Whole genome resequencing data and grain quality traits of the rice cultivar Mahsuri and its blast disease resistant mutant line, Mahsuri Mutant

In Malaysia, rice mutant varieties that are genetically altered to confer resistance against blast disease have been substantially developed through mutational breeding program. However, due to the limited accessible information on the mutant lines, mutant gene variants corresponding to the disease resistance and other useful agronomic traits are yet to be exploited. Here, we conducted whole genome re-sequencing of blast resistance with kernel elongation traits in mutant line, Mahsuri Mutant (87,639,446 bp raw reads), and its parental line, Mahsuri (85,156,783 bp raw reads) using Illumina Novaseq 6000 sequencing platform with 30x sequencing coverage. The generated genome sequences are aimed to facilitate the discovery of causal mutation and single nucleotide polymorphisms (SNPs) related to the intended traits. The identified SNPs can be further employed to develop allele-specific SNP molecular markers to locate the mutant gene regions. The NGS data obtained (FASTQ format) of the parental and mutant lines have been deposited in the National Center for Biotechnology Information (NCBI) database under sequence read archive (SRA) xwith accession numbers SRR24388814 (Mahsuri) and SRR22952097 (Mahsuri Mutant) respectively.

Data on genome resequencing of the rice cultivar MR219 and its abiotic stress tolerant mutant lines, NMR152 and NMR151

The genomics and genetic information of Malaysian rice (Oryza sativa L.) and their mutant lines are very limited. Therefore, the genome resequencing of two drought and submergence tolerant mutant rice lines, NMR152 and NMR151 and their parental line, MR219 was performed using Illumina Hi Seq 4000 platform with 20x sequencing coverage to facilitate the identification of causal mutations and the discovery of candidate variants of single nucleotide polymorphisms (SNPs) from their genome. The identification of SNPs would be useful in developing functional SNP markers related to drought and submergences resistance traits. Genome sequence data (FASTQ format) of the mutants and their parental line have been deposited into the National Center for Biotechnology Information (NCBI) database under sequence read archive (SRA) data with accessions SRR20824202 (NMR152), SRR20995190 (NMR151) and SRR21043964 (MR219), respectively.

Comparative Genomics: Insights on the Pathogenicity and Lifestyle of Rhizoctonia solani

Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. Rhizoctonia solani is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft R. solani AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies R. solani’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.