Genome wide association study for growth in Pakistani dromedary camels using genotyping-by-sequencing

Sabahat, Sajida; Nadeem, Asif; Brauning, Rudiger; Thomson, Peter C.; Khatkar, Mehar Singh

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Article

https://doi.org/10.5713/ab.22.0181 [Accepted] Published online November 14, 2022.

Genome wide association study for growth in Pakistani dromedary camels using genotyping-by-sequencing

Sajida Sabahat^1,2

, Asif Nadeem^1,3

, Rudiger Brauning⁴

, Peter C. Thomson^1,2

, Mehar Singh Khatkar^5,*

¹Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani (Outfall) Road, Lahore 54000, Pakistan
²The University of Sydney, School of Life and Environmental Sciences, 425 Werombi Road, Camden NSW 2570, Australia
³Department of Biotechnology, Virtual University of Pakistan, Lahore 54000, Pakistan
⁴AgResearch, Invermay Agricultural Centre, 176 Puddle Alley, Mosgiel 9092, New Zealand
⁵The University of Sydney, Sydney School of Veterinary Science, University of Sydney, 425 Werombi Road, Camden NSW 2570, Australia

Correspondence: Mehar Singh Khatkar, Tel: +61-2-9351 1687, Fax: +61-2-9351 1687, Email: mehar.khatkar@sydney.edu.au

Received: 2 May 2022 • Revised: 2 September 2022 • Accepted: 28 October 2022

Abstract

Objective
Growth performance and growth-related traits have a crucial role in livestock due to their inﬂuence on productivity. This genome-wide association study (GWAS) in Pakistani dromedary camels was conducted to identify SNPs associated with growth at specific camel ages, and for selected SNPs, to investigate in detail how their effects change with increasing camel age. This is the first GWAS conducted on dromedary camels in this region.
Methods
Two Pakistani breeds, Marecha and Lassi, were selected for this study. A genotyping-by-sequencing method was used and a total of 65,644 SNPs were identified. For GWAS, weight records data with several body weight traits, namely, birthweight, weaning weight, and weights of camels at 1, 2, 4 and 6 years of age were analysed by using model-based growth curve analysis. Age-specific weight data were analysed with a linear mixed model that included ﬁxed effects of SNP genotype as well as sex.
Results
Based on the q-value method for false discovery control, for Marecha camels, five SNPs at q < 0.01 and 96 at q < 0.05 were signiﬁcantly associated with the weight traits considered, while three (q < 0.01) and seven (q < 0.05) SNP associations were identified for Lassi camels. Several candidate genes harbouring these SNP were discovered.
Conclusion
These results will help to better understand the genetic architecture of growth including how these genes are expressed at different phases of their life. This will serve to lay the foundations for applied breeding programs of camels by allowing the genetic selection of superior animals to serve as future breeding candidates.

Keywords: Dromedary; Growth; GWAS; Lassi; Marecha