Generation, functional analysis and utility of Citrus grandis EST from a flower-derived cDNA library

Abstract

Pummelo (Citrus grandis) is one of the most important species found in the genus Citrus and one of the ancestors of sweet oranges. We used flower buds at different developmental stages to construct the first cDNA library for this species. A total of 3,758 EST sequences were generated from the cDNA library and clustered into 2,228 unigenes, comprising 451 contigs and 1,777 singletons. Among these unigene sequences, 1,266 have significant homology to the non-redundant protein database, from which 891 were assigned to one or more gene ontology categories. Functional categorization of the annotated unigenes showed that 760 genes were involved in molecular function, 1,189 in biological processes and 1,154 in cellular component categorization. Homologs of genes regulating many aspects of flower development were also identified, including those for organ development, cell-cycle control and cell and tissue differentiation. The majority of these genes (e.g., embryo relatives, YABBY-like, MAD Box, SKP-like and SRNAs) are the first representatives in Citrus, providing an opportunity to explore the cause of self incompatibility and embryo development in Citrus. Patterns of transcript accumulation were characterized by real-time qPCR for 13 of these genes. Many potential molecular markers were also identified in this EST data set; 212 Simple Sequences Repeats (SSRs), 717 transposon elements and 115 candidate single nucleotide polymorphisms (SNPs) were found. An assessment of a set of 212 SSR primer pairs on 16 citrus genotypes showed polymorphism with 122 (57.82%) markers. Similarly, a set of eight contigs were used to confirm in silico predicated SNPs in a set of five genotypes using wet lab experiments, three contigs were generated as scorable and sequenceable amplicons and no PCR amplicons were obtained from five contigs. The outcome of this study could aid in the discovery of genes involved in reproductive developments. Identified candidate genes can be experimentally tested for their functions in various important processes. SSR, SNP and transposon element-containing data sets may facilitate marker development and can be used for citrus molecular breeding, linkage map construction, evolutionary, phylogenetic and population genetic studies.