Detecting selection signatures on the X chromosome of the Chinese Debao pony

Liu, X.-X.; Pan, Jianfei; Zhao, Qianjun; He, Xiaohong; Yun, Pu; Han, Jiangang; Ma, Yue; Jiang, Lin

doi:10.1111/jbg.12314

Cited by 11 publications

(8 citation statements)

References 29 publications

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“…TGF-β1 [25] and TMED2 (transmembrane emp24 domain) were also differentially expressed in embryonic cells and placenta [32], proven by the morphogenesis of the embryo and placenta, as well as skeletal muscle physiology [33]. CACNA1F (L-type voltage-dependent calcium channel a1F), involved in the differentiation of adipocytes and related to the etiology of obesity [34], was found to be under selection in the Chinese Debao pony [35]. EDN3 (endothelin-3) was reported to be associated with enteric neuron development and blood circulation, thereby influencing the racing performance of Swedish-Norwegian coldblooded trotter horses [36].…”

Section: Discussionmentioning

confidence: 99%

Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds

Yun

Zhang

et al. 2020

Animals

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As a nutrient sensor, the placenta plays a key role in regulating fetus growth and development. Long non-coding RNAs (lncRNAs) have been shown to regulate growth-related traits. However, the biological function of lncRNAs in horse placentas remains unclear. To compare the expression patterns of lncRNAs in the placentas of the Chinese Ningqiang (NQ) and Yili (YL) breeds, we performed a transcriptome analysis using RNA sequencing (RNA-seq) technology. NQ is a pony breed with an average adult height at the withers of less than 106 cm, whereas that of YL is around 148 cm. Based on 813 million high-quality reads and stringent quality control procedures, 3011 transcripts coding for 1464 placental lncRNAs were identified and mapped to the horse reference genome. We found 107 differentially expressed lncRNAs (DELs) between NQ and YL, including 68 up-regulated and 39 down-regulated DELs in YL. Six (TBX3, CACNA1F, EDN3, KAT5, ZNF281, TMED2, and TGFB1) out of the 233 genes targeted by DELs were identified as being involved in limb development, skeletal myoblast differentiation, and embryo development. Two DELs were predicted to target the TBX3 gene, which was found to be under strong selection and associated with small body size in the Chinese Debao pony breed. This finding suggests the potential functional significance of placental lncRNAs in regulating horse body size.

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Section: Discussionmentioning

confidence: 99%

Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds

Yun

Zhang

et al. 2020

Animals

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“…sites that are still polymorphic in one population but are fixed in another [16]. Both approaches have been applied in different horse breeds such as Asian [27] and Shetland ponies [28], where growth, height, feed efficiency and fat deposition related genes appeared to have been under selective pressure. Furthermore, racing performance and locomotion have been targeted in gaited breeds and Quarter Horses [29].…”

Section: Introductionmentioning

confidence: 99%

Selection signatures in four German warmblood horse breeds: Tracing breeding history in the modern sport horse

2019

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The study of selection signatures helps to find genomic regions that have been under selective pressure and might host genes or variants that modulate important phenotypes. Such knowledge improves our understanding of how breeding programmes have shaped the genomes of livestock. In this study, 942 stallions were included from four, exemplarily chosen, German warmblood breeds with divergent historical and recent selection focus and different crossbreeding policies: Trakehner (N = 44), Holsteiner (N = 358), Hanoverian (N = 319) and Oldenburger (N = 221). Those breeds are nowadays bred for athletic performance and aptitude for show-jumping, dressage or eventing, with a particular focus of Holsteiner on the first discipline. Blood samples were collected during the health exams of the stallion preselections before licensing and were genotyped with the Illumina EquineSNP50 BeadChip. Autosomal markers were used for a multi-method search for signals of positive selection. Analyses within and across breeds were conducted by using the integrated Haplotype Score (iHS), cross-population Extended Haplotype Homozygosity (xpEHH) and Runs of Homozygosity (ROH). Oldenburger and Hanoverian showed very similar iHS signatures, but breed specificities were detected on multiple chromosomes with the xpEHH. The Trakehner clustered as a distinct group in a principal component analysis and also showed the highest number of ROHs, which reflects their historical bottleneck. Beside breed specific differences, we found shared selection signals in an across breed iHS analysis on chromosomes 1, 4 and 7. After investigation of these iHS signals and shared ROH for potential functional candidate genes and affected pathways including enrichment analyses, we suggest that genes affecting muscle functionality ( TPM1 , TMOD2-3 , MYO5A , MYO5C ), energy metabolism and growth ( AEBP1 , RALGAPA2 , IGFBP1 , IGFBP3-4 ), embryonic development ( HOXB -complex) and fertility ( THEGL , ZPBP1-2 , TEX14 , ZP1 , SUN3 and CFAP61 ) have been targeted by selection in all breeds. Our findings also indicate selection pressure on KITLG , which is well-documented for influencing pigmentation.

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“…In recent years, methods for detecting selection signals using chip data have been widely used in livestock (Liu et al . 2018; Zhao et al .…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis reveals signatures of selection for gait traits in Yili horse

Liu

Fang

Meng

et al. 2018

Preprint

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10High quality gaits play an important role in many breeding programs, but the genes of gait 11 were limited at the moment. Here, we present an analysis of genomic selection signatures 12 in 53 individuals from two breeds, using genotype data from the Affymetrix Equine 670K 13 SNP genotyping array. The 11 selection regions of Yili horse were identified using an FST 14 statistic and XP-EHH calculated in 200-kb windows across the genome. In total, 50 genes 15 could be found in the 11 regions, and two candidate genes related to locomotory behavior 16 (CLN6, FZD4). The genome of Yili horse and Russian horse were shaped by natural and 17 artificial selection. Our results suggest that gait trait of Yili horse may related to two genes. 18 This is the first time when whole genome array data is utilized to study genomic regions 19 affecting gait in Yili horse breed.20

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Detecting selection signatures on the X chromosome of the Chinese Debao pony

Cited by 11 publications

References 29 publications

Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds

Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds

Selection signatures in four German warmblood horse breeds: Tracing breeding history in the modern sport horse

Genome-wide analysis reveals signatures of selection for gait traits in Yili horse

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