Genome wide association mapping for key agronomic traits in Brassica juncea
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB57434 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10483700_1.fastq.gz | Fastqsanger.gz | |||
| ERR10483700_2.fastq.gz | Fastqsanger.gz | |||
| ERR10483701_1.fastq.gz | Fastqsanger.gz | |||
| ERR10483701_2.fastq.gz | Fastqsanger.gz | |||
| ERR10479402_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 590 |
Similar Datasets
Project description:Indian mustard (Brassica juncea L.) Transcriptome or Gene expression
| PRJNA312980 | ENA
Project description:Microarray analysis of Indian mustard plants subjected to arsenate stress
| PRJNA277020 | ENA
Project description:Peanut is one of the most important cash crops with high quality oil, high protein content, and many other nutritional elements, and grown globally. Cultivated peanut (Arachis hypogaea L.) is allotetraploid with a narrow genetic base, and its genetics and molecular mechanisms controlling the agronomic traits are poorly understood. The array SNP data was used for revaling of key candidate loci and genes associated with important agronomic traits in peanut
2022-02-22 | GSE197103 | GEO
Project description:Soybean is the world's leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but the genetic architecture of yield and key agronomic traits is poorly understood. We developed a 40-mating soybean nested association mapping (NAM) population of 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers and six agronomic traits in field trials in 22 environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. A higher frequency of estimated positive yield alleles was evident from elite founder parents than from exotic founders, although unique desirable alleles from the exotic group were identified, demonstrating the value of expanding the genetic base of US soybean breeding.
| S-EPMC6169381 | biostudies-other
Project description:De novo transcriptome profiling of cold-stressed siliques during pod filling stages in Indian mustard (Brassica juncea L.)
| PRJNA296365 | ENA
Project description:In a single vascular plant species, the ubiquitin system consists of thousands of different proteins involved in attaching ubiquitin to substrates, recognizing or processing ubiquitinated proteins, or constituting or regulating the 26S proteasome. The ubiquitin system affects plant health, reproduction, and responses to the environment, processes that impact important agronomic traits. Here we summarize three agronomic traits influenced by ubiquitination: induction of flowering, seed size, and pathogen responses. Specifically, we review how the ubiquitin system affects expression of genes or abundance of proteins important for determining when a plant flowers (focusing on FLOWERING LOCUS C, FRIGIDA, and CONSTANS), highlight some recent studies on how seed size is affected by the ubiquitin system, and discuss how the ubiquitin system affects proteins involved in pathogen or effector recognition with details of recent studies on FLAGELLIN SENSING 2 and SUPPRESSOR OF NPR CONSTITUTIVE 1, respectively, as examples. Finally, we discuss the effects of pathogen-derived proteins on plant host ubiquitin system proteins. Further understanding of the molecular basis of the above processes could identify possible genes for modification or selection for crop improvement.
| S-EPMC7535913 | biostudies-literature
Project description:Identification of trait-associated metabolites will advance the knowledge and understanding of the biosynthetic and catabolic pathways that are relevant to the complex traits of interest. In the past, the association between metabolites (treated as quantitative traits) and genetic variants (e.g., SNPs) has been extensively studied using metabolomic quantitative trait locus (mQTL) mapping. Nevertheless, the research on the association between metabolites with agronomic traits has been inadequate. In practice, the regular approaches for QTL mapping analysis may be adopted for metabolites-phenotypes association analysis due to the similarity in data structure of these two types of researches. In the study, we compared four regular QTL mapping approaches, i.e., simple linear regression (LR), linear mixed model (LMM), Bayesian analysis with spike-slab priors (Bayes B) and least absolute shrinkage and selection operator (LASSO), by testing their performances on the analysis of metabolome-phenotype associations. Simulation studies showed that LASSO had the higher power and lower false positive rate than the other three methods. We investigated the associations of 839 metobolites with five agronomic traits in a collection of 533 rice varieties. The results implied that a total of 25 metabolites were significantly associated with five agronomic traits. Literature search and bioinformatics analysis indicated that the identified 25 metabolites are significantly involved in some growth and development processes potentially related to agronomic traits. We also explored the predictability of agronomic traits based on the 839 metabolites through cross-validation, which showed that metabolomic prediction was efficient and its application in plant breeding has been justified.
