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1.
Plant J ; 100(1): 114-127, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31169939

RESUMO

Phytol is one of the key precursors for tocopherol synthesis in plants, however, the underlying mechanisms concerning the accumulation of tocopherol remain poorly understood. In this study, qVE5, a major QTL affecting tocopherol accumulation in maize kernels was identified via a positional cloning approach. qVE5 encodes a protochlorophyllide oxidoreductase (ZmPORB2), which localizes to the chloroplast. Overexpression of ZmPORB2 increased tocopherol content in both leaves and kernels. Candidate gene association analysis identified a 5/8-bp insertion/deletion (InDel058) in the 5' untranslated region (UTR) as the causal polymorphism in affecting ZmPORB2 expression and being highly associated with tocopherol content. We showed that higher expression of ZmPORB2 correlated with more chlorophyll metabolites in the leaf following pollination. RNA-sequencing and metabolic analysis in near isogenic lines (NILs) support that ZmPORB2 participates in chlorophyll metabolism enabling the production of phytol, an important precursor of tocopherol. We also found that the tocopherol content in the kernel is mainly determined by the maternal genotype, a fact that was further confirmed by in vitro culture experiments. Finally, a PCR-based marker based on Indel058 was developed in order to facilitate the high tocopherol (vitamin E) maize breeding.

2.
BMC Genomics ; 20(1): 443, 2019 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-31159731

RESUMO

BACKGROUND: Trait ontology (TO) analysis is a powerful system for functional annotation and enrichment analysis of genes. However, given the complexity of the molecular mechanisms underlying phenomes, only a few hundred gene-to-TO relationships in plants have been elucidated to date, limiting the pace of research in this "big data" era. RESULTS: Here, we curated all the available trait associated sites (TAS) information from 79 association mapping studies of maize (Zea mays L.) and rice (Oryza sativa L.) lines with diverse genetic backgrounds and built a large-scale TAS-derived TO system for functional annotation of genes in various crops. Our TO system contains information for up to 18,042 genes (6345 in maize at the 25 k level and 11,697 in rice at the 50 k level), including gene-to-TO relationships, which covers over one fifth of the annotated gene sets for maize and rice. A comparison of Gene Ontology (GO) vs. TO analysis demonstrated that the TAS-derived TO system is an efficient alternative tool for gene functional annotation and enrichment analysis. We therefore combined information from the TO, GO, metabolic pathway, and co-expression network databases and constructed the TAS system, which is publicly available at http://tas.hzau.edu.cn . TAS provides a user-friendly interface for functional annotation of genes, enrichment analysis, genome-wide extraction of trait-associated genes, and crosschecking of different functional annotation databases. CONCLUSIONS: TAS bridges the gap between genomic and phenomic information in crops. This easy-to-use tool will be useful for geneticists, biologists, and breeders in the agricultural community, as it facilitates the dissection of molecular mechanisms conferring agronomic traits in an easy, genome-wide manner.


Assuntos
Genoma de Planta , Genômica/métodos , Oryza/genética , Proteínas de Plantas/genética , Zea mays/genética , Produtos Agrícolas/genética , Estudo de Associação Genômica Ampla , Oryza/fisiologia , Fenótipo , Locos de Características Quantitativas , Zea mays/fisiologia
3.
Plant J ; 99(2): 216-230, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30888713

RESUMO

It is generally recognized that many favorable genes which were lost during domestication, including those related to both nutritional value and stress resistance, remain hidden in wild relatives. To uncover such genes in teosinte, an ancestor of maize, we conducted metabolite profiling in a BC2 F7 population generated from a cross between the maize wild relative (Zea mays ssp. mexicana) and maize inbred line Mo17. In total, 65 primary metabolites were quantified in four tissues (seedling-stage leaf, grouting-stage leaf, young kernel and mature kernel) with clear tissue-specific patterns emerging. Three hundred and fifty quantitative trait loci (QTLs) for these metabolites were obtained, which were distributed unevenly across the genome and included two QTL hotspots. Metabolite concentrations frequently increased in the presence of alleles from the teosinte genome while the opposite was observed for grain yield and shape trait QTLs. Combination of the multi-tissue transcriptome and metabolome data provided considerable insight into the metabolic variations between maize and its wild relatives. This study thus identifies favorable genes hidden in the wild relative which should allow us to balance high yield and quality in future modern crop breeding programs.

