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1.
Talanta ; 235: 122776, 2021 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-34517633

RESUMO

Agriculture and food crops monitoring is extremely important for securing the food supply chain to human society. Here, we developed a highly specific detection method for monitoring pathogenic fungus Colletotrichum gloeosporioides using necrotrophic DNA biomarker as the recognition element and surface plasmon resonance (SPR) as transducing mechanism in the prism coupling configuration. The sensor shows its response for a wide range of concentrations from pM to µM of target DNA sequence using a complementary DNA probe immobilized on the sensor surface, which could detect concentrations as low as 7 pM. The detection limit is found to be comparable with conventional molecular-based detection platforms, achieved due to optimized spectral SPR bimetallic substrate with subpixel resolution obtained by post processing. The response time of the sensor for detection is less than 30 min at room temperature. The quick detection scheme of the sensor may facilitate the screening of a large number of samples acquired for the sorting of harvested produce. This sensor is fast, reliable, cost-effective, and can be miniaturized for portability for the screening of real samples (mRNA) in the field and packaging house.


Assuntos
Colletotrichum , Marcadores Genéticos , Humanos , Doenças das Plantas , Ressonância de Plasmônio de Superfície
2.
Ann Clin Lab Sci ; 51(4): 451-460, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34452883

RESUMO

OBJECTIVE: To reduce the incidence of Opioid Use Disorder (OUD), multiple guidelines recommend assessing the risk of OUD prior to prescribing oral opioids. Although subjective risk assessments are available to help classify subjects at risk for OUD, we are aware of no clinically validated objective risk assessment tools. An objective risk assessment based on genetics may help inform shared decision-making prior to prescribing short-duration oral opioids. METHODS: A multicenter, observational cohort of adults exposed to prescription oral opioids for 4-30 days was conducted to determine the performance of an OUD classifier derived from machine learning (ML). From this cohort, the demographics of the U.S. adult opioid-prescribed population were used to create a blinded, random, representative group of subjects (n=385) for analysis to accurately estimate the performance characteristics in the intended use population. Genotyping was performed via a qualitative SNP microarray on DNA extracted from buccal samples. RESULTS: In the study subjects, the classifier demonstrated 82.5% sensitivity (95% confidence intervals: 76.1%-87.8%) and 79.9% specificity (73.7-85.2%), with no statistically significant differences in clinical performance observed based on gender, age, length of follow-up from opioid exposure, race, or ethnicity. CONCLUSION: This study demonstrates an ML classifier may provide additional objective information regarding a patient's risk of developing OUD. This information may enable subjects and healthcare providers to make more informed decisions when considering the use of oral opioids.


Assuntos
Analgésicos Opioides/efeitos adversos , Marcadores Genéticos , Aprendizado de Máquina , Transtornos Relacionados ao Uso de Opioides/epidemiologia , Medição de Risco/métodos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Feminino , Seguimentos , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Transtornos Relacionados ao Uso de Opioides/etiologia , Transtornos Relacionados ao Uso de Opioides/genética , Transtornos Relacionados ao Uso de Opioides/patologia , Prognóstico , Estudos Prospectivos , Estados Unidos/epidemiologia , Adulto Jovem
3.
BMC Genomics ; 22(1): 595, 2021 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-34353285

RESUMO

BACKGROUND: Cannabis sativa L., a dioecious plant derived from China, demonstrates important medicinal properties and economic value worldwide. Cannabis properties have been usually harnessed depending on the sex of the plant. To analyse the genetic structure of Chinese Cannabis and identify sex-linked makers, genome-wide insertion-deletion (InDel) markers were designed and used. RESULTS: In this study, a genome-wide analysis of insertion-deletion (InDel) polymorphisms was performed based on the recent genome sequences. In total, 47,558 InDels were detected between the two varieties, and the length of InDels ranged from 4 bp to 87 bp. The most common InDels were tetranucleotides, followed by pentanucleotides. Chromosome 5 exhibited the highest number of InDels among the Cannabis chromosomes, while chromosome 10 exhibited the lowest number. Additionally, 31,802 non-redundant InDel markers were designed, and 84 primers evenly distributed in the Cannabis genome were chosen for polymorphism analysis. A total of 38 primers exhibited polymorphisms among three accessions, and of the polymorphism primers, 14 biallelic primers were further used to analyse the genetic structure. A total of 39 fragments were detected, and the PIC value ranged from 0.1209 to 0.6351. According to the InDel markers and the flowering time, the 115 Chinese germplasms were divided into two subgroups, mainly composed of cultivars obtained from the northernmost and southernmost regions, respectively. Additional two markers, "Cs-I1-10" and "Cs-I1-15", were found to amplify two bands (398 bp and 251 bp; 293 bp and 141 bp) in the male plants, while 389-bp or 293-bp bands were amplified in female plants. Using the two markers, the feminized and dioecious varieties could also be distinguished. CONCLUSION: Based on the findings obtained herein, we believe that this study will facilitate the genetic improvement and germplasm conservation of Cannabis in China, and the sex-linked InDel markers will provide accurate sex identification strategies for Cannabis breeding and production.


