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Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis.

Petersen R, Djozgic H, Rieger B, Rapp S, Schmidt ER - BMC Plant Biol. (2015)

Bottom Line: Radicles mainly express genes associated with primary metabolism, 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany. peterser@uni-mainz.de.

ABSTRACT

Background: Primary 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.

Results: Radicles 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.

Conclusions: The 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).

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Genotypes of primary roots. The genotype of 119 apple primary roots was determined by marker PCRs with regard to the presence of the Gypsy-44 retrotransposon insertion.
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Fig1: Genotypes of primary roots. The genotype of 119 apple primary roots was determined by marker PCRs with regard to the presence of the Gypsy-44 retrotransposon insertion.

Mentions: 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. As the trees were grown surrounded by other columnar apple varieties, the chance of pollination by a columnar father was high. After about 12 weeks of incubation at 4°C, the germination rate of the seeds was approximately 80%. No obvious phenotypic differences could be observed between individual radicles. The radicle genotype with regard to the presence of the columnar-specific Gypsy-44 transposable element (TE), which most likely represents the original Co mutation [10], was determined via PCRs. The diagnostic PCR assays as established by Otto et al. discriminate unambiguously between the non-columnar, the heterozygous columnar and the homozygous columnar genotype [10]. Of 119 seedlings subjected to genotyping, 40 seedlings were detected to be non-columnar, 59 showed a heterozygous columnar genotype, while the remaining 20 seedlings carried the columnar-specific Gypsy-44 insertion homozygously. These results could be confirmed by PCR assays using our indel-based markers I2_3_M1 and H1_M1 that are tightly linked to the Co mutation [37]. In total, 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.Figure 1


Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis.

Petersen R, Djozgic H, Rieger B, Rapp S, Schmidt ER - BMC Plant Biol. (2015)

Genotypes of primary roots. The genotype of 119 apple primary roots was determined by marker PCRs with regard to the presence of the Gypsy-44 retrotransposon insertion.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4352258&req=5

Fig1: Genotypes of primary roots. The genotype of 119 apple primary roots was determined by marker PCRs with regard to the presence of the Gypsy-44 retrotransposon insertion.
Mentions: 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. As the trees were grown surrounded by other columnar apple varieties, the chance of pollination by a columnar father was high. After about 12 weeks of incubation at 4°C, the germination rate of the seeds was approximately 80%. No obvious phenotypic differences could be observed between individual radicles. The radicle genotype with regard to the presence of the columnar-specific Gypsy-44 transposable element (TE), which most likely represents the original Co mutation [10], was determined via PCRs. The diagnostic PCR assays as established by Otto et al. discriminate unambiguously between the non-columnar, the heterozygous columnar and the homozygous columnar genotype [10]. Of 119 seedlings subjected to genotyping, 40 seedlings were detected to be non-columnar, 59 showed a heterozygous columnar genotype, while the remaining 20 seedlings carried the columnar-specific Gypsy-44 insertion homozygously. These results could be confirmed by PCR assays using our indel-based markers I2_3_M1 and H1_M1 that are tightly linked to the Co mutation [37]. In total, 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.Figure 1

Bottom Line: Radicles mainly express genes associated with primary metabolism, 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, Johannes Gutenberg-University, Mainz, D-55128, Germany. peterser@uni-mainz.de.

ABSTRACT

Background: Primary 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.

Results: Radicles 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.

Conclusions: The 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).

Show MeSH