4.
J Exp Bot ; 70(6): 1859-1873, 2019 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-30759246

RESUMO

The use of mixed nitrate and ammonium as a nitrogen source can improve plant growth. Here, we used metabolomics and transcriptomics to study the underlying mechanisms. Maize plants were grown hydroponically in the presence of three forms of nitrogen (nitrate alone, 75%/25% nitrate/ammonium, and ammonium alone). Plants grown with mixed nitrogen had a higher photosynthetic rate than those supplied only with nitrate, and had the highest leaf area and shoot and root biomass among the three nitrogen treatments. In shoot and root, the concentration of nitrogenous compounds (ammonium, glutamine, and asparagine) and carbohydrates (sucrose, glucose, and fructose) in plants with a mixed nitrogen supply was higher than that with nitrate supply, but lower than that with ammonium supply. The activity of the related enzymes (glutamate synthase, asparagine synthase, phosphoenolpyruvate carboxylase, invertase, and ADP-glucose pyrophosphorylase) changed accordingly. Specifically, the mixed nitrogen source enhanced auxin synthesis via the shikimic acid pathway, as indicated by the higher levels of phosphoenolpyruvate and tryptophan compared with the other two treatments. The expression of corresponding genes involving auxin synthesis and response was up-regulated. Supply of only ammonium resulted in high levels of glutamine and asparagine, starch, and trehalose hexaphosphate. We conclude that, in addition to increased photosynthesis, mixed nitrogen supply enhances leaf growth via increasing auxin synthesis to build a large sink for carbon and nitrogen utilization, which, in turn, facilitates further carbon assimilation and nitrogen uptake.

5.
Mol Plant ; 12(3): 426-437, 2019 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-30597214

RESUMO

Deciphering the genetic mechanisms underlying agronomic traits is of great importance for crop improvement. Most of these traits are controlled by multiple quantitative trait loci (QTLs), and identifying the underlying genes by conventional QTL fine-mapping is time-consuming and labor-intensive. Here, we devised a new method, named quantitative trait gene sequencing (QTG-seq), to accelerate QTL fine-mapping. QTG-seq combines QTL partitioning to convert a quantitative trait into a near-qualitative trait, sequencing of bulked segregant pools from a large segregating population, and the use of a robust new algorithm for identifying candidate genes. Using QTG-seq, we fine-mapped a plant-height QTL in maize (Zea mays L.), qPH7, to a 300-kb genomic interval and verified that a gene encoding an NF-YC transcription factor was the functional gene. Functional analysis suggested that qPH7-encoding protein might influence plant height by interacting with a CO-like protein and an AP2 domain-containing protein. Selection footprint analysis indicated that qPH7 was subject to strong selection during maize improvement. In summary, QTG-seq provides an efficient method for QTL fine-mapping in the era of "big data".


Assuntos
Mapeamento Cromossômico/métodos , Genoma de Planta , Locos de Características Quantitativas , Sequenciamento Completo do Genoma/métodos , Zea mays/genética , Cromossomos de Plantas/genética , Genômica , Fenótipo , Zea mays/crescimento & desenvolvimento
6.
Med Sci Monit ; 25: 333-340, 2019 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-30633736

