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1.
BMC Plant Biol ; 19(1): 341, 2019 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-31382871

RESUMO

BACKGROUND: Barley is a low phosphorus (P) demand cereal crop. Tibetan wild barley, as a progenitor of cultivated barley, has revealed outstanding ability of tolerance to low-P stress. However, the underlying mechanisms of low-P adaption and the relevant genetic controlling are still unclear. RESULTS: We identified low-P tolerant barley lines in a doubled-haploid (DH) population derived from an elite Tibetan wild barley accession and a high-yield cultivar. The tolerant lines revealed greater root plasticity in the terms of lateral root length, compared to low-P sensitive lines, in response to low-P stress. By integrating the QTLs associated with root length and root transcriptomic profiling, candidate genes encoding isoflavone reductase, nitrate reductase, nitrate transporter and transcriptional factor MYB were identified. The differentially expressed genes (DEGs) involved the growth of lateral root, Pi transport within cells as well as from roots to shoots contributed to the differences between low-P tolerant line L138 and low-P sensitive lines L73 in their ability of P acquisition and utilization. CONCLUSIONS: The plasticity of root system is an important trait for barley to tolerate low-P stress. The low-P tolerance in the elite DH line derived from a cross of Tibetan wild barley and cultivated barley is characterized by enhanced growth of lateral root and Pi recycling within plants under low-P stress.


Assuntos
Hordeum/fisiologia , Fósforo/metabolismo , Raízes de Plantas/fisiologia , Adaptação Fisiológica , Perfilação da Expressão Gênica , Genes de Plantas/genética , Genes de Plantas/fisiologia , Hordeum/genética , Hordeum/crescimento & desenvolvimento , Hordeum/metabolismo , Fósforo/deficiência , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/metabolismo , Locos de Características Quantitativas/genética , Estresse Fisiológico
2.
Nat Commun ; 10(1): 2680, 2019 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-31213597

RESUMO

Genetic studies of complex traits in animals have been hindered by the need to generate, maintain, and phenotype large panels of recombinant lines. We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions of unique recombinant individuals. We use ceX-QTL to map a drug resistance locus with high resolution. We also map differences in gene expression in live worms and discovered that mutations in the co-chaperone sti-1 upregulate the transcription of HSP-90. Lastly, we use ceX-QTL to map loci that influence fitness genome-wide confirming previously reported causal variants and uncovering new fitness loci. ceX-QTL is fast, powerful and cost-effective, and will accelerate the study of complex traits in animals.


Assuntos
Caenorhabditis elegans/genética , Mapeamento Cromossômico/métodos , Aptidão Genética/genética , Locos de Características Quantitativas/genética , Característica Quantitativa Herdável , Animais , Mapeamento Cromossômico/economia , Resistência a Medicamentos/genética , Feminino , Regulação da Expressão Gênica/genética , Masculino , Fatores de Tempo
3.
Nat Commun ; 10(1): 2633, 2019 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-31201330

RESUMO

Long-range chromatin interactions are important for transcriptional regulation of genes, many of which are related to complex agronomics traits. However, the pattern of three-dimensional chromatin interactions remains unclear in plants. Here we report the generation of chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) data and the construction of extensive H3K4me3- and H3K27ac-centered chromatin interaction maps in maize. Results show that the interacting patterns between proximal and distal regulatory regions of genes are highly complex and dynamic. Genes with chromatin interactions have higher expression levels than those without interactions. Genes with proximal-proximal interactions prefer to be transcriptionally coordinated. Tissue-specific proximal-distal interactions are associated with tissue-specific expression of genes. Interactions between proximal and distal regulatory regions further interweave into organized network communities that are enriched in specific biological functions. The high-resolution chromatin interaction maps will help to understand the transcription regulation of genes associated with complex agronomic traits of maize.


