A study conducted in the Forest and Forest-Savannah transition zones of Ghana during the 2018–2019 cropping seasons to investigate the profitability of integrating pigeonpea into yam described as a pigeonpea-yam cropping system consisted of; yam planted with pigeonpea in alleys (PA) and as a border (PB) compared with sole yam (SY). PA, PB, and SY plots were further divided into sub-plots, and subjected to three inorganic fertilizer treatments of 0–0–0, 23–23–30, 45–45–60 N–P 2 O 5 –K 2 O kg ha −1 as no, half, and full fertilizer rates, respectively. Three farmer-practiced scenarios of access to no, half, and full recommended fertilizer rates were evaluated with profitability indicators of Income Equivalent Ratio, Net Present Value (NPV) and Benefit-Cost Ratio (BCR). The results revealed that planting yam in PA with half and full fertilizer rates resulted in IRR (the discounted rate at which NPV equals zero) of 5.67 and 5.90 respectively at Fumesua and 5.66 and 5.88 respectively at Ejura in both seasons. Interestingly, planting yam in PA with half and full fertilizer rates resulted in a similar BCR. Even when yams were planted without fertilizer, the presence of the pigeonpea resulted in a better BCR than when half and full fertilizer rates were used on SY for both locations and seasons. Thus, adopting the proposed technologies even without fertilizer will be profitable for each Gh₵ 1.00 spent. As such, the Pigeonpea-yam cropping system can be promoted as a viable option for soil fertility management and a readily available source of stakes for sustainable yam production.

Bean rust is a devastating disease of snap beans in Sri Lanka. Our study endeavored to develop snap beans with resistance to Uromyces appendiculatus, the bean rust pathogen reported to have numerous virulent races. Accordingly, we needed a detailed understanding of the virulence of U. appendiculatus and to identify genes conferring effective rust resistance. To investigate the virulence, we collected leaves of snap bean with rust symptoms from four snap bean producing districts of Sri Lanka. From these samples we established 57 single pustule isolates. Each isolate was inoculated on a set of 12 differential cultivars, six from the Andean and six from the Middle American gene pools of common bean. The virulence of the isolates segregated into four distinct groups that comprised the first four reported races of U. appendiculatus in Sri Lanka, 23-5, 31-1, 31-11, and 63-21. All races were significantly more virulent on the Andean than on the Middle American differential cultivars. PI 1819966, a Middle American differential cultivar containing the Ur-11 gene, conferred resistance to all four races. Three other Middle American cultivars were resistant to three races. Conversely, five Andean differential cultivars were susceptible to all four races. PI 160418 was the only Andean differential cultivar with resistance to three races. The results suggested that rust resistance genes from the Middle American differential cultivars could be combined in different ways with the resistance of Andean PI 260418 to develop snap bean varieties with broad resistance to all races of U. appendiculatus in Sri Lanka.

Bean rust is one of the major diseases of the common bean (Phaseolus vulgaris) reported in Sri Lanka and at the global level. This study aimed to develop rust-resistant snap bean breeding lines via gene pyramiding assisted by molecular markers. Resistant sources; PI 181996, BelMiNeb-RMR-8, and BelDakMi-RMR-19, enriched with the rust-resistant genes Ur-3 and Ur-11, were selected as donor parents to obtain a wide range of resistance to the rust pathogen. Resistant genotypes were crossed with popular local varieties Kappetipola nil and Galpalama Kalu (Capri) to introgress Ur-3 and Ur-11 resistant genes. Successive F1, F2, and BC (backcross) generations were obtained with the self-pollination and backcrossing processes. Standard phenotypic disease screening methods were applied to identify resistant lines. Phenotypically resistant plants obtained from these crosses were tested with sequence-characterized amplified region (SCAR) markers linked to two rust-resistant genes: SK 14 (linked to Ur-3) and SI 19 (linked to Ur-11). Molecular marker SI-19 showed higher reproducibility (50% to 80%) with the availability of relevant banding patterns for phenotypically resistant F1, F2, and BC1 progenies. However, SK 14 showed lower reproducibility (30–60%) for the same progenies. Approximately 450 genotypes introgressed with rust-resistant genes (Ur-3 and Ur-11)were produced. Among them, four advanced resistant lines obtained from the different cross combinations (Kappetipola nil x BelDakMi-RMR-19, Galpalama Kalu x BelMiNeb RMR-8, Kappetipola nil x PI 181996, and Kappetipola nil x BelMiNeb RMR-8) with preferred agronomic characters were selected for further variety development. All new genotypes will be important for future bean-resistant breeding programs in Sri Lanka.