RESUMO

BACKGROUND The aim of this study was to determine the efficacy of sublingual administration of Dermatophagoides farinae drops for the treatment of allergic rhinitis (AR) accompanied by adenoid hypertrophy and the effect on immune function in children. MATERIAL AND METHODS Eosinophil counts in peripheral blood before and after treatment were determined; serum levels of immunoglobulin E (IgE), total IgE (T-IgE), immunoglobulin G4 (IgG4), interleukin-2 (IL-2), and interleukin-6 (IL-6) before and after treatment were detected by enzyme-linked immunosorbent assay. RESULTS The total effective rate in the study group was significantly higher than that in the control group (P<0.05). In both the study and control groups, symptom scores, medication scores, eosinophil counts in the peripheral blood, and serum levels of IgE, T-IgE, and IL-6 were significantly lower than those before treatment (P<0.05), while the serum levels of IgG4 and IL-2 were significantly higher than those before treatment (P<0.05). After treatment, symptom scores, medication scores, eosinophil counts in the peripheral blood, and serum levels of IgE, T-IgE, and IL-6 in the study group were significantly lower than those in the control group (P<0.05), while the serum levels of IgG4 and IL-2 were significantly higher in the study group than those in the control group (P<0.05). CONCLUSIONS Sublingual administration of D. farinae drops improved the clinical symptoms of pediatric AR caused by Dermatophagoides mites and improved the immune functions in children.


Assuntos
Dermatophagoides farinae/imunologia , Dessensibilização Imunológica/métodos , Rinite Alérgica/terapia , Tonsila Faríngea/efeitos dos fármacos , Tonsila Faríngea/fisiopatologia , Administração Sublingual , Animais , Asma/imunologia , Criança , Pré-Escolar , Eosinófilos/efeitos dos fármacos , Feminino , Humanos , Imunoglobulina E/análise , Imunoglobulina E/sangue , Imunoglobulina G/análise , Imunoglobulina G/sangue , Interleucina-2/análise , Interleucina-2/sangue , Interleucina-6/análise , Interleucina-6/sangue , Masculino , Estudos Retrospectivos , Imunoterapia Sublingual/métodos , Resultado do Tratamento
7.
J Integr Plant Biol ; 2018 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-30117291

RESUMO

Long non-coding RNAs (lncRNAs), whose sequences are approximately 200 bp or longer and unlikely to encode proteins, may play an important role in eukaryotic gene regulation. Although the latest maize (Zea mays L.) reference genome provides an essential genomic resource, genome-wide annotations of maize lncRNAs have not been updated. Here, we report on a large transcriptomic dataset collected from 749 RNA sequencing experiments across different tissues and stages of the maize reference inbred B73 line and 60 from its wild relative teosinte. We identified 18,165 high-confidence lncRNAs in maize, of which 6,873 are conserved between maize and teosinte. We uncovered distinct genomic characteristics of conserved lncRNAs, non-conserved lncRNAs, and protein-coding transcripts. Intriguingly, Shannon entropy analysis showed that conserved lncRNAs are likely to be expressed similarly to protein-coding transcripts. Co-expression network analysis revealed significant variation in the degree of co-expression. Furthermore, selection analysis indicated that conserved lncRNAs are more likely than non-conserved lncRNAs to be located in regions subject to recent selection, indicating evolutionary differentiation. Our results provide the latest genome-wide annotation and analysis of maize lncRNAs and uncover potential functional divergence between protein-coding, conserved lncRNA, and non-conserved lncRNA genes, demonstrating the high complexity of the maize transcriptome.

8.
BMC Plant Biol ; 18(1): 66, 2018 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-29673320

RESUMO

BACKGROUND: Residual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies. However, knowledge of factors affecting the genome-wide distribution of RH remains limited. RESULTS: A set of 2196 heterogeneous inbred family (HIF) maize lines derived from 12 recombinant inbred line (RIL) populations was genotyped using the Maize50K SNP chip. A total of 18,615 unique RH intervals were identified, ranging from 505 to 2095 intervals per population, with average maize genome coverage of 94.8%. Across all populations, there were 8.6 RH intervals per HIF line on average, ranging from 1.8 to 14 intervals; the average size of an RH interval was approximately 58.7 Mb, ranging from 7.2 to 74.1 Mb. A given RH region was present in an average of 5 different individuals within a population. Seven RH hotspots, where RH segments were enriched in the genome, were found to be subject to selection during population development. The RH patterns varied significantly across populations, presumably reflecting differences in the genetic background of each population, and 8 QTLs were found to affect heterozygosity levels in the RH hotspots. The potential use of this HIF library for the fine mapping of QTLs was assessed based on publicly available QTL information, achieving a ≤ 1 Mb resolution on average. CONCLUSION: The examined library of HIF lines offers insight into the RH landscape and its intraspecific variation and provides a useful resource for the QTL cloning of important agronomic traits in maize.


