Traits Of Economic Importance Research Articles

TARGET OF EAT3 (TOE3) specifically regulates fruit spine initiation in cucumber (Cucumis sativus L.).

The presence or absence of spines is an important economic trait of cucumber fruit. Spines are believed to be a type of specialized trichome on the fruit surface and all the identified cucumber trichome-less mutants lack fruit spines. However, genes that specifically regulate fruit spine initiation remain to be identified. Here, we found that knocking out cucumber TARGET OF EAT3 homolog (CsTOE3), belonging to the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) family, affected flower development, and more interestingly, inhibited cucumber fruit spine initiation. On analyzing expression patterns by qRT-PCR and in situ hybridization assay, CsTOE3 was found to be highly expressed in male and female flowers, and its mRNA accumulated in the tips of sepal and petal primordia and in the cells of fruit spines and peels. Biochemical analyses indicated that CsTOE3 directly interacts with GLABRA1 (CsGL1) and TRANSPARENT TESTA GLABRA1 (CsTTG1), which are positive regulators of trichome formation. In addition, RNA-seq showed that the transcription levels of eight ERFs were significantly upregulated in CsTOE3 knockout lines. Phytohormone content analysis also revealed a significant increase in the amount of ethylene released by CsTOE3 knockout lines; treatment with the ethylene synthesis inhibitor aminoethoxyvinyl-glycine (AVG) partly restored the spineless phenotype. Our results suggest that CsTOE3 specifically regulates fruit spine initiation but does not affect the formation of trichomes on other organs in cucumber. Our findings may have a far-reaching significance for cucumber germplasm improvement and quality breeding using fruit spines as the target trait.

Investigating the genetic components of tuber bruising in a breeding population of tetraploid potatoes

BackgroundTuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economic importance, as it affects tubers’ fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype. Here, we used capture sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis (GWAS) for tuber bruising. In addition, we collected transcriptomic data to enrich the GWAS results. However, there is currently no satisfactory method to represent both GWAS and transcriptomics analysis results in a single visualisation and to compare them with existing knowledge about the biological system under study.ResultsWhen investigating population structure, we found that the STRUCTURE algorithm yielded greater insights than discriminant analysis of principal components (DAPC). Importantly, we found that markers with the highest (though non-significant) association scores were consistent with previous findings on tuber bruising. In addition, new genomic regions were found to be associated with tuber bruising. The GWAS results were backed by the transcriptomics differential expression analysis. The differential expression notably highlighted for the first time the role of two genes involved in cellular strength and mechanical force sensing in tuber resistance to bruising. We proposed a new visualisation, the HIDECAN plot, to integrate the results from the genomics and transcriptomics analyses, along with previous knowledge about genomic regions and candidate genes associated with the trait.ConclusionThis study offers a unique genome-wide exploration of the genetic components of tuber bruising. The role of genetic components affecting cellular strength and resistance to physical force, as well as mechanosensing mechanisms, was highlighted for the first time in the context of tuber bruising. We showcase the usefulness of genomic data from breeding programmes in identifying genomic regions whose association with the trait of interest merit further investigation. We demonstrate how confidence in these discoveries and their biological relevance can be increased by integrating results from transcriptomics analyses. The newly proposed visualisation provides a clear framework to summarise of both genomics and transcriptomics analyses, and places them in the context of previous knowledge on the trait of interest.

41 A preliminary investigation of candidate genes from a GWAS identified QTL for relative body size in the American Quarter Horse