| S-EPMC5842221 | biostudies-literature
Project description:Plant breeders have played an essential role in improving agricultural crops, and their efforts will be critical to meet the increasing demand for cellulosic bioenergy feedstocks. However, a major concern is the potential development of novel invasive species that result from breeders' efforts to improve agronomic traits in a crop. We use reed canarygrass as a case study to evaluate the potential of plant breeding to give rise to invasive species. Reed canarygrass has been improved by breeders for use as a forage crop, but it is unclear whether breeding efforts have given rise to more vigorous populations of the species. We evaluated cultivars, European wild, and North American invader populations in upland and wetland environments to identify differences in vigor between the groups of populations. While cultivars were among the most vigorous populations in an agricultural environment (upland soils with nitrogen addition), there were no differences in above- or below-ground production between any populations in wetland environments. These results suggest that breeding has only marginally increased vigor in upland environments and that these gains are not maintained in wetland environments. Breeding focuses on selection for improvements of a specific target population of environments, and stability across a wide range of environments has proved elusive for even the most intensively bred crops. We conclude that breeding efforts are not responsible for wetland invasion by reed canarygrass and offer guidelines that will help reduce the possibility of breeding programs releasing cultivars that will become invasive.
| S-EPMC3185028 | biostudies-literature
Project description:BackgroundFlax (Linum usitatissimum. L) is an ancient oilseed and natural fiber crop. It could be divided into three categories by use, namely oil flax, fiber flax and oil-fiber dual purpose (OF). Cultivated flax is widely used in the food and textile industry. It is of great significance to elucidate the genetic characteristics of flax collections for accelerating the process of breeding improvement in this dual purpose crop. With the development of next-generation sequencing, we can use new methods, such as SLAF-seq (specific-locus amplified fragment sequencing), to decode unknown genomes of species. In this study, a high-through sequencing of flax collections using SLAF-seq was conducted. The evolutionary tendency was defined and candidate genes associated with agronomic traits of flax species were identified by Genome-Wide Association Studying (GWAS).ResultsA flax collection consisting of 224 varieties were sequenced by SLAF-seq. In total, 346,639 SLAF tags were developed from all accessions, with an average sequencing depth of 7.19 for each accession. A total of 584,987 SNPs (single nucleotide polymorphism) with an MAF > 0.05 were identified from these SLAFs. The population structure division and phylogenetic analysis indicated a strong divergence among three kinds of flax groups. The genome-wide variation uncovered that oil flax had the highest genetic diversity and was considered to be the ancestor of fiber flax and oil-fiber flax. Sixteen associated peak SNPs for six traits were obtained by GWAS of oil-related traits using EMMAX (efficient mixed-model association eXpedited). Candidate genes and their related pathway were evaluated. A new GWAS was developed for fiber properties using the GLM (General linear model) model and a number of loci were identified.ConclusionsTo our knowledge, this is the first study on discovery multiple loci for important agronomic traits of flax species using GWAS strategy. These results will provide the highest possibility of incorporating both high fiber and good oil traits in a single variety.
| S-EPMC6029072 | biostudies-literature
Project description:Peach (Prunus persica L.) is a highly valuable crop species and is recognized by molecular researchers as a model fruit for the Rosaceae family. Using whole-genome sequencing data generated from 129 peach accessions, here we perform a comprehensive genome-wide association study for 12 key agronomic traits. We show that among the 10 qualitative traits investigated, nine exhibit consistent and more precise association signals than previously identified by linkage analysis. For two of the qualitative traits, we describe candidate genes, one potentially involved in cell death and another predicted to encode an auxin-efflux carrier, that are highly associated with fruit shape and non-acidity, respectively. Furthermore, we find that several genomic regions harbouring association signals for fruit weight and soluble solid content overlapped with predicted selective sweeps that occurred during peach domestication and improvement. Our findings contribute to the large-scale characterization of genes controlling agronomic traits in peach.
| S-EPMC5105138 | biostudies-literature