Assuntos
Cromatina/metabolismo , Regulação da Expressão Gênica de Plantas , Sequências Reguladoras de Ácido Nucleico/genética , Transcrição Genética/genética , Zea mays/genética , Cromatina/genética , Imunoprecipitação da Cromatina , Mapeamento Cromossômico , Produção Agrícola , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Histonas/genética , Histonas/imunologia , Regiões Promotoras Genéticas , Locos de Características Quantitativas/genética
4.
Nat Commun ; 10(1): 2632, 2019 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-31201335

RESUMO

Chromatin loops connect regulatory elements to their target genes. They serve as bridges between transcriptional regulation and phenotypic variation in mammals. However, spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, we characterize epigenetic features of active promoter proximal regions and candidate distal regulatory elements to construct high-resolution chromatin interaction maps for maize via long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). The maps indicate that chromatin loops are formed between regulatory elements, and that gene pairs between promoter proximal regions tend to be co-expressed. The maps also demonstrated the topological basis of quantitative trait loci which influence gene expression and phenotype. Many promoter proximal regions are involved in chromatin loops with distal regulatory elements, which regulate important agronomic traits. Collectively, these maps provide a high-resolution view of 3D maize genome architecture, and its role in gene expression and phenotypic variation.


Assuntos
Cromatina/genética , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes/genética , Locos de Características Quantitativas/genética , Zea mays/genética , Cromatina/metabolismo , Imunoprecipitação da Cromatina , Mapeamento Cromossômico , Produção Agrícola , Elementos Facilitadores Genéticos/genética , Epigênese Genética , Epigenômica/métodos , Genoma de Planta/genética , Estudo de Associação Genômica Ampla , Mutação , Fenótipo , Regiões Promotoras Genéticas/genética
5.
Nat Commun ; 10(1): 2760, 2019 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-31235787

RESUMO

Heart failure is a leading cause of mortality, yet our understanding of the genetic interactions underlying this disease remains incomplete. Here, we harvest 1352 healthy and failing human hearts directly from transplant center operating rooms, and obtain genome-wide genotyping and gene expression measurements for a subset of 313. We build failing and non-failing cardiac regulatory gene networks, revealing important regulators and cardiac expression quantitative trait loci (eQTLs). PPP1R3A emerges as a regulator whose network connectivity changes significantly between health and disease. RNA sequencing after PPP1R3A knockdown validates network-based predictions, and highlights metabolic pathway regulation associated with increased cardiomyocyte size and perturbed respiratory metabolism. Mice lacking PPP1R3A are protected against pressure-overload heart failure. We present a global gene interaction map of the human heart failure transition, identify previously unreported cardiac eQTLs, and demonstrate the discovery potential of disease-specific networks through the description of PPP1R3A as a central regulator in heart failure.


Assuntos
Redes Reguladoras de Genes/genética , Insuficiência Cardíaca/genética , Miócitos Cardíacos/patologia , Fosfoproteínas Fosfatases/metabolismo , Animais , Benzenoacetamidas , Células Cultivadas , Conjuntos de Dados como Assunto , Modelos Animais de Doenças , Feminino , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica , Técnicas de Silenciamento de Genes , Estudo de Associação Genômica Ampla , Insuficiência Cardíaca/etiologia , Insuficiência Cardíaca/metabolismo , Insuficiência Cardíaca/patologia , Humanos , Masculino , Redes e Vias Metabólicas/genética , Camundongos , Camundongos Knockout , Pessoa de Meia-Idade , Fosfoproteínas Fosfatases/genética , Cultura Primária de Células , Piridinas , Locos de Características Quantitativas/genética , Ratos , Ratos Sprague-Dawley , Análise de Sequência de RNA/métodos
6.
Nat Commun ; 10(1): 2773, 2019 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-31235808

RESUMO

Dental caries and periodontitis account for a vast burden of morbidity and healthcare spending, yet their genetic basis remains largely uncharacterized. Here, we identify self-reported dental disease proxies which have similar underlying genetic contributions to clinical disease measures and then combine these in a genome-wide association study meta-analysis, identifying 47 novel and conditionally-independent risk loci for dental caries. We show that the heritability of dental caries is enriched for conserved genomic regions and partially overlapping with a range of complex traits including smoking, education, personality traits and metabolic measures. Using cardio-metabolic traits as an example in Mendelian randomization analysis, we estimate causal relationships and provide evidence suggesting that the processes contributing to dental caries may have undesirable downstream effects on health.


