Читать книгу Biotechnology of Fruit and Nut Crops - Группа авторов - Страница 113

Little is known about the physiological and molecular basis for tissue development in coconut (Liang et al., 2014). A coconut bacterial artificial chromosome library has been reported (Baudouin et al., 2005); however, this genomic tool has not been exploited (Meerow et al., 2012). Using a super-matrix of seven WRKY transcription factor loci, Meerow et al. (2009) demonstrated that Syagrus is the most closely related genus to Cocos.

Direct sequencing of cDNA fragments is now possible without the construction of clone libraries. Parallel sequencing (RNA-seq) methods have been employed to gain a global overview of the C. nucifera transcriptome. One study (Fan et al., 2013) used Illumina sequencing to collect 54.9 million short reads and that underwent de novo assembly to produce 57,304 unigenes with a mean length of 752 bp. When these unigenes were examined further, 347 were involved in fatty acid synthesis and metabolism, and 23,168 were mapped into 215 KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways, including galactose metabolism, plant-pathogen interaction and plant hormone signal transduction pathways.

Xia et al. (2014) used transcriptome sequencing to ascertain the distribution of gene-based microsatellite loci and obtain a series of SSR markers for coconut. Of the 6608 SSRs identified across 57,304 unigenes, there was approximately one expressed sequence tag-derived SSR locus for every ten unigenes. Polymorphic markers were used to examine coconut varieties from different regions of Asia and nine markers were significantly linked to coconut height.

Huang et al. (2014) examined gene expression in embryos, endosperm and leaves of Dwarf coconuts, using de novo transcript assembly from RNA-seq data. In 10 Gb of collected sequence data, there were 58,211 unigenes reported from the embryo, 61,152 from the endosperm and 33,446 from leaf tissue. In each unigene group, 24,857 were annotated to the embryo, 29,731 to the endosperm and 26,064 to leaves. KEGG analysis identified 138 pathways for both embryo and endosperm and 139 for leaf tissues. The results indicate that RNA-directed DNA methylation is important for coconut seed development, especially when the endosperm is maturing. Transcript profiles established for those tissues revealed a number of highly expressed genes with further potential to uncover strong tissue-specific promoters.

Research by Liang et al. (2014) functionally annotated genes that were differentially expressed during three coconut pulp development stages using bioinformatics analysis. This has provided a valuable understanding of gene function and involvement in regulatory networks during coconut fruit development. A total of 1272 clones were analysed from four suppression subtractive hybridization libraries, with 63% showing a likeness to known proteins. Out of a total of 737 unigenes, 103 of the identified enzymes were linked to fatty acid and carbohydrate biosynthesis and metabolism.

A study by Armero et al. (2017) used oil palm as a reference species for coconut comparative genomics to improve transcriptomic data and provide a proteome that could be used to address functional or evolutionary queries. The method generated 29,366 proteins, 1246 of which were derived from new contigs. The coconut proteome had a functional profile similar to that of rice and metabolic pathways related to secondary metabolism and biotic stress were also identified.

These transcriptomic studies provide the groundwork for future coconut molecular genetic research and breeding, as well as for isolation and characterization of functional genes involved in different biochemical pathways.