MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

Abstract

Background: Zhengdan 958 (Zheng 58 × Chang 7-2), a commercial hybrid that is produced in a large area in China, is the result of the successful use of the heterotic pattern of Reid × Tang-SPT. The jointing stage of maize is the key period from vegetative to reproductive growth, which determines development at later stages and heterosis to a certain degree. MicroRNAs (miRNAs) play vital roles in the regulation of plant development, but how they function in the sixth leaf at the six-leaf (V6) stage to influence jointing stage heterosis is still unclear.

Result: Our objective was to study miRNAs in four hybrid combinations developed in accordance with the Reid × Tang-SPT pattern, Zhengdan 958, Anyu 5 (Ye 478 × Chang 7-2), Ye 478 × Huangzaosi, Zheng 58 × Huangzaosi, and their parental inbred lines to explore the mechanism related to heterosis. A total of 234 miRNAs were identified in the sixth leaf at the V6 stage, and 85 miRNAs were differentially expressed between the hybrid combinations and their parental inbred lines. Most of the differentially expressed miRNAs were non-additively expressed, which indicates that miRNAs may participate in heterosis at the jointing stage. miR164, miR1432 and miR528 families were repressed in the four hybrid combinations, and some miRNAs, such as miR156, miR399, and miR395 families, exhibited different expression trends in different hybrid combinations, which may result in varying effects on the heterosis regulatory mechanism.

Conclusions: The potential targets of the identified miRNAs are related to photosynthesis, the response to plant hormones, and nutrient use. Different hybrid combinations employ different mature miRNAs of the same miRNA family and exhibit different expression trends that may result in enhanced or repressed gene expression to regulate heterosis. Taken together, our results reveal a miRNA-mediated network that plays a key role in jointing stage heterosis via posttranscriptional regulation.

Keywords: Jointing stage heterosis; Maize; Photosynthesis; Sixth leaf; V6 stage; miRNA.

Fig. 1

Characteristics of the leaf area, net photosynthesis rate of the sixth leaf at the V6 stage and grain yield of hybrid combinations and inbred lines. The lowercase letters indicate significant differences at P < 0.05 (least significant difference)

Fig. 2

Length distribution of sRNAs in the sixth leaf at the V6 stage of the four hybrid combinations and inbred lines

Fig. 3

Expression of the total identified known miRNAs in the four hybrid combinations and the four inbred lines

Fig. 4

Characteristics of differentially expressed miRNAs between hybrid combinations and their parental lines and classification of the differentially expressed miRNAs. a-d Venn diagram of differentially expressed miRNAs between the four hybrid combinations and parental lines. e Expression pattern classification of the differentially expressed miRNAs in the four hybrid combinations. “++”, extremely high parental expression; “+”, high parental expression; “+−”, additive expression; “-”, low parental expression; “--”, extremely low parental expression. f Venn diagram of the expression patterns of scaled miRNAs in the four hybrid combinations

Fig. 5

Major GO categories of biological processes for the target genes identified by the degradome of the scaled miRNAs. a Zhengdan 958; b Anyu 5; c Ye 478 × Huangzaosi; d Zheng 58 × Huangzaosi

Fig. 6

Examples of T-plots of miRNA targets confirmed by degradome sequencing. he T-plots show the distribution of the degradome reads along the full length of the target mRNA. The red point indicates the cleavage site of each transcript. a The cleavage features in SPL11 (Zm00001d014698_T001) mRNA by miR156a-5p. b Cleavage features in NAC domain-containing protein 79 (Zm00001d050893_T001) mRNA by miR164e-5p. c Cleavage features in sulfate transporter 2.2 (Zm00001d028164_T001) mRNA by miR395b-3p. d Cleavage features in a cupredoxin superfamily protein member (Zm00001d021850_T001) mRNA by miR528a-5p

Fig. 7

Verification of the expression patterns of selected miRNAs and their target genes in Zhengdan 958. The different lowercase letters above the columns indicate significant differences (P < 0.05)

Fig. 8

Model for miRNAs and their target genes associated with photosynthesis, hormone effects, and nutrient use. The black letters in the yellow block indicate upregulation, and the black letters in the green block indicate downregulation. The black arrows represent the direction of regulation. ELIP: early light-induced protein; SULTR, sulfate transporter; PHO2, PHOSPHATE 2; SPL, SQUAMOSA promoter-binding-like family transcription factors; NAC1, NAC domain-containing protein