Assuntos
Locos de Características Quantitativas/genética , Zea mays/genética , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Heterozigoto
9.
Plant Biotechnol J ; 16(8): 1464-1475, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29356296

RESUMO

Although tocopherols play an important role in plants and animals, the genetic architecture of tocopherol content in maize kernels has remained largely unknown. In this study, linkage and association analyses were conducted to examine the genetic architecture of tocopherol content in maize kernels. Forty-one unique quantitative trait loci (QTLs) were identified by linkage mapping in six populations of recombinant inbred lines (RILs). In addition, 32 significant loci were detected via genome-wide association study (GWAS), 18 of which colocalized with the QTLs identified by linkage mapping. Fine mapping of a major QTL validated the accuracy of GWAS and QTL mapping results and suggested a role for nontocopherol pathway genes in the modulation of natural tocopherol variation. We provided genome-wide evidence that genes involved in fatty acid metabolism, chlorophyll metabolism and chloroplast function may affect natural variation in tocopherols. These findings were confirmed through mutant analysis of a particular gene from the fatty acid pathway. In addition, the favourable alleles for many of the significant SNPs/QTLs represented rare alleles in natural populations. Together, our results revealed many novel genes that are potentially involved in the variation of tocopherol content in maize kernels. Pyramiding of the favourable alleles of the newly elucidated genes and the well-known tocopherol pathway genes would greatly improve tocopherol content in maize.

10.
Nat Commun ; 8(1): 1874, 2017 11 30.
Artigo em Inglês | MEDLINE | ID: mdl-29187731

RESUMO

Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana, including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17 × 10-8 ~3.87 × 10-8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.


Assuntos
Evolução Molecular , Genoma de Planta/genética , Zea mays/genética , Haplótipos
11.
Front Plant Sci ; 8: 2063, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29250099

RESUMO

Recombination is a vital characteristic for quantitative trait loci mapping and breeding to enhance the yield potential of maize. However, recombination characteristics in globally used segregating populations have never been evaluated at similar genetic marker densities. This study aimed to divulge the characteristics of recombination events, recombinant chromosomal segments, and recombination frequency for four dissimilar populations. These populations were doubled haploid (DH), recombination inbred line (RIL), intermated B73xMo17 (IBM), and multi-parent advanced generation inter-cross (MAGIC), using the Illumina MaizeSNP50 BeadChip to provide markers. Our results revealed that the average number of recombination events was 16, 41, 72, and 86 per line in DH, RIL, IBM, and MAGIC populations, respectively. Accordingly, the average length of recombinant chromosomal segments was 84.8, 47.3, 29.2, and 20.4 Mb in DH, RIL, IBM, and MAGIC populations, respectively. Furtherly, the recombination frequency varied in different genomic regions and population types [DH (0-12.7 cM/Mb), RIL (0-15.5 cM/Mb), IBM (0-24.1 cM/Mb), MAGIC (0-42.3 cM/Mb)]. Utilizing different sub-sets of lines, the recombination bin number and size were analyzed in each population. Additionally, different sub-sets of markers and lines were employed to estimate the recombination bin number and size via formulas for relationship in these populations. The relationship between recombination events and recombination bin length was also examined. Our results contribute to determining the most suitable number of genetic markers, lines in each population, and population type for successful mapping and breeding.