Artificial selection during domestication has influenced an array of morphological traits in the horse, many that are now important economic traits for the horse industry. Growth and skeletal phenotypes impact the desirability and function of horses in diverse disciplines and are often key characteristics in the development of breeds. Skeletal traits also impact functionality: benefitting horses for specialized work or predisposing them to musculoskeletal injury. To investigate variations in body size and shape, we utilized measurements taken at 2 years of age (+/− one week) from 91 American Quarter Horses bred and owned by the University of Florida. We summarized 32 body measures from each horse using a principal component analysis followed by a varimax rotation. Factor 1 summarizes 19.5% of the variation and describes overall body size, except for head measurements which are better captured in Factor 2. Factor 1 traits encompass body proportions, heavily loading on the measure's height at dock and croup. DNA was extracted from blood and hair through previously published methods and genotyped at GeneSeek Inc. (Lansing, MI) using the Affymetrix Axiom Equine HD 670k array. We recently reported results from a preliminary genome-wide association study with 311,085 high-quality SNPs (poly-high resolution, MAF >0.05)suggesting a quantitative trait locus for the Body Factor 1 trait on chromosome 6 (raw P = 1.356e-09, Bonferroni P = 4.51e-07) and defines a candidate region spanning 1.5Mb. The QTL is in a region unrelated to a previously characterized HMGA2 body height locus. The candidate region contains 5 protein-coding genes, influencing human height and skeletal traits including one associated with Noonan Syndrome- a disease impacting height and facial morphology, an interesting parallel to the phenotype observed in our population. None of the 16,860 variants found in the European Nucleotide Archive for our candidate region had a functional impacted on a protein coding region. Therefore, we sequenced 2 whole genomes from American Quarter Horses to discover variants specific to the haplotype bearing this new body size QTL. Using the 10x Chromium library prep with 150bp paired end reads on an Illumina HiSeq2500, the 2 genomes totaled 1.5 billion reads. Following alignment and variant calling using the LongRanger package (v2.2, 10x Genomics Inc.), we observed 4,703 SNPs in the candidate region. Future investigation aims to investigate additional loci relevant to body morphological variations and develop predictive phenotype models in the horse.

Relationship between Single Nucleotide Polymorphism of IGF-1 Gene in Nile Tilapia (Oreochromis niloticus) and Weight Gain

Production and consumption of Nile tilapia (Oreochromis niloticus) have been growing. Insulin-like growth factor-1 (IGF-1) is a hormone that affects animal weight. Traditional breeding combined with molecular marker technology-assisted selective breeding has long been used to cultivate new fish strains and produce high-quality Nile tilapia. Moreover, molecular markers or genes related to important economic traits can be identified with the help of molecular-assisted selection breeding. A total of 152 Nile tilapia fish fin samples were collected from Janghang fish farm and classified according to their weight and sex. A total of 9 single nucleotide polymorphisms (SNPs) were identified in the Nile tilapia IGF-1 gene in this study. One SNP was located in the promoter region, three in the 5

Seed yield improvement in navy bean: Registration of ‘ND Polar’

Abstract‘ND Polar’ (Reg. no. CV‐349, PI 700767) is a new navy bean (Phaseolus vulgaris L.) cultivar developed by the Dry Edible Bean Breeding Program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. ND Polar was developed using a modified pedigree method (F1–F5), followed by pure line selection based on agronomic performance, disease resistance, and seed quality characteristics. With ∼16% of the total dry bean production in the United States, navy bean is the third most important market class after pinto and black. Accounting for 35% of the total production, North Dakota is the largest producer of dry bean in the United States. Between 2015 and 2021, ND Polar was tested across 23 environments in North Dakota, where seed yield was significantly higher than ‘HMS Medalist’, ‘Blizzard’, and ‘Ensign’ and similar to ‘T9905’. ND Polar is resistant to Bean common mosaic virus and has intermediate resistance to common bacterial blight. ND Polar has desirable upright architecture to facilitate direct harvest. Under North Dakota environments, ND Polar shows an average plant height of 52 cm, has a 100‐seed weight of 18.3 g, and matures in 102 days. Canning quality was rated as acceptable. Similar to the commercial checks, ND Polar is susceptible to local races/strains of the bean rust pathogen, anthracnose, and white mold. Other traits of agronomic and economic importance are within acceptable ranges.

