REGULAR ARTICLES Single nucleotide polymorphisms at heat shock protein 90 gene and their association with thermo-tolerance potential in selected indigenous Nigerian cattle Gbolabo O. Onasanya 1,2,3,4 & George M. Msalya 3,5 & Aranganoor K. Thiruvenkadan 3 & Chirukandoth Sreekumar 4 & Gopalan K. Tirumurugaan 6 & Timothy M. Sanni 2 & John S. Decampos 7 & Samuel A. Amusan 8 & Olajide Olowofeso 2 & Adeboye O. Fafiolu 9 & Moses Okpeku 10 & Abdulmojeed Yakubu 11 & Christian O. Ikeobi 2 Received: 12 September 2019 /Accepted: 17 January 2020 # Springer Nature B.V. 2020 Abstract Heat shock protein (HSP) 90 gene provides protection and adaptation to thermal assault and certain polymorphisms have been associated to heat tolerance in humans and animals. Single nucleotide polymorphisms (SNPs) of HSP 90 gene were used to evaluate the scientific basis of heat tolerance in four zebu breeds of Nigeria. The DNA was extracted from skin tissue of 90 adult bulls representing White Fulani (WF), Sokoto Gudali (SG), Red Bororo (RB), and Ambala (AM). The SNPs were determined in DNAs using PCR, sequencing, and visualization and bio-editing by chromatogram in SeqMan Ngen tool. Subsequently, respective genotypes were constructed and genotypic and allelic frequencies were computed. Also, body parameters related to heat stress (HS) including body temperature (BT), rectal temperature (RT), and respira- tory rates (RR) were taken for each animal before biological sampling and heat tolerance coefficient (HTC) was calculated. We detected four SNPs distinct/specific for each breed as follows: change from thymine (T) to guanine (G) at position 116 (T116G) in RB, G to cytosine (C) at 220 (G220C) in SG, G to adenine (A) at two positions, 346 (G346A) and 390 (G390A) in AM and WF, respectively. Heterozygous SNPs showed significantly lower values (P <0.0001) for BT, RT, RR, and HTC than homozygous genotypes at all positions. We hypothesize that animals with heterozygous SNPs in exon 3 of HSP 90 may be tolerant to HS. These SNPs can be used as bio-markers for screening large populations of cattle for tolerance to hot tropical conditions in Nigeria and other sub-humid places. Keywords Heat stress . Insertion-deletion . SNP variants . Transversion . Zebu * George M. Msalya msalya@sua.ac.tz 1 Department of Animal Science, Federal University Dutse, Dutse, Nigeria 2 Deparment of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria 3 Mecheri Sheep Research Station, Pottaneri, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India 4 Biotechnology Center, Postgraduate Research Institute in Animal Sciences, Kattupakkum, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India 5 Department of Animal, Aquaculture and Range Sciences (DAARS), Sokoine University of Agriculture (SUA), PO Box 3004, Morogoro, Tanzania 6 Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India 7 Department of Animal Production, University of Ilorin, Ilorin, Kwara State, Nigeria 8 Department of Animal production, Federal College of Animal Health and Production Technology, Moor Plantation, Ibadan, Nigeria 9 Department of Animal Nutrition, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria 10 Department of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westvile Campus, Durban, South Africa 11 Department of Animal Science, Faculty of Agriculture, Nasarawa State University, Keffi, Shabu-Lafia Campus, Lafia, Nigeria Tropical Animal Health and Production https://doi.org/10.1007/s11250-020-02222-9