共查询到20条相似文献，搜索用时 15 毫秒
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Hong Wang Shutu Xu Yaming Fan Nannan Liu Wei Zhan Haijun Liu Yingjie Xiao Kun Li Qingchun Pan Wenqiang Li Min Deng Jie Liu Min Jin Xiaohong Yang Jiansheng Li Qing Li Jianbing Yan 《Plant biotechnology journal》2018,16(8):1464-1475
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. 相似文献
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Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae 总被引：1，自引：0，他引：1 
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下载免费PDF全文 Houxiang Kang Yue Wang Shasha Peng Yanli Zhang Yinghui Xiao Dan Wang Shaohong Qu Zhiqiang Li Shuangyong Yan Zhilong Wang Wende Liu Yuese Ning Pavel Korniliev Hei Leung Jason Mezey Susan R. McCouch Guo‐Liang Wang 《Molecular Plant Pathology》2016,17(6):959-972
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Min Liu Xiaolong Tan Yan Yang Peng Liu Xiaoxiang Zhang Yinchao Zhang Lei Wang Yu Hu Langlang Ma Zhaoling Li Yanling Zhang Chaoying Zou Haijian Lin Shibin Gao Michael Lee Thomas Lübberstedt Guangtang Pan Yaou Shen 《Plant biotechnology journal》2020,18(1):207-221
Kernel size‐related traits are the most direct traits correlating with grain yield. The genetic basis of three kernel traits of maize, kernel length (KL), kernel width (KW) and kernel thickness (KT), was investigated in an association panel and a biparental population. A total of 21 single nucleotide polymorphisms (SNPs) were detected to be most significantly (P < 2.25 × 10?6) associated with these three traits in the association panel under four environments. Furthermore, 50 quantitative trait loci (QTL) controlling these traits were detected in seven environments in the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, of which eight were repetitively identified in at least three environments. Combining the two mapping populations revealed that 56 SNPs (P < 1 × 10?3) fell within 18 of the QTL confidence intervals. According to the top significant SNPs, stable‐effect SNPs and the co‐localized SNPs by association analysis and linkage mapping, a total of 73 candidate genes were identified, regulating seed development. Additionally, seven miRNAs were found to situate within the linkage disequilibrium (LD) regions of the co‐localized SNPs, of which zma‐miR164e was demonstrated to cleave the mRNAs of Arabidopsis CUC1, CUC2 and NAC6 in vitro. Overexpression of zma‐miR164e resulted in the down‐regulation of these genes above and the failure of seed formation in Arabidopsis pods, with the increased branch number. These findings provide insights into the mechanism of seed development and the improvement of molecular marker‐assisted selection (MAS) for high‐yield breeding in maize. 相似文献
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A genome‐wide association study (GWAS) was conducted on 15 milk production traits in Chinese Holstein. The experimental population consisted of 445 cattle, each genotyped by the GGP (GeneSeek genomic profiling)‐BovineLD V3 SNP chip, which had 26 151 public SNPs in its manifest file. After data cleaning, 20 326 SNPs were retained for the GWAS. The phenotypes were estimated breeding values of traits, provided by a public dairy herd improvement program center that had been collected once a month for 3 years. Two statistical models, a fixed‐effect linear regression model and a mixed‐effect linear model, were used to estimate the association effects of SNPs on each of the phenotypes. Genome‐wide significant and suggestive thresholds were set at 2.46E‐06 and 4.95E‐05 respectively. The two statistical models concurrently identified two genome‐wide significant (P < 0.05) SNPs on milk production traits in this Chinese Holstein population. The positional candidate genes, which were the ones closest to these two identified SNPs, were EEF2K (eukaryotic elongation factor 2 kinase) and KLHL1 (kelch like family member 1). These two genes could serve as new candidate genes for milk yield and lactation persistence, yet their roles need to be verified in further function studies. 相似文献
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Plants have served as sources providing humans with metabolites for food and nutrition, biomaterials for living, and treatment for pain and disease. Plants produce a huge array of metabolites, with an immense diversity at both the population and individual levels. Dissection of the genetic bases for metabolic diversity has attracted increasing research attention. The concept of genome‐wide association study (GWAS) was extended to studies on the diversity of plant metabolome that benefitted from the development of mass‐spectrometry‐based analytical systems and genome sequencing technologies. Metabolic genome‐wide association study (mGWAS) is one of the most powerful tools for global identification of genetic determinants for diversity of plant metabolism. Recently, mGWAS has been performed for various species with continuous improvements, providing deeper insights into the genetic bases of metabolic diversity. In this review, we discuss fully the achievements to date and remaining challenges that are associated with both mGWAS and mGWAS‐based multi‐dimensional analysis. We begin with a summary of GWAS and its development based on statistical methods and populations. As variation in targeted traits is essential for GWAS, we review metabolic diversity and its rise at both the population and individual levels. Subsequently, the application of mGWAS for plants and its corresponding achievements are fully discussed. We address the current knowledge on mGWAS‐based multi‐dimensional analysis and emerging insights into the diversity of metabolism. 相似文献
