A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheep

Smith, Wendy; Li, Yutao; Ingham, Aaron; Collis, E.; McWilliam, Sean; Dixon, Tom; Norris, Belinda J.; Mortimer, SI; Moore, Robert J.; Reverter, Antônio

doi:10.1186/1746-6148-6-27

Cited by 27 publications

(30 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…During the past decade there has been a dramatic increase in our knowledge on the molecular control of fiber initiation and development in mice and humans (Botchkarev and Paus, 2003;Schmidt-Ullrich and Paus, 2005;Bostjancic and Glavac, 2008;Wang et al, 2012;Cadau et al, 2013). Gene expression profiles of sheepskin have also been generated by the sequencing of ESTs and cDNA microarray (Adelson et al, 2004;Norris et al, 2005;Smith et al, 2010;Burgess et al, 2012). However, molecular regulation of these developmental processes has been hampered by the paucity of information on the sheep genome and skin transcriptome (Jager et al, 2011) However, comparative analyses of gene expression patterns in skin suggest that the molecular regulation of the basic mechanisms of follicle initiation and development and fiber production are similar in most mammals.…”

Section: Discussionmentioning

confidence: 99%

“…Gene expression profiles of sheepskin have also been generated by sequencing of ESTs and cDNA microarray (Adelson et al, 2004;Norris et al, 2005;Smith et al, 2010;Burgess et al, 2012). However, hybridization-based microarray technology is restricted to known sequences, which are unable to detect new transcripts.…”

Section: Discussionmentioning

confidence: 99%

“…The pathways or maps with the highest representation were metabolic pathways (1977 unigenes, 11.56%, ko01100), focal adhesion (966 unigenes, 5.65%, ko04510), and regulation of the actin cytoskeleton (840 unigenes, 4.91%, ko04810). Signaling pathways related to hair follicle development included, for example, the hedgehog signaling, insulin signaling, Jak-STAT signaling, MAPK signaling, melanogenesis, notch signaling, TGF-beta signaling, Toll-like receptor signaling, VEGF signaling, and Wnt signaling pathways (Botchkarev and Paus, 2003;Adelson et al, 2004;Norris et al, 2005;Schmidt-Ullrich and Paus, 2005;Bostjancic and Glavac, 2008;Smith et al, 2010;Penagaricano et al, 2012;Wang et al, 2012) (Table 5). DEGs = differentially expressed genes; Jak-STAT = Janus kinase/signal transducers and activators of transcription; MAPK = mitogen-activated protein kinase; PPAR = peroxisome proliferator-activated receptor; VEGF = vascular endothelial growth factor; Wnt = wingless.…”

Section: Functional Annotation Of Sheepskin Transcriptomementioning

confidence: 99%

“…In sheep, wool follicle induction and morphogenesis have been characterized in a number of studies (McCloghry et al, 1992;Bond et al, 1994;Hynd et al, 1999). Gene expression profiles of sheepskin have also been generated by sequencing expressed sequence tages (ESTs) and complementary DNA (cDNA) microarray (Adelson et al, 2004;Norris et al, 2005;Smith et al, 2010;Burgess et al, 2012;Peñagaricano et al, 2012). However, molecular regulation of these developmental processes has been hampered by the paucity of information on the sheep genome and skin transcriptome (Jager et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

“…In 2009, total wool imports into China reached 327 kt, accounting for 33% of the world's output (Liu et al, 2011). Therefore, there is an urgent need to improve the quantity and quality of wool by researching the genetics, endocrinology, and ectoparasitic diseases of sheep (Smith et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries)

Yuan¹,

Liu²,

Yang³

et al. 2015

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. Wool is produced via synthetic processes of wool follicles, which are embedded in the skin of sheep. The development of new-generation sequencing and RNA sequencing provides new approaches that may elucidate the molecular regulation mechanism of wool follicle development and facilitate enhanced selection for wool traits through gene-assisted selection or targeted gene manipulation. We performed de novo transcriptome sequencing of skin using the Illumina Hiseq 2000 sequencing system in sheep (Ovis aries). Transcriptome de novo assembly was carried out via short-read assembly programs, including SOAPdenovo and ESTScan. The protein function, clusters of orthologous group function, gene ontology function, metabolic pathway analysis, and protein coding region prediction of unigenes were annotated by BLASTx, BLAST2GO, and ESTScan. More than 26,266,670 clean reads were collected and assembled into 79,741 unigene sequences, with a final assembly length of 35,447,962 nucleotides. A total of 22,164 unigenes were annotated, accounting for Y.J. Yue et al. 1372©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (1): 1371-1384 (2015) 36.27% of the total number of unigenes, which were divided into 25 classes belonging to 218 signaling pathways. Among them, there were 17 signal paths related to hair follicle development. Based on mass sequencing data of sheepskin obtained by RNA-Seq, many unigenes were identified and annotated, which provides an excellent platform for future sheep genetic and functional genomic research. The data could be used for improving wool quality and as a model for human hair follicle development or disease prevention.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Functional Annotation Of Sheepskin Transcriptomementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries)

Yuan¹,

Liu²,

Yang³

et al. 2015

Genet. Mol. Res.

View full text Add to dashboard Cite

show abstract

A Novel Missense SNP in the Fatty Acid-Binding Protein 4 (FABP4) Gene is Associated with Growth Traits in Karakul and Awassi Sheep

Alwan,

Aljubouri,

Al-Shuhaib

2023

Biochem Genet

View full text Add to dashboard Cite

Allelic variation in ovine fatty acid-binding protein (FABP4) gene

et al. 2012

View full text Add to dashboard Cite

The fatty acid-binding protein 4 (FABP4) plays a role in lipid metabolism and has been implicated in intra-cellular lipid transport. While FABP4 variation has been reported in some species, variation in the coding sequence has not been reported in sheep. In this study two regions of ovine FABP4 were analysed using PCR-SSCP and sequencing. Five different PCR-SSCP patterns, representing five specific sequences (A ( 1 )-E ( 1 )) were detected in region 1 (exon 2-intron 2) with sequence analysis revealing three nucleotide substitutions and one deletion in the intron. In region 2 (exon 3-intron 3), four different PCR-SSCP patterns (A ( 2 )-D ( 2 )) were observed and four nucleotide substitutions were revealed. In total, fourteen haplotypes through both regions were defined. There was a difference (P < 0.001) in allele frequencies between two selection lines of Coopworth sheep that have been bred over many generations to be lean or fat. In region 1, A ( 1 ) and B ( 1 ) were most common (at a frequency of 50 and 30 % respectively) in the fat line, whereas these two variants were absent or rare in the lean line in which C ( 1 ) predominated (89 %). In region 2, C ( 2 ) was the most common variant (59 %) in the lean line but was absent in the fat line, whereas B ( 2 ) was predominant (83 %) in the fat line but was rare (3 %) in the lean line. These results indicate that ovine FABP4 is polymorphic and suggest further analysis is required to see if the variation detected affects fat deposition in sheep.

show abstract

A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheep

Cited by 27 publications

References 37 publications

De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries)

De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries)

A Novel Missense SNP in the Fatty Acid-Binding Protein 4 (FABP4) Gene is Associated with Growth Traits in Karakul and Awassi Sheep

Allelic variation in ovine fatty acid-binding protein (FABP4) gene

Contact Info

Product

Resources

About