Assuntos
Cárie Dentária/genética , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Periodontite/genética , Cárie Dentária/epidemiologia , Genômica , Hereditariedade , Humanos , Análise da Randomização Mendeliana , Periodontite/epidemiologia , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas/genética , Autorrelato/estatística & dados numéricos
7.
Plant Sci ; 285: 122-131, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31203876

RESUMO

Domestication and subsequent breeding have eroded genetic diversity in the modern chickpea crop by ˜100-fold. Corresponding reductions to trait variation create the need, and an opportunity, to identify and harness the genetic capacity of wild species for crop improvement. Here we analyze trait segregation in a series of wild x cultivated hybrid populations to delineate the genetic underpinnings of domestication traits. Two species of wild chickpea, C. reticulatum and C. echinospermum, were crossed with the elite, early flowering C. arietinum cultivar ICCV96029. KASP genotyping of F2 parents with an FT-linked molecular marker enabled selection of 284 F3 families with reduced phenological variation: 255 F3 families of C. arietinum x reticulatum (AR) derived from 17 diverse wild parents and 29 F3 families of C. arietinum x echinospermum (AE) from 3 wild parents. The combined 284 lineages were genotyped using a genotyping-by-sequencing strategy and phenotyped for agronomic traits. 50 QTLs in 11 traits were detected from AR and 35 QTLs in 10 traits from the combined data. Using hierarchical clustering to assign traits to six correlated groups and mixed model based multi-trait mapping, four pleiotropic loci were identified. Bayesian analysis further identified four inter-trait relationships controlling the duration of vegetative growth and seed maturation, for which the underlying pleiotropic genes were mapped. A random forest approach was used to explore the most extreme trait differences between AR and AE progenies, identifying traits most characteristic of wild species origin. Knowledge of the genomic basis of traits that segregate in wild-cultivated hybrid populations will facilitate chickpea improvement by linking genetic and phenotypic variation in a quantitative genetic framework.


Assuntos
Cicer/genética , Genes de Plantas/genética , Melhoramento Vegetal/métodos , Teorema de Bayes , Cicer/crescimento & desenvolvimento , DNA de Plantas/genética , Domesticação , Estudos de Associação Genética , Ligação Genética/genética , Hibridização Genética/genética , Locos de Características Quantitativas/genética , Característica Quantitativa Herdável , Sementes/crescimento & desenvolvimento
8.
Plant Sci ; 285: 151-164, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31203880

RESUMO

Enhancing the accumulation of essential mineral elements in cereal grains is of prime importance for combating human malnutrition. Biofortification by breeding holds great potential for improving nutrient accumulation in grains. However, conventional breeding approaches require element analysis of many grain samples, which causes high costs. Here we applied hyperspectral imaging to estimate the concentration of 15 grain elements (C, B, Ca, Cd, Cu, Fe, K, Mg, Mn, Mo, N, Na, P, S, Zn) in high-throughput in the wild barley nested association mapping (NAM) population HEB-25, comprising 1,420 BC1S3 lines derived from crossing 25 wild barley accessions with the cultivar 'Barke'. Nutrient concentrations varied largely with a multitude of lines having higher micronutrient concentration than 'Barke'. In a genome-wide association study (GWAS), we located 75 quantitative trait locus (QTL) hotspots, whereof many could be explained by major genes such as NO APICAL MERISTEM-1 (NAM-1) and PHOTOPERIOD 1 (Ppd-H1). The GWAS approach revealed exotic alleles that were able to increase grain element concentrations. Remarkably, a QTL linked to GIBBERELLIN 20 OXIDASE 2 (HvGA20ox2) significantly increased several grain elements without yield loss. We conclude that introgressing promising exotic alleles into elite breeding material can assist in improving the nutritional value of barley grains.