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Jin‐Yang Liu Pei Li Ya‐Wen Zhang Jian‐Fang Zuo Guo Li Xu Han Jim M. Dunwell Yuan‐Ming Zhang 《The Plant journal : for cell and molecular biology》2020,103(3):1103-1124
Although the biochemical and genetic basis of lipid metabolism is clear in Arabidopsis, there is limited information concerning the relevant genes in Glycine max (soybean). To address this issue, we constructed three‐dimensional genetic networks using six seed oil‐related traits, 52 lipid metabolism‐related metabolites and 54 294 SNPs in 286 soybean accessions in total. As a result, 284 and 279 candidate genes were found to be significantly associated with seed oil‐related traits and metabolites by phenotypic and metabolic genome‐wide association studies and multi‐omics analyses, respectively. Using minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) analyses, six seed oil‐related traits were found to be significantly related to 31 metabolites. Among the above candidate genes, 36 genes were found to be associated with oil synthesis (27 genes), amino acid synthesis (four genes) and the tricarboxylic acid (TCA) cycle (five genes), and four genes (GmFATB1a, GmPDAT, GmPLDα1 and GmDAGAT1) are already known to be related to oil synthesis. Using this information, 133 three‐dimensional genetic networks were constructed, 24 of which are known, e.g. pyruvate–GmPDAT–GmFATA2–oil content. Using these networks, GmPDAT, GmAGT and GmACP4 reveal the genetic relationships between pyruvate and the three major nutrients, and GmPDAT, GmZF351 and GmPgs1 reveal the genetic relationships between amino acids and seed oil content. In addition, GmCds1, along with average temperature in July and the rainfall from June to September, influence seed oil content across years. This study provides a new approach for the construction of three‐dimensional genetic networks and reveals new information for soybean seed oil improvement and the identification of gene function. 相似文献
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《Addiction biology》2018,23(5):1145-1159
Excessive alcohol use is extremely prevalent in the United States, particularly among trauma‐exposed individuals. While several studies have examined genetic influences on alcohol use and related problems, this has not been studied in the context of trauma‐exposed populations. We report results from a genome‐wide association study of alcohol consumption and associated problems as measured by the alcohol use disorders identification test (AUDIT) in a trauma‐exposed cohort. Results indicate a genome‐wide significant association between total AUDIT score and rs1433375 [N = 1036, P = 2.61 × 10−8 (dominant model), P = 7.76 × 10−8 (additive model)], an intergenic single‐nucleotide polymorphism located 323 kb upstream of the sodium channel and clathrin linker 1 (SCLT1) at 4q28. rs1433375 was also significant in a meta‐analysis of two similar, but independent, cohorts (N = 1394, P = 0.0004), the Marine Resiliency Study and Systems Biology PTSD Biomarkers Consortium. Functional analysis indicated that rs1433375 was associated with SCLT1 gene expression and cortical‐cerebellar functional connectivity measured via resting state functional magnetic resonance imaging. Together, findings suggest a role for sodium channel regulation and cerebellar functioning in alcohol use behavior. Identifying mechanisms underlying risk for problematic alcohol use in trauma‐exposed populations is critical for future treatment and prevention efforts. 相似文献
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A. Arakawa N. Okumura M. Taniguchi T. Hayashi K. Hirose K. Fukawa T. Ito T. Matsumoto H. Uenishi S. Mikawa 《Animal genetics》2015,46(5):571-575
Because of increasing litter size in Western pig breeds, additional teats are desirable to increase the capacity for nursing offspring. We applied genome‐wide SNP markers to detect QTL regions that affect teat number in a Duroc population. We phenotyped 1024 animals for total teat number. A total of 36 588 SNPs on autosomes were used in the analysis. The estimated heritability for teat number was 0.34 ± 0.05 on the basis of a genomic relationship matrix constructed from all SNP markers. Using a BayesC method, we identified a total of 18 QTL regions that affected teat number in Duroc pigs; 9 of the 18 regions were newly detected. 相似文献
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Y. L. Bernal Rubio J. L. Gualdrón Duarte R. O. Bates C. W. Ernst D. Nonneman G. A. Rohrer A. King S. D. Shackelford T. L. Wheeler R. J. C. Cantet J. P. Steibel 《Animal genetics》2016,47(1):36-48
