The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq

Abstract

Background: The chloroplast genome has the potential to be genetically engineered to enhance the agronomic value of major crops. As a crop plant with major economic value, it is important to understand every aspect of the genetic inheritance pattern among Elaeis guineensis individuals to ensure the traceability of agronomic traits.

Methods: Two parental E. guineensis individuals and 23 of their F₁ progenies were collected and sequenced using the next-generation sequencing (NGS) technique on the Illumina platform. Chloroplast genomes were assembled de novo from the cleaned raw reads and aligned to check for variations. The sequences were compared and analyzed with programming language scripting and relevant bioinformatic softwares. Simple sequence repeat (SSR) loci were determined from the chloroplast genome.

Results: The chloroplast genome assembly resulted in 156,983 bp, 156,988 bp, 156,982 bp, and 156,984 bp. The gene content and arrangements were consistent with the reference genome published in the GenBank database. Seventy-eight SSRs were detected in the chloroplast genome, with most located in the intergenic spacer region.The chloroplast genomes of 17 F₁ progenies were exact copies of the maternal parent, while six individuals showed a single variation in the sequence. Despite the significant variation displayed by the male parent, all the nucleotide variations were synonymous. This study show highly conserve gene content and sequence in Elaeis guineensis chloroplast genomes. Maternal inheritance of chloroplast genome among F₁ progenies are robust with a low possibility of mutations over generations. The findings in this study can enlighten inheritance pattern of Elaeis guineensis chloroplast genome especially among crops' scientists who consider using chloroplast genome for agronomic trait modifications.

Keywords: Chloroplast genome; Chloroplast inheritance; Gene content; Oil palm; Simple sequence repeat.

Figure 1. Summary visualization of nucleotide variations in the sequences generated in this study compared to J4-25.

J4-25 serve as reference genome on the bottom. The numbers on the top diagram are alignment position for each variation. The box in dark grey color are InDels variation with ‘i’ is insertion and ‘d’ is deletion. The number in the dark grey box shows the number of inserted nucleotide. For example, GB3341 has one insertion in position 6,902, ML161 has one deletion in position 12,995. Additionally, SNP variations were also specified in the diagram.

Figure 2. Visualization of the circular structure of E. guineensis (J4-25) chloroplast genome.

The arrows show the transcription direction of the genes. Genes positioned on the outside are transcribed counterclockwise, conversely, genes positioned on the inside are transcribed clockwise. The bands on the inside represent SNPs and InDels of different individuals in this study. Red: deletion; orange: Insertion; brown: SNP ‘G’; green: SNP ‘A’; blue: SNP ‘T’; yellow: SNP ‘C’.

Figure 3. TCS network of haplotypes in this study.

Haplotypes individuals with SNPs variation can be viewed in Table 2 and the details in Table S2. The hash lines between different haplotypes are nucleotide SNPs. Both Hap_6 (GB3331,GB3347) and Hap_4 (GB3311) showed one SNP, Hap_3 (ML-161) showed 15 SNPs, and Hap_1 (NC_017602) showed 35 SNPs compared to J4-25 sequence.

Figure 4. Bar chart shows SSR distribution in J4-25 chloroplast genome regions.

(A) Bar chart shows SSR distribution in J4-25 chloroplast genome regions. y-axis is the SSR number, x-axis is the sequence region in the chloroplast region. On the top of each bar is a total SSR number for that region. (B) Horizontal chart analysis of repeated sequences in J4-25 chloroplast genome regions. y-axis is the repeat types, x-axis is the number of sequences in the chloroplast genome.