Abstract
India is home to a large and diverse buffalo population. The Murrah breed of North India is known for its milk production, and it has been used in breeding programs in several countries. Selection signature analysis yield valuable information about how the natural and artificial selective pressures have shaped the genomic landscape of modern-day livestock species. Genotype information was generated on six buffalo breeds of India, namely, Murrah, Bhadawari, Mehsana, Pandharpuri, Surti, and Toda using ddRAD sequencing protocol. Initially, the genotypes were used to carry out population diversity and structure analysis among the six breeds, followed by pair-wise comparisons of Murrah with the other five breeds through XP-EHH and F ST methodologies to identify regions under selection in Murrah. Admixture results showed significant levels of Murrah inheritance in all the breeds except Pandharpuri. The selection signature analysis revealed six regions in Murrah, which were identified in more than one pair-wise comparison through both XP-EHH and F ST analyses. The significant regions overlapped with QTLs for milk production, immunity, and body development traits. Genes present in these regions included SLC37A1, PDE9A, PPBP, CXCL6, RASSF6, AFM, AFP, ALB, ANKRD17, CNTNAP2, GPC5, MYLK3, and GPT2. These genes emerged as candidates for future polymorphism studies of adaptability and performance traits in buffaloes. The results also suggested ddRAD sequencing as a useful cost-effective alternative for whole-genome sequencing to carry out diversity analysis and discover selection signatures in Indian buffalo breeds.
Highlights
Water buffalo is considered as an important livestock resource in tropical and sub-tropical countries due to its high milk production ability along with adaptability to hot and humid environment, and high feed conversion efficiency (Kumar et al, 2019)
As the Murrah breed is mainly found in the northern part of India, the random samples were collected from three institutional farms of the area, i.e., the Livestock Research Station (LRS) ICAR-IVRI situated in Izatnagar, Bareilly (Uttar Pradesh), the Buffalo Farm at livestock research station of GBPUA and T, Pantnagar (Uttarakhand), and the Livestock Farm, GADVASU Ludhiana
Total 397.8 million paired-end reads of 150bp length were obtained for the 96 buffalo breeds, averaging 4.14 million reads per sample
Summary
Water buffalo is considered as an important livestock resource in tropical and sub-tropical countries due to its high milk production ability along with adaptability to hot and humid environment, and high feed conversion efficiency (Kumar et al, 2019). Buffaloes are the major contributors of milk production in India accounting for 49.2% of 187.7 million tons of total milk production (DAHD&F, 2018). India possesses a remarkably large and diverse buffalo population with 109.85 million buffaloes and 17 registered breeds (DAHD&F, 2018; NBAGR Karnal, 2021). Murrah is the most important buffalo breed of India, constituting about 44.3% of the total buffalo population of the country. The main breeding area of this breed is the northern states of India, namely Punjab, Haryana, and Western Uttar Pradesh. Due to its high milk potential in varied
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