Yam production along the West African yam belt is challenged with deteriorating soil fertility and unavailability of stakes, resulting in decreased yam productivity, and farmers' livelihood. This study evaluated resource use and yam productivity in pigeonpea-yam cropping systems in Ghana's forest and forest-savannah transition zones from 2017 through 2019 cropping seasons. Pigeonpea was established either in an alley or as a border during the 2017 cropping season, while yam was cultivated in 2018 and 2019. A split-plot design of cropping system (yam planted in alleys of pigeonpea—PA; yam planted with pigeonpea as a border—PB and sole yam) as main-plot treatments and chemical fertilizer (0–0–0; 23–23–30; 45–45–60 N-P2O5-K2O kg ha−1) as subplot treatments were used for the study. Productivity data on pigeonpea and yam were collected. The results revealed significantly higher leafy biomass and correspondent higher N content and N due to fixation in PA fields than PB fields in both locations and seasons. The presence of the pigeonpea and its biomass resulted in a significant suppression of ridge erosion and weeds, while soil moisture and nutrients improved, resulting in increased yam tuber productivity than in sole yam production. Further, planting yam with pigeonpea and half (23–23–30 N-P2O5-K2O kg ha−1) the recommended fertilizer rate significantly improved tuber yield and productivity than planting sole yam with full recommended fertilizer level in both locations and seasons. Promoting and adopting the pigeonpea-yam cropping system could sustain soil fertility, provide readily available stakes to address the constraint of deforestation and land degradation associated with yam production.

Consumers hesitate to purchase field-grown shoot-tops of amaranths in Sri Lanka, citing the low-cleanliness making growers focus on greenhouse farming. However, the photosynthetic and growth variations in relation to the organoleptic preference of the greenhouse-grown amaranths in comparison to field-grown counterparts have not been studied. Also, the species delimits of the amaranths in Sri Lanka have not been identified, limiting our ability to interpret species-specific production characteristics. Thus, we assessed the common types of amaranths under greenhouse and field conditions. The photosynthesis was measured using a MultispeQ device of the PhotosynQ phenomic platform, which records chlorophyll fluorescence-based parameters. The shoot-tops were harvested and prepared as dishes according to the typical recipe for amaranths in Sri Lanka. The dishes were subjected to an organoleptic assessment for the parameters color, aroma, bitterness, texture, and overall taste. The differences in plant and the shoot-top biomass were also assessed. The markers atpB-rbcL, matk-trnT, and ITS were used to define the species delimits. The field-grown and greenhouse-grown amaranths exhibited species/cultivar-specific photosynthetic variations. The texture and overall taste of the dishes were different among greenhouse and field-grown material. The tasters preferred the texture and the overall taste of the greenhouse-grown shoot-tops. The greenhouse-grown plants also yielded higher shoot-top harvests compared to field-grown counterparts. Out of the tested markers, ITS defines the delimits of amaranth species. The higher organoleptic preference, the appreciable yield levels, unique photosynthetic patterns of the greenhouse-grown amaranths, and species definitions provide the much-needed platform for clean shoot-top production guaranteeing the highest end-user trust.

