Project description:Kernel development is accompanied by complex gene networks. Expression quantitative trait loci (eQTL) analysis is an efficient way to detect the regulatory elements of genes, especially the trans-eQTLs help to construct the regulatory networks of genes and contribute to a better understanding of the intrinsic mechanisms of biological processes. Till now, the 15 DAP (day after pollination) eQTL has been elucidated in maize kernel, but little is known about the early stage. Here, we conduct eQTL analysis for 5 DAP maize kernel using 318 maize inbred lines. The results will provide insights into the genetic basis of early kernel development.
2019-10-01 | GSE110315 | GEO
Project description:Analysis of eQTLs in 5 DAP maize kernel reveals complex regulatory networks of gene expression
Project description:Kernel development is accompanied by complex gene networks. Expression quantitative trait loci (eQTL) analysis is an efficient way to detect the regulatory elements of genes, especially the trans-eQTLs help to construct the regulatory networks of genes and contribute to a better understanding of the intrinsic mechanisms of biological processes. Till now, the 15 DAP (day after pollination) eQTL has been elucidated in maize kernel, but little is known about the early stage. Here, we analyzed the SNP and gene expression profiles and conducted eQTL analysis for 5 DAP maize kernel using 282 maize inbred lines. The results will provide insights into the genetic basis of early kernel development.
Project description:Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the gene regulatory networks that control endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the kernel. Comparisons of these mRNA populations revealed the diverged gene expression programs between filial and maternal compartments, and an unexpected close correlation between embryo and the aleurone layer of endosperm. Gene co-expression network analysis identified co-expression modules associated with single or multiple kernel compartments including modules for the endosperm cell types, some of which showed enrichment of previously identified temporally activated and/or imprinted genes. Detailed analyses of a co-expression module highly correlated with the basal endosperm transfer layer (BETL) identified a regulatory module activated by MRP-1, a regulator of BETL differentiation and function. These results provide a high-resolution atlas of gene activity in the compartments of the maize kernel and help to uncover the regulatory modules associated with the differentiation of the major endosperm cell types. RNAs from ten compartments of the maize kernel including the central starchy endosperm (CSE), conducting zone (CZ), aleurone (AL), basal endosperm transfer layer (BETL), embryo-surrounding region (ESR), nucellus (NU), pericarp (PE), placenta-chalazal region (PC), the vascular region of the pedicel (PED), and the embryo (EMB) were isolated at 8 days after pollination (DAP) using laser-capture microdissection and sequenced using an Illumina HiSeq 2000 platform.
Project description:Two maize inbred lines, DAN3130 and JI63, with different patterns of folate accumulation and different total folate contents in mature kernels were used to investigate the transcriptional regulation of folate metabolism during late stages of kernel formation by comparative transcriptome analysis; The fresh kernel samples of each inbred line were collected on DAP 24, DAP 35 days, respectively. Mature kernel samples were harvested after all the plants turned yellow. Three biological replicates of each sample were collected, and total RNA with high quality was pooled and sent for sequencing. Total RNA of high quality was pooled for transcriptome analysis, and raw RNA-seq data of DAP 24, DAP35 and mature kernels for both two inbred lines were obtained. The folate accumulation during DAP 24 to mature kernels could be controlled by circumjacent pathways of folate biosynthesis, such as pyruvate metabolism, glutamate metabolism and serine/glycine metabolism. In addition, the folate variation between these two inbred lines was related to those genes among folate metabolism, such as genes in the pteridine branch, ρ-ABA branch, serine/THF/5-M-THF cycle and the conversion of tetrahydrofolate monoglutamate to tetrahydrofolate polyglutamate; The findings provided insight into folate accumulation mechanisms during maize kernel formation to promote folate biofortification.
Project description:We explored the gene expression profiles of developing maize kernel by RNA sequencing. Our purpose was to explore the sequence diversity across the inbred lines, especially in the gene regions, and to discover the gene regulatory networks employed in immature maize kernels.
Project description:In this study, protein was extracted from maize kernel at 10 and 25 DAP with three biological replicates. All maize kernel samples under the two water treatments were collected at 09:00 h for proteomics analysis.
Project description:Endosperm is a filial structure resulting from a second fertilization event in angiosperms. As an absorptive storage organ, endosperm plays an essential role in support of embryo development or seedling germination. The accumulation of carbohydrate and protein storage products in cereal endosperm provides humanity with a major portion of its food, feed and renewal resources. However, little is known regarding the regulatory gene networks controlling endosperm proliferation and differentiation. As a first step towards understanding these processes, we have profiled all mRNAs in kernel and endosperm of maize at eight successive stages during the first 12 days after pollination. Analysis of these gene sets has identified temporal programs of gene expression including hundreds of transcription-factor genes. We also show a close correlation of these sequentially expressed gene sets with distinct spatial programs of expression in distinct compartments of the developing endosperm. The results constitute a preliminary atlas of spatiotemproal patterns of endosperm gene expression in support of future efforts for understanding the underlying mechanisms that control seed yield and quality. The unpollinated kernels (0 DAP), the kernels of 2, 3, 4, 6 DAP and hand dissected endosperms of 8, 10, 12 DAP from the B73 were used to perform high-throughput sequencing using the SOLiD platform
Project description:Transcriptome profiles of MATZ and BETL tissues are compared across three stages of development. Sugars and other nutrients unloaded from vascular tissues in the MATZ are imported by the BETL for utilization by the developing endosperm. Pronounced changes in gene expression occur in both tissues during kernel development. RNAseq data were obtained from duplicate tissue samples isolated by cryomicrodissection of developing maize kernels at three developmental time points; 8 days post-pollination (DAP), 14 DAP and 20 DAP.