Assuntos
Grão Comestível/genética , Hordeum/genética , Produção Agrícola , Grão Comestível/crescimento & desenvolvimento , Estudo de Associação Genômica Ampla , Hordeum/crescimento & desenvolvimento , Hordeum/metabolismo , Valor Nutritivo/genética , Locos de Características Quantitativas/genética , Característica Quantitativa Herdável , Análise Espectral/métodos
9.
BMC Plant Biol ; 19(1): 243, 2019 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-31174472

RESUMO

BACKGROUND: Green flesh color, resulting from the accumulation of chlorophyll, is one of the most important commercial traits for the fruits. The genetic network regulating green flesh formation has been studied in tomato, melon and watermelon. However, little is known about the inheritance and molecular basis of green flesh in cucumber. This study sought to determine the main genomic regions associated with green flesh. Three F2 and two BC1 populations derived from the 9110Gt (cultivated cucumber, green flesh color) and PI183967 (wild cucumber, white flesh color) were used for the green flesh genetic analysis. Two F2 populations of them were further employed to do the map construction and quantitative trait loci (QTL) study. Also, a core cucumber germplasms population was used to do the GWAS analysis. RESULTS: We identified three indexes, flesh color (FC), flesh extract color (FEC) and flesh chlorophyll content (FCC) in three environments. Genetic analysis indicated that green flesh color in 9110Gt is controlled by a major-effect QTL. We developed two genetic maps with 192 and 174 microsatellite markers respectively. Two novel inversions in Chr1 were identified between cultivated and wild cucumbers. The major-effect QTL, qgf5.1, was identified using FC, FEC and FCC index in all different environments used. In addition, the same qgf5.1, together with qgf3.1, was identified via GWAS. Further investigation of two candidate regions using pairwise LD correlations, combined with genetic diversity of qgf5.1 in natural populations, it was found that Csa5G021320 is the candidate gene of qgf5.1. Geographical distribution revealed that green flesh color formation could be due to the high latitude, which has longer day time to produce the photosynthesis and chlorophyll synthesis during cucumber domestication and evolution. CONCLUSIONS: We first reported the cucumber green flesh color is a quantitative trait. We detected two novel loci qgf5.1 and qgf3.1, which regulate the green flesh formation in cucumber. The QTL mapping and GWAS approaches identified several candidate genes for further validation using functional genomics or forward genetics approaches. Findings from the present study provide a new insight into the genetic control of green flesh in cucumber.


Assuntos
Cucumis sativus/fisiologia , Estudo de Associação Genômica Ampla , Fenótipo , Pigmentação/genética , Locos de Características Quantitativas/genética , Mapeamento Cromossômico , Cor , Cucumis sativus/genética , Redes Reguladoras de Genes/fisiologia
10.
J Dairy Sci ; 102(8): 7237-7247, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31155255

RESUMO

Relatedness between reference and test animals has an important effect on the reliability of genomic prediction for test animals. Because genomic prediction has been widely applied in practical cattle breeding and bulls have been selected according to genomic breeding value without progeny testing, the sires or grandsires of candidates might not have phenotypic information and might not be in the reference population when the candidates are selected. The objective of this study was to investigate the decreasing trend of the reliability of genomic prediction given distant reference populations, using genomic best linear unbiased prediction (GBLUP) and Bayesian variable selection models with or without including the quantitative trait locus (QTL) markers detected from sequencing data. The data used in this study consisted of 22,242 bulls genotyped using the 54K SNP array from EuroGenomics. Among them, 1,444 Danish bulls born from 2006 to 2010 were selected as test animals. Different reference populations with varying relationships to test animals were created according to pedigree-based relationships. The reference individuals having a relationship with one or more test animals higher than 0.4 (scenario ρ < 0.4), 0.2 (ρ < 0.2), or 0.1 (ρ < 0.1, where ρ = relationship coefficient) were removed from reference sets; these represented the distance between reference and test animals being 2 generations, 3 generations, and 4 generations, respectively. Imputed whole-genome sequencing data of bulls from Denmark were used to conduct a genome-wide association study (GWAS). A small number of significant variants (QTL markers) from the GWAS were added to the array data. To compare the effects of different models, the basic GBLUP model, a Bayesian selection variable model, a GBLUP model with 2 components of genetic effects, and a Bayesian model with pooled array data and QTL markers were used for estimating genomic estimated breeding values (GEBV) of test animals. The reliability of genomic prediction decreased when the test animals were more generations away from the reference population. The reliability of genomic prediction was 0.461 for 1 generation away and 0.396 for 3 generations away, with the same number of individuals in the reference set, using a GBLUP model with chip markers only. The results showed that using the Bayesian method and QTL markers improved the reliability of genomic prediction in all scenarios of relationship between test and reference animals, in a range of 1.3% and 65.1% (4 generations away with only 841 individuals in the reference set). However, most gains were for predictions of milk yield and fat yield. There was little improvement for predictions of protein yield and mastitis, and no improvement for prediction of fertility, except for scenario ρ < 0.1, in which there was a large improvement for predictions of all traits. On the other hand, models including more than 10% polygenic effect decreased prediction reliability when the relationship between test and reference animals was distant.