12.
Sci Rep ; 7(1): 16482, 2017 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-29184085

RESUMO

Fibroblast growth factor 21 (FGF21), a stress-induced hormone in the liver, has been shown the protective functions in pathological conditions. The study investigated the association of circulating FGF21 with hepatitis B virus (HBV) infection and its related diseases. Serum FGF21 levels were measured in 33 acute hepatitis B (AHB), 75 chronic hepatitis B (CHB) and 66 CHB patients with advanced liver diseases including liver cirrhosis, acute-on-chronic liver failure (ALCF) and hepatocellular carcinoma (HCC) together with 200 age- and BMI-matched healthy controls. FGF21 levels were significantly increased in AHB patients and rapidly returned to normal levels after treatment. FGF21 levels reflected the degree of liver injury caused by AHB. However, serum FGF21 levels were decreased in CHB patients especially in those who developed cirrhosis and were associated with hepatic protein synthesis capacity. Serum FGF21 in CHB patients were increased with the occurrence of ACLF. Notably, in CHB patients who developed HCC, serum FGF21 exhibited a dramatic increase, which may provide important information on monitoring tumorigenesis in CHB patients. In conclusion, we revealed the diverse changes of circulating FGF21 in HBV-related diseases. FGF21 may be a useful biomarker in monitoring the tumorigenesis in patients with CHB.

13.
Plant Physiol ; 175(2): 858-873, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28838954

RESUMO

Plant architecture is a key factor affecting planting density and grain yield in maize (Zea mays). However, the genetic mechanisms underlying plant architecture in diverse genetic backgrounds have not been fully addressed. Here, we performed a large-scale phenotyping of 10 plant architecture-related traits and dissected the genetic loci controlling these traits in 10 recombinant inbred line populations derived from 14 diverse genetic backgrounds. Nearly 800 quantitative trait loci (QTLs) with major and minor effects were identified as contributing to the phenotypic variation of plant architecture-related traits. Ninety-two percent of these QTLs were detected in only one population, confirming the diverse genetic backgrounds of the mapping populations and the prevalence of rare alleles in maize. The numbers and effects of QTLs are positively associated with the phenotypic variation in the population, which, in turn, correlates positively with parental phenotypic and genetic variations. A large proportion (38.5%) of QTLs was associated with at least two traits, suggestive of the frequent occurrence of pleiotropic loci or closely linked loci. Key developmental genes, which previously were shown to affect plant architecture in mutant studies, were found to colocalize with many QTLs. Five QTLs were further validated using the segregating populations developed from residual heterozygous lines present in the recombinant inbred line populations. Additionally, one new plant height QTL, qPH3, has been fine-mapped to a 600-kb genomic region where three candidate genes are located. These results provide insights into the genetic mechanisms controlling plant architecture and will benefit the selection of ideal plant architecture in maize breeding.


Assuntos
Genoma de Planta/genética , Locos de Características Quantitativas/genética , Zea mays/genética , Mapeamento Cromossômico , Epistasia Genética , Pleiotropia Genética , Endogamia , Fenótipo , Zea mays/anatomia & histologia
14.
Plant Physiol ; 175(2): 774-785, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28811335

RESUMO

Maize (Zea mays) is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight, and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation. To provide candidate genes for these QTLs, we identified 30 maize genes that are orthologs of 18 rice (Oryza sativa) genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are located in the identified QTLs or within 1 Mb of the significant single-nucleotide polymorphisms. We further confirmed the effects of five genes on maize kernel size/weight in an independent association mapping panel with 540 lines by candidate gene association analysis. Lastly, the function of ZmINCW1, a homolog of rice GRAIN INCOMPLETE FILLING1 that affects seed size and weight, was characterized in detail. ZmINCW1 is close to QTL peaks for kernel size/weight (less than 1 Mb) and contains significant single-nucleotide polymorphisms affecting kernel size/weight in the association panel. Overexpression of this gene can rescue the reduced weight of the Arabidopsis (Arabidopsis thaliana) homozygous mutant line in the AtcwINV2 gene (Arabidopsis ortholog of ZmINCW1). These results indicate that the molecular mechanisms affecting seed development are conserved in maize, rice, and possibly Arabidopsis.