Assuntos
Cannabis , Cannabis/genética , China , Marcadores Genéticos , Genoma , Mutação INDEL , Melhoramento Vegetal
4.
Int J Mol Sci ; 22(16)2021 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-34445527

RESUMO

Primary ciliary dyskinesia (PCD) is a disease caused by impaired function of motile cilia. PCD mainly affects the lungs and reproductive organs. Inheritance is autosomal recessive and X-linked. PCD patients have diverse clinical manifestations, thus making the establishment of proper diagnosis challenging. The utility of next-generation sequencing (NGS) technology for diagnostic purposes allows for better understanding of the PCD genetic background. However, identification of specific disease-causing variants is difficult. The main aim of this study was to create a unique guideline that will enable the standardization of the assessment of novel genetic variants within PCD-associated genes. The designed pipeline consists of three main steps: (1) sequencing, detection, and identification of genes/variants; (2) classification of variants according to their effect; and (3) variant characterization using in silico structural and functional analysis. The pipeline was validated through the analysis of the variants detected in a well-known PCD disease-causing gene (DNAI1) and the novel candidate gene (SPAG16). The application of this pipeline resulted in identification of potential disease-causing variants, as well as validation of the variants pathogenicity, through their analysis on transcriptional, translational, and posttranslational levels. The application of this pipeline leads to the confirmation of PCD diagnosis and enables a shift from candidate to PCD disease-causing gene.


Assuntos
Dineínas do Axonema/genética , Transtornos da Motilidade Ciliar/diagnóstico , Marcadores Genéticos , Proteínas Associadas aos Microtúbulos/genética , Mutação , Estudos de Casos e Controles , Transtornos da Motilidade Ciliar/classificação , Transtornos da Motilidade Ciliar/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos
5.
Fa Yi Xue Za Zhi ; 37(3): 372-377, 2021 Jun.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-34379907

RESUMO

Abstract: Objective To derive the probability distribution formula of combined identity by state (CIBS) score among individuals with different relationships based on population data of autosomal multiallelic genetic markers. Methods The probabilities of different identity by state (IBS) scores occurring at a single locus between two individuals with different relationships were derived based on the principle of ITO method. Then the distribution probability formula of CIBS score between two individuals with different relationships when a certain number of genetic markers were used for relationship identification was derived based on the multinomial distribution theory. The formula was compared with the CIBS probability distribution formula based on binomial distribution theory. Results Between individuals with a certain relationship, labelled as RS, the probabilities of IBS=2, 1 and 0 occurring at a certain autosomal genetic marker x (that is, p2(RSx), p1(RSx) and p0(RSx)), can be calculated based on the allele frequency data of that genetic marker and the probability of two individuals with the corresponding RS relationship sharing 0, 1 or 2 identity by descent (IBD) alleles (that is, φ0, φ1 and φ2). For a genotyping system with multiple independent genetic markers, the distribution of CIBS score between pairs of individuals with relationships other than parent-child can be deducted using the averages of the 3 probabilities of all genetic markers (that is, p2(RS), p1(RS) and p0(RS)), based on multinomial distribution theory. Conclusion The calculation of CIBS score distribution formula can be extended to all kinships and has great application value in case interpretation and system effectiveness evaluation. In most situations, the results based on binomial distribution formula are similar to those based on the formula derived in this study, thus, there is little difference between the two methods in actual work.


