Abstract
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo.
Highlights
Pummelo (Citrus grandis (L.) Osbeck), known as the female parent of sweet orange, is an important economical cultivated species and a valuable germplasm for citrus breeding
The length distribution of the unigenes indicates that the assembled unigenes with lengths varying from 200 to 300 bp, 300 to 1000 bp and above 1000 bp accounted for 22.41%, 40.69% and 36.90% of the total, respectively (S1B Fig.)
next-generation sequencing (NGS) technology, which is characterized by unprecedented high throughput, convenience and cost-effectiveness, is likely to become the method of choice for transcriptome sequencing, which is an important molecular biology tool that is widely used in various studies, such as in generating different dynamic views of gene expression [25,26,27], the discovery of novel genes or transcripts [28,29], splicing activity [30], and molecular marker mining [31,32,33,34]
Summary
Pummelo (Citrus grandis (L.) Osbeck), known as the female parent of sweet orange, is an important economical cultivated species and a valuable germplasm for citrus breeding. Pummelo is commercially cultivated in many countries, such as China, Thailand, Japan, Mexico and Israel, because pummelo fruits and juice have abundant antioxidant compounds, including vitamin C, carotenoids, flavonoids and limonoids, which can reduce the risk of oxidative-related diseases [1,2,3,4]. De Novo Transcriptome and Molecular Markers Development of Pummelo
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