Genome‐wide association (GWA) studies based on GBLUP models are a common practice in animal breeding. However, effect sizes of GWA tests are small, requiring larger sample sizes to enhance power of detection of rare variants. Because of difficulties in increasing sample size in animal populations, one alternative is to implement a meta‐analysis (MA), combining information and results from independent GWA studies. Although this methodology has been used widely in human genetics, implementation in animal breeding has been limited. Thus, we present methods to implement a MA of GWA, describing the proper approach to compute weights derived from multiple genomic evaluations based on animal‐centric GBLUP models. Application to real datasets shows that MA increases power of detection of associations in comparison with population‐level GWA, allowing for population structure and heterogeneity of variance components across populations to be accounted for. Another advantage of MA is that it does not require access to genotype data that is required for a joint analysis. Scripts related to the implementation of this approach, which consider the strength of association as well as the sign, are distributed and thus account for heterogeneity in association phase between QTL and SNPs. Thus, MA of GWA is an attractive alternative to summarizing results from multiple genomic studies, avoiding restrictions with genotype data sharing, definition of fixed effects and different scales of measurement of evaluated traits. 相似文献
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Alexander Feiner Nicholi Pitra Paul Matthews Klaus Pillen Ludger A. Wessjohann David Riewe 《Plant, cell & environment》2021,44(1):323-338
Downy mildew in hop (Humulus lupulus L.) is caused by Pseudoperonospora humuli and generates significant losses in quality and yield. To identify the biochemical processes that confer natural downy mildew resistance (DMR), a metabolome‐ and genome‐wide association study was performed. Inoculation of a high density genotyped F1 hop population (n = 192) with the obligate biotrophic oomycete P. humuli led to variation in both the levels of thousands of specialized metabolites and DMR. We observed that metabolites of almost all major phytochemical classes were induced 48 hr after inoculation. But only a small number of metabolites were found to be correlated with DMR and these were enriched with phenylpropanoids. These metabolites were also correlated with DMR when measured from the non‐infected control set. A genome‐wide association study revealed co‐localization of the major DMR loci and the phenylpropanoid pathway markers indicating that the major contribution to resistance is mediated by these metabolites in a heritable manner. The application of three putative prophylactic phenylpropanoids led to a reduced degree of leaf infection in susceptible genotypes, confirming their protective activity either directly or as precursors of active compounds. 相似文献
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Mathew Littlejohn Talia Grala Kathryn Sanders Caroline Walker Garry Waghorn Kevin Macdonald Richard Spelman Steve Davis Russell Snell 《Animal genetics》2012,43(6):781-784
Animal growth relative to food energy input is of key importance to agricultural production. Several recent studies highlighted genetic markers associated with food conversion efficiency in beef cattle, and there is now a requirement to validate these associations in additional populations and to assess their potential utility for selecting animals with enhanced food‐use efficiency. The current analysis tested a population of dairy cattle using 138 DNA markers previously associated with food intake and growth in a whole‐genome association analysis of beef animals. Although seven markers showed point‐wise significance at P < 0.05, none of the single‐nucleotide polymorphisms tested were significantly associated with food conversion efficiency after correction for multiple testing. These data do not support the involvement of this subset of previously implicated markers in the food conversion efficiency of the physiologically distinct New Zealand Holstein‐Friesian dairy breed. 相似文献
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L. Fontanesi G. Schiavo M. Gallo C. Baiocco G. Galimberti S. Bovo V. Russo L. Buttazzoni 《Animal genetics》2017,48(1):103-107
Protected designation of origin dry‐cured hams are the most important productions of the Italian heavy pig industry. Hams capable of minimal seasoning losses produce better quality dry‐cured hams. Ham weight loss during the first 7 days in brine (first salting) is highly correlated with the total loss of weight up to the end of seasoning, and it has quite high heritability (0.30–0.61). For these reasons, ham weight loss at first salting has been included as a meat quality trait in the Italian heavy pig selection program. In this work, we carried out a genome‐wide association study for this parameter in the Italian Large White pig breed by genotyping 1365 animals with the Illumina BeadChip PorcineSNP60 chip. A total of 44 single nucleotide polymorphisms (SNPs) had a Pnominal value below 5.0E‐04, five of which were below 5.0E‐05 and one of them (ALGA0057985 on chromosome 10) was associated with this trait at a PBonferroni threshold of 0.10. These SNPs identified a total of at least 29 putative QTLs that were located on most porcine autosomal chromosomes. This study provides genomic information that could be useful in dissecting this complex trait by identifying potential candidate genes whose function could contribute to understanding the biological mechanisms affecting meat quality for seasoning aptitude. 相似文献
