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Riverine buffaloes are major livestock species contributing greatly to the dairy sector of our country. Till date, no
suitable reference genes are available to normalize the transcriptional data across tissues of riverine buffaloes. Also the
expression profiling of alpha1 sodium-potassium adenosine triphosphatase (ATP1A1) gene, an important candidate for its
key role in adaptation and heat tolerance is not known across various tissues of riverine buffaloes. In the present study, a
panel of 10 reference genes (GAPDH, ACTB, UXT, RPS15, RPL4, RPS9, RPS23, HMBS, �²2M and EEF1A1) were evaluated
using three different algorithms, geNorm, NormFinder and BestKeeper to identify most stable reference in tissue samples
(mammary gland, kidney, spleen, liver, heart, intestine, ovary, lung, muscle, brain and fat). The M-value given by geNorm
ranged from 0.9797 (RPS9 and UXT) to 1.7362 (RPS15). From the most stable to the least stable, genes were ranked as: UXT/
RPS9>RPL4>RPS23>EEF1A1>B-ACTIN>HMBS>GAPDH>B2M>RPS15. NormFinder analysis ranked the reference genes
according to the stability value as: UXT>RPS23>RPL4>RPS9>EEF1A1>HMBS>�²-ACTIN>�²2M>GAPDH>RPS15. Based
on the crossing point SD value and range of fold change expression, BestKeeper analysis classified the genes from most to
least stable as: RPS9> RPS23/UXT>RPL4>GAPDH>EEF1A1>�²-ACTIN>HMBS>�²2M>RPS15. Our data identified RPS23,
RPS9, RPL4 and UXT gene to be the most stable and appropriate reference genes that could be utilized for normalization of
transcriptional data in various tissues of buffalo. Our data showed expression of ATP1A1 in all the tissues though expression
level varied in the following order: Kidney>heart>brain>lung>ovary>liver>fat>mammary glands>intestine>spleen> muscle.
Relative expression of mRNA ATP1A1 in kidney was 4 folds higher expression thanin muscles. Hence the present study
provides panel of stably expressed reference genes that can be utilized for functional studies in riverine buffaloes. In future
such study will pave way to study functional aspects of buffalo specific genes including ATP1A1 that will enrich the bubaline
genome.