scholarly journals Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 773 ◽  
Author(s):  
Fuping Zhao ◽  
Tianyu Deng ◽  
Liangyu Shi ◽  
Wenwen Wang ◽  
Qin Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Coat Color ◽  
Reproductive Traits ◽  
Bioinformatic Analysis ◽  
Selection Signatures ◽  
Selection Signature ◽  
Positional Candidate ◽  
Indigenous Sheep ◽  
Tibetan Sheep ◽  
Genomic Regions

It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep.

scholarly journals Title: Meta-Analysis of Heifer Traits Identified Reproductive Pathways in Bos indicus Cattle

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 768
Author(s):  
Muhammad S. Tahir ◽  
Laercio R. Porto-Neto ◽  
Cedric Gondro ◽  
Olasege B. Shittu ◽  
Kimberley Wockner ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Meta Analysis ◽  
Reproductive Traits ◽  
Significant Snps ◽  
Genomic Region ◽  
Chromosome 8 ◽  
Positional Candidate ◽  
Brahman Cattle ◽  
Genomic Regions

Fertility traits measured early in life define the reproductive potential of heifers. Knowledge of genetics and biology can help devise genomic selection methods to improve heifer fertility. In this study, we used ~2400 Brahman cattle to perform GWAS and multi-trait meta-analysis to determine genomic regions associated with heifer fertility. Heifer traits measured were pregnancy at first mating opportunity (PREG1, a binary trait), first conception score (FCS, score 1 to 3) and rebreeding score (REB, score 1 to 3.5). The heritability estimates were 0.17 (0.03) for PREG1, 0.11 (0.05) for FCS and 0.28 (0.05) for REB. The three traits were highly genetically correlated (0.75–0.83) as expected. Meta-analysis was performed using SNP effects estimated for each of the three traits, adjusted for standard error. We identified 1359 significant SNPs (p-value < 9.9 × 10−6 at FDR < 0.0001) in the multi-trait meta-analysis. Genomic regions of 0.5 Mb around each significant SNP from the meta-analysis were annotated to create a list of 2560 positional candidate genes. The most significant SNP was in the vicinity of a genomic region on chromosome 8, encompassing the genes SLC44A1, FSD1L, FKTN, TAL2 and TMEM38B. The genomic region in humans that contains homologs of these genes is associated with age at puberty in girls. Top significant SNPs pointed to additional fertility-related genes, again within a 0.5 Mb region, including ESR2, ITPR1, GNG2, RGS9BP, ANKRD27, TDRD12, GRM1, MTHFD1, PTGDR and NTNG1. Functional pathway enrichment analysis resulted in many positional candidate genes relating to known fertility pathways, including GnRH signaling, estrogen signaling, progesterone mediated oocyte maturation, cAMP signaling, calcium signaling, glutamatergic signaling, focal adhesion, PI3K-AKT signaling and ovarian steroidogenesis pathway. The comparison of results from this study with previous transcriptomics and proteomics studies on puberty of the same cattle breed (Brahman) but in a different population identified 392 genes in common from which some genes—BRAF, GABRA2, GABR1B, GAD1, FSHR, CNGA3, PDE10A, SNAP25, ESR2, GRIA2, ORAI1, EGFR, CHRNA5, VDAC2, ACVR2B, ORAI3, CYP11A1, GRIN2A, ATP2B3, CAMK2A, PLA2G, CAMK2D and MAPK3—are also part of the above-mentioned pathways. The biological functions of the positional candidate genes and their annotation to known pathways allowed integrating the results into a bigger picture of molecular mechanisms related to puberty in the hypothalamus–pituitary–ovarian axis. A reasonable number of genes, common between previous puberty studies and this study on early reproductive traits, corroborates the proposed molecular mechanisms. This study identified the polymorphism associated with early reproductive traits, and candidate genes that provided a visualization of the proposed mechanisms, coordinating the hypothalamic, pituitary, and ovarian functions for reproductive performance in Brahman cattle.

