Abstract
To identify the genetic variation between Citrus trifoliata and Citrus clementina, we performed genome resequencing on the two citrus species. Compared with the citrus reference genome, a total of 9,449,204 single-nucleotide polymorphisms (SNPs) and 846,615 insertion/deletion polymorphisms (InDels) were identified in the two citrus species, while 1,868,115 (19.77%) of the SNPs and 190,199 (22.47%) of the InDels from the two citrus species were located in the genic regions. Meanwhile, a total of 8,091,407 specific SNPs and 692,654 specific InDels were identified in the two citrus genotypes, yielding an average of 27.32 SNPs/kb and 2.34 InDels/kb. We identified and characterized the patterns of gene exchanges in the grafted citrus plants by using specific genetic variation from genome resequencing. A total of 4396 transporting genes across graft junctions was identified. Some specific genetic variation and mobile genes was also confirmed by Sanger sequencing. Furthermore, these mobile genes could move directionally or bidirectionally between the scions and the rootstocks. In addition, a total of 1581 and 2577 differentially expressed genes were found in the scions and the rootstocks after grafting compared with the control, respectively. These genetic variations provide fundamental information on the genetic basis of important traits between C. trifoliata and C. clementina, as the transport of genes would be applicable to horticulture crops.
Highlights
Grafting has been used in a number of plant species, including fruits, vegetables, and ornamentals, for over 2000 years of history to improve plant production, water-use efficiency, and other fruit quality traits, as well as deal with abiotic stress [1,2]
A total of 9,449,204 single-nucleotide polymorphisms (SNPs) and 846,615 insertion/deletion polymorphisms (InDels) were identified in the two citrus species
A total of 8,091,407 specific SNPs and 692,654 specific InDels were identified in the two citrus genotypes
Summary
Grafting has been used in a number of plant species, including fruits, vegetables, and ornamentals, for over 2000 years of history to improve plant production, water-use efficiency, and other fruit quality traits, as well as deal with abiotic stress [1,2]. Grafting is employed to fuse material from two different plants: a part of a plant (scions) is joined to another plant (rootstocks) for the two parts to grow together [3]. When a graft takes successfully, the rootstock and scions appear to grow as a single unit in cultivation. Graft compatibility between the scions and rootstocks is a key factor affecting the success rate of grafting. Grafting is a common means to clonally propagate desirable scions in many fruit trees, because the seeds from these plants cannot reproduce the original cultivar due to genomic heterogeneity [4]. The mechanisms behind the physiological interactions between rootstocks and scions in fruit trees have been studied for some time, Biomolecules 2018, 8, 182; doi:10.3390/biom8040182 www.mdpi.com/journal/biomolecules
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