Abstract
Columnar apples trees, originated from a bud mutation ‘Wijcik McIntosh,’ develop a simple canopy and set fruit on spurs. These characteristics make them an important genetic resource for improvement of tree architecture. Genetic studies have uncovered that columnar growth habit is a dominant trait and is caused by a retroposon insertion that induces the expression of the neighboring gene Co encoding a 2OG-Fe(II) oxygenase. Here we report the genetic mapping of two loci of recessive suppressors (genes) c2 (on Chr10) and c3 (on Chr9) that are linked to repression of the retroposon-induced Co gene expression and associated columnar phenotype in 275 F1 seedlings, which were developed from a reciprocal cross between two columnar selections heterozygous at the Co locus. The mapping was accomplished by sequencing a genomic pool comprising 18 columnar seedlings and another pool of 16 standard seedlings that also carry the retroposon insertion, and by exploring DNA variants of segregation types that are informative for mapping recessive traits in apple. The informative segregation types include <hk × hk>, <lm × ll>, <nn × np>, <lm × mm>, and <pp × np>, where each letter denotes one of the four DNA bases and the letters in bold represent variants in relation to the reference genome. The alleles in each first and third positions are assumed in linkage with the recessive suppressors’ allele in the two parents, respectively. Using RNA-seq analysis, we further revealed that the Co gene together with the differentially expressed genes under loci c2 and c3 formed a co-expression gene-network module associated with growth habit, in which 12 MapMan Bins were enriched.
Highlights
In the mid-20th century, the successful genetic improvement in plant architecture had led to a drastic yield increase worldwide in field crops, corn, rice and wheat
To identify the columnar suppressors, we explored and identified DNA variants of segregation types suitable for mapping recessive traits in apple by pooled genome sequencing, an adaptation from a previous approach developed for mapping dominant traits (Dougherty et al, 2018)
Using RNA-seq analysis, we further revealed that suppressed columnar phenotype is coupled with a strong expression repression of the Co gene, which together with the differentially expressed genes (DEGs) under c2 and c3 formed a co-expression gene-network module highly associated with growth habit
Summary
In the mid-20th century, the successful genetic improvement in plant architecture had led to a drastic yield increase worldwide in field crops, corn, rice and wheat. To keep apple trees in optimal shape for fruit production in orchards, horticulturists have. Phenotypic Suppression of Columnar Apples been improving tree pruning and training systems and developing different dwarfing rootstocks (Robinson et al, 2013). Such efforts are effective for productivity improvement in modern orchards, apple production costs have been increased markedly due to manual tree pruning and fruit harvest (West et al, 2012; Taylor and Granatstein, 2013). There is a strong demand for automation of labor-intensive orchard tasks, especially fruit harvest. The complex and dynamic tree canopy and variable fruit bearing sites have been the major challenges to automating fruit harvest motorized platforms that can improve fruit harvest efficiency are available and promising prototypes of robotic fruit harvesters are being tested
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