Assuntos
Genótipo , Alelos , Frequência do Gene , Marcadores Genéticos , Humanos , Probabilidade
6.
Int J Mol Sci ; 22(15)2021 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-34360619

RESUMO

qRT-PCR still remains the most widely used method for quantifying gene expression levels, although newer technologies such as next generation sequencing are becoming increasingly popular. A critical, yet often underappreciated, problem when analysing qRT-PCR data is the selection of suitable reference genes. This problem is compounded in situations where up to 25% of all genes may change (e.g., due to leukocyte invasion), as is typically the case in ARDS. Here, we examined 11 widely used reference genes for their suitability in commonly used models of acute lung injury (ALI): ventilator-induced lung injury (VILI), in vivo and ex vivo, lipopolysaccharide plus mechanical ventilation (MV), and hydrochloric acid plus MV. The stability of reference gene expression was determined using the NormFinder, BestKeeper, and geNorm algorithms. We then proceeded with the geNorm results because this is the only algorithm that provides the number of reference genes required to achieve normalisation. We chose interleukin-6 (Il-6) and C-X-C motif ligand 1 (Cxcl-1) as the genes of interest to analyse and demonstrate the impact of inappropriate normalisation. Reference gene stability differed between the ALI models and even within the subgroup of VILI models, no common reference gene index (RGI) could be determined. NormFinder, BestKeeper, and geNorm produced slightly different, but comparable results. Inappropriate normalisation of Il-6 and Cxcl1 gene expression resulted in significant misinterpretation in all four ALI settings. In conclusion, choosing an inappropriate normalisation strategy can introduce different kinds of bias such as gain or loss as well as under- or overestimation of effects, affecting the interpretation of gene expression data.


Assuntos
Lesão Pulmonar Aguda/genética , Algoritmos , Modelos Animais de Doenças , Perfilação da Expressão Gênica/normas , Regulação da Expressão Gênica , Marcadores Genéticos , Lesão Pulmonar Aguda/patologia , Animais , Feminino , Camundongos , Padrões de Referência
7.
Adv Gerontol ; 34(3): 360-366, 2021.
Artigo em Russo | MEDLINE | ID: mdl-34409814

RESUMO

For the first time in the ethnic group of Abkhazians, the association analysis of polymorphic DNA-markers of the antioxidant genes CAT (rs1001179), MSRA (rs10098474), GPX1 (rs1050450), GSR (rs1002149), GSTP1 (rs1695), SOD1 (rs2070424), SOD2 (rs4880), PON1 (rs662), PON2 (rs7493) with age was performed. Using ROC-analysis and logistic regression, it was found that the spectrum of alleles and genotypes frequencies of PON1 and GSTP1 genes polymorphic markers change throughout the studied age period (21-107 years old); the distribution of allele and genotype frequencies of CAT and SOD2 genes polymorphic markers changes within the age of 60 years. Multilocus genetic markers of longevity were determined by the Monte Carlo Markov chain method. Among persons in the age range 60-107 years, the frequency of observation of the patterns GSTP1*G/G+PON1*G (OR=6,59, PFDR=0,018) and GSTP1*G/G+SOD1*A (OR=3,4, PFDR=0,041) is statistically significantly increased; the GSTP1*A allele in various combinations with the PON1*A, PON2*C and CAT*C alleles are less common (OR=0,3, PFDR<0,05).


Assuntos
Antioxidantes , Grupos Étnicos , Alelos , Arildialquilfosfatase/genética , DNA , Grupos Étnicos/genética , Marcadores Genéticos , Predisposição Genética para Doença , Genótipo , Humanos , Polimorfismo de Nucleotídeo Único
8.
BMC Plant Biol ; 21(1): 388, 2021 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-34416870

RESUMO

BACKGROUND: Soybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil. Seed protein content (SPC) is a valuable quality trait controlled by multiple genes in soybean. RESULTS: In this study, we performed quantitative trait loci (QTL) mapping, QTL-seq, and RNA sequencing (RNA-seq) to reveal the genes controlling protein content in the soybean by using the high protein content variety Nanxiadou 25. A total of 50 QTL for SPC distributed on 14 chromosomes except chromosomes 4, 12, 14, 17, 18, and 19 were identified by QTL mapping using 178 recombinant inbred lines (RILs). Among these QTL, the major QTL qSPC_20-1 and qSPC_20-2 on chromosome 20 were repeatedly detected across six tested environments, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. 329 candidate DEGs were obtained within the QTL region of qSPC_20-1 and qSPC_20-2 via gene expression profile analysis. Nine of which were associated with SPC, potentially representing candidate genes. Clone sequencing results showed that different single nucleotide polymorphisms (SNPs) and indels between high and low protein genotypes in Glyma.20G088000 and Glyma.16G066600 may be the cause of changes in this trait. CONCLUSIONS: These results provide the basis for research on candidate genes and marker-assisted selection (MAS) in soybean breeding for seed protein content.


