Identification of genes alternatively spliced in developing maize endosperm

Abstract

The process of alternative splicing is critical for the regulation of growth and development of plants. Thus far, little is known about the role of alternative splicing in the regulation of maize (Zea mays L.) endosperm development. RNA sequencing (RNA-seq) data of endosperms from two maize inbred lines, Mo17 and Ji419, at 15 and 25 days after pollination (DAP), respectively, were used to identify genes that were alternatively spliced during endosperm development. Intron retention (IR) in GRMZM2G005887 was further validated using PCR and re-sequencing technologies. In total, 49,000 alternatively spliced events and ca. 20,000 alternatively spliced genes were identified in the two maize inbred lines. Of these, 30 genes involved in amino acid biosynthesis and starch biosynthesis were identified, with IR occurring only in a specific sample, and were significantly co-expressed with ten well-known genes related to maize endosperm development. Moreover, IR in GRMZM2G005887, which encodes a cysteine synthase, was confirmed to occur only in the endosperm of Mo17 at 15 DAP, resulting in the retention of a 121-bp fragment in its 5' untranslated region. Two cis-acting regulatory elements, CAAT-box and TATA-box were observed in the retained fragment in Mo17 at 15 DAP; this could regulate the expression of this gene and influence endosperm development. The results suggest that the 30 genes with IR identified herein might be associated with maize endosperm development, and are likely to play important roles in the developing maize endosperm.

Genome-Wide Profiling of Alternative Splicing and Gene Fusion during Rice Black-Streaked Dwarf Virus Stress in Maize (Zea mays L.)

“…Alternative splicing (AS) was first identified in calcitonin and immunoglobulin genes [ 25 , 38 , 39 ]. Previous studies detected AS in 60% of plant genes [ 25 , 40 ].…”

“…Alternative splicing (AS) was first identified in calcitonin and immunoglobulin genes [ 25 , 38 , 39 ]. Previous studies detected AS in 60% of plant genes [ 25 , 40 ]. AS events typically include signal transduction, growth, abiotic stresses, and circadian rhythms [ 41 , 42 ], and AS has recently been found to play a major role in these processes during stress events, such as drought, heat, and disease [ 43 , 44 , 45 , 46 , 47 ].…”

“…AS events typically include signal transduction, growth, abiotic stresses, and circadian rhythms [ 41 , 42 ], and AS has recently been found to play a major role in these processes during stress events, such as drought, heat, and disease [ 43 , 44 , 45 , 46 , 47 ]. In maize, AS events were identified that responded to drought [ 48 , 49 ], development [ 29 ], and endosperm [ 25 ]. AS events can provide a novel strategy for plant response to virus stresses.…”

“…The structures, functions, and subcellular locations of these proteins can be altered by AS transcripts [ 20 , 21 , 22 ]. AS plays a significant role in post-transcriptional responses to biotic and abiotic stresses in plants [ 23 , 24 ], including development in maize endosperm [ 25 ], the evolution of maize or soybean [ 26 , 27 ], drought and heat in maize or wheat [ 22 , 28 , 29 ], and plant-virus interactions in Brachypodium distachyon [ 30 ] and wheat [ 31 ]. However, there are no reports about whether AS plays a role in maize response to RBSDV.…”

Integrated transcriptome, small RNA, and degradome analysis reveals the complex network regulating starch biosynthesis in maize

“…These two lines differ significantly in endosperm starch content and starch granule structure (Additional file 3: Figure S2; Additional file 6: Figure S5). Further details of the kernel morphological characteristics of Mo17 and Ji419 have been detailed in our previous study [74]. The experimental field consisted of 40 rows that were 3 m long and 0.6 m wide, with spacing of 0.3 m between plants within rows.…”