Bean rust caused by Uromyces appendiculatus fungus is one of the most destructive diseases reported in temperate, tropical, and sub-tropical regions, affecting the quality and quantity of common bean (Phaseolus vulgaris L) yield. The present study aimed to improve the breeding process of snap beans for rust resistance by identification of inheritance patterns of resistant genes using phenotypic and molecular markers. Among the different genes identified, Ur-11 has wide-spectrum resistance to 89 out of 90 reported races of the rust pathogen. Therefore, the common bean cultivar PI 181996, having the Ur-11 gene was used as the rust resistance donor parent while the local popular snap bean variety Kappetipola nil, susceptible to all locally reported races of the rust pathogen in Sri Lanka, was selected as the susceptible (Recurrent) parent. The introgression of the Ur-11 gene from the cultivar PI 181996 in F1, F2, and BC1F1 populations were phenotypically evaluated using standard screening method while validating random amplified polymorphic DNA (RAPD) marker, OPAC 20 and sequence characterized amplified region (SCAR) marker, SAE 19 and GT 2. Coupling markers (OPAC 20 and GT-2) and repulsion marker (SAE 19) showed 95% and 100% of expected results for phenotypically resistant and susceptible lines respectively. The results showed that the Ur-11 gene in PI 181996 can be tagged with SCAR marker GT-2 and SAE 19 and can be used for markerassisted selection to identify the presence of the Ur-11 gene in the snap bean rust-resistance breeding program. Introgression of the Ur-11 gene helped to develop genetic resistance to local races of the rust pathogen, and the selected progenies could be developed as new resistant snap bean breeding lines.

Asiatic pennyworts (AP) (Centella asiatica) are among the most popular leafy vegetable species in Sri Lanka. Five AP cultivars, namely, Lowland AP (LAP), Giant AP1 (GAP1), Giant AP2 (GAP2), Salad AP (SAP), and Medicinal AP (MAP) are grown in the country. Two other leafy vegetable species, water pennyworts (WP) (Hydrocotyle verticillata) and Korean pennyworts (KP) (Adenophora triphylla), are also designated under ‘pennyworts’ in Sri Lanka. The consumerpreference on the pennywort bunches available in the market and the salad properties are yet to be studied. Also, no attempts have been reported for the identification of species delimits and phylogenetic relationships among the different cultivars of C. asiatica. In the present study, consumer preference on the appearance of leaf bunches and salads of pennyworts were assessed. The intra- and interspecific variation of pennyworts grown in Sri Lanka were also studied. The genomic DNA extracted from the immature leaves was PCR amplified for the DNA barcoding markers matK-trnT, atpB-rbcL, and rbcL. The PCR products were sequenced and used to assess the intraand interspecific variation. The consumers mostly preferred to purchase the leaf bunches of GAP2 because of its large leaf size and appealing look. However, the highest preference for salads was reported for the dishes prepared using LAP, MAP, and WP. The clade structure of the phylogenetic tree drawn for AP cultivars shows an intraspecific variation. Our study also highlights the importance of producing an improved AP cultivar with larger leaf size, improved flavor properties, and sinuate leaf margin.

Purpose: The nomenclature of the wild strawberries inhabited in Sri Lanka is ambiguous. In Sri Lanka, this species is still named Duchesnea indica which needs a revision. Wild strawberries grow well in natural habitats of upcountry in Sri Lanka. Since the commercial strawberry cultivations gain a popularity in upcountry, the studies on wild strawberry is essential for crop improvement and management. Research Method: In the present study, we conducted extensive field sampling followed by a phylogenetic analysis with the DNA barcoding markers ITS and, trnL-F by using a representative sample of wild strawberry plants in Sri Lanka. The distribution of the species was identified using maximum entropy modeling approaches. Findings: Sri Lankan wild strawberry got placed at subtribe: Potentilla, and clade: Reptans and show a shallow divergence with the species Potentilla indica reported. Thus, we reposition the genus of wild strawberries in Sri Lanka from Duchesnea to Potentilla and hereafter name it as P. indica. The niche model analysis predicted a highly restricted distribution of Sri Lankan wild strawberry in Nuwara-Eliya district over an area of 166.36 km2 in the altitude range of 1546 - 2524 m in a small climatic envelop highlighting the need for urgent conservation measures. Research Limitations: The pop-set for available in literature of P. indica is limited for comparison. Extensive studies based on DNA sequencing is needed for further validation. Originality / Value: Taxonomy, narrow distribution, need of conservation, and phylogenetic distance to Fragaria chiloensis, a progenitor species of cultivated strawberry, are defined for Sri Lankan wild strawberries.