Assuntos
Mapeamento Cromossômico , Estudos de Associação Genética , Proteínas de Plantas/análise , Proteínas de Plantas/genética , Sementes/química , Soja/química , Soja/genética , Produtos Agrícolas/química , Produtos Agrícolas/genética , Regulação da Expressão Gênica de Plantas , Marcadores Genéticos , Variação Genética , Genótipo , Locos de Características Quantitativas , Análise de Sequência de RNA
9.
Nat Commun ; 12(1): 5071, 2021 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-34417470

RESUMO

Identification of causal variants and genes underlying genome-wide association study (GWAS) loci is essential to understand the biology of alcohol use disorder (AUD) and drinks per week (DPW). Multi-omics integration approaches have shown potential for fine mapping complex loci to obtain biological insights to disease mechanisms. In this study, we use multi-omics approaches, to fine-map AUD and DPW associations at single SNP resolution to demonstrate that rs56030824 on chromosome 11 significantly reduces SPI1 mRNA expression in myeloid cells and lowers risk for AUD and DPW. Our analysis also identifies MAPT as a candidate causal gene specifically associated with DPW. Genes prioritized in this study show overlap with causal genes associated with neurodegenerative disorders. Multi-omics integration analyses highlight, genetic similarities and differences between alcohol intake and disordered drinking, suggesting molecular heterogeneity that might inform future targeted functional and cross-species studies.


Assuntos
Alcoolismo/genética , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Genômica , Doenças Neurodegenerativas/genética , Encéfalo/metabolismo , Epigênese Genética , Feto/metabolismo , Redes Reguladoras de Genes , Loci Gênicos , Marcadores Genéticos , Humanos , Desequilíbrio de Ligação/genética , Análise da Randomização Mendeliana , Mapeamento Físico do Cromossomo , Regiões Promotoras Genéticas/genética , Locos de Características Quantitativas/genética
10.
BMC Plant Biol ; 21(1): 311, 2021 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-34210282

RESUMO

BACKGROUND: Mineral elements are important for maintaining good human health besides heavy metals. Mining genes that control mineral elements are paramount for improving their accumulation in the wheat grain. Although previous studies have reported some loci for beneficial trace elements, they have mainly focused on Zn and Fe content. However, little information is available regarding the genetic loci differences in dissecting synchronous accumulation of multiple mineral elements in wheat grains, including beneficial and heavy elements. Therefore, a genome-wide association study (GWAS) was conducted on 205 wheat accessions with 24,355 single nucleotide polymorphisms (SNPs) to identify important loci and candidate genes for controlling Ca, Fe, Zn, Se, Cu, Mn, Cd, As, and Pb accumulation in wheat grains. RESULTS: A total of 101 marker-trait associations (MTAs) (P < 10-5) loci affecting the content of nine mineral elements was identified on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 3D, 4A, 4B, 5A, 5B, 5D, 6B, 7A, 7B, and 7D. Among these, 17 major MTAs loci for the nine mineral elements were located, and four MTAs loci (P < 10-5) were found on chromosomes 1B, 6B, 7B, and 7D. Eight multi-effect MTAs loci were detected that are responsible for the control of more than one trait, mainly distributed on chromosomes 3B, 7B, and 5A. Furthermore, sixteen candidate genes controlling Ca, Fe, Zn, Se, Cd, and Pb were predicted, whose functions were primarily related to ion binding, including metals, Fe, Ca, Cu, Mg, and Zn, ATP binding, ATPase activity, DNA binding, RNA binding, and protein kinase activity. CONCLUSIONS: Our study indicated the existence of gene interactions among mineral elements based on multi-effect MTAs loci and candidate genes. Meanwhile this study provided new insights into the genetic control of mineral element concentrations, and the important loci and genes identified may contribute to the rapid development of beneficial mineral elements and a reduced content of harmful heavy metals in wheat grain.