scholarly journals Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yingyue Zhang ◽  
Xianglan Xue ◽  
Yue Liu ◽  
Adam Abied ◽  
Yangyang Ding ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Coat Color ◽  
Genomic Diversity ◽  
Mean Corpuscular Hemoglobin ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Selection Signatures ◽  
Corpuscular Hemoglobin ◽  
Genome Wide ◽  
Tibetan Sheep

AbstractThe identification of genome-wide selection signatures can provide insights on the mechanisms of natural and/or artificial selection and uncover genes related to biological functions and/or phenotypes. Tibetan sheep are an important livestock in Tibet, providing meat and wool for Tibetans who are renown for breeding livestock that adapt well to high altitudes. Using whole-genome sequences with an effective sequencing depth of 5×, we investigated the genomic diversity and structure and, identified selection signatures of White Tibetan, Oula and Poll Dorset sheep. We obtained 30,163,679 Single Nucleotide Polymorphisms (SNPs) and 5,388,372 indels benchmarked against the ovine Oar_v4.0 genome assembly. Next, using FST, ZHp and XP-EHH approaches, we identified selection signatures spanning a set of candidate genes, including HIF1A, CAPN3, PRKAA1, RXFP2, TRHR and HOXA10 that are associated with pathways and GO categories putatively related to hypoxia responses, meat traits and disease resistance. Candidate genes and GO terms associated with coat color were also identified. Finally, quantification of blood physiological parameters, revealed higher levels of mean corpuscular hemoglobin measurement and mean corpuscular hemoglobin concentration in Tibetan sheep compared with Poll Dorset, suggesting a greater oxygen-carrying capacity in the Tibetan sheep and thus better adaptation to high-altitude hypoxia. In conclusion, this study provides a greater understanding of genome diversity and variations associated with adaptive and production traits in sheep.

scholarly journals Whole genome sequences reveal multiple functions of PAT1 gene on environment adaptation and coat coloration in Tibetan sheep populations

2019 ◽  
Author(s):  
Jianbin Liu ◽  
Xuezhi Ding ◽  
Chao Yuan ◽  
Yufeng Zeng ◽  
Tingting Guo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Coat Color ◽  
Body Height ◽  
Multiple Traits ◽  
Adaptive Traits ◽  
Environment Adaptation ◽  
Tibetan Sheep ◽  
Genomic Regions ◽  
The Tropics ◽  
Productive Trait

Abstract Background: Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of both productive and adaptive traits. However, the genetic mechanism regulating the multiple biological process remain unclear. Results: In this study, we report a novel PAT1 gene that simultaneously explained the variations of productive trait (coat color), adaptive traits (altitude and geography response) in 15 indigenous Tibetan sheep populations. Overlapped genomic regions harboring 6 candidate genes across three traits were identified at 27 chromosomes, with the top 1% of Fst and |Zph| values. The SNP/INDELs and expression of these candidate genes were further analyzed, and we find that only PAT1 gene, a CSDE1 homologue was consistent with the variation of multiple traits regarding. Haplotype analysis of PAT1 reveal that Tibetan sheep breeds with C-type of PAT1 have significantly greater body weight, shear amount, chest width and body length, but have lower body height, than those with CA-type of PAT1. Conclusions: We emphasized that PAT1 gene could be a potentially selective target used for the improvements of environmental adaption and coat coloration in the future. These results contribute to the knowledge of adaptive response in Tibetan sheep populations and will help to guide future conservation programs for Tibetan sheep native to Qinghai-Tibetan Plateau.

scholarly journals Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 938 ◽  
Author(s):  
Islam ◽  
Li ◽  
Liu ◽  
Berihulay ◽  
Abied ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Positive Selection ◽  
Candidate Genes ◽  
Runs Of Homozygosity ◽  
Selection Signatures ◽  
Effective Population ◽  
Signature Of Selection ◽  
Genomic Regions ◽  
Insight Into

: Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

Using soybean pedigrees to identify genomic selection signatures associated with long-term breeding for cultivar improvement

2018 ◽  
Vol 98 (5) ◽  
pp. 1176-1187 ◽  
Author(s):  
Christopher M. Grainger ◽  
Jocelyne Letarte ◽  
Istvan Rajcan
Keyword(s):  
In Silico Analysis ◽  
Selection Signatures ◽  
Selection Signature ◽  
Breeding Lines ◽  
Genomic Regions ◽  
Elite Breeding Lines ◽  
Silico Analysis ◽  
Simple Sequence ◽  
Introgressive Breeding