Genome-wide association study for numbers of vertebrae in Dezhou donkey population reveals new candidate genes

Numbers of vertebrae is an important economic trait associated with body size and meat productivity in animals. However, the genetic basis of vertebrae number in donkey remains to be well understood. The aim of this study was to identify candidate genes affecting the number of thoracic (TVn) and the number of lumbar vertebrae (LVn) in Dezhou donkey. A genome-wide association study was conducted using whole genome sequence data imputed from low-coverage genome sequencing. For TVn, we identified 38 genome-wide significant and 64 suggestive SNPs, which relate to 7 genes (NLGN1, DCC, SLC26A7, TOX, WNT7A, LOC123286078, and LOC123280142). For LVn, we identified 9 genome-wide significant and 38 suggestive SNPs, which relate to 8 genes (GABBR2, FBXO4, LOC123277146, LOC123277359, BMP7, B3GAT1, EML2, and LRP5). The genes involve in the Wnt and TGF-β signaling pathways and may play an important role in embryonic development or bone formation and could be good candidate genes for TVn and LVn.

A genome-wide scan to identify signatures of selection in Lueyang black -bone chicken

Lueyang black-bone chicken is a domestic breed in China. The genetic mechanism of the formation of important economic traits of this breed has not been studied systematically. Therefore, in this study, whole genome resequencing was used to systematically analyze and evaluate the genetic diversity of the black-feather and white-feather populations, and to screen and identify key genes related to phenotypes. The results of principal component analysis and population structure analysis showed that Lueyang black-feathered chickens and white-feathered chickens could be divided into 2 subgroups, and the genetic diversity of black-feathered chicken was richer than that of white-feathered chickens. Linkage disequilibrium analysis also showed that the selection intensity of black-feathered chickens was lower than for white-feathered chickens, which was mainly due to the small population size of white-feathered chickens and a certain degree of inbreeding. Fixation index (FST) analysis revealed that the candidate genes related to feather color traits were G-gamma, FA, FERM, Kelch, TGFb, Arf, FERM, and melanin synthesis-related gene tyrosinase (TYR). Based on Kyoto Encyclopedia of Genes and Genomes enrichment analysis, Jak-STAT, mTOR, and TGF-β signaling pathways were mainly related to melanogenesis and plume color. The findings of this study supported important information for the evaluation and protection of chicken genetic resources and help to analyze the unique genetic phenotypes such as melanin deposition and feather color of Lueyang black-bone chicken. Additionally, it could provide basic research data for the improvement and breeding of Lueyang black-bone chicken with characteristic traits.

Metabolomic and Transcriptomic Analysis Reveals the Mechanisms Underlying the Difference in Anthocyanin Accumulation in Apple Fruits at Different Altitudes

The red color of apple peel is an important phenotypic and economic trait mainly attributed to anthocyanin accumulation. Apples show a deeper red color at higher altitudes than at lower ones; however, the molecular regulatory network underlying color variation along altitudinal gradients has not been investigated. In this study, the effects of environmental conditions associated with low (124 m) and high (1901 m) altitudes on peel color were assessed through physiological, metabolomic, transcriptomic, and qRT-PCR analyses in Huashuo apple and its sister line, Huarui apple. The content of cyanidin-3-O-galactoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-xyloside was abundant in the high-altitude environment and may contribute to the deeper red color. Transcript levels of structural genes in the anthocyanin synthesis pathway, especially MdCHI, MdCHS, MdANS, and MdDFR, in apple peel were significantly higher at high altitude than at low altitude. Based on the protein interaction prediction and correlation analyses, four transcription factors (MDP0000127691, MDP0000284922, MDP0000758053, and MDP0000074681) could interact with anthocyanin synthesis-related proteins, showing high correlation with anthocyanin accumulation. Therefore, the abovementioned four genes and four transcription factors were predicted to account for the color differences between high and low altitudes. These results provide genetic resources and a theoretical basis for color-oriented fruit improvement.

KNOX Genes Were Involved in Regulating Axillary Bud Formation of Chrysanthemum × morifolium.

