Transcriptomic analysis of maize mature embryos from an elite maize hybrid Zhengdan958 and its parental lines

Abstract

Utilization of heterosis is one of the most outstanding advancements in plant breeding. However, its genetic basis is not well understood. We used digital gene expression technology to investigate the transcriptomes of the mature maize embryo of an elite maize hybrid Zhengdan958 and its parental lines to screen differentiallyexpressed genes and to study their relationship to heterosis. In the study, we found five expression patterns, including co-silence expression of parental lines (754 genes), parental-specific expression (2,200 genes), hybrid-specific expression (704 genes), single-parental consistent expression (2,431 genes), and co-expression of the hybrid and parental lines (15,628 genes). Genes showing hybrid-specific expression pattern were enriched in photosynthesis related pathways. Those over-dominance expressed genes in co-expression pattern were striking enriched in protein metabolic process, and those under-dominance expressed genes in co-expression pattern were signally enriched in biosynthetic process. Those results indicated that mature embryo of Zhengdan958 has higher photosynthetic efficiency and better regulation ability in protein metabolic and biosynthetic process for better preparation for growth recover, and those enriched genes can be related with heterosis of maize mature embryos.

Comparative transcriptome analysis reveals important roles of nonadditive genes in maize hybrid An’nong 591 under heat stress

“…According to the differences in expression between hybrids and their parental lines, genes can be classified into five expression patterns, namely co-silence expression of the parental lines (Type I: genes are expressed in both of the parental lines, but not in F 1 hybrid), parental-specific expression (Type II: genes are expressed only in one of the parental lines), hybrid-specific expression (Type III: genes are expressed only in F 1 hybrid), single-parental consistent expression (Type IV: genes are expressed in F 1 and one of the parental lines), and co-expression of the hybrid and parental lines (Type V) [26]. In the present study, under the control conditions, a total of 288, 1459, 93, and 1713 genes were identified for Types I to IV, respectively, whereas 116, 1478, 153, and 2321 genes were detected for the four groups under heat treatment (Fig.…”

“…Previous studies have indicated that Types I to IV are associated with qualitative differences in gene expression, meanings presence/absence variation of these genes. Type V is associated with quantitative differences in gene expression, and the difference in expression patterns between hybrids and their parental lines is predominantly associated with this type [3, 26]. A total of 12 classes of DEGs were defined according to the expression pattern in the hybrid relative to its parental lines in the present study (Table 1).…”

“…Three main genetic models, comprising dominance, overdominance, and epistasis hypotheses, have been proposed to explain heterosis in classical quantitative genetics [4–6, 9]; however, the molecular and genetic mechanisms of this complex biological phenomenon remain poorly understood [3]. Increasing evidence has indicated that differential gene expression between hybrids and their parental lines may be responsible for heterosis [3, 23, 26]. In the present study, RNA-Seq was adopted to investigate the relationship between expression patterns and heterosis in seedlings of the maize hybrid An’nong 591 and its parental lines CB25 and CM1 grown under control and heat stress conditions.…”

“…Nonadditive gene expression in hybrids includes levels of transcripts equal to the high or low parent (high or low parent dominance), above the high parent (overdominance), or below the low parent (underdominance) [3, 15, 21–25]. For example, using transcriptome analysis of the mature embryo, a total of 4766 and 4081 transcripts were identified as DEGs between the maize hybrid Zhengdan 958 and its parental lines (Chang 7–2 and Zheng 58, respectively) and were further divided into additive, paternal dominance, maternal dominance, overdominance, and underdominance in accordance with the different expression patterns [26].…”

Comparative Study on the Transcriptome of Maize Mature Embryos from Two China Elite Hybrids Zhengdan958 and Anyu5

“…This result showed that a large portion of differential genes were not expressed in mature embryos. In the present study, several DEGs detected by digital gene expression profiling were already validated by quantitative RT-PCR [ 13 ].…”