Foot-and-mouth disease (FMD) affects the livestock industry in a transboundary manner. It is essential to understand the FMD phylodynamics to assist in the disease-eradication. FMD critically affects the Sri Lankan cattle industry causing substantial economic losses. Even though many studies have covered the serotyping and genotyping of FMD virus (FMDV) in Sri Lanka, there is a significant knowledge gap exists in understanding the FMDV phylodynamics in the country. In the present study, the VP1 genomic region of FMD viral isolates belonging to serotype C from Sri Lanka and other South Asian countries were sequenced. All the published VPI sequences of serotype C and most of the published VP1 sequences for lineage ME-SA/Ind-2001d of serotype O from Sri Lanka, India, and other South Asian countries were retrieved. The datasets of serotype C and serotype O were separately analyzed using Bayesian, maximum likelihood, and phylogenetic networking methods to infer the transboundary movements and evolutionary aspects of the FMDV incursions in Sri Lanka. A model-based approach was used to detect any possible recombination events of FMDV incursions. Our results revealed that the invasions of the topotype ASIA of serotype C and the lineage ME-SA/Ind-2001d have a similar pattern of transboundary movement and evolution. The haplotype networks and phylogenies developed in the present study confirmed that FMDV incursions in Sri Lanka mainly originate from the Indian subcontinent, remain quiet after migration, and then cause outbreaks in a subsequent year. Since there are no recombination events detected among the different viral strains across serotypes and topotypes, we can assume that the incursions tend to show the independent evolution compared to the ancestral viral populations. Thus, we highlight the need for thorough surveillance of cattle/ruminants and associated product-movement into Sri Lanka from other regions to prevent the transboundary movement of FMDV.

Cassava (Manihot esculenta Crantz), an important dietary staple in many countries, supplies food for one billion people in the world. Due to dietary importance, currently cassava cultivation is promoted in Sri Lanka. Even though there are different cassava cultivars grown, no studies have been conducted on cultivar discrimination and preference on their tubers for consumption. Therefore, the present study was conducted to study the morphological and genetic diversity, and assess the consumer preference of cassava cultivars grown in Sri Lanka. Morphological traits of leaves, stems and tubers, chlorophyll content, ascorbic acid content of leaves, dry matter content of leaves and tubers were recorded. The genetic diversity was assessed by sequencing and analyzing the ITS, a DNA barcoding locus. The leaf morphology of wild-accession and Landrace cultivars were considerably different from the rest. The stem morphology was highly different, mainly in the internodal length. A significantly high number of tubers were observed in the cultivar Suranimala. The significant associations were observed from color, aroma, texture, bitterness, hardness and overall taste vs. cassava cultivars. The nine cultivars were separated through ITS polymorphism. In phylogenetic analysis, wild-accession was the most genetically distant type having nine unique SNPs and one INDEL. Other cultivars were mainly divided into two clusters. Thus, it is possible to employ ITS barcoding marker to discriminate the cultivars of M. esculenta.

Yield improvement is a major aspect in rice breeding programs. Ghd7 is a pleiotropic gene which regulates yield, plant height, and heading date in rice. Although Ghd7 has been previously cloned and sequenced in several other rice cultivars, none of the studies have been conducted for Sri Lankan rice germplasm. Therefore, in this study, we assessed the yield performance of 12 rice cultivars, genetic polymorphism of Ghd7 locus and associations between DNA markers and yield traits. Breeder seeds of the selected cultivars were obtained from RRDI, Bathalagoda, and established under greenhouse conditions at Peradeniya, Sri Lanka in Maha and Yala seasons, 2017. The cultivars were subjected to morphometric analysis, genotyped for 12 DNA markers and sequenced at Seq7-8 locus. Morphometric data were subjected to single marker analysis using General Linear Model (GLM) in SAS 9.4. Here we reported six marker haplotypes based on the arrangement of 13 DNA maker alleles at Ghd7. Moreover, twenty-three SNP/INDEL variations at Seq7-8 locus revealed close genetic relationships between the rice cultivars Bg 90-2, Bg 352 and At 307, Bg310. Four polymorphic markers (Seq7-8, Seq1-2, RM5436 and RM5346) were significantly associated with rice yield traits so that they could be used in marker assisted selection. The SNPs/INDELs of Ghd7 were significantly associated with all the yield traits except 100 seed weight and 100 endosperm weight. Thus the present study demonstrate the possibility of employing marker assisted breeding to improve rice yield using the polymorphic genomic information at Ghd7 locus.Keywords: DNA markers for rice, Rice marker haplotypes, Pleiotropic genes in rice, Rice breeding in Sri Lanka, SNP and INDEL in rice breeding.

Plant patents (PPs) and Plant Breeders' Rights (PBR) are two forms of Intellectual Property Rights (IPRs) granted to improved novel crop varieties. The government of the state of authority issues PPs and PBR after confirming the uniqueness of varietal identity. The uniqueness relies on distinctiveness, uniformity, and stability of the new variety. Morphological, physiological and biochemical descriptors are less capable in varietal discrimination to obtain IPR in the presence of large number of closely related varieties as the reference collections, but advanced molecular tools such as DNA fingerprinting and sequencing have high potentials to detect the uniqueness. DNA fingerprinting and sequencing have identified varietal identities of many crops such as rice, apple, wheat, and soybean revealing the potential of the successful use of molecular descriptors in granting patents or PBR. The novelty verification is the first step in the process of allowing patents or PBRs. The patent or plant variety protection office requires an application from the breeder that includes all the details of the plant variety fulfilling all statutory requirements to grant varietal ownership via a patent certificate or a plant variety protection certificate. Currently, Sri Lanka has no developed system of IPRs to allow PBR or patents for improved crop varieties. The efforts made by breeders in developing novel varieties can be justified and appreciated by granting plant varietal ownerships. For this purpose, molecular descriptors must be used instead of inefficient morphological, physiological and biochemical characters to avoid ambiguities and to clearly define the inventor of a particular variety.

Rice Research and Development Institute (RRDI) at Bathalagoda and its' substations are solely conducting rice breeding in Sri Lanka. Recently, RRDI has identified five exportable rice varieties/lines. As rice export in Sri Lanka is undertaken by the private sector, the RRDI does not receive any foreign revenues or credit for breeding rice genotypes. Therefore, RRDI currently is in need of a reliable protocol to claim the Plant Breeders' Rights (PBR) of these exportable genotypes. The first step of establishing such a protocol based on DNA fingerprinting is depending on the ability to extract good quality DNA from rice caryopses. Therefore, the present study compared the suitability of commonly available DNA extraction methods to purify DNA from rice caryopsis. Three rice genotypes; Bg 250 and At 353 (varieties for local consumption) and Bw-Bs-1-2-31 (with export potential) were selected. Three parboiled rice samples each from long-and short-grain groups were also selected. The DNA extraction, quantification and purity assessment were carried out using four methods viz., CTAB, modified CTAB, Promega kit and Qiagen kit. The extracted DNA was subjected to simplex and multiplex PCR using four rice specific DNA markers. Although positive PCR bands were obtained for all four methods, the modified CTAB method yielded the significantly highest DNA yield (6196.67µg/ml) compared to other methods. Thus, RRDI can employ modified CTAB method in the protocol to claim its PBR and rice varietal ownerships.