Assuntos
Genoma de Planta , Minerais/metabolismo , Estações do Ano , Sementes/genética , Triticum/genética , Alelos , Mapeamento Cromossômico , Loci Gênicos , Marcadores Genéticos , Estudo de Associação Genômica Ampla , Fenótipo
11.
BMC Plant Biol ; 21(1): 313, 2021 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-34215178

RESUMO

BACKGROUND: Harnessing heterosis is one of the major approaches to increase rice yield and has made a great contribution to food security. The identification and selection of outstanding parental genotypes especially among male sterile lines is a key step for exploiting heterosis. Two-line hybrid system is based on the discovery and application of photoperiod- and thermo-sensitive genic sensitive male sterile (PTGMS) materials. The development of wide-range of male sterile lines from a common gene pool leads to a narrower genetic diversity, which is vulnerable to biotic and abiotic stress. Hence, it is valuable to ascertain the genetic background of PTGMS lines and to understand their relationships in order to select and design a future breeding strategy. RESULTS: A collection of 118 male sterile rice lines and 13 conventional breeding lines from the major rice growing regions of China was evaluated and screened against the photosensitive (pms3) and temperature sensitive male sterility (tms5) genes. The total gene pool was divided into four major populations as P1 possessing the pms3, P2 possessing tms5, P3 possessing both pms3 and tms5 genes, and P4 containing conventional breeding lines without any male sterility allele. The high genetic purity was revealed by homozygous alleles in all populations. The population admixture, principle components and the phylogenetic analysis revealed the close relations of P2 and P3 with P4. The population differentiation analysis showed that P1 has the highest differentiation coefficient. The lines from P1 were observed as the ancestors of other three populations in a phylogenetic tree, while the lines in P2 and P3 showed a close genetic relation with conventional lines. A core collection of top 10% lines with maximum within and among populations genetic diversity was constructed for future research and breeding efforts. CONCLUSION: The low genetic diversity and close genetic relationship among PTGMS lines in P2, P3 and P4 populations suggest a selection sweep and they might result from a backcrossing with common ancestors including the pure lines of P1. The core collection from PTGMS panel updated with new diverse germplasm will serve best for further two-line hybrid breeding.


Assuntos
Oryza/genética , Fotoperíodo , Infertilidade das Plantas/genética , Sementes/genética , Temperatura , Núcleo Celular/genética , Núcleo Celular/efeitos da radiação , Análise por Conglomerados , Ontologia Genética , Estudos de Associação Genética , Marcadores Genéticos , Luz , Nucleotídeos/genética , Oryza/efeitos da radiação , Filogenia , Infertilidade das Plantas/efeitos da radiação , Polimorfismo de Nucleotídeo Único/genética , Análise de Componente Principal , Reprodutibilidade dos Testes , Sementes/efeitos da radiação
12.
BMC Plant Biol ; 21(1): 312, 2021 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-34215182

RESUMO

BACKGROUND: Peanut smut is a disease caused by the fungus Thecaphora frezii Carranza & Lindquist to which most commercial cultivars in South America are highly susceptible. It is responsible for severely decreased yield and no effective chemical treatment is available to date. However, smut resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring smut resistance within a tetraploid genetic background, this study evaluated a RIL population {susceptible Arachis hypogaea subsp. hypogaea (JS17304-7-B) × resistant synthetic amphidiploid (JS1806) [A. correntina (K 11905) × A. cardenasii (KSSc 36015)] × A. batizocoi (K 9484)4×} segregating for the trait. RESULTS: A SNP based genetic map arranged into 21 linkage groups belonging to the 20 peanut chromosomes was constructed with 1819 markers, spanning a genetic distance of 2531.81 cM. Two consistent quantitative trait loci (QTLs) were identified qSmIA08 and qSmIA02/B02, located on chromosome A08 and A02/B02, respectively. The QTL qSmIA08 at 15.20 cM/5.03 Mbp explained 17.53% of the phenotypic variance, while qSmIA02/B02 at 4.0 cM/3.56 Mbp explained 9.06% of the phenotypic variance. The combined genotypic effects of both QTLs reduced smut incidence by 57% and were stable over the 3 years of evaluation. The genome regions containing the QTLs are rich in genes encoding proteins involved in plant defense, providing new insights into the genetic architecture of peanut smut resistance. CONCLUSIONS: A major QTL and a minor QTL identified in this study provide new insights into the genetic architecture of peanut smut resistance that may aid in breeding new varieties resistant to peanut smut.


