ALBERT

Description: Sugarcane has a high potential to support second-generation ethanol production and environmentally friendly by-products for use in chemical, pharmaceutical, medical, cosmetic and food industries. A crucial challenge for a long-term economic viability is to optimise the crop for production of a biomass composition that will ensure maximum economic benefit. Transcriptome data analysis provides a relevant explanation of phenotypic variances and gives a more accurate prediction of phenotypes than genomic information. This multi-omic approach, with an integrated transcriptomics and metabolomics analysis may reveal details of biological mechanisms and pathways. A global view of transcriptional regulation and the identification differentially expressed genes (DEGs) and metabolites may help the feasibility of tailoring engineering targeted biosynthetic pathways to improve the production of these bio-products from sugarcane. We propose a profiling analysis workflow (pipeline) to generate empirical correlations between gene expression, metabolites, proteins and phenotypic traits and pathway analysis, with a highlight focus on data visualisation. This study of genetic variation in gene expression and correlations with metabolic and protein phenotype relies on high-throughput methodology, measurement and analysis of 360 samples, 24 commercial sugarcane cultivars with different phenotypic characteristics at 5 different development stages with 3 replicates.

Description: Jojoba (Simmondsia Chinensis) is a perennial stress tolerant desert shrub that has oil containing seeds and inhabits the Sonoran desert in the southwest of the United States and northwest Mexico. It has attracted a growing worldwide interest for multi-purpose uses. However, the most attractive characteristics of Jojoba are the richness of the oil content of the seed and the superior stress tolerance of the plant. Little has been done towards Jojoba genetic improvement. The exploration of jojoba genetic resources will define a molecular and biochemical fingerprint for jojoba and will aid sustainable crop commercialisation define. In this research, we aim to establish a reference genome database for Jojoba, which will help to facilitate crop improvement. Besides, the contribution to reveal the molecular background of its outstanding drought tolerance using transcriptional profiling during a water stress. RNA sequencing will be performed for samples collected under moderate and severe stress. The genetic database of jojoba will help to reveal the genetic mechanism of response and identify the genes responsible for the drought tolerant phenotype of this crop. Application of this knowledge will support the researchers, farmers, and the Jojoba industry.

Description: Sucrose and fibre in sugarcane share a very dynamic relationship depending largely upon the genetic makeup of the genotypes and growth environment. To investigate the molecular basis of carbon flux into sucrose and fibre that makes the genotypes high sugared or high fibred, or dual purposed, an extensive transcriptomics study was undertaken using a set of sugarcane genotypes differing in sugar and fibre contents. Differential gene expression analyses were performed using 50 transcriptomes revealing a complex network of transcripts associated with growth, defence, vacuole, sucrose and fibre. Rather than merely being a storage sugar of the culms, sucrose might play a significant regulatory role in controlling the expression of several thousand genes including those related to fibre. The high sugar genotypes were not always low in fibre and the fibre might to an extent provide structural framework for maintaining high sugar levels as seen by the high expression of fibre related genes. The study suggests that there could exist certain threshold levels of sugar or fibre contents beyond which an inverse relation would occur. In addition, analysis of the transcriptomes resulted in the identification of a new isoform of sucrose synthase genes, SuSy 7 that was not reported earlier. With the availability of a monoploid reference genome, there is a need for in-depth transcriptome studies to understand and identify finer details of genes, and their transcripts in entirety and regulatory elements of sugarcane genome which is challenging the current capabilities of sequencing technologies unlike any other plant genomes sequenced thus far.

Description: Lignocellulosic biomasses available in abundance is the most promising raw material for alternate energy production considering the issues of dwindling oil prices, and global warming. Recently, Erianthus arundinaceous has been identified as a potential target for second generation biofuel crop due to its high biomass production, and adaptability to extreme growth environments. Lignin is a major plant cell wall polymer indispensable for plant growth and development, however it hinders the saccharification of lignocellulosic biomass. Based on the previous transcriptome studies in a set of sugarcane genotypes differing for lignin content, genes encoding cinnamyl alcohol dehydrogenase (CAD), and Phenylalanine ammonia lyase (PAL) genes playing major roles in genetic regulation of lignin production have been cloned and characterized from an Erianthus clone IK 76-81. The genomic region of EriCAD was 3524 bp sequence containing four exons and three introns, among which the exon 1&2 of 88 and 80 bp were conserved with sorghum and Miscanthus CADs. The coding region of CAD was identified with 1086 bp open reading frame (ORF), a 68 bp 5′ untranslated region (UTR), and a 86 bp 3′ untranslated region (UTR). In the PROSITE analysis, a zinc-containing alcohol dehydrogenase signature (GHEVVGEVVEVGPEV) and an NADP-binding domain motif (GLGGLG) was identified. Similarly sequence analysis of PAL showed an ORF of 2106 bp encoding for 702 amino acid residues. It was flanked by 172 bp of 5′ UTR and 121 bp of 3′ UTR. This sequence information on PAL and CAD from Erianthus might be useful for subsequent research on lignin modification for improved biomass conversion.