Branching is an important agronomic and economic trait in cut chrysanthemums. The axillary meristem (AM) formation of the axillary buds of cut chrysanthemums has a decisive role in its branching characteristics. However, little is known about the regulation mechanism of axillary meristem formation in chrysanthemums at the molecular level. Members of the Homeobox gene family especially genes belonging to the class I KNOX branch play a key role in regulating the axillary bud growth and development processes of plants. In this study, three genes belonging to the class I KNOX branch, CmKNAT1, CmKNAT6, and CmSTM were cloned from chrysanthemums, and their functions in regulating axillary bud formation were examined. The subcellular localization test showed that these three KNOX genes were expressed in the nucleus, so all of them might function as transcription factors. The results of the expression profile analysis showed that these three KNOX genes were highly expressed in the AM formation stage of axillary buds. Overexpression of KNOX genes result in a wrinkled leaf phenotype in tobacco and Arabidopsis, which may be related to the excessive division of leaf cells, resulting in the proliferation of leaf tissue. Furthermore, overexpression of these three KNOX genes enhances the regeneration ability of tobacco leaves, indicating that these three KNOX genes may participate in the regulation of cell meristematic ability, thus promoting the formation of buds. In addition, the results of fluorescence quantitative testing showed that these three KNOX genes may promote the formation of chrysanthemum axillary buds by promoting the cytokinin pathway while inhibiting the auxin and gibberellin pathways. In conclusion, this study demonstrated that CmKNAT1, CmKNAT6, and CmSTM genes were involved in regulating axillary bud formation of Chrysanthemum × morifolium and preliminarily revealed the molecular mechanism of their regulation of AM formation. These findings may provide a theoretical basis and candidate gene resources for genetic engineering breeding of new varieties of cut chrysanthemums without lateral branches.

Identification of Key Functional Genes and LncRNAs Influencing Muscle Growth and Development in Leizhou Black Goats.

Meat yield and quality are important economic traits of livestock. Herein, longissimus dorsi (LD) muscles of Leizhou black goats aged 0, 3, and 6 months were used to identify differentially expressed messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) by high-throughput RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to analyze differentially expressed genes. Expression levels of regulator of calcineurin 1 (RCAN1) and olfactory receptor 2AP1 (OR2AP1) were significantly different in LD muscles of goats aged 0, 3, and 6 months, indicating potentially important roles in postnatal muscle development. Differentially expressed lncRNAs and mRNAs were mainly enriched in biological processes and pathways related to cellular energy metabolism, consistent with previous studies. Three lncRNAs, TCONS_00074191, TCONS_00074190, and TCONS_00078361, may play a cis-acting role with methyltransferase-like 11B (METTL11B) genes and participate in the methylation of goat muscle proteins. Some of the identified genes may provide valuable resources for future studies on postnatal meat development in goat muscles.

Whole genome sequencing of simmental cattle for SNP and CNV discovery

BackgroudThe single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity.ResultsIn this study, we performed a comprehensive analysis to explore the genetic variations (SNPs and CNVs) of high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls using the high-coverage (25×) short-read next generation sequencing and single-molecule long reads sequencing data. A total of ~ 15 million SNPs and 2,944 CNV regions (CNVRs) were detected in Simmental bulls, and a set of positive selected genes (PSGs) and CNVRs were found to be overlapped with quantitative trait loci (QTLs) involving immunity, muscle development, reproduction, etc. In addition, we detected two new variants in LEPR, which may be related to the artificial breeding to improve important economic traits. Moreover, a set of genes and pathways functionally related to male fertility were identified. Remarkably, a CNV on SPAG16 (chr2:101,427,468 − 101,429,883) was completely deleted in all poor sperm motility (PSM) bulls and half of the bulls in high sperm motility (HSM), which may play a crucial role in the bull-fertility.ConclusionsIn conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.

