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 were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. 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.
Highlights
The accuracy of the BRR model was more than Bayes A, B, and C (r > 0.65) based on the 99 associated SNPs. the accuracy of GEBVs of body weight was less than birth weight and daily gain based on the 99 associated SNPs (Fig. 8)
We performed a GWAS for growth traits in dromedary camels using the genotypes of 96 calves of the central desert of Iran. this is the first GWAS for birth weight, daily gain, and body weight of camels using GBS
The candidate genes for Dry Matter Intake, Average Daily Gain, and Metabolic Body Weight based on the imputed 7.8 M WGS in chattels were reported: SNORA70, B3GALT1, DDR2, GPR37, SYT1, LYZL1, RGS2, F13A1, SNORA31, LCORL, DPH6, PARD3, MOS, CRB1, CUL1, CCND2, ARRDC3, PLAG1, STC2, CARD11, TMEM72, SCGB1A1, ERICH6, ARRDC3, GALNT14, PLAG1, ERGIC1, AP3S2, A1CF40
Summary
Among 256 male calves, we recorded 96 samples from 5 regions including: Bafgh (n = 41) Bahabad (n = 8), Khatam (n = 17), Mehriz (n = 8), and Ardakan (n = 22). The meta data collected for any calf included: ID number, characteristics of owner, geographical region, recording date, birth date, parental names, and body weight. The 18 calves belong to National Research and Development Station on Dromedary Camel (Bafgh), measured in 8 -times, the others were recorded 2 or 3-times including: Bafgh (n = 164), Bahabad (n = 8), Khatam (n = 26), Mehriz (n = 9), Ardakan (45). The association between the SNPs and the traits were tested using mixed linear models with PCA and kinship matrix in TASSEL software[28]. We used 3:1 size ratio of training set and validation set randomly selected from the 96 camels, which is a three-folds cross-validation, and repeated 100 times for evaluation of models by the 99 associated SNPs35,36
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