Genomic Prediction for Growth Using Low-Density SNP Panel in Dromedary Camels

Abstract

For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs located in 36 candidate genes were associated with birth weight, daily gain, and body weight (p-value < 0.001). The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.

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

“…The current work builds on the study by Bitaraf Sani et al [12] who reported the results of a GWAS on 96 dromedaries of several breeds in Iran. When the results of the Bitaraf Sani et al paper and the current study are compared, it was noted that a number of SNP associations within a ± 1 Mb window were in common, notably on chromosomes 7, 11, 18, 25, 31 and 33 (see S2 Table 2).…”

“…Guo et al [11] published a GWAS on haematological traits in the Bactrian camel in China. Recently, Bitaraf Sani et al [12] presented a GWAS for an Iranian dromedary population for birth weight and average growth. However, there is no study, that the authors are aware of, in the dromedary camel, that undertake a GWAS across a range of weight-for-age traits.…”

“…The PDF file 'Supporting Table2' contains a list of SNP associations mapped in the current study with SNPs that were within 1 Mb of those mapped in the study on Iranian breeds of dromedary by Bitaraf Sani et al[12].…”