The impact of Box-Cox transformation on phenotypic and genomic characteristics of litter size variability in Landrace pigs

The genetic background of variability remains of interest especially in traits of high economic importance, e.g. litter size in pigs. It has been indicated that the data transformation can affect the variability phenotype. This study aims to evaluate the phenotypic and genomic background of variability of litter size obtained from data before and after the Box-Cox transformation. In total, 67 500 records on the total number born (TNB) in Landrace pig population were used. Since the data presented skewness, the decision was made to perform Box-Cox transformation on TNB and obtain bcTNB. Next, the phenotypic variability was estimated as log-transformed variance of residuals (LnVar) for both TNB (LnVar_TNB) and bcTNB (LnVar_bcTNB). The variability traits were further used in the genome-wide association study (GWAS) performed on 10 688 sows genotyped with Axiom porcine 660 K or imputed to 660 K SNP-chip. The substantial difference in skewness was observed after data transformation, represented as a change from −0.46 to −0.02. Heritability for TNB was 0.118 vs 0.125 for bcTNB. The heritability for LnVar_TNB was 0.0025 vs 0.0037 for LnVar_bcTNB. The change in the genetic variance was confirmed when genetic coefficients on SD level were compared: 2% for LnVar_TNB vs 4% for LnVar_bcTNB. In bivariate analysis, the genetic correlation between the additive genetic effects of the mean TNB and its variability changed from 0.38 to 0.63. The observed positive genetic correlations indicated that selection focused on increasing the litter size will simultaneously cause an increase in litter size variability. Based on GWAS, 14 SNPs were detected for LnVar_TNB and eight for LnVar_bcTNB, with two of them indicating the most promising candidate genes. First candidate gene located on Sus scrofa chromosome (SSC) 3 is STAG3, which plays an essential role in gametogenesis. Second gene located on SSC 10 is ESRRG, which affects placenta development. The additional post-GWAS analysis indicated even more candidate genes for LnVar_TNB and LnVar_bcTNB. The most promising candidate gene was located on SSC 13 – MFN1, which is involved in embryonic development. The results of this study indicated a substantial change in variance components for variability when the Box-Cox transformation was applied to data presenting skewness. Moreover, the data transformation changed the phenotype substantially enough that only part of SNP overlapped between two variability traits. Our investigation shows that it is essential to perform Box-Cox transformation for skewed data in order to properly describe phenotypic and genomic properties of litter size variability in Landrace pigs.

Potentiality of Growth Traits for Selection to Improve Productivity in Nilotic Cattle

Selection for traits of economic importance is crucial for improving productivity and reproductivity in livestock, including cattle. We investigated the prospects of using growth traits; viz: live-body weight (BW), absolute growth rate (AGR), relative growth rate (RGR), absolute maturing rate (AMR), and Kleiber ratio (KR) as bases for selection in Nilotic cattle, by examining the phenotypic correlations among these traits, using 125 male and 136 female calves reared under traditional husbandry system. In the experimental procedure, the heart girth (HG) and body length (BL) of each calf was measured at birth, and at the age of 2, 4, 6, 8, 10, 12, 14, and 16 months; then the BW at each age was derived, and used for estimating AGR, RGR, AMR, KR, and dry matter intake for maintenance (DMIm). AGR, RGR, AMR, or KR was calculated from 0~8 months (AGRα, RGRα, AMRα, KRα), 8~12 months (AGRβ, RGRβ, AMRβ, KRβ), and 12~16 months (AGRγ, RGRγ, AMRγ, KRγ). Phenotypic correlations were determined using the Pearson's correlation method. The results revealed that, BW, AGR, RGR, AMR, KR, and DMIm were inter-correlated. In particular, calf weaning weight (CWW at 8 months), and post-weaning AGRβ, RGRβ, AMRβ, and KRβ (all at 8~12 months` interval) were positively correlated among themselves and with post-weaning BW, but negatively correlated with birth weight and DMIm, and thus, considered the most appropriate selection indices in Nilotic cattle, since these would decrease calf birth weight, thereby reducing dystocia incidences, and increase post-weaning growth, with less DMIm. These results provide the first evidence for possible selection using growth traits to improve productive efficiency in Nilotic cattle.

