Genome and Comparative Transcriptomics of African Wild Rice Oryza longistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility

Neelam

et al. 2020

Sci Rep

Rice bran, a by-product after milling, is a rich source of phytonutrients like oryzanols, tocopherols, tocotrienols, phytosterols, and dietary fibers. Moreover, exceptional properties of the rice bran oil make it unparalleled to other vegetable oils. However, a lipolytic enzyme Phospholipase D alpha1 (OsPLDα1) causes rancidity and 'stale flavor' in the oil, and thus limits the rice bran usage for human consumption. To improve the rice bran quality, sequence based allele mining at OsPLDα1 locus (3.6 Kb) was performed across 48 accessions representing 11 wild Oryza species, 8 accessions of African cultivated rice, and 7 Oryza sativa cultivars. From comparative sequence analysis, 216 SNPs and 30 InDels were detected at the OsPLDα1 locus. Phylogenetic analysis revealed 20 OsPLDα1 cDNA variants which further translated into 12 protein variants. The O. officinalis protein variant, when compared to Nipponbare, showed maximum variability comprising 22 amino acid substitutions and absence of two peptides and two β-sheets. Further, expression profiling indicated significant differences in transcript abundance within as well as between the OsPLDα1 variants. Also, a new OsPLDα1 transcript variant having third exon missing in it, Os01t0172400-06, has been revealed. An O. officinalis accession (IRGC101152) had lowest gene expression which suggests the presence of novel allele, named as OsPLDα1-1a (GenBank accession no. MF966931). The identified novel allele could be further deployed in the breeding programs to overcome rice bran rancidity in elite cultivars.

Section: Phylogenetic Relationships Of Ospldα1 Gene Among Diverese Wisupporting

confidence: 91%

Novel allelic variation in the Phospholipase D alpha1 gene (OsPLDα1) of wild Oryza species implies to its low expression in rice bran

Neelam

et al. 2020

Sci Rep

G3 Genes|Genomes|Genetics

“…To this end, we isolated a 65 bp sequence from the NB reference genome centered on the location around the SNP. This sequence was then used as a query for a BLASTN search in the recently published OL genome (Zhang et al 2015), retaining the best three hits. Out of 301 sequences covering the SNP positions, 206 had their best BLASTN hit on the same chromosome in both NB and OL, indicating that there is a syntenic relationship (Table S3).…”

Section: Resultsmentioning

confidence: 99%

Adapting Genotyping-by-Sequencing for Rice F2 Populations

Furuta

Ashikari

Jena

et al. 2017

Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata. While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536 cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories.

“…and ~0.6 million years ago (Zhang et al 2015). In the case without any reference, we can start with a draft genome obtained by a DBG method.…”

Section: Discussionmentioning

confidence: 99%

“…It can be seen that BAUM had significant improvements over the other assemblers in terms of contig N50 and scaffold N50. The contig and scaffold N50 were even better than the hybrid assembly reported in (Zhang et al 2015), which integrated the Illumina sequencing reads and 454 sequencing reads. After the deletion of the scaffolds shorter than 1Kbp, the total size of the BAUM assembly was still close to the estimated value given by the cytometry test, while those corresponding to SOAPdenovo2 and Allpaths-LG were obviously smaller; the non-N base numbers of the three assemblers were only around 200M.…”

Section: Assessment Of Initial Contigs By Simulationsmentioning

confidence: 94%

See 1 more Smart Citation

BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach

Wang

et al. 2018

Bioinformatics