Assuntos
Teorema de Bayes , Bovinos/genética , Estudo de Associação Genômica Ampla/veterinária , Mastite Bovina/genética , Leite/metabolismo , Locos de Características Quantitativas/genética , Animais , Cruzamento , Dinamarca , Feminino , Fertilidade/genética , Marcadores Genéticos/genética , Genômica , Genótipo , Masculino , Herança Multifatorial/genética , Linhagem , Fenótipo , Reprodutibilidade dos Testes
11.
J Dairy Sci ; 102(8): 7263-7276, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31155265

RESUMO

Genetic effects on milk production traits in dairy cattle might change during lactation. However, most genome-wide association studies (GWAS) for milk production traits assume that genetic effects are constant during lactation. This assumption might lead to missing these quantitative trait loci (QTL) whose effects change during lactation. This study aimed to screen the whole genome specifically for QTL whose effects change during lactation. For this purpose, 4 different GWAS approaches were performed using test-day milk protein content records: (1) separate GWAS for specific lactation stages, (2) GWAS for estimated Wilmink lactation curve parameters, (3) a GWAS using a repeatability model where SNP effects are assumed constant during lactation, and (4) a GWAS for genotype by lactation stage interaction using a repeatability model and accounting for changing genetic effects during lactation. Separate GWAS for specific lactation stages suggested that the detection power greatly differs between lactation stages and that genetic effects of some QTL change during lactation. The GWAS for estimated Wilmink lactation curve parameters detected many chromosomal regions for Wilmink parameter a (protein content level), whereas 2 regions for Wilmink parameter b (decrease in protein content toward nadir) and no regions for Wilmink parameter c (increase in protein content after nadir) were detected. Twenty chromosomal regions were detected with effects on milk protein content; however, there was no evidence that their effects changed during lactation. For 5 chromosomal regions located on chromosomes 3, 9, 10, 14, and 27, significant evidence was observed for a genotype by lactation stage interaction and thus their effects on milk protein content changed during lactation. Three of these 5 regions were only identified using a GWAS for genotype by lactation stage interaction. Our study demonstrated that GWAS for genotype by lactation stage interaction offers new possibilities to identify QTL involved in milk protein content. The performed approaches can be applied to other milk production traits. Identification of QTL whose genetic effects change during lactation will help elucidate the genetic and biological background of milk production.


Assuntos
Bovinos/genética , Estudo de Associação Genômica Ampla/veterinária , Proteínas do Leite/metabolismo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Animais , Bovinos/fisiologia , Feminino , Genótipo , Lactação/genética , Fenótipo
12.
J Dairy Sci ; 102(8): 7189-7203, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31178181

RESUMO

The aim of this study was to investigate the feasibility of using mid-infrared (MIR) spectroscopy analysis of milk samples to increase the power and precision of genome-wide association studies (GWAS) for milk composition and to better distinguish linked quantitative trait loci (QTL). To achieve this goal, we analyzed phenotypic data of milk composition traits, related MIR spectra, and genotypic data comprising 626,777 SNP on 5,202 Holstein, Jersey, and crossbred cows. We performed a conventional GWAS on protein, lactose, fat, and fatty acid concentrations in milk, a GWAS on individual MIR wavenumbers, and a partial least squares regression (PLS), which is equivalent to a multi-trait GWAS, exploiting MIR data simultaneously to predict SNP genotypes. The PLS detected most of the QTL identified using single-trait GWAS, usually with a higher significance value, as well as previously undetected QTL for milk composition. Each QTL tends to have a different pattern of effects across the MIR spectrum and this explains the increased power. Because SNP tracking different QTL tend to have different patterns of effect, it was possible to distinguish closely linked QTL. Overall, the results of this study suggest that using MIR data through either GWAS or PLS analysis applied to genomic data can provide a powerful tool to distinguish milk composition QTL.


