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

• Published in: PeerJ (San Francisco, CA) Vol. 12; p. e17335
• Main Authors: Mohd Talkah, Nurul Shakina, Aziz, Nur Afieqah Kaz Abdul, Rahim, Muhammad Farid Abdul, Hanafi, Nurul Fatiha Farhana, Ahmad Mokhtar, Mohd Azinuddin, Othman, Ahmad Sofiman
• Format: Journal Article
• Language: English
• Published: United States PeerJ Inc 27.05.2024
• Subjects: Agricultural Science; Bioinformatics; Chloroplast genome; Chloroplast inheritance; Gene content; Genetics; Genome, Chloroplast - genetics; Genomics; High-Throughput Nucleotide Sequencing; Inheritance Patterns; Microsatellite Repeats - genetics; Oil palm; Plant Science; Simple sequence repeat; Chloroplast inheritance; Gene content; Simple sequence repeat; Chloroplast genome; Oil palm
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.17335

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 individuals to ensure the traceability of agronomic traits. Two parental individuals and 23 of their F progenies were collected and sequenced using the next-generation sequencing (NGS) technique on the Illumina platform. Chloroplast genomes were assembled 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. 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 F 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 chloroplast genomes. Maternal inheritance of chloroplast genome among F progenies are robust with a low possibility of mutations over generations. The findings in this study can enlighten inheritance pattern of chloroplast genome especially among crops' scientists who consider using chloroplast genome for agronomic trait modifications.