Recent advances in understanding genetic variants associated with economically important traits in sheep (<i>Ovis aries</i>) revealed by high-throughput screening technologies

doi:10.15302/J-FASE-2017151

Front. Agr. Sci. Eng.

2017, Vol. 4

Issue (3) : 279-288 https://doi.org/10.15302/J-FASE-2017151

REVIEW

Recent advances in understanding genetic variants associated with economically important traits in sheep (Ovis aries) revealed by high-throughput screening technologies

Song-Song XU^1,², Meng-Hua LI¹(

)

¹. CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
². University of Chinese Academy of Sciences, Beijing 100049, China

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Abstract

Sheep are one of the most economically important domesticated animals for human society. However, genetic improvements for the key traits associated with meat, growth, milk, wool, reproduction, horns and tails progress slowly using conventional crossbreeding methods. With the development and utilization of high-throughput screening technologies over the last decade, a list of functional genes and genetic variants associated with these traits has been identified. This review covers recent genome-wide studies on sheep productive traits using high-throughput screening technologies, including those based on single-nucleotide polymorphisms and copy number variants at the whole-genome level (e.g., genome-wide association studies), transcriptome and DNA methylation sequences. Additionally, comprehensive information on functional genes and genetic variants associated with economically important traits in sheep is provided.

Keywords sheep high-throughput screening productive traits genome-wide studies

Corresponding Author(s): Meng-Hua LI

Just Accepted Date: 16 March 2017 Online First Date: 13 April 2017 Issue Date: 12 September 2017

Cite this article:

Song-Song XU,Meng-Hua LI. Recent advances in understanding genetic variants associated with economically important traits in sheep (Ovis aries) revealed by high-throughput screening technologies[J]. Front. Agr. Sci. Eng. , 2017, 4(3): 279-288.

URL:

https://academic.hep.com.cn/fase/EN/10.15302/J-FASE-2017151
https://academic.hep.com.cn/fase/EN/Y2017/V4/I3/279

