrium (LD) across the genome and also the persistence of LD phase between populations. In the present study LD between adjacent SNPs and LD decay between SNPs was calculated in three Iranian water buffalo populations. Persistence of LD phase was evaluated across these populations and effective population size (Ne) was estimated from corrected r2 information. A set of 404 individuals from three Iranian buffalo populations were genotyped with the Axiom Buffalo Genotyping 90K Array. Average r2 and |D’| between adjacent SNP pairs across all chromosomes was 0.27 and 0.66 for AZI, 0.29 and 0.68 for KHU, and 0.32 and 0.72 for MAZ. The LD between the SNPs decreased with increasing physical distance from 100Kb to 1Mb between markers, from 0.234 to 0.018 for AZI, 0.254 to 0.034 for KHU, and 0.297 to 0.119 for MAZ, respectively. These results indicate that a density of 90K SNP is sufficient for genomic analyses relying on long range LD (e.g. GWAS and genomic selection). The persistence of LD phase decreased with increasing marker distances across all the populations, but remained above 0.8 for AZI and KHU for marker distances up to 100Kb. For multi-breed genomic evaluation, the 90K SNP panel is suitable for AZI and KHU buffalo breeds. Estimated effective population sizes for AZI, KHU and MAZ were 477, 212 and 32, respectively, for recent generations. The estimated effective population sizes indicate that the MAZ is at risk and requires careful management.

Partial Text

The water buffalo (B. bubalis) is an important livestock resource in many regions of the world, particularly in tropical and subtropical countries. Water buffalo produce milk and meat, and are used as draught animals in developing countries [1,2]. There are two types of domestic water buffalo. The river buffalo, which originated in the Indian sub-continent and are now spread widely from India to Europe. The swamp buffalo, which originated in Northern Thailand or Laos, is the most common buffalo type in Asia, from India to the Philippines. Water buffalo and cattle (Bos taurus) belong to the sub-family, Bovinae. While cattle were domesticated between 8000 and 10,000 years ago [3], domestication of river and swamp buffalo was more recent and has been estimated to have been between 5000 and 7000 years ago [2,4,5].




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