A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167–0.9952, low nucleotide diversity ranging from 0.0288–0.3434, and high FST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are likely attributed to geographical distance, past historical events, allopatric speciation, dispersal ability and water currents. For instance, the mixture of haplotypes revealed an extraordinary migration ability of T. jarbua (>1200 km) via ancient river connectivity. The negative overall value of the neutrality test and a non-significant mismatch distribution are consistent with demographic expansion(s) in the past. The median-joining network concurred with the maximum likelihood haplotype tree with three major clades resolved. The scarcity of information on this species is an obstacle for future management and conservation purposes. Hence, this study aims to contribute information on the population structure, genetic diversity, and historical demography of T. jarbua in Malaysia.
Aims: Sheath blight disease (Rhizoctonia solani) is an important rice disease that causes heavy yield losses in rice annually. To date, no rice variety has been found to be completely resistant to this disease. The most desirable approach for the management of sheath blight disease is to introgress genes with major and durable resistance into the rice genome. Therefore, this study aims to identify disease resistance and defence genes within qShb 9-2, a major QTL found within moderately resistant rice population via in silico analysis. Methodology and results: The sequences of tightly linked markers of qShb 9-2 from GRAMENE database was used to derive the 10.24 Mbp QTL region that contains 1581 genes according to MSU Rice Genome Annotation Project database. BLAST results showed that 11.4% of these genes were transposable elements which may be involved in gene duplication. Through Blast2GO, fifty-four (2.9%) defence-related genes were annotated within this QTL and can be classified into 5 major defence mechanisms. Further, fifty (2.7%) disease resistance genes were identified in qShb 9-2 based on the presence of NB-ARC, LRR-receptor kinase, Ser/Thr protein kinase and protein kinase domains. Lastly, directed acyclic graphs showing the interaction between all the disease resistance and defence-related genes were generated. Conclusion, significance and impact of study: The presence of these genes indicates that qShb 9-2 region may contribute towards the defence against sheath blight disease. By deciphering the gene landscape within the QTL, it may be possible to further fine map the QTL into a smaller region for QTL pyramiding in breeding programmes. The resistance and defence genes are also a source for genetic engineering studies and a good source for marker development.
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