Yam, a major food crop for West Africa, has not been managed to reach its potential productivity. The current practice of planting yam continuously for years after clear-cutting a field is not sustainable and has led to deforestation and nutrient depletion. By examining the effect of improved management on yam cultivation in Ghana, this study aimed to solve the tradeoff between improving yam yield and sustaining soil organic carbon (SOC). We used a calibrated and validated process-based crop simulation model, Systems Approach to Land Use Sustainability, to assess the impact of four management treatments: continuous unfertilized rainfed yam (control), pigeonpea-yam rotation, yam with 3 Mg/ha pigeonpea residue incorporated and yam with 23-23 N-P2O5 kg/ha fertilizer added. We modeled 10 years of yam yield and SOC across cropland in Ghana with varying levels of soil carbon, rainfall amount, and precipitation pattern. On average, simulated yam tuber yield was the highest with a pigeonpea residue incorporation treatment (4.1-11.9 Mg/ha, average of 7.5 Mg/ha). The rotation (average yield of 6.4 Mg/ha) and fertilizer (average of 7.0 Mg/ha) treatments produced comparable increases in yam yield over the control treatment (1.9-9.2 Mg/ha, average of 4.9 Mg/ha). The low yam yield of the control treatment was mostly attributed to nutrient deficiency (nitrogen and phosphorus). Drought also limited yam growth, particularly in northern Ghana. The three improved management treatments increased soil nutrient availability and thus improved yield. SOC declined under all four tested treatments over the simulated 10 years, but declined least with residue incorporation (average rate -0.3 Mg/ha/year), followed by fertilizer addition (-0.43 Mg/ha/year), rotation (-0.42 Mg/ha/year), and the control (-0.51 Mg/ha/year) management. Our work provides a benchmark for yam yield response to alternative management across Ghana, and highlights pigeonpea's contribution to sustainable intensification of yam. Further research is needed to untangle the interacting effects of land use and agronomic management on SOC.

The wood adulteration is a common problem and under-studied aspect in the timber industry of Sri Lanka. Hence we conducted a survey to assess the status of timber adulteration and check the applicability of morphometric parameters and DNA barcoding to detect the adulterated timber sources. We interviewed the stakeholders of the timber industry to collect information regarding timber adulterations. We measured the morphometric parameters; wood density and sizes of the xylem elements of the standard and adulterant species. For DNA barcoding, DNA was extracted from the wood of the selected standard and adulterant species and subjected to PCR using the markers, matK-trnT and atpB-rbcL. The PCR products were subjected to DNA sequencing. According to the survey, 92.5% of patrons, 73.7% of manufacturers and 96.7% of carpenters said timber adulteration is taking place in the country. The respondents said that the standard timber species; Tectona grandis, Artocarpus heterophyllus, and Swietenia macrophylla, profoundly undergo adulteration in Sri Lanka. The morphometric parameters did not discriminate the adulterant species from the standard species. The DNA barcodes matK-trnT and atpB-rbcL provided unique polymorphic DNA sequences with specific lengths for each species permitting the precise establishment of species identity and enabling the accurate detection of timber adulterations.

Genus Ipomoea is the largest of the family Convolvulaceae. It is a highly diverse genus distributed all around the world. In Sri Lanka, 13 members have been identified in Ipomoea; however, most of them have not been morpho-genetically characterized. In the present study, we selected I. batatas, I. aquatica, I. nil, and I. pes-caprae for the assessment based on certain criteria viz., food security, leafy vegetable, emergent weed, and coastal conservation capabilities. The morphological variation, species delimits, and phylogenetic relationships among these four species were assessed. The DNA was extracted from young leaf samples using CTAB method and subjected to PCR using ITS and rbcL as markers. The PCR products were subjected to sequencing. The DNA sequences were analyzed, and phylogenetic trees were generated by using PAUP to define the species delimits, identify the speciation and evolutionarily relationships in comparison to the homologous Ipomoea sequences available in GenBank. The tuber bearing ability, flower colour, and leaf shape are the key morphological descriptors that can be used to delimit the selected species. Both rbcL and ITS markers could be used to identify the four species studied distinctively. However, among the two markers, ITS provides a greater variation to identify the four species and their evolutionary relationships. Thus, the present study provides a key platform with usable morphological traits and DNA barcoding markers to characterize all Ipomoea species in Sri Lanka.