Genetic diversity and signatures of selection in BoHuai goat revealed by whole-genome sequencing

BackgroundCross breeding is an important way to improve livestock performance. As an important livestock and poultry resource in Henan Province of China, Bohuai goat was formed by crossing Boer goat and Huai goat. After more than 20 years of breeding, BoHuai goats showed many advantages, such as fast growth, good reproductive performance, and high meat yield. In order to better develop and protect Bohuai goats, we sequenced the whole genomes of 30 BoHuai goats and 5 Huai goats to analyze the genetic diversity, population structure and genomic regions under selection of BoHuai goat. Furthermore, we used 126 published genomes of world-wide goat to characterize the genomic variation of BoHuai goat.ResultsThe results showed that the nucleotide diversity of BoHuai goats was lower and the degree of linkage imbalance was higher than that of other breeds. The analysis of population structure showed that BoHuai goats have obvious differences from other goat breeds. In addition, the BoHuai goat is more closely related to the Boer goat than the Huai goat and is highly similar to the Boer goat. Group by selection signal in the BoHuai goat study, we found that one region on chromosome 7 shows a very strong selection signal, which suggests that it could well be the segment region under the intense artificial selection results. Through selective sweeps, we detected some genes related to important traits such as lipid metabolism (LDLR, STAR, ANGPTL8), fertility (STAR), and disease resistance (CD274, DHPS, PDCD1LG2).ConclusionIn this paper, we elucidated the genomic variation, ancestry composition, and selective signals related to important economic traits in BoHuai goats. Our studies on the genome of BoHuai goats will not only help to understand the characteristics of the crossbred but also provide a basis for the improvement of cross-breeding programs.

Whole-genome DNA methylation analysis of the sperm in relation to bull fertility.

Bull fertility is an important economic trait, this study identified some DNA methylation biomarkers that are associated with bull fertility. Subfertile bulls may cause huge economic losses in dairy production since their semen could be used to inseminate thousands of cows by artificial insemination. This study adopted whole-genome enzymatic methyl sequencing and aimed to identify candidate DNA methylation markers in bovine sperm that correlate with bull fertility. Twelve bulls were selected (high bull fertility = 6; low bull fertility = 6) based on the industry's internally used Bull Fertility Index. After sequencing, a total of 450 CpG had a DNA methylation difference higher than 20% (q < 0.01) had been screened. The 16 most significant differentially methylated regions (DMRs) were identified using a 10% methylation difference cut-off (q < 5.88 × 10-16). Interestingly, most of the differentially methylated cytosines (DMCs) and DMRs were distributed on the X and Y chromosomes, demonstrating that the sex chromosomes play essential roles in bull fertility. Additionally, the functional classification showed that the beta-defensin family, zinc finger protein family, and olfactory and taste receptors could be clustered. Moreover, the enriched G protein-coupled receptors such as neurotransmitter receptors, taste receptors, olfactory receptors, and ion channels indicated that the acrosome reaction and capacitation processes are pivotal for bull fertility. In conclusion, this study identified the sperm-derived bull fertility-associated DMRs and DMCs at the whole genome level, which could complement and integrate into the existing genetic evaluation methods, increasing our decisive capacity to select good bulls and explain bull fertility better in the future.

Genome-wide association study reveals new QTL and functional candidate genes for the number of ribs and carcass length in pigs.