Trait	Approach	Genes, miRNAs and signaling pathways	References
Meat and carcass	GWAS	Lean meat yield: GDF8 Marbling: ALDOA, STK32B and FAM190A Meat myoglobin content and fatty acid composition: FASN, MLXIPL, EVOLV6, ACACA, SYNRG, APOL6, MB, ACSL1, ISYNA1, SGK2 and AGPAT9 Meat production and quality: GHR Muscling and shear force: MEG3, MEG8 and DLK1	[ 11–16]
	RNA-seq	Fat metabolism: NELL1, FMO3, AACS, ACACA, ACACB, ACOT6, ELOVL6, FASN, HSD17B12 and SCD Muscle growth and development: HSPA6, ZIM3, SLC5A12, FGF1, IGF2BP2, IGF-2, TCF4, MRFs, GXP1 and STAC3; and miRNAs miR-10, miR-let-7 family, oar-miR-3955-5p, oar-miR-410-3p, bta-miR-183 and bta-miR-182	[ 17–22]
	DNA methylation	Muscle development: 399 different methylated regions and LTBP1	[ 23,24]
Growth	GWAS and selective sweeps	Body size: NPR2, HMGA2, BMP2, GPX3, FSTL1, PVR, EXT2, ALT4, SOX6, HAND2, PDGFD, BMPR2, GHR, ANKS1B; and Signal pathways HIF-1, VSMC and GH/IGF-1 Post-weaning gain: GRM1, POL, MBD5, UBR2, RPL7, SMC2, DAAM1 and APIP Bodyweight: GSTRBP, TRAMIL1, PHF15, PRSS12, MAN1A1, SYNE1, WAPAL, DAAM1, OST/SPP1, MEPE, IBSP, NCAPG and LCORL Bone-related traits: SPP1, MEPE, IBSP, LCORL and NCAPG	[ 11,16,25–29]
Wool	GWAS and selective sweeps	Coat pigmentation: KIT, ASIP, KITLG, EDN3, MITF, MC1R, HERC2-like, TYRP1, ASIP and MITF Growing wing hairs: FRY Wool fiber diameter: TSPEAR, PIK3R4, KRTCAP3, YWHAZ and CCNY Fiber diameter coefficient of variation and fineness dispersion: gKIF16B Crimp: PTPN3, TCF9, GPRC5A, DDX47, EPHA5, TPTE2 and NBEA	[ 11,27,30–36]
	RNA-seq	Hair/fleece development and function: KRTs, KRTAPs families, CST3, CSTB, S100A11, PPARD, CSTA, SIVA1, CCDC85B, FOXE1, VAX2, BAK1, ADRA1B, PKIA and HNF4A Coat color regulation: DCT, MATP, TYR and TYRP1 Fiber diameter: GNPAT, LPIN2, CHKA, PLD2, PLA2G3, SMPD2, UGCG, PIP4K2A, ACOT8, SLC25A17, NCOR1, FABP6, HSD11B1, STAR, FABP4 and SLC25A20 Follicle bulb regression and regeneration: Wnt, Jak-STAT, MAPK, Notch, TGF-β, Toll-like receptor and VEGF pathways Telogen hair follicles development and growth: 1910 known miRNAs and 2261 novel mature miRNAs	[ 37–41]
Milk	GWAS and selective sweeps	Milk protein and fat contents: LALBA Milk production performances: PALMD and RFP145 Milk production traits: ABCG2, SPP1, SCD and SOCS2, PKD2, MEPE and IBSP	[ 34,42–44]
	RNA-seq	Higher cheese yield: CSN2, CSN3 and LALBA Lipid metabolism: BTN1A1, XDH, FASN, ADFP, SCD, H-FABP and ACSS2 High protein production: FABP4, SUCNR1, HSP70 and HSPB8 Milk secretion: 2764 genes	[ 45^–48]
Reproduction	GWAS and selective sweeps	Mammalian reproduction: PRLP Metabolic regulation and reproduction: TSHR Increased ovulation rate/litter size: GDF9 and BMP15 Oocyte development: CCNB2 and SLC8A3 Pre-weaning gain: POL, RPL7, MSL1 and SHISA9	[ 11,13,49–52]
	RNA-seq	Fecundity: BAX, BAD, NDUFA13, CAV1, LOC101117112, PAX8, IFI6, PRLR, PGR, ESR2, CYP19A1, CYP11A1, HSD17B12, INHBA, BMPR1B and BMPR2 receptors; and miRNAs oar-miR-665-5p, oar-miR-411a-5p, oar-miR-1197-3p and oar-miR-134-3p Fecundity and prolificacy: signaling pathways Wnt, MAPK, G-protein, TGF-b and PPAR	[ 53–57]
	DNA methylation	Reproductive traits: ADIPOQ, ABCG1, BRWD1, GRIN2B, METTL6, SIAH2, SLCO2A1, TNIK and UMODL1	[ 58]
Horn	GWAS and selective sweeps	Horn development: RXFP2, MTX2, HOX clusters, EVX2 and KIAA1715	[ 11,27,32–34,59–68]
Tail	Selective sweeps	Fat deposition or tail morphology: PPP2CA, SKP1, TCF7, RXFP2, PPP1CC, PDGFD, BMP2, VNRT, PPARA, RXRA, KLF11, HOXA11, BMP2, PPP1CC, SP3, SP9, WDR92, PROKR1 and ETAA1	[ 34,69–72]
	RNA-seq	Lipid metabolism: NELL1, FMO3, ACACA, ELOVL6, HSD17B12, CYP11A1, GDE1, ACACB, ACOT6, FASN, SCD and ACOT2; and miRNAs bta-miR-18a, hsa-miR-29b-1-5p, ssc-miR-22-3p, and hsa-miR-4749-5p	[ 17,18,20,73 ]

Tab.1 Summary of high-throughput screening studies on economically important traits in sheep

Fig.1 Workflow of identification, validation and application of candidate function genes or variants

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