Purpose : Elaeocarpus ganitrus and E. serratus are two significant tropical fruit tree species. E. ganitrus is also important for its endocarps that are popularly known as Rudraksha. However, these are underutilized species in Sri Lanka. Therefore, present study was conducted to assess the morphometric diversity of fruits and endocarps and the phylogenetic relationships of two species using DNA barcoding markers. Research Method : The ripe fruits were collected from a set of trees of two species in Matale and Kandy districts. The fruit and endocarp size parameters were measured in two seasons and subjected to statistical analysis. The trnH-psbA and trnL-trnF sequences were obtained from the selected trees and subjected to phylogenetic analysis. Findings : The fruit size traits were predominantly affected by the intraspecific variation than the environment. The length and diameter of the endocarps were seasonal independent and tree specific. Except colour, people preferred E. serratus fruits than E. ganitrus fruits. The markers, trnH-psbA and trnL-trnF unravelled the species delimits of E. ganitrus and E. serratus. The trnL-trnF based phylogeny positioned the trees of E. ganitrus in the respective clade. E. serratus trees were cladded with E. stipularis, E. tectorius, E. dongnaiensis and E. glaber. Research Limitations: A limited sequence pop-set for Elaeocarpus spp. is available in literature for comparison. The meta-scale attempts are needed to resolve the phylogenetic relationships of Elaeocarpus germplasm. Originality / Value : The revealed morphological and phylogenetic relationships of E. ganitrus and E. serratus lay the platform for germplasm conservation and crop improvement programs in Sri Lanka.

The development of phosphorous deficiency tolerance (PDT) in rice cultivars is important for sustainable rice production. If the performances (PDT indicators) of the rice cultivars can be correlated with Pup1 (major QTL linked to PDT in rice) haplotypes, marker assisted breeding (MAB) programmes could be launched to produce phosphorous deficiency tolerant rice varieties. In the present study, 27 rice cultivars (nine landraces and 18 improved varieties) were screened under P-deficient soil conditions in two seasons (Yoh and Alaha, the major cropping seasons in Sri Lanka) based on shoot dry weight and P-utilisation efficiency. To establish the basis for MAB of PDT, the Pup1 haplotypes were assessed using 17 Pup1 linked DNA markers and sequence polymorphism of the two marker loci, K29 and RM28102. The PDT screening results revealed that the performance of the rice cultivars is season-dependent. The landrace Madathawalu and the old-improved variety 11-4 showed the highest trait values for yield, shoot dry weight, and P utilisation efficiency in both Yala and Alaha seasons. Remarkably, Madathawalu and H-4 share a common Pup1 haplotype demonstrating that MAB for PDT is possible using these two rice cultivars as parents. The Pup1 linked marker haplotypes and variation of the PDT indicators of the studied cultivars can be used to conduct MAB programmes to develop improved rice varieties.

The demand for apple is higher than other fruits in Sri Lanka, and the total of the requirement is achieved through imports causing a massive economic expenditure. A few low-performing apple trees can be seen in local upcountry regions. However, the feasibility of growing apple in Sri Lanka has not received any attention. The present study was conducted to (1) to assess the quantity imported and the costs associated with importing to Sri Lanka using the statistics available in the National Plant Quarantine Service (NPQS), and (2) observe currently growing apple trees to identify the status of production and their S-allele genotypes to understand whether pollination is likely among the trees. It was further examined the climatic conditions of agro-ecological regions in Sri Lanka to identify suitable areas for apple growing. Nearly 25,000 metric tons of apples are annually imported to Sri Lanka costing USD 32.2 million, a burden to the economy. The apple trees cultivated in Sri Lanka perform well below the standards, and the application of the standard agronomic practices is seldom noticed. We found through PCR and restriction digestion that the trees do not have self-compatible genotypes for pollination. However, the observed apple trees undergo flowering and fruiting at the substandard level implying that local apple production is possible. Apple trees can be grown anywhere in the tropics; however, the best quality apples can be achieved only under the conditions available in up and mid countries of wet and intermediate zones especially in agroecological regions WU1, WU2a, WU2b and WU3. In world-wide information sources, many apple cultivars such as Anna, Dorsett-Golden, and Wambugu are listed for tropical environments. As James Taylor started tea plantations in 1867, on which Sri Lanka became the world leader in tea production, a dedicated scientific effort must be made to establish an apple industry in Sri Lanka.