The number of ribs (NR) and carcass length (CL) are important economic traits in pig breeding programs. Pigs with a higher NR and longer CL produce greater pork yields. In the present study, Suhuai pigs with NR and CL phenotypes were genotyped using the Neogen® GGP Porcine 80 K SNP array to identify the QTL affecting NR and CL and dissect the candidate genes for the two traits. The SNP-chip data was imputed to the whole-genome sequence (iWGS) to increase the probability of identifying causal variants. Through genome-wide association studies (GWAS) based on both chip and iWGS data, significant SNPs were detected on Sus scrofa chromosome (SSC) 1, SSC4 and SSC7 for NR and on SSC5, SSC16 and SSC17 for CL. Moreover, two SNPs (H3GA0022644 and WU_10.2_7_103460706) on SSC7 detected in chip-based GWAS were significantly associated with both NR and CL. Through Bayes fine mapping, one reported QTL for NR on SSC7 and two reported QTLfor CL on SSC17 were verified, and two new QTL(SSC1: 14.05-15.84Mb and SSC4: 64.83-66.59Mb) affecting NR and two new QTL(SSC5: 58.31-59.84Mb and SSC16: 22.98-23.43Mb) affecting CL were detected. According to the biological functions of genes, MTHFD1L on SSC1 and SULF1 on SSC4 are novel functional candidate genes for NR, and EMP1 on SSC5 and EGFLAM on SSC16 are novel functional candidate genes for CL. Overall, our findings provide a basis for identifying new causal genes and mutations affecting NR and CL.

Integration of Transcriptomics and Non-Targeted Metabolomics Reveals the Underlying Mechanism of Skeletal Muscle Development in Duck during Embryonic Stage

Skeletal muscle is an important economic trait in duck breeding; however, little is known about the molecular mechanisms of its embryonic development. Here, the transcriptomes and metabolomes of breast muscle of Pekin duck from 15 (E15_BM), 21 (E21_BM), and 27 (E27_BM) days of incubation were compared and analyzed. The metabolome results showed that the differentially accumulated metabolites (DAMs), including the up-regulated metabolites, l-glutamic acid, n-acetyl-1-aspartylglutamic acid, l-2-aminoadipic acid, 3-hydroxybutyric acid, bilirubin, and the significantly down-regulated metabolites, palmitic acid, 4-guanidinobutanoate, myristic acid, 3-dehydroxycarnitine, and s-adenosylmethioninamine, were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, biosynthesis of cofactors, protein digestion and absorption, and histidine metabolism, suggesting that these pathways may play important roles in the muscle development of duck during the embryonic stage. Moreover, a total of 2142 (1552 up-regulated and 590 down-regulated), 4873 (3810 up-regulated and 1063 down-regulated), and 2401 (1606 up-regulated and 795 down-regulated) DEGs were identified from E15_BM vs. E21_BM, E15_BM vs. E27_BM and E21_BM vs. E27_BM in the transcriptome, respectively. The significantly enriched GO terms from biological processes were positive regulation of cell proliferation, regulation of cell cycle, actin filament organization, and regulation of actin cytoskeleton organization, which were associated with muscle or cell growth and development. Seven significant pathways, highly enriched by FYN, PTK2, PXN, CRK, CRKL, PAK, RHOA, ROCK, INSR, PDPK1, and ARHGEF, were focal adhesion, regulation of actin cytoskeleton, wnt signaling pathway, insulin signaling pathway, extracellular matrix (ECM)-receptor interaction, cell cycle, and adherens junction, which participated in regulating the development of skeletal muscle in Pekin duck during the embryonic stage. KEGG pathway analysis of the integrated transcriptome and metabolome indicated that the pathways, including arginine and proline metabolism, protein digestion and absorption, and histidine metabolism, were involved in regulating skeletal muscle development in embryonic Pekin duck. These findings suggested that the candidate genes and metabolites involved in crucial biological pathways may regulate muscle development in the Pekin duck at the embryonic stage, and increased our understanding of the molecular mechanisms underlying the avian muscle development.

Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs.

Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed, synthesized between HN pigs and American Duroc, and are subjected to selection for important traits, such as fast growth and excellent meat quality. However, the genomic differences, selection signatures and loci associated with important economic traits in YN black pigs and HN pigs are still not well understood. In this study, based on high-density SNP chip analysis of 159 samples covering commercial DLY (Duroc × Landrace × Large White) pigs, HN pigs and YN black pigs, we performed a comprehensive analysis of phylogenetic relationships and genetic diversity among the three breeds. Furthermore, we used composite likelihood ratio tests (CLR) and F-statistics (Fst) to identify specific signatures of selection associated with important economic traits and potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes based on genetic differentiation (Fst) in the YN-DLY group. In the HN-DLY group, 169 selected regions harbored 58 genes. In the YN-HN group, 179 selected regions harbored 77 genes. In addition, the QTLs database with the most overlapping regions was associated with triglyceride level, number of mummified pigs, hemoglobin and loin muscle depth for YN black pigs, litter size and intramuscular fat content for HN pigs, and humerus length, linolenic acid content and feed conversion ratio mainly in DLY pigs. Of note, overlapping 14 tissue-specific promoters' annotation with the top Fst 1% selective regions systematically demonstrated the muscle-specific and hypothalamus-specific regulatory elements in YN black pigs. Taken together, these results contribute to an accurate knowledge of crossbreeding, thus benefitting the evaluation of production performance and improving the genome-assisted breeding of other important indigenous pig in the future.

Genome-wide association study to identify SNPs and candidate genes associated with body size traits in donkeys.

The Yangyuan donkey is a domestic animal breed mainly distributed in the northwest region of Hebei Province. Donkey body shape is the most direct production index, can fully reflect the donkey's growth status, and is closely related to important economic traits. As one of the main breeding selection criteria, body size traits have been widely used to monitor animal growth and evaluate the selection response. Molecular markers genetically linked to body size traits have the potential to accelerate the breeding process of animals via marker-assisted selection. However, the molecular markers of body size in Yangyuan donkeys have yet to be explored. In this study, we performed a genome-wide association study to identify the genomic variations associated with body size traits in a population of 120 Yangyuan donkeys. We screened 16 single nucleotide polymorphisms that were significantly associated with body size traits. Some genes distributed around these significant SNPs were considered candidates for body size traits, including SMPD4, RPS6KA6, LPAR4, GLP2R, BRWD3, MAGT1, ZDHHC15, and CYSLTR1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these genes were mainly involved in the P13K-Akt signaling pathway, Rap1 signaling pathway, regulation of actin cytoskeleton, calcium signaling pathway, phospholipase D signaling pathway, and neuroactive ligand-receptor interactions. Collectively, our study reported on a list of novel markers and candidate genes associated with body size traits in donkeys, providing useful information for functional gene studies and offering great potential for accelerating Yangyuan donkey breeding.

Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs

Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms. As the major indicators of growth performance, the backfat thickness (BFT), loin eye area (LEA), and days to 100 kg (D100) traits are commonly used to the genetics improvement in pigs. However, the available genetic markers for these traits are limited. To uncover novel loci and candidate genes associated with growth performance, we collected the phenotypic information of BFT, LEA, and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K BeadChip. We performed a genome-wide association study (GWAS) using 4 statistical models, including mixed linear models (MLM), fixed and random model circulating probability unification (FarmCPU), settlement of MLM under progressively exclusive relationships (SUPER), Bayesian-information and linkage-disequilibrium Iteratively nested keyway (Blink), and identified 5, 3, and 6 high-confidence single nucleotide polymorphisms (SNPs) associated with BFT, LEA, and D100, respectively. Variant annotation and quantitative trait locus (QTL) mapping analysis suggested that 6 genes (SKAP2, SATB1, PDE7B, PPP1R16B, WNT3, and WNT9B) were potentially associated with growth performance in pigs. Transcriptome analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2 (SKAP2) was higher in prenatal muscles than in postnatal muscles, and the expression of Phosphodiesterase 7B (PDE7B) continuously increased during the prenatal stages and gradually decreased after birth, implying their potential roles in prenatal skeletal muscle development. Overall, this study provides new candidate loci and genes for the genetic improvement of pigs.