Assuntos
Arachis/genética , Arachis/microbiologia , Mapeamento Cromossômico , Resistência à Doença/genética , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Locos de Características Quantitativas/genética , Estudos de Associação Genética , Marcadores Genéticos , Endogamia , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Recombinação Genética/genética
13.
Int J Mol Sci ; 22(13)2021 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-34281266

RESUMO

Bone marrow stromal cells (BMSCs) are multipotent cells which can differentiate into chondrocytes, osteoblasts, and fat cells. Under pathological stress, reduced bone formation in favour of fat formation in the bone marrow has been observed through a switch in the differentiation of BMSCs. The bone/fat switch causes bone growth defects and disordered bone metabolism in bone marrow, for which the mechanisms remain unclear, and treatments are lacking. Studies suggest that small non-coding RNAs (microRNAs) could participate in regulating BMSC differentiation by disrupting the post-transcription of target genes, leading to bone/fat formation changes. This review presents an emerging concept of microRNA regulation in the bone/fat formation switch in bone marrow, the evidence for which is assembled mainly from in vivo and in vitro human or animal models. Characterization of changes to microRNAs reveals novel networks that mediate signalling and factors in regulating bone/fat switch and homeostasis. Recent advances in our understanding of microRNAs in their control in BMSC differentiation have provided valuable insights into underlying mechanisms and may have significant potential in development of new therapeutics.


Assuntos
Adipogenia/genética , Adipogenia/fisiologia , Células-Tronco Mesenquimais/citologia , Células-Tronco Mesenquimais/metabolismo , Osteogênese/genética , Osteogênese/fisiologia , Animais , Proteínas Morfogenéticas Ósseas/genética , Proteínas Morfogenéticas Ósseas/metabolismo , Sinalização do Cálcio/genética , Diferenciação Celular/genética , Diferenciação Celular/fisiologia , Marcadores Genéticos , Humanos , MicroRNAs/genética , MicroRNAs/metabolismo , Modelos Biológicos , Transdução de Sinais/genética , Proteínas Smad/genética , Proteínas Smad/metabolismo , Fator de Crescimento Transformador beta/genética , Fator de Crescimento Transformador beta/metabolismo , Via de Sinalização Wnt/genética
14.
Methods Mol Biol ; 2288: 49-72, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34270004

RESUMO

Molecular markers are employed for doubled haploid (DH) technology by researchers and applied plant breeders in many crops. In the 1990s, isozymes and RFLPs were commonly used marker technologies to characterize DHs and were later replaced by PCR- based markers (e.g., RAPDs, AFLPs, ISSRs, SSRs) and today by SNPs. Markers are used for multiple purposes in DH production, that is, for the study of genes underlying haploid induction and confirming homozygous plants of gametophytic origin. Furthermore, they are tools for investigating segregation in DH populations and for mapping simple and complex traits using DHs. The deployment of DHs and markers for developing trait-linked markers are demonstrated with examples from rapeseed, wheat, and barley. Marker development for resistance to viruses derived from genetic resources and their use in, for example, pyramiding of resistance genes, are given as an example for the combination of DH-technology and marker development in research. Today, marker systems amenable to automation are frequently used in applied plant breeding. Practical examples are given from Lantmännen (LM) ( https://Lantmannen.com ) using large-scale genotyping for variety development based on SSRs and SNPs.


Assuntos
Produtos Agrícolas/genética , Melhoramento Vegetal/métodos , Brassica napus/genética , Produtos Agrícolas/virologia , DNA de Plantas/genética , Diploide , Resistência à Doença/genética , Genes de Plantas , Marcadores Genéticos , Haploidia , Homozigoto , Hordeum/genética , Isoenzimas/genética , Biologia Molecular/métodos , Doenças das Plantas/genética , Doenças das Plantas/virologia , Reação em Cadeia da Polimerase , Polimorfismo de Fragmento de Restrição , Polimorfismo de Nucleotídeo Único , Triticum/genética
15.
BMC Plant Biol ; 21(1): 344, 2021 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-34289812

