Genome-Wide Association Study of Body Weight Traits in Chinese Fine-Wool Sheep

Lu, Zengkui; Yuan, Yongna; Yuan, Chao; Liu, Jianbin; Chen, Zhiqiang; Niu, Chune; Sun, Xiaoping; Zhu, Shijia; Zhao, Hongchang; Guo, Tingting; Yang, Bo‐Yi

doi:10.3390/ani10010170

Cited by 43 publications

(50 citation statements)

References 52 publications

(45 reference statements)

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“…The QTL regions and the genes: ADAMTSL3, CAPN2, CAPN2, FABP6, ZEB2 were detected using GWAS in Colombian Brahman cattle that in uencing growth and weight traits 37 . Lu et al 11 (2020) reported SLCO2A1, LY6K, RALYL, AADACL3, C17H4orf45, BICC1, SHROOM2 as candidate genes for birth weight in Chinese Fine-Wool Sheep 11 . 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, A1CF 38 .…”

Section: Discussionmentioning

confidence: 99%

“…A number of 28 SNPs were found to be associated with birth weight, daily gain, and body weight of dromedaries (p value < 0.001) ( Table 4). For birth weight, 12 correlated SNPs (p value < 0.001) were detected on the chromosomes 7,8,9,11,19, and 34 were annotated to 9 genes (Table 4). For daily gain, 7 correlated SNPs (p value < 0.001) on the chromosomes 10, 16, 12, 19, and 14, were annotated to 11 genes (Table 4).…”

Section: Genome Wide Association Studymentioning

confidence: 99%

“…The availability of reference genome assemblies coupled with GBS enables us to explore in greater detail of dromedary populations and to identify genetic associations with different phenotypic traits 10 . Genome-wide association studies (GWAS) are used to screen the whole genome for target genes that correlate with phenotypic traits, using SNPs and an important method for identifying candidate genes for important economic traits in livestock 11 . GWAS have a greater capability than QTL mapping to detect causal SNPs in a smaller genetic range 12 .…”

Section: Introductionmentioning

confidence: 99%

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

Sani

Harofte

Banabazi

et al. 2020

Preprint

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Genome Wide Association Studymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Sani

Harofte

Banabazi

et al. 2020

Preprint

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“…Human pathologies in this gene lead to mucopolysaccharidosis type I, which presents a global phenotype that includes coarse hair (Scott et al ., 1995; Kloska et al ., 2005). Furthermore, an alternative allele of GLIS1 , an enhancer of pluripotency markers (Maekawa et al ., 2011), and the reference allele of AADACL3 , which is associated with fat deposition in Chinese sheep breeds (Lu et al ., 2020), were found in the regions under selection with support from F ST . The reference allele of GPR179 , highlighted by H1 / H2 statistics, which is linked to genetic blindness, was also found under selection in Tuva sheep (Audo et al ., 2012).…”

Section: Figurementioning

confidence: 92%

Resequencing and signatures of selection scan in two Siberian native sheep breeds point to candidate genetic variants for adaptation and economically important traits

et al. 2020

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SummaryRussian sheep breeds represent an important economic asset by providing meat and wool, whilst being adapted to extreme climates. By resequencing two Russian breeds from Siberia: Tuva (n = 20) and Baikal (n = 20); and comparing them with a European (UK) sheep outgroup (n = 14), 41 million variants were called, and signatures of selection were identified. High‐frequency missense mutations on top of selection peaks were found in genes related to immunity (LOC101109746) in the Baikal breed and wool traits (IDUA), cell differentiation (GLIS1) and fat deposition (AADACL3) in the Tuva breed. In addition, genes found under selection owing to haplotype frequency changes were related to wool traits (DSC2), parasite resistance (CLCA1), insulin receptor pathway (SOCS6) and DNA repair (DDB2) in the Baikal breed, and vision (GPR179) in the Tuva breed. Our results present candidate genes and SNPs for future selection programmes, which are necessary to maintain and increase socioeconomic gain from Siberian breeds.

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Section: Introductionmentioning

confidence: 99%

Genomic prediction for growth using a low-density SNP panel in dromedary camels

Sani

Harofte

Banabazi

et al. 2021

Sci Rep

View full text Add to dashboard Cite

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.

show abstract

Genome-Wide Association Study of Body Weight Traits in Chinese Fine-Wool Sheep

Cited by 43 publications

References 52 publications

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

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

Resequencing and signatures of selection scan in two Siberian native sheep breeds point to candidate genetic variants for adaptation and economically important traits

Genomic prediction for growth using a low-density SNP panel in dromedary camels

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