Читать книгу Biotechnology of Fruit and Nut Crops - Группа авторов - Страница 132

Molecular marker technologies can greatly improve the breeding efficiency of oil palm. DNA markers and genetic linkage maps are essential resources for MAS to accelerate genetic improvement. The identification of expressed sequence tags–simple sequence repeats (EST-SSRs) that detect polymorphisms in elite breeding material provides tools for molecular breeding strategies. The identification of SSRs within transcripts, in particular those that encode proteins involved in transcriptional and post-transcriptional regulation, would allow insight into the functional roles of these proteins by revealing how phenotypic traits cosegregate with these markers. Tranbarger et al. (2012) reported 6103 non-redundant ESTs derived from cDNA libraries of developing vegetative and reproductive tissues were annotated and searched for SSRs. Primer pairs from sequences flanking 289 EST-SSRs were tested to detect polymorphisms in elite breeding parents and their crosses. Among 230 of these amplified PCR products, 88 were polymorphic within the breeding material tested. A detailed analysis and annotation of the EST-SSRs revealed the locations of the polymorphisms within the transcripts, and that the main functional category was related to transcription and post-transcriptional regulation. SSR polymorphisms were found in sequences encoding AP2-like, bZIP, zinc finger, MADS-box and NAC-like transcription factors in addition to other transcriptional regulatory proteins and several RNA interacting proteins.

In order to identify QTLs for fatty acid composition of palm oil, Montoya et al. (2013) studied an Elaeis interspecific pseudo-backcross of first generation (E. oleifera × E. guineensis) × E. guineensis. A dense microsatellite linkage map of 362 loci spanned 1.485 cM, representing the 16 pairs of homologous chromosomes in the Elaeis genus from which the authors traced segregating alleles from both E. oleifera and E. guineensis grandparents. The relative linear orders of mapped loci suggested the probable absence of chromosome rearrangements between the E. oleifera and E. guineensis genomes. There were 19 QTLs associated with palm oil fatty acid composition. The QTL positions and the species origin as well as the estimated effects of the QTL marker alleles were in coherence with the oil biosynthesis pathway in plants and with the individual phenotypic correlations between the traits. The mapping of chosen Elaeis key genes related to oleic acid C18:1, using intra-gene single nucleotide polymorphisms (SNPs), supported several QTLs underlying notably FATA and SAD enzymes. The high number of hypervariable SSR loci of known relative linear orders and the QTL information make these resources valuable for mapping in other Elaeis breeding materials.

Several linkage maps have been constructed using dominant and codominant markers to facilitate mapping of QTLs in oil palm; however, dominant markers are not easily transferable among different laboratories. Lee et al. (2015) constructed a consensus linkage map for oil palm using codominant markers, i.e. microsatellite and SNPs, and two F1 breeding populations generated by crossing dura and pisifera individuals. Four hundred and forty-four microsatellites and 36 SNPs were mapped onto 16 linkage groups. The map length was 1565.6 cM, with an average marker space of 3.72 cM. A genome-wide scan of QTLs identified a major QTL for stem height on linkage group 5, which explained 51% of the phenotypic variation. Genes in the QTL were predicted using the palm genome sequence and bioinformatic tools. The linkage map supplies a base for mapping QTLs for accelerating genetic improvement and will be also useful for improving the assembly of genome sequences. Markers linked to the QTLs may be used for selecting dwarf trees, and genes within the QTL will be characterized to understand the mechanisms underlying dwarfing (Lee et al., 2015).

SNPs are widespread nucleotide variations in genomes, the most abundant type of DNA marker and easily detected at high-throughput in genomes. By taking advantage of the recently developed reference genome sequence of the oil palm (Singh et al., 2013a,b), it is possible to develop genome-wide DNA markers with gene information resources (Ting, 2014). Furthermore, gene-based SNP markers could themselves be causative SNPs for traits and have been used for developing transcript maps, QTL analysis, association mapping and synteny analysis (Pootakham et al., 2015).

Using both SNPs and microsatellites markers, Bai et al. (2018) constructed a linkage map containing 10,023 markers covering 16 chromosomes. The map length was 2938.2 cM with an average marker space of 0.29 cM. Such a large number of SNPs will supply ample choices of DNA markers in analysing the genetic diversity, population structure and evolution of oil palm. This high-density linkage map will contribute to mapping QTLs for important traits, thus accelerating oil palm genetic improvement. Gan et al. (2018) reported the first use of the DArTseq platform to genotype two closely related self-pollinated oil palm populations. Identification of the sh marker demonstrated the robustness of using the DArTseq platform to generate high-density genetic maps of oil palm with adequate genome coverage. Both genetic maps and integrated maps are of paramount interest for QTL analysis of important yield traits as well as potentially assisting the anchoring of genetic maps to genomic sequences.