RESUMO

BACKGROUND: Maize (Zea mays ssp. mays) is the most abundantly cultivated and highly valued food commodity in the world. Oil from maize kernels is highly nutritious and important for the diet and health of humans, and it can be used as a source of bioenergy. A better understanding of genetic basis for maize kernel oil can help improve the oil content and quality when applied in breeding. RESULTS: In this study, a KUI3/SC55 recombinant inbred line (RIL) population, consisting of 180 individuals was constructed from a cross between inbred lines KUI3 and SC55. We phenotyped 19 oil-related traits and subsequently dissected the genetic architecture of oil-related traits in maize kernels based on a high-density genetic map. In total, 62 quantitative trait loci (QTLs), with 2 to 5 QTLs per trait, were detected in the KUI3/SC55 RIL population. Each QTL accounted for 6.7% (qSTOL1) to 31.02% (qBELI6) of phenotypic variation and the total phenotypic variation explained (PVE) of all detected QTLs for each trait ranged from 12.5% (OIL) to 52.5% (C16:0/C16:1). Of all these identified QTLs, only 5 were major QTLs located in three genomic regions on chromosome 6 and 9. In addition, two pairs of epistatic QTLs with additive effects were detected and they explained 3.3 and 2.4% of the phenotypic variation, respectively. Colocalization with a previous GWAS on oil-related traits, identified 19 genes. Of these genes, two important candidate genes, GRMZM2G101515 and GRMZM2G022558, were further verified to be associated with C20:0/C22:0 and C18:0/C20:0, respectively, according to a gene-based association analysis. The first gene encodes a kinase-related protein with unknown function, while the second gene encodes fatty acid elongase 2 (fae2) and directly participates in the biosynthesis of very long chain fatty acids in Arabidopsis. CONCLUSIONS: Our results provide insights on the genetic basis of oil-related traits and a theoretical basis for improving maize quality by marker-assisted selection.


Assuntos
Óleo de Milho/genética , Óleo de Milho/metabolismo , Produtos Agrícolas/genética , Zea mays/genética , Mapeamento Cromossômico , Marcadores Genéticos , Variação Genética , Genótipo , Fenótipo , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único
16.
BMC Plant Biol ; 21(1): 350, 2021 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-34303361

RESUMO

BACKGROUND: Lycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. However, genetic analysis of this plant and molecular breeding for quality improvement are limited by the lack of sufficient molecular markers. RESULTS: In this study, two parental strains, 'Ningqi No. 1' (Lycium barbarum L.) and 'Yunnan Gouqi' (Lycium yunnanense Kuang et A.M. Lu), and 200 F1 hybrid individuals were resequenced for genetic analysis. In total, 8,507 well-selected SNPs were developed, and a high-density genetic map (NY map) was constructed with a total genetic distance of 2,122.24 cM. A consensus genetic map was established by integrating the NY map and a previously published genetic map (NC map) containing 15,240 SNPs, with a total genetic distance of 3,058.19 cM and an average map distance of 0.21 cM. The 12 pseudochromosomes of the Lycium reference genome were anchored using this consensus genetic map, with an anchoring rate of 64.3%. Moreover, weak collinearities between the consensus map and the pepper, potato, and tomato genomes were observed. Twenty-five stable QTLs were identified for leaf- and fruit-related phenotypes, including fruit weight, fruit longitude, leaf length, the fruit index, and the leaf index; these stable QTLs were mapped to four different linkage groups, with LOD scores ranging from 2.51 to 19.37 and amounts of phenotypic variance explained from 6.2% to 51.9%. Finally, 82 out of 188 predicted genes underlying stable QTLs for fruit-related traits were differentially expressed according to RNA-seq analysis. CONCLUSIONS: A chromosome-level assembly can provide a foundation for further functional genomics research for wolfberry. The genomic regions of these stably expressed QTLs could be used as targets for further fine mapping and development of molecular markers for marker-assisted selection (MAS). The present study provided valuable information on saturated SNP markers and reliable QTLs for map-based cloning of functional genes related to yield and morphological traits in Lycium spp.


Assuntos
Mapeamento Cromossômico , Frutas/genética , Ligação Genética , Marcadores Genéticos , Lycium/genética , Folhas de Planta/genética , Locos de Características Quantitativas , China , Produtos Agrícolas/genética , Variação Genética , Fenótipo , Sintenia/genética
17.
Int J Mol Sci ; 22(13)2021 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-34281252

RESUMO

Cardiovascular diseases have attracted our full attention not only because they are the main cause of mortality and morbidity in many countries but also because the therapy for and cure of these maladies are among the major challenges of the medicine in the 21st century [...].