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Fumio Matsuda Ryo Nakabayashi Zhigang Yang Yozo Okazaki Jun‐ichi Yonemaru Kaworu Ebana Masahiro Yano Kazuki Saito 《The Plant journal : for cell and molecular biology》2015,81(1):13-23
Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome‐wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications. 相似文献
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Previously, a single nucleotide polymorphism (SNP) related to gait type was identified at position 22 999 655 of chromosome 23 in the coding region of DMRT3 (DMRT3:Ser301Ter) by showing that a cytosine (C) to adenine (A) mutation of this SNP induced pace in the Icelandic horse. We investigated the effect of DMRT3:Ser301Ter on the gait of Hokkaido Native Horses, a Japanese native breed, and examined genetic factors other than DMRT3 by exploring genome‐wide SNPs related to gait determination. All animals exhibiting pace were AA for DMRT3:Ser301Ter, confirming the association of DMRT3:Ser301Ter with gait determination; however, 14.3% of the animals exhibiting trot also had AA for DMRT3:Ser301Ter, suggesting the presence of another factor(s) cooperatively working with DMRT3:Ser301Ter for gait determination. SNPs on chromosomes 13 and 23 were detected by genome‐wide association analysis (false discovery rate <0.05), although SNPs on chromosome 23 were all located in the vicinity of DMRT3:Ser301Ter, confirming the association with DMRT3. A genome‐wide association study targeting only animals with AA for DMRT3:Ser301Ter to examine genetic factors cooperatively working with DMRT3:Ser301Ter for gait determination suggested associations of 23 SNPs on six chromosomes. In a series of analyses of the effect of a maternal factor (dam's gait) on gait determination, the effect was suggested in comparison of the frequencies of exhibiting pace in gait checks in only two animal groups having dams with different DMRT3:Ser301Ter genotypes (P < 0.05), suggesting that the gait of the dam does not have a major effect on whether progeny homozygous for the DMRT3:Ser301Ter mutation will preferentially pace or trot. 相似文献
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Body pigmentation in insects and other organisms is typically variable within and between species and is often associated with fitness. Regulatory variants with large effects at bab1, t and e affect variation in abdominal pigmentation in several populations of Drosophila melanogaster. Recently, we performed a genome wide association (GWA) analysis of variation in abdominal pigmentation using the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP). We confirmed the large effects of regulatory variants in bab1, t and e; identified 81 additional candidate genes; and validated 17 candidate genes (out of 28 tested) using RNAi knockdown of gene expression and mutant alleles. However, these analyses are imperfect proxies for the effects of segregating variants. Here, we describe the results of an extreme quantitative trait locus (xQTL) GWA analysis of female body pigmentation in an outbred population derived from light and dark DGRP lines. We replicated the effects on pigmentation of 28 genes implicated by the DGRP GWA study, including bab1, t and e and 7 genes previously validated by RNAi and/or mutant analyses. We also identified many additional loci. The genetic architecture of Drosophila pigmentation is complex, with a few major genes and many other loci with smaller effects. 相似文献
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Matthew W. Horton Eriko Sasaki Maarten Koornneef Magnus Nordborg 《Plant, cell & environment》2016,39(11):2570-2579
The capacity to tolerate freezing temperatures limits the geographical distribution of many plants, including several species of agricultural importance. However, the genes involved in freezing tolerance remain largely unknown. Here, we describe the variation in constitutive freezing tolerance that occurs among worldwide accessions of Arabidopsis thaliana. We found that although plants from high latitudes tend to be more freezing tolerant than plants from low latitudes, the environmental factors that shape cold adaptation differ across the species range. Consistent with this, we found that the genetic architecture of freezing tolerance also differs across its range. Conventional genome‐wide association studies helped identify a priori and other promising candidate genes. However, simultaneously modelling climate variables and freezing tolerance together pinpointed other excellent a priori candidate genes. This suggests that if the selective factor underlying phenotypic variation is known, multi‐trait mixed models may aid in identifying the genes that underlie adaptation. 相似文献
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