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Comparative transcriptome analysis reveals mechanisms of folate accumulation in maize grains

ABSTRACT: 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.

ORGANISM(S): Zea mays

PROVIDER: GSE195815 | GEO | 2022/04/19

REPOSITORIES: GEO

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Project description:Maize kernel is an important source of food, feed and industrial raw materials. The illustration of the molecular mechanisms of maize kernel development will be helpful for the manipulation of maize improvements. Although a great many researches based on molecular biology and gecetics have greatly increased our understanding on the kernel development, many of the mechanisms controlling this important process remain elusive. In current study, a microarray with approximately 58,000 probes was used to study the dynamic gene expression during kernel development from the fertilization to physiological maturity. Samples from two consecutive time-points were paired and labeled using different fluorescent dyes (Cy3 and Cy5) and hybridized in the same array. Hybridization of slides was performed according to the manufacturer’s instructions (http://www.maizearray.org/). The hybridized slides were scanned by a Genepix 4000B (Axon, USA). A loop design was applied for running the microarray. Two replicates of each pair of samples were carried out to test both the reproducibility and quality of the chip hybridizations. By comparing six consecutive time-points, namely 1, 5, 10, 15, 25 and 35 days after pollination (DAP), 3,445 differentially expressed genes were identified. These genes were then grouped into 10 clusters showing specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes expanded our understanding of the regulation mechanism underlying the important developmental processes, cell division and kernel filling. The differential expression of genes involved in plant hormone signaling pathways suggested that phytohormone might play a critical role in the kernel developmental process. Moreover, regulation of some transcription factors and protein kinases might be involved in the whole developmental process. To obtain the global gene expression profile during maize kernel development, a microarray with approximately 58,000 probes was used. The maize inbred line X178 was planted on the field. Each plant was self-pollinated by hand. The ears were harvested from healthy plants at 1, 5, 10, 15, 25 and 35 days after pollination (DAP), respectively. In order to increase the consistency & uniformity of the isolated kernels, the upper half and about one sixth of ears from the bottom were cut and discarded, the kernels were isolated from the rest part of the ears. Samples at each time-point were collected from at least thirty ears and pooled to represent the line characteristics of X178. Two sub-samples for replication in the microarray analysis were randomly drawn. Samples from two consecutive time-points were paired and labeled using different fluorescent dyes (Cy3 and Cy5) and hybridized in the same array. A loop design was applied for running the microarray. Two replicates of each pair of samples were carried out to test both the reproducibility and quality of the chip hybridizations.

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Comparative transcriptome analysis reveals mechanisms of folate accumulation in maize grains

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