Soybean has long been a part of the traditional cuisine of Indonesian people since the 12 th century as the main ingredient used for a number of processed foods. As an important source of protein for food and feed, soybean demand is always high and exceeds the national production capacity. The deficit production requires imports to ensure food security. Therefore, Indonesian government has implemented many efforts to increase the national production due to some opportunities: high market demand, land and superior varieties availability. In order to seize this opportunity and be able to increase production, government should consider some strategies: securing suitable land for soybean cultivation including determination the centers for soybean production, expanding soybean cultivation to commercial scale, and providing sufficient water for farmers; applying technology to increase land and plant productivities the use of superior varieties and agronomic approach, applying integrated pest management, using specific and suitable machineries to increase plant stand, reduce grain lost, and increase grain quality; providing and strengthen market-producer network including post-harvest management, ensuring continuous supply for market, good process for both parties, and producing seed which meet market demand. Efforts in increasing soybean production will face some challenges: low fertility of the available land, lack of market driven quality traits in existing soybean varieties, and the unfavorable price paid for locally produced soybean. Facing these challenges, government should not focus only on enhancing production capacity but also strengthening farmer institutional, involving farmer in this effort (participation), and working with all parties including local government in synergy.

The genus Artocarpus J.R. Forster & G. Forster shows a higher diversity along the tropics of Indo Malayan region to Australasia. The Artocarpus phylogeny is resolved in previous studies. According to morpho-genetic assessments, Artocarpus spp. have been subdivided into subgenera and sections. However, the published phylogenies did not comprise the Artocarpus spp. found in Sri Lanka, leaving an ambiguity of their phylogenetic positions. The morphology was observed in many trees in natural range, and the line diagrams were drawn to showcase the morphological features that can be used to classify the Artocarpus spp. into subgenera and sections. We collected leaf samples from the Artocarpus spp. in Sri Lanka. The genomic DNA was extracted, and PCR amplified for five markers (trnH-psbA, rbcL, trnL-F spacer, trnSGCU-trnGUUC, and ITS1-4) followed by sequencing. The Artocarpus phylogeny was constructed in Maximum Likelihood and Bayesian framework using the generated sequences and the related sequence-popsets. Moreover, a divergence dating analysis was also carried out to check the evolutionary history of Sri Lankan Artocarpus spp. According to the morphology and phylogeny, the subgeneric classification of A. heterophyllus Lam, A. altilis (Parkinson) Fosberg, and, A. camansi Blanco was in line with previous studies. The dating analysis revealed a recent introduction of A. heterophyllus, A. altilis, and, A. camansi into Sri Lanka because of the associated food values. We positioned A. nobilis Thwaites, an endemic species to Sri Lanka, in the Artocarpus phylogeny under section Duricarpus. The nomenclatural status of A. gomezianus Wall. Ex Trécul coming under subspecies zeylanicus was verified as it does not clade closely with true A. gomezianus. However, we kept the species name as A. gomezianus as both true A. gomezianus, and Sri Lankan species got 10–13 pairs of lateral veins and the whitish hair underneath the leaf. We also recognized three ancient lineages of subgenera Artocarpus and Pseudojaca. These species naturally occur in India and Sri Lanka where they might be close descendants of the common ancestors of the subgenera Artocarpus and Pseudojaca.

