Similar Datasets
Project description:Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages in rice seed embryo with profile of miRNA-seq. Methods: Oryza sativa. L miRNA profiles of two different ecotypes with 3 different maturation stages of rice seed embryo were generated by NGS, in duplicate, following Illumina NGS workflow. Results: We found the differentially expressed microRNAs between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. Target transcripts of differentially expressed microRNAs have been predicted via psRNATarget web server, and a part of those target genes are likely to be regulated by microRNAs, affecting overall responses to heat stress and the regulation of seed dormancy during maturation. Conclusions: Our study represents the analysis of rice seed small RNAs, specifically microRNAs, under two different ecotypes, three different seed maturation stages in rice seed embryo. Our results show that microRNAs are involved in response to heat stress and the regulation of seed dormancy. This study will provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.
2021-07-04 | GSE175561 | GEO
Project description:Introduction: Pre-harvest Sprouting (PHS) seriously affects wheat quality and yield. However, to date there have been limited reports. It is of great urgency to breed resistance varieties via quantitative trait nucleotides (QTNs) or genes for PHS resistance in white-grained wheat. Methods: 629 Chinese wheat varieties, including 373 local wheat varieties from 70 years ago and 256 improved wheat varieties were phenotyped for spike sprouting (SS) in two environments and genotyped by wheat 660K microarray. These phenotypes were used to associate with 314,548 SNP markers for identifying QTNs for PHS resistance using several multi-locus genome-wide association study (GWAS) methods. Their candidate genes were verified by RNA-seq, and the validated candidate genes were further exploited in wheat breeding. Results: As a result, variation coefficients of 50% and 47% for PHS in 629 wheat varieties, respectively, in 2020-2021 and 2021-2022 indicated large phenotypic variation, in particular, 38 white grain varieties appeared at least medium resistance, such as Baipimai, Fengchan 3, and Jimai 20. In GWAS, 22 significant QTNs, with the sizes of 0.06% ~ 38.11%, for PHS resistance were stably identified by multiple multi-locus methods in two environments, e.g., AX-95124645 (chr3D:571.35Mb), with the sizes of 36.390% and 45.850% in 2020-2021 and 2021-2022, respectively, was detected by several multi-locus methods in two environments. As compared with previous studies, the AX-95124645 was used to develop Kompetitive Allele-Specific PCR marker QSS.TAF9-3D (chr3D:569.17Mb~573.55Mb) for the first time, especially, it is available in white-grain wheat varieties. Around this locus, nine genes were significantly differentially expressed, and two of them (TraesCS3D01G466100 and TraesCS3D01G468500) were found by GO annotation to be related to PHS resistance and determined as candidate genes. Discussion: The QTN and two new candidate genes related to PHS resistance were identified in this study. The QTN can be used to effectively identify the PHS resistance materials, especially, all the white-grained varieties with QSS.TAF9-3D-TT haplotype are resistant to spike sprouting. Thus, this study provides candidate genes, materials, and methodological basis for breeding wheat PHS resistance in the future.
2023-01-08 | GSE222342 | GEO
Project description:The widespread agricultural problem of pre-harvest sprouting (PHS) could potentially be overcome by improving seed dormancy. Here, we report that miR156, an important grain yield regulator, also controls seed dormancy in rice. We found that mutations in one MIR156 subfamily enhance seed dormancy and suppress PHS with negligible effects on shoot architecture and grain size, whereas mutations in another MIR156 subfamily modify shoot architecture and increase grain size but have minimal effects on seed dormancy. Mechanistically, mir156 mutations enhance seed dormancy by suppressing the gibberellin (GA) pathway through de-represssion of the miR156 target gene Ideal Plant Architecture 1 (IPA1), which directly regulates multiple genes in the GA pathway. These results provide an effective method to suppress PHS without compromising productivity, and will facilitate breeding elite crop varieties with ideal plant architectures.
2019-09-03 | GSE131243 | GEO
Project description:To determine the extent of alternative 3' end cleavage during Drosophila spermatogenesis, we performed 3' end sequencing of Drosophila testes from flies at different time points post heat shock (pHS) that were mutant for bam and also had a heat shock inducible transgene expressing Bam. We then performed Polysome profiling of testes at 24, 48 and 72 hours PHS and created 3' end sequencing libraries from the free, 40S, 60s, 80S, 2-3 ribosomes, and 4+ ribosomes fractions for each dataset
2024-05-14 | GSE267303 | GEO
Project description:The goal of this study is to find out how Yarrowia lipolytica W29’s transcriptome changes in response to different pHs in certain medium, where the production of citric acid and lipid vary significantly at different pHs. The changes in transcriptome will give us insight about the mechanism of citric acid and/or lipid production are regulated. We harvested Y. lipolytica cells from bioreactor cultures from three different pHs: 2.0, 4.0 and 6.0 in triplicates. We sequenced the mRNA by Illumina HiSeq 2500 and generated an average of 20 million reads for each sample. We did not find distinct gene expression changes for the enzymes right downstream the intersection where citrate is cleaved into acetyl-CoA. Instead, from gene ontology enrichment analysis, we observed proteins with transport activities were overrepresented in gene groups that were up-regulated higher pH conditions, where citric acid secretion is favored.
2019-04-26 | GSE80717 | GEO
Project description:Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages and two different tissues, embryo and endosperm of rice seeds with profile of RNA-seq. Methods: Oryza sativa. L mRNA profiles of two different ecotypes with 3 different maturation stages and 2 different tissues were generated by NGS, in duplicate, following Illumina NGS workflow. qRT–PCR validation was performed using SYBR Green assays. Results: We found the differentially expressed genes (DEGs) between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. In DEGs, gene ontology (GO) analysis and Mapman analysis were performed, and we discovered genes related to plant hormones and heat stress, which are not yet reported. These genes were validated through qRT-PCR, and it is likely to be highly related to seed dormancy. Conclusions: Our study represents the analysis of rice seed transcriptomes under two different ecotypes, three different seed maturation stages and two different tissues (Embryo and endosperm). Our results show that seed dormancy is affected and regulated by a plant hormones and heat stress. This study might provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.
2021-05-07 | GSE174017 | GEO