Genetic hitchhiking methods used to uncover selection signatures related to traits of agronomic importance in crops have primarily been used at the level of domestication by comparing groups of wild germplasm to landraces or elite breeding lines. In this study, two groups of cultivars defined by an elite Canadian soybean cultivar, ‘OAC Bayfield’, were compared to identify selection signatures related to long-term breeding within a specific region. Cultivars were assigned to either a pre- or post-OAC Bayfield group. Of the 162 simple sequence repeat markers used to genotype members of the pedigree, 14 were fixed and 19 exhibited a selective signature. An in silico analysis compared the results in this study to quantitative trait loci (QTL) reported in SoyBase and showed that 18 out of the 19 markers with a selective signature were associated with at least one QTL. From the 80 QTL associated with the 18 markers, half were related to plant architecture, yield, or maturity. In addition, the number and type of QTL associated with the fixed versus selected loci differed, particularly for yield. Genomic regions exhibiting a selection signature may contain important loci that either need to be conserved for agronomic performance or be targeted for introgressive breeding and germplasm enrichment.

scholarly journals Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam

2021 ◽  
Author(s):  
Janet Higgins ◽  
Bruno Santos ◽  
Tran Dang Khanh ◽  
Khuat Huu Trung ◽  
Tran Duy Duong ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Continuous Improvement ◽  
Rice Genome ◽  
Selection Signatures ◽  
Genome Scanning ◽  
Selective Pressures ◽  
Rice Landraces ◽  
Rich Diversity ◽  
Genomic Regions ◽  
New Generation

Background and aims: Vietnam harnesses a rich diversity of rice landraces adapted to a broad range of conditions, which constitute a largely untapped source of genetic diversity for the continuous improvement of rice cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica-5 group. Here, we leveraged on that strong differentiation, and the 672 rice genomes generated, to identify genes within genomic regions putatively selected during domestication and breeding of rice in Vietnam. Methodology: We identified significant distorted patterns in allele frequency (XP-CLR method) and population differentiation scores (FST), resulting from differential selective pressures between native subpopulations, and compared them with QTLs previously identified by GWAS in the same panel. We particularly focused on the outlying Indica-5 subpopulation because of its likely novelty and differential evolution. Results: We identified selection signatures in each of the Vietnamese subpopulations and carried out a comprehensive annotation of the 52 regions selected in Indica-5, which represented 8.1% of the rice genome. We annotated the 4,576 genes in these regions, verified the overlap with QTLs identified in the same diversity panel and the comparison with a FST analysis between subpopulations, to select sixty-five candidate genes as promising breeding targets, several of which harboured alleles with non-synonymous substitutions. Conclusions: Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.

scholarly journals Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242200
Author(s):  
Natalia Anatolievna Zinovieva ◽  
Arsen Vladimirovich Dotsev ◽  
Alexander Alexandrovich Sermyagin ◽  
Tatiana Evgenievna Deniskova ◽  
Alexandra Sergeevna Abdelmanova ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Candidate Genes ◽  
High Density ◽  
Fixation Index ◽  
Nucleotide Polymorphism ◽  
Selection Signatures ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
Native Cattle ◽  
Genomic Regions

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

scholarly journals Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guoyao Zhao ◽  
Yuqiang Liu ◽  
Qunhao Niu ◽  
Xu Zheng ◽  
Tianliu Zhang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Average Length ◽  
Snp Array ◽  
Reproductive Traits ◽  
Farm Animals ◽  
Production Traits ◽  
Runs Of Homozygosity ◽  
Exact Test ◽  
Genomic Regions

Abstract Background Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. Results We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher’s exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. Conclusions Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.

scholarly journals Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Elisabeth Le Bihan-Duval ◽  
Christelle Hennequet-Antier ◽  
Cécile Berri ◽  
Stéphane A. Beauclercq ◽  
Marie Christine Bourin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Chicken Meat ◽  
Selection Signatures ◽  
Genomic Regions ◽  
Combined Detection
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