Assuntos
Oryza/genética , Locos de Características Quantitativas/genética , Zea mays/genética , Oryza/crescimento & desenvolvimento , Fenótipo , Sementes/genética , Sementes/crescimento & desenvolvimento , Zea mays/crescimento & desenvolvimento
15.
Sci Rep ; 7(1): 1205, 2017 04 26.
Artigo em Inglês | MEDLINE | ID: mdl-28446764

RESUMO

Recombinations occur nonuniformly across the maize genome. To dissect the genetic mechanisms underlying the nonuniformity of recombination, we performed quantitative trait locus (QTL) mapping using recombinant inbred line populations. Genome-wide QTL scan identified hundreds of QTLs with both cis-prone and trans- effects for recombination number variation. To provide detailed insights into cis- factors associated with recombination variation, we examined the genomic features around recombination hot regions, including density of genes, DNA transposons, retrotransposons, and some specific motifs. Compared to recombination variation in whole genome, more QTLs were mapped for variations in recombination hot regions. The majority QTLs for recombination hot regions are trans-QTLs and co-localized with genes from the recombination pathway. We also found that recombination variation was positively associated with the presence of genes and DNA transposons, but negatively related to the presence of long terminal repeat retrotransposons. Additionally, 41 recombination hot regions were fine-mapped. The high-resolution genotyping of five randomly selected regions in two F2 populations verified that they indeed have ultra-high recombination frequency, which is even higher than that of the well-known recombination hot regions sh1-bz and a1-sh2. Taken together, our results further our understanding of recombination variation in plants.

16.
Plant Biotechnol J ; 15(10): 1250-1263, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28218981

RESUMO

Amino acids are both constituents of proteins, providing the essential nutrition for humans and animals, and signalling molecules regulating the growth and development of plants. Most cultivars of maize are deficient in essential amino acids such as lysine and tryptophan. Here, we measured the levels of 17 different total amino acids, and created 48 derived traits in mature kernels from a maize diversity inbred collection and three recombinant inbred line (RIL) populations. By GWAS, 247 and 281 significant loci were identified in two different environments, 5.1 and 4.4 loci for each trait, explaining 7.44% and 7.90% phenotypic variation for each locus in average, respectively. By linkage mapping, 89, 150 and 165 QTLs were identified in B73/By804, Kui3/B77 and Zong3/Yu87-1 RIL populations, 2.0, 2.7 and 2.8 QTLs for each trait, explaining 13.6%, 16.4% and 21.4% phenotypic variation for each QTL in average, respectively. It implies that the genetic architecture of amino acids is relative simple and controlled by limited loci. About 43.2% of the loci identified by GWAS were verified by expression QTL, and 17 loci overlapped with mapped QTLs in the three RIL populations. GRMZM2G015534, GRMZM2G143008 and one QTL were further validated using molecular approaches. The amino acid biosynthetic and catabolic pathways were reconstructed on the basis of candidate genes proposed in this study. Our results provide insights into the genetic basis of amino acid biosynthesis in maize kernels and may facilitate marker-based breeding for quality protein maize.


Assuntos
Aminoácidos/metabolismo , Genes de Plantas , Zea mays/genética , Zea mays/metabolismo , Mapeamento Cromossômico , Estudo de Associação Genômica Ampla , Locos de Características Quantitativas
18.
Theor Appl Genet ; 129(8): 1465-77, 2016 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-27154588

RESUMO

KEY MESSAGE: Sixteen major QTLs regulating maize kernel traits were mapped in multiple environments and one of them, qKW - 9.2 , was restricted to 630 Kb, harboring 28 putative gene models. To elucidate the genetic basis of kernel traits, a quantitative trait locus (QTL) analysis was conducted in a maize recombinant inbred line population derived from a cross between two diverse parents Zheng58 and SK, evaluated across eight environments. Construction of a high-density linkage map was based on 13,703 single-nucleotide polymorphism markers, covering 1860.9 cM of the whole genome. In total, 18, 26, 23, and 19 QTLs for kernel length, width, thickness, and 100-kernel weight, respectively, were detected on the basis of a single-environment analysis, and each QTL explained 3.2-23.7 % of the phenotypic variance. Sixteen major QTLs, which could explain greater than 10 % of the phenotypic variation, were mapped in multiple environments, implying that kernel traits might be controlled by many minor and multiple major QTLs. The major QTL qKW-9.2 with physical confidence interval of 1.68 Mbp, affecting kernel width, was then selected for fine mapping using heterogeneous inbred families. At final, the location of the underlying gene was narrowed down to 630 Kb, harboring 28 putative candidate-gene models. This information will enhance molecular breeding for kernel traits and simultaneously assist the gene cloning underlying this QTL, helping to reveal the genetic basis of kernel development in maize.


