Abstract
BackgroundPrimary roots (radicles) represent the first visible developmental stages of the plant and are crucial for nutrient supply and the integration of environmental signals. Few studies have analyzed primary roots at a molecular level, and were mostly limited to Arabidopsis. Here we study the primary root transcriptomes of standard type, heterozygous columnar and homozygous columnar apple (Malus x domestica) by RNA-Seq and quantitative real-time PCR. The columnar growth habit is characterized by a stunted main axis and the development of short fruit spurs instead of long lateral branches. This compact growth possesses economic potential because it allows high density planting and mechanical harvesting of the trees. Its molecular basis has been identified as a nested Gypsy-44 retrotransposon insertion; however the link between the insertion and the phenotype as well as the timing of the phenotype emergence are as yet unclear. We extend the transcriptomic studies of columnar tissues to the radicles, which are the earliest developmental stage and investigate whether homozygous columnar seedlings are viable.ResultsRadicles mainly express genes associated with primary metabolism, growth and development. About 200 genes show differential regulation in a comparison of heterozygous columnar radicles with non-columnar radicles, whereas the comparison of homozygous columnar radicles with non-columnar radicles yields about 300 differentially regulated genes. Genes involved in cellulose and phenylpropanoid biosynthesis, cell wall modification, transcription and translation, ethylene and jasmonate biosynthesis are upregulated in columnar radicles. Genes in the vicinity of the columnar-specific Gypsy-44 insertion experience an especially strong differential regulation: the direct downstream neighbor, dmr6-like, is downregulated in heterozygous columnar radicles, but strongly upregulated in columnar shoot apical meristems.ConclusionsThe transcriptomic profile of primary roots reflects their pivotal role in growth and development. Homozygous columnar embryos are viable and form normal radicles under natural conditions, and selection towards heterozygous plants most likely occurs due to breeders’ preferences. Cell wall and phytohormone biosynthesis and metabolism experience differential regulation in columnar radicles. Presumably the first step of the differential regulation most likely happens within the region of the retrotransposon insertion and its tissue-specificity suggests involvement of one (or several) tissue-specific regulator(s).Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0356-6) contains supplementary material, which is available to authorized users.
Highlights
Primary roots represent the first visible developmental stages of the plant and are crucial for nutrient supply and the integration of environmental signals
Homozygous columnar apple seedlings are viable To investigate whether homozygous columnar apple seedlings show reduced viability or phenotypic effects compared to standard-type seedlings in early developmental stages, seeds obtained from apples of the heterozygous columnar cultivar ‘Procats 28’ (P28) that had been subjected to open pollination were germinated
A genotype ratio of non-columnar : heterozygous columnar : homozygous columnar seedlings of 2 : 3 : 1 (Figure 1) was detected. This suggests that homozygous columnar apple embryos are viable and most likely germinate at normal ratios
Summary
Primary roots (radicles) represent the first visible developmental stages of the plant and are crucial for nutrient supply and the integration of environmental signals. The columnar growth habit is characterized by a stunted main axis and the development of short fruit spurs instead of long lateral branches This compact growth possesses economic potential because it allows high density planting and mechanical harvesting of the trees. Columnar apple trees show a characteristic pillar-like growth habit with a thick, stunted main axis and short lateral fruit spurs [1,2]. This growth habit could be of potential benefit to apple growers because columnar trees can be planted closer together and require less pruning than standard tree types [2,3]. Whether the lack of homozygous individuals (Co/Co) is due to a decreased viability of homozygous columnar seeds/seedlings or just the decision of apple growers to preferentially choose non-columnar breeding partners is unclear
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