Assuntos
Bovinos/fisiologia , Estudo de Associação Genômica Ampla/veterinária , Leite/química , Locos de Características Quantitativas/genética , Animais , Bovinos/genética , Ácidos Graxos/análise , Feminino , Genótipo , Glicolipídeos/análise , Glicoproteínas/análise , Raios Infravermelhos , Lactose/análise , Leite/efeitos da radiação , Proteínas do Leite/análise , Fenótipo
13.
BMC Plant Biol ; 19(1): 259, 2019 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-31208337

RESUMO

BACKGROUND: Cultivated rice (Oryza sativa L.) is one of the staple food for over half of the world's population. Thus, improvement of cultivated rice is important for the development of the world. It has been shown that abundant elite genes exist in rice landraces in previous studies. RESULTS: A genome-wide association study (GWAS) performed with EMMAX for 12 agronomic traits measured in both Guangzhou and Hangzhou was carried out using 150 accessions of Ting's core collection selected based on 48 phenotypic traits from 2262 accessions of Ting's collection, the GWAS included more than 3.8 million SNPs. Within Ting's core collection, which has a simple population structure, low relatedness, and rapid linkage disequilibrium (LD) decay, we found 32 peaks located closely to previously cloned genes such as Hd1, SD1, Ghd7, GW8, and GL7 or mapped QTL, and these loci might be natural variations in the cloned genes or QTL which influence potentially agronomic traits. Furthermore, we also detected 32 regions where new genes might be located, and some peaks of these new candidate genes such as the signal on chromosome 11 for heading days were even higher than that of Hd1. Detailed annotation of these significant loci were shown in this study. Moreover, according to the estimated LD decay distance of 100 to 350 kb on the 12 chromosomes in this study, we found 13 identical significant regions in the two locations. CONCLUSIONS: This research provided important information for further mining these elite genes within Ting's core collection and using them for rice breeding.


Assuntos
Oryza/genética , Característica Quantitativa Herdável , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Genes de Plantas/genética , Estudos de Associação Genética , Estudo de Associação Genômica Ampla , Desequilíbrio de Ligação/genética , Locos de Características Quantitativas/genética
14.
Int J Mol Sci ; 20(9)2019 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-31083584

RESUMO

Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses.


Assuntos
Brachypodium/genética , Brachypodium/metabolismo , Variação Genética , Metaboloma/genética , Sementes/genética , Sementes/metabolismo , Mapeamento Cromossômico , Cruzamentos Genéticos , Genótipo , Endogamia , Locos de Características Quantitativas/genética , Vitamina B 6/metabolismo
16.
Nat Plants ; 5(5): 471-479, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31061537

RESUMO

Genome editing technologies are being widely adopted in plant breeding1. However, a looming challenge of engineering desirable genetic variation in diverse genotypes is poor predictability of phenotypic outcomes due to unforeseen interactions with pre-existing cryptic mutations2-4. In tomato, breeding with a classical MADS-box gene mutation that improves harvesting by eliminating fruit stem abscission frequently results in excessive inflorescence branching, flowering and reduced fertility due to interaction with a cryptic variant that causes partial mis-splicing in a homologous gene5-8. Here, we show that a recently evolved tandem duplication carrying the second-site variant achieves a threshold of functional transcripts to suppress branching, enabling breeders to neutralize negative epistasis on yield. By dissecting the dosage mechanisms by which this structural variant restored normal flowering and fertility, we devised strategies that use CRISPR-Cas9 genome editing to predictably improve harvesting. Our findings highlight the under-appreciated impact of epistasis in targeted trait breeding and underscore the need for a deeper characterization of cryptic variation to enable the full potential of genome editing in agriculture.