Description: Due to the importance of the rice crop in Iraq, this study was conducted to determine the origin of the major varieties and understand the evolutionary relationships between Iraqi rice varieties and other Asian rice accessions that could be significant in the improvement of this crop. Five varieties of Oryza sativa were obtained from Baghdad/Iraq, and the whole genomic DNA was sequenced, among these varieties, Amber33, Furat, Yasmin, Buhooth1 and Amber al-Baraka. Raw sequence reads of 33 domesticated Asian rice accessions were obtained from the Sequence Read Archive (SRA-NCBI). The sequence of the whole chloroplast-genome was assembled while only the sequence of 916 concatenated nuclear-genes was assembled. The phylogenetic analysis of both chloroplast and nuclear genomes showed that two main clusters, Indica and Japonica, and further five sub-clusters based upon their ecotype, indica, aus, tropical-japonica, temperate-japonica and basmati were created; moreover, Amber33, Furat, Yasmin and Buhooth1 belonged to the basmati, indica and japonica ecotypes, respectively, where Amber33 was placed in the basmati group as a sister of cultivars from Pakistan and India. This confirms the traditional story that Amber was transferred by a group of people who had migrated from India and settled in southern Iraq a long time ago.

Description: Asian and African rice gene pools vary in many traits that are important in rice breeding. The genetic basis of these differences was evaluated by analysis of important agronomic traits in crosses between African and Asian rice. Trait-associated variants (TAVs) influencing three quantitative agronomic traits, heading date (Hd), tiller number at maturity (T), and 1000 grain weight (TGW), were identified by association analysis of crosses between Asian and African rice. Populations were developed by crossing WAB56-104 (Oryza sativa) and CG14 (Oryza glaberrima). DNA from plants with extremely high or low values for these phenotypes was bulked and sequenced. The reference genome of O. sativa cv Nipponbare was used in general association analysis and candidate gene analysis. A total of 5152 non-synonymous single nucleotide polymorphisms (SNPs) across 3564 genes distinguished the low and the high bulks for Hd, T, and TGW traits; 611 non-synonymous SNPs across 447 genes were found in KEGG pathways. Six non-synonymous SNPs were found in the sequences of LOC107275952, LOC4334529, LOC4326177, LOC107275432, LOC4335790, and LOC107275425 genes associated with Hd, T, and TGW traits. These genes were involved in: abscisic-acid biosynthesis, carotenoid biosynthesis, starch and sucrose metabolism, and cytokinin biosynthesis. Analysis of 24 candidate genes associated with Hd, T, and TGW traits showed seven non-synonymous variations in the sequence of Hd3a and Ehd2 from the Hd genes (not in a KEGG pathway), D10 and D53 from the T genes (strigolactones biosynthetic pathway), and Gn1a and GIF1 from the TGW genes (cytokinin biosynthetic and starch and sucrose metabolism pathways). This study identified significant differences in allele frequencies supported by high sequence depth in analysis of bulks displaying high and low values for these key traits. These trait-associated variants are likely to be useful in rice improvement.

Description: Plants have leaves as specialised organs that capture light energy by photosynthesis. However, photosynthesis is also found in other plant organs. Photosynthesis may be found in the petiole, stems, flowers, fruits, and seeds. All photosynthesis can contribute to the capture of carbon and growth of the plant. The benefit to the plant of photosynthesis in these other tissues or organs may often be associated with the need to re-capture carbon especially in storage organs that have high respiration rates. Some plants that conduct C3 photosynthesis in the leaves have been reported to use C4 photosynthesis in petioles, stems, flowers, fruits, or seeds. These pathways of non-leaf photosynthesis may be especially important in supporting plant growth under stress and may be a key contributor to plant growth and survival. Pathways of photosynthesis have directionally evolved many times in different plant lineages in response to environmental selection and may also have differentiated in specific parts of the plant. This consideration may be useful in the breeding of crop plants with enhanced performance in response to climate change.