Biology subjects

Songsomboon, K.

Publications and source records attributed to Songsomboon, K..

3 recordsLinked to original sources

bioRxiv2025

Utilizing a pan-transcriptome reveals genotype-specific responses to iron deficiency in Sorghum bicolor

IntroductionSweet sorghum genotypes are distinguished from non-sweet types by their ability to accumulate high concentrations of sugar in their stems, which makes them valuable for both bioenergy production and as an alternative source of sugar. Previous work has reported numerous gene copy number differences in metal metabolism and iron transport genes between the sweet and non-sweet genotypes. The objective of this study was to investigate which genes are differentially expressed by the sweet and non-sweet genotypes under varying iron conditions. MethodsThree sweet and three non-sweet sorghum genotypes were grown hydroponically under two conditions (control and low iron), and root tissue from the plants was harvested for RNA extraction and sequencing after 9 days. To obtain a more complete picture of diverse iron-response mechanisms in sorghum, we constructed a pan-transcriptome from 10 founder parents of the Carbon-Partitioning Nested Association Mapping population. ResultsDifferential expression analysis using the pan-transcriptome revealed 209 genes that responded differently to iron stress in the sweet and non-sweet types, which was more than twice as many genes found using only a single reference genome. Enrichment analysis based on age of duplication event showed that duplicate gene copies that are differentially expressed due to genotype effect appear to be specific to sorghum while most duplicate gene copies that are differentially expressed due to iron treatment appear to be more evolutionary conserved across plants. DiscussionThis study highlights the importance of the non-core genome and the utility of the pan-transcriptome in sorghum. It also revealed that different sorghum genotypes respond to iron stress differently.

plant biology↗

bioRxiv2022

Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes

Sorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations. Expanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs).These resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism. We show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes.

genomics↗

bioRxiv2018

Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum)

Switchgrass (Panicum virgatum L.), a northern native perennial grass, suffers from yield reduction from Bipolaris leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoe-maker. This study aimed for determining the resistant populations via multiple phenotyping approaches and identifying potential resistance genes to the disease from genome-wide association studies in the switchgrass northern association panel. The disease resistance was evaluated from both natural (field evaluations in NY and PA) and artificial inoculations (detached leaf and leaf disk assays). There are ten out of the 66 populations showed the most resistant based on a combination of detached leaf, leaf disk, and mean from two locations. The GWAS from five subgroups from the association panel to different disease evaluation combinations yielded 27 significant SNPs on 12 chromosomes: 1K, 2K, 2N, 3K, 3N, 4N, 5K, 5N, 6N, 7K, 7N, and 9N accumulatively explaining phenotypic variance of BLUPs of detached leaf percent lesion via image analysis 26.52% at most and BLUPs of leaf disk percent lesion via image analysis 3.28% at least. Within linkage disequilibrium of 20 kb, these SNP markers linked with the potential resistance genes including genes encoding for NBS-LRR, PPR, cell wall related proteins, homeostatic proteins, anti-apoptotic proteins, and ABC transporters.

bioinformatics↗