Conservation & local programs

Genome-wide Analysis of Runs of Homozygosity in six Indian Buffalo Breeds

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Abstract

Genomic analyses provide a powerful framework for quantifying autozygosity, inbreeding, and population structure in livestock, particularly in populations with incomplete pedigree records. Runs of homozygosity (ROH), defined as continuous homozygous segments resulting from identity-by-descent, enable the dissection of recent and historical inbreeding events. Indian water buffalo (Bubalus bubalis) represent a major livestock resource for dairy production and draught power, yet genome-wide characterizations of autozygosity across indigenous breeds remain limited. This study aimed to (i) characterize the genomic distribution and length-class patterns of ROH in six Indian buffalo breeds, (ii) estimate genomic inbreeding coefficients (FROH), and (iii) evaluate genomic relationships within and between breeds. A uniformly processed SNP dataset was used for analysis. The data were generated using the MAHISHCHIP microarray developed by the NATIONAL Dairy Development Board (NDDB), India. After quality control, 54,909 autosomal SNPs were retained, providing sufficient marker density for ROH detection and genomic inbreeding estimation. ROH were identified using standard criteria (minimum length 1 Mb and ≥35 consecutive SNPs), and individual-level metrics including ROH count and total length were computed. Genomic inbreeding was estimated using FROH and partitioned into ROH length classes (1-4, 4-8, 8-16, and ≥16 Mb), with ROH >4 Mb reflecting recent-to-intermediate inbreeding. Genomic relationships were assessed using the genomic relationship matrix. A total of 3,429 animals representing Jafarabadi (1,512), Banni (432), Nili-Ravi (408), Pandharpuri (527), Surti (362), and Toda (188) were analyzed, yielding 39,124 ROH segments. Mean genomic inbreeding across breeds was FROH = 0.024, with FROH > 4 Mb accounting for ~68% of total autozygosity, indicating a substantial contribution from recent-to-intermediate inbreeding. ROH burden varied across breeds, with higher ROH counts and total ROH length observed in Toda and lower values in Nili-Ravi and Jafarabadi. Mean ROH length was highest in Surti, which also harbored the longest ROH (130.95 Mb) on chromosome 2. ROH were non-uniformly distributed across the genome, with chromosomes 2, 3, 5, 7, and 12 showing consistently elevated ROH density, suggestive of selection or historical drift. Breed-specific ROH length profiles indicated contrasting demographic histories, with Surti and Toda enriched for long ROH ( >16 Mb), Pandharpuri dominated by intermediate ROH (4-16 Mb), and Jafarabadi and Nili-Ravi showing an excess of short ROH (1-4 Mb). GRM-based estimates supported these patterns, revealing highest within-breed relatedness in Toda and lowest in Jafarabadi and Nili-Ravi. Together, these results provide the first large-scale ROH and length-specific FROH ( >4 Mb) landscape for Indian buffalo breeds, establishing a genomic baseline for monitoring recent inbreeding conserving genetic diversity, and guiding sustainable genomic breeding and conservation strategies in indigenous buffalo populations.

Keywords: 2026

How to Cite:

Mahajan, A., Nayee, N., Gupta, R., Gajjar, S., Sudhakar, A., Kesharwani, A. & Trivedi, K., (2026) “Genome-wide Analysis of Runs of Homozygosity in six Indian Buffalo Breeds”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286810. doi: https://doi.org/10.31274/wcgalp.24129

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