Assuntos
Domesticação , Epistasia Genética/genética , Duplicação Gênica/genética , Lycopersicon esculentum/genética , Proteína 9 Associada à CRISPR , Sistemas CRISPR-Cas , Flores/crescimento & desenvolvimento , Duplicação Gênica/fisiologia , Edição de Genes/métodos , Variação Genética/genética , Variação Genética/fisiologia , Lycopersicon esculentum/crescimento & desenvolvimento , Lycopersicon esculentum/fisiologia , Melhoramento Vegetal , Plantas Geneticamente Modificadas , Locos de Características Quantitativas/genética , Reprodução/genética , Reprodução/fisiologia
17.
Genet Test Mol Biomarkers ; 23(6): 393-400, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31063404

RESUMO

Background: The protein AXIN2 is involved in the negative feedback regulation of the Wnt/ß-catenin signaling pathway; it functions by promoting ß-catenin degradation. AXIN2 mutations have been studied in various cancers. In this study, we genotyped three single nucleotide polymorphisms in the AXIN2 gene and investigated their association with the risk of breast cancer (BC) in the Chinese Han population. Methods: In a population of 415 BC patients and 528 controls the expression of AXIN2 was measured using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and compared with the overall survival (OS) of BC patients analyzed through Oncomine and Kaplan-Meier plotter databases. Bioinformatic analyses demonstrated that AXIN2 mRNA levels were downregulated in BC patients; this in turn correlated with a poorer survival rate for BC patients. Results: The polymorphisms rs11079571 and rs3923087, but not rs3923086, were associated with an increased risk of BC. The minor allele containing genotypes of polymorphism rs3923087 were positively associated with lymph node metastases. A haplotype analysis demonstrated that the ATA haplotype was correlated with an increased risk of BC. Conclusion: In conclusion, the downregulation of AXIN2 is related to poorer OS for BC patients. Its polymorphisms rs11079571 and rs3923087 confer susceptibility to BC. These findings should be confirmed with larger studies that include more diverse ethnic populations.


Assuntos
Proteína Axina/genética , Neoplasias da Mama/genética , Adulto , Alelos , Grupo com Ancestrais do Continente Asiático/genética , Proteína Axina/fisiologia , Neoplasias da Mama/metabolismo , Estudos de Casos e Controles , China , Grupos Étnicos/genética , Feminino , Frequência do Gene/genética , Predisposição Genética para Doença/genética , Variação Genética/genética , Genótipo , Haplótipos/genética , Humanos , Metástase Linfática/genética , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Fatores de Risco , Taxa de Sobrevida , Via de Sinalização Wnt/genética
18.
Genet Test Mol Biomarkers ; 23(6): 380-386, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31063409

RESUMO

Background: Hallux valgus (HV) is a type of forefoot deformity affecting ∼23% of adults. Previous studies have shown that HV is highly heritable. Tumor necrosis factor (TNF) is an important proinflammatory cytokine involved in bone remodeling and plays essential roles in osteoarthritis and chronic inflammatory bone diseases, including HV. Methods: A total of 1,788 Chinese women comprising 637 HV subjects and 1,151 controls were recruited. Twelve single nucleotide polymorphisms (SNPs) located in TNF and its promoter regions were selected and genotyped. Genetic association analyses were performed to investigate potential susceptibility SNPs. Bioinformatic and expression quantitative trait loci (eQTL) analyses were conducted to examine the functional consequences of the SNPs identified as being significantly associated with HV. Results: SNP rs1800629, which is located at the 5' end of the promoter region of TNF, was identified as significantly associated with HV status in Chinese women (OR = 0.56, p = 2.12 × 10-6). Bioinformatic analyses using RegulomeDB indicated that this SNP has important functional significance, but subsequent eQTL analyses did not identify a significant association between rs1800629 and TNF gene expression. In addition, 26 genes with cis-eQTL for rs1800629 were identified. Conclusions: This study identified a susceptibility SNP for HV located within the promoter region of the TNF gene. Bioinformatic and eQTL analyses linked this SNP to 26 genes but not to TNF. Functional studies are needed to more fully characterize the effects of this SNP.


