| dc.description.abstract | Foxtail millet is a potential cereal crop with the second-highest yield potential among millets. However, abiotic stress may lead to potential yield loss in foxtail millet production. Stem lodging is one of the abiotic stresses that is difficult to predict and measure in the field. Various stress factors such as wind, drought, extreme rainfall, and plant genetic factors determine the degree of stem lodging. Stem lodging in foxtail millet has been reported to decrease yield potential. One approach to minimizing losses due to stem lodging was identifying accessions with an ideal idiotype related to resistance to stem lodging. Key characteristics associated with stem lodging include morphological traits, biochemical traits, or genetic marker associations. The ideal idiotype was a plant with strong stems and high yield but a low tendency for stem lodging. The general objective of this study was to identify and obtain foxtail millet accessions resistant to stem lodging stress.
This study consisted of two experiments. The first experiment was conducted from March to September 2023 at the Cikabayan Bawah Experimental Farm, Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University. The objective of this experiment was to determine the lodging resistance of five Indonesian foxtail millet accessions and identify important traits determining the stem lodging resistance of those accessions. The experiment used a split-plot randomized complete block design with four replications. The main plot was the type of stem lodging stress, which included no lodging stress, temporal stem lodging stress (24 hours at 10 days after anthesis), and permanent stem lodging stress (10 days after anthesis until harvest). The subplot factor was five accessions of foxtail millet, namely Botok-10, Botok-4, NTB-1, Mauliru-2, and Hambapraing. Observations were made on three main character classes: panicle traits, stem strength, and cellulose-lignin content in stems. The analyses used included tolerance indices, Pearson correlation, and dendrograms. The results indicated that accessions Botok-10 and Botok-4 had higher resistance levels compared to other accessions, with an ideal idiotype of plant height, mechanical stem strength, cellulose content, and yield index. Tolerance index analysis also suggested that Botok-10 and Botok-4 had higher adaptability and resistance to stem lodging based on TOL, SSI, STI, SSPI, and YI indices. The Pearson correlation analysis revealed a significant negative correlation between the stem lodging index and stem breaking strength, stem mechanical strength, and cellulose content. Dendrogram analysis classified the resistant group (Botok-10 and Botok-4) and the susceptible group (NTB-1, Mauliru, and Hambapraing) based on TOL indices and potential yield loss.
The second experiment was conducted from September 2023 to February 2024 at the Plant Molecular Biology Laboratory (PMB 2), Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University. The aim was to characterize genes responsible for cellulose and lignin biosynthesis in nine Indonesian foxtail millet accessions. The genetic material used included accessions Botok-10, Botok-4, NTB-1, Mauliru-2, Hambapraing, ICERI-5, ICERI-6, Buru, and Toraja. Characterization was carried out on the SiCesA4 gene with a sequence length of 4,775 bp amplified in seven fragments and the SiCCR1 gene with a sequence length of 2,447 bp amplified in two fragments. Characterization included similarity levels of the SiCesA4 and SiCCR1 genes among the nine foxtail millet accessions with two reference accessions (IC-403579 and Yugu1), nucleotide variation for SNP sites, phylogenetic tree analysis, and prediction of conserved domains. The characterization of the SiCesA4 gene revealed 100% similarity between the nine foxtail millet accessions and the two reference accessions, whereas similarity with other species ranged from 70-86%. No nucleotide base variation was found in the SiCesA4 gene sequences aligned with the reference accessions. Only four out of seven SiCes4 gene fragments were successfully sequenced using the Sanger method in this study. Thus, it is suspected that there may still be potential base variations in the fragments that were not successfully isolated. Phylogenetic tree analysis showed that the SiCesA4 gene from the nine accessions clustered in the same group as the two reference sequences, with the closest similarity found to the CeS4 gene from wheat (TaCesA4) and barley (HvCesA4). Prediction of conserved domains for the SiCesA4 gene identified the cellulose synthase conserved domain within the PLN02189 superfamily.
Characterization of the SiCCR1 gene in the nine foxtail millet accessions showed a 98-99% similarity with the reference accessions and 85-97% with other species in the Poaceae family. Alignment of SiCCR1 gene sequences from the nine accessions with the reference accessions revealed several nucleotide base variations. Identified nucleotide base variations (SNPs) in the SiCCR1 gene included synonymous SNPs in intron 1 (nucleotide 40, 41, and 42) and intron 4 (nucleotide 1,398), as well as non-synonymous SNPs in exon 6 (nucleotide 2,029). The nucleotide variation at position 2,029 changes the amino acid translation from valine to leucine in the NTB-1 accession. Phylogenetic tree analysis showed that the SiCCR1 gene from the nine foxtail millet accessions clustered in the same group as the reference accessions, except for the Botok-10 accession. This is suspected to be due to Botok-10 having the shortest isolated sequence length compared to other accessions. The SiCCR1 gene showed closeness to the CCR1 genes of Panicum virgatum, Panicum hallii, Zea mays, and Sorghum bicolor. Prediction of conserved domains for the SiCCR1 gene identified the NADB Rossman superfamily domain. The NADB domain is frequently found in various proteins involved in redox reactions and various enzymes participating in metabolic pathways. | |