Assuntos
Doenças Cardiovasculares/etiologia , Animais , Doenças Cardiovasculares/genética , Doenças Cardiovasculares/metabolismo , Complemento C3/genética , Complemento C3/metabolismo , Vesículas Extracelulares/metabolismo , Marcadores Genéticos , Humanos , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , Modelos Cardiovasculares , Cadeias Leves de Miosina/genética , Cadeias Leves de Miosina/metabolismo , Fatores de Risco
18.
BMC Genomics ; 22(1): 495, 2021 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-34215185

RESUMO

BACKGROUND: The clearhead icefish, Protosalanx hyalocranius, is an economically important fishery species in China. Since 1980s, P. hyalocranius was widely introduced into lakes and reservoirs of northern China for aquaculture. However, the lack of a rapid and cost-effective sex identification method based on sex specific genetic markers has hindered study on sex determination mechanisms and breeding applications. RESULTS: Female-specific genomic regions were discovered by comparing whole genome re-sequencing data of both males and females. Two female-specific genomic regions larger than 50 bp were identified, and one (598 bp) contained a putative FOXI gene, which was paralogous to another FOXI gene with sex-associated SNPs. The two FOXI sequences displayed significant length difference with nine deletions of total length of 230 bp. This deletion-type structural variation could be easily and efficiently detected by traditional PCR and agarose gel electrophoresis with one 569 bp band for males and two bands (569 and 339 bp) for females, which were validated in 50 females and 40 males with known phenotypic sexes. CONCLUSIONS: The results provided structural genomic evidence for the ZZ/ZW sex determination system in P. hyalocranius discovered in our previous study with association analysis of SNPs. Moreover, the female-specific markers and rapid and cost-effective PCR-based genetic sex identification method should have applications in further studies of sex determination mechanism for this species.


Assuntos
Genoma , Osmeriformes , Animais , China , Feminino , Marcadores Genéticos , Genômica , Masculino , Osmeriformes/genética , Processos de Determinação Sexual
19.
Int J Mol Sci ; 22(13)2021 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-34201603

RESUMO

Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.


Assuntos
Cucumis melo/genética , Marcadores Genéticos , Polimorfismo de Nucleotídeo Único , Variação Genética , Genética Populacional , Genoma de Planta , Estudo de Associação Genômica Ampla , Haplótipos/genética , Desequilíbrio de Ligação , Fenótipo , Filogenia , Sementes/genética
20.
Cytogenet Genome Res ; 161(3-4): 213-222, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34233333

RESUMO

The genera of the tribe Triticeae (family Poaceae), constituting many economically important plants with abundant genetic resources, carry genomes such as St, H, P, and Y. The genome symbol of Roegneria C. Koch (Triticeae) is StY. The St and Y genomes are crucial in Triticeae, and tetraploid StY species participate extensively in polyploid speciation. Characterization of St and Y nonhomologous chromosomes in StY-genome species could help understand variation in the chromosome structure and differentiation of StY-containing species. However, the high genetic affinity between St and Y genome and the deficiency of a complete set of StY nonhomologous probes limit the identification of St and Y genomes and variation of chromosome structures among Roegneria species. We aimed to identify St- and Y-enhanced repeat clusters and to study whether homoeologous chromosomes between St and Y genomes could be accurately identified due to high affinity. We employed comparative genome analyses to identify St- and Y-enhanced repeat clusters and generated a FISH-based karyotype of R. grandis (Keng), one of the taxonomically controversial StY species, for the first time. We explored 4 novel repeat clusters (StY_34, StY_107, StY_90, and StY_93), which could specifically identify individual St and Y nonhomologous chromosomes. The clusters StY_107 and StY_90 could identify St and Y addition/substitution chromosomes against common wheat genetic backgrounds. The chromosomes V_St, VII_St, I_Y, V_Y, and VII_Y displayed similar probe distribution patterns in the proximal region, indicating that the high affinity between St and Y genome might result from chromosome rearrangements or transposable element insertion among V_St/Y, VII_St/Y, and I_Y chromosomes during allopolyploidization. Our results can be used to employ FISH further to uncover the precise karyotype based on colinearity of Triticeae species by using the wheat karyotype as reference, to analyze diverse populations of the same species to understand the intraspecific structural changes, and to generate the karyotype of different StY-containing species to understand the interspecific chromosome variation.


Assuntos
Cromossomos de Plantas/genética , Elymus/genética , Genoma de Planta/genética , Hibridização in Situ Fluorescente/métodos , Evolução Molecular , Marcadores Genéticos/genética , Cariótipo , Região Organizadora do Nucléolo/genética , Poliploidia , Sequências Repetitivas de Ácido Nucleico/genética , Tetraploidia , Triticum/genética
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