Assuntos
Hallux Valgus/genética , Fator de Necrose Tumoral alfa/genética , Adulto , Alelos , Grupo com Ancestrais do Continente Asiático/genética , Estudos de Casos e Controles , China , Grupos Étnicos/genética , Feminino , Predisposição Genética para Doença/genética , Variação Genética/genética , Genótipo , Hallux Valgus/metabolismo , Haplótipos/genética , Humanos , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Fatores de Risco , Fator de Necrose Tumoral alfa/fisiologia
19.
BMC Plant Biol ; 19(1): 201, 2019 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-31096901

RESUMO

BACKGROUND: The kernel row number (KRN) of an ear is an important trait related to yield and domestication in maize. Exploring the underlying genetic mechanisms of KRN has great research significance and application potential. RESULTS: In the present study, N531 with a KRN of 18-22 and SLN with a KRN of 4-6 were used as the recurrent parent and the donor parent, respectively, to develop two introgression lines (ILs), IL_A and IL_B, both of which have common negative-effect alleles from SLN on chromosomes 1, 5 and 10 and significantly reduced inflorescence meristem (IM) diameter and KRN compared with those of N531. We used RNA-Seq to investigate the transcriptome profiles of 5-mm immature ears of N531, IL_A and IL_B. We identified a total of 2872 differentially expressed genes (DEGs) between N531 and IL_A, 2428 DEGs between N531 and IL_B and 1811 DEGs between IL_A and IL_B. A total of 1252 DEGs were detected as overlapping DEGs, and 89 DEGs were located on the common introgression fragments. Furthermore, three DEGs (Zm00001d013277, Zm00001d015310 and Zm00001d015377) containing three SNPs associated with KRN were identified using regional association mapping. CONCLUSIONS: These results will facilitate our understanding of ear development and provide important candidate genes for further study on KRN.


Assuntos
Grão Comestível/crescimento & desenvolvimento , Zea mays/genética , Mapeamento Cromossômico/métodos , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/genética , Genes de Plantas/fisiologia , Estudos de Associação Genética , Locos de Características Quantitativas/genética , Característica Quantitativa Herdável , Reação em Cadeia da Polimerase em Tempo Real
20.
J Anim Sci ; 97(7): 2793-2802, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31087081

RESUMO

The objectives of this study were to identify informative genomic regions that affect the exterior traits of purebred Korean Yorkshire pigs and to investigate and compare the accuracy of genomic prediction for response variables. Phenotypic data on body height (BH), body length (BL), and total teat number (TTN) from 2,432 Yorkshire pigs were used to obtain breeding values including as response variable the estimated breeding value (EBV) and 2 types of deregressed EBVs-one including the parent average (DEBVincPA) and the other excluding it (DEBVexcPA). A final genotype panel comprising 46,199 SNP markers was retained for analysis after quality control for common SNPs. The BayesB and BayesC methods-with various π and weighted response variables (EBV, DEBVincPA, or DEBVexcPA)-were used to estimate SNP effects, through the genome-wide association study. The significance of genomic windows (1 Mb) was obtained at 1.0% additive genetic variance and was subsequently used to identify informative genomic regions. Furthermore, SNPs with a high model frequency (≥0.90) were considered informative. The accuracy of genomic prediction was estimated using a 5-fold cross-validation with the K-means clustering method. Genomic accuracy was measured as the genomic correlation between the molecular breeding value and the individual weighted response variables (EBV, DEBVincPA, or DEBVexcPA). The number of identified informative windows (1 Mb) for BH, BL, and TTN was 4, 3, and 4, respectively. The number of significant SNPs for BH, BL, and TTN was 6, 4, and 5, respectively. Diversity π did not influence the accuracy of genomic prediction. The BayesB method showed slightly higher genomic accuracy for exterior traits than BayesC method in this study. In addition, the genomic accuracy using DEBVincPA as response variable was higher than that using other response variables. Therefore, the genomic accuracy using BayesB (π = 0.90) with DEBVinPA as a response variable was the most effective in this study. The genomic accuracy values for BH, BL, and TTN were calculated to be 0.52, 0.60, and 0.51, respectively.


Assuntos
Estudo de Associação Genômica Ampla/veterinária , Genoma/genética , Genômica , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Suínos/genética , Animais , Cruzamento , Análise por Conglomerados , Confiabilidade dos Dados , Feminino , Marcadores Genéticos/genética , Testes Genéticos/veterinária , Genótipo , Masculino , Glândulas Mamárias Animais/anatomia & histologia , Fenótipo , Suínos/anatomia & histologia
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