Assuntos
Mapeamento Cromossômico , Interação Gene-Ambiente , Locos de Características Quantitativas , Zea mays/genética , DNA de Plantas/genética , Meio Ambiente , Ligação Genética , Fenótipo , Sementes/genética
19.
New Phytol ; 210(3): 1083-94, 2016 May.
Artigo em Inglês | MEDLINE | ID: mdl-26720856

RESUMO

Meiotic recombination is a major driver of genetic diversity, species evolution, and agricultural improvement. Thus, an understanding of the genetic recombination landscape across the maize (Zea mays) genome will provide insight and tools for further study of maize evolution and improvement. Here, we used c. 50 000 single nucleotide polymorphisms to precisely map recombination events in 12 artificial maize segregating populations. We observed substantial variation in the recombination frequency and distribution along the ten maize chromosomes among the 12 populations and identified 143 recombination hot regions. Recombination breakpoints were partitioned into intragenic and intergenic events. Interestingly, an increase in the number of genes containing recombination events was accompanied by a decrease in the number of recombination events per gene. This kept the overall number of intragenic recombination events nearly invariable in a given population, suggesting that the recombination variation observed among populations was largely attributed to intergenic recombination. However, significant associations between intragenic recombination events and variation in gene expression and agronomic traits were observed, suggesting potential roles for intragenic recombination in plant phenotypic diversity. Our results provide a comprehensive view of the maize recombination landscape, and show an association between recombination, gene expression and phenotypic variation, which may enhance crop genetic improvement.


Assuntos
Genoma de Planta , Recombinação Genética , Zea mays/anatomia & histologia , Zea mays/genética , Mapeamento Cromossômico , Regulação da Expressão Gênica de Plantas , Loci Gênicos , Genótipo , Fenótipo
20.
Plant Physiol ; 170(1): 136-46, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26556794

RESUMO

Metabolic quantitative trait locus (QTL) studies have allowed us to better understand the genetic architecture underlying naturally occurring plant metabolic variance. Here, we use two recombinant inbred line (RIL) populations to dissect the genetic architecture of natural variation of 155 metabolites measured in the mature maize (Zea mays) kernel. Overall, linkage mapping identified 882 metabolic QTLs in both RIL populations across two environments, with an average of 2.1 QTLs per metabolite. A large number of metabolic QTLs (more than 65%) were identified with moderate effects (r(2) = 2.1%-10%), while a small portion (less than 35%) showed major effects (r(2) > 10%). Epistatic interactions between these identified loci were detected for more than 30% of metabolites (with the proportion of phenotypic variance ranging from 1.6% to 37.8%), implying that genetic epistasis is not negligible in determining metabolic variation. In total, 57 QTLs were validated by our previous genome-wide association study on the same metabolites that provided clues for exploring the underlying genes. A gene regulatory network associated with the flavonoid metabolic pathway was constructed based on the transcriptional variations of 28,769 genes in kernels (15 d after pollination) of 368 maize inbred lines. A large number of genes (34 of 58) in this network overlapped with previously defined genes controlled by maize PERICARP COLOR1, while three of them were identified here within QTL intervals for multiple flavonoids. The deeply characterized RIL populations, elucidation of metabolic phenotypes, and identification of candidate genes lay the foundation for maize quality improvement.


Assuntos
Redes Reguladoras de Genes , Zea mays/genética , Zea mays/metabolismo , Mapeamento Cromossômico , Flavonoides/genética , Flavonoides/metabolismo , Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Recombinação Genética , Espectrometria de Massas em Tandem/métodos
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