Canna indica is a tuber crop which has many medicinal values. In Sri Lanka, C. indica tubers are consumed in rural areas and mainly available in street-markets of Nuwara-Eliya and Kandy Districts. In the present study, we assessed the phylogenetics of C. indica, starch granule morphology and consumer preference of C. indica tubers in comparison to the popular tuber crops. The phylogenetic analysis was conducted based on the sequence polymorphism at rbcL, atpB gene, trnL-trnF and trnH-psbA marker-loci with respect to the ornamental Canna spp. in Sri Lanka and the previously published sequences of Canna spp. The starch granules were isolated and observed under optical and scanning electron microscopes. The diameter and the surface area of the starch granules were measured under the optical microscope and subjected to analysis of variance. As C. indica tubers are consumed as boiled tuber pieces in Sri Lanka, the consumer preference analysis was conducted using the boiled tuber pieces C. indica, Xanthosoma sagittifolium, Manihot esculenta, Solanum tuberosum, and Ipomoea batatas. The phylogenetic tree based on rbcL marker revealed that C. indica in Sri Lanka is slightly divergent from the other Canna spp. Only the polymorphism of the atpB gene can be used to differentiate C. indica from the ornamental Canna sp. in Sri Lanka. The morphological analysis of starch granules revealed that C. indica has the biggest scallop-seashell shaped starch granules compared to other tuber species. The boiled C. indica tubers were accepted better than that of X. sagittifolium, rated equally to the tubers of S. tuberosum and M. esculenta, and rated less than I. batatas. The hardy and fibrous nature of C. indica tubers must be the major limiting factors for achieving the highest consumer preference highlighting the need of breeding for better texture in tubers

The development of rice cultivars with desirable traits is essential. The decision-making is a crucial step in rice breeding programs. Breeders can make efficient and pragmatic decisions if an organized pedigree visualization platform is available for the accessions and cultivars in rice breeding germplasm. In the present study, the available data of all the rice varieties released by Rice Research and Development Institute, Sri Lanka, and the related landraces and genotypes were arranged in Pedimap, a pedigree visualization tool. Pedimap can showcase pedigree relationships, phenotypic, and molecular data. The identity by descent probabilities were calculated using FlexQTL software and included in the Pedimap database. The parentage selection based on the variations of phenotypic traits, selection of marker alleles for molecular breeding, and detection of the founders of genetic effects can be swiftly conducted using Pedimap. However, the power of harnessing the value of Pedimap for making breeding decisions relies on the availability of data for the traits, markers, and genomic sequences. Thus, it is imperative to characterize the breeding germplasms using standard phenomic and genomic characterization procedures such as the assessment of before organized into Pedimap. Thereby, the worldwide breeding programs can benefit from each other to produce improved varieties to meet global challenges.

The Rice Research and Development Institute (RRDI) of Sri Lanka has developed five exportable rice cultivars; At 362, Bg 94-1, Bg 360, Bg 1165-2, and Bw-Bs-1-2-31.The present study was conducted to establish the identities of these five cultivars at caryopsis level in comparison compared to those of mega rice cultivars (Bg 352, Bg 300, Bg 358, Bg 359, Bg 357, Bg 379-2, and At 353) in Sri Lanka using DNA fingerprinting and sequencing. These rice cultivars were grown in a greenhouse and a field using breeder-seeds. The seeds were harvested and subjected to a morphometric analysis using decision tree algorithms based on the size and colour of seeds and caryopses. The algorithms estimated the percentage accuracy of detection based on morphometric analysis ranged from 3.13-84.38 %. Similar seed and caryopsis combinations were grouped and exposed them to a panel of human subjects to discriminate the samples in each combination and subjected the data to calculate Kappa (K) and inter-rater reliability (IRR) statistics. The K was always 0.00, and IRR was 27% implying the inability of accurate visual differentiation. In the DNA fingerprinting analysis, a set of six SSR markers (RM206, RM246, RM251, RM335, RM475, and RM23744) were selected that can establish the cultivar identity. In addition, the combined analysis of DNA sequencing of 12 cultivars with three selected loci, (Seq 7-8, HvSSR12-34 and RM23744) authenticated the varietal identities.

Table S4. Calculations of segregation ratios for progeny families from all possible phenotype/genotype parental combinations for a two-locus model to explain repeat fruiting vs once-fruiting of strawberry. Calculations assume the primary, already mapped locus, has a dominant allele (RB) conferring repeat fruiting, and a recessive allele (jb) conferring once-fruiting. Repeat-fruiting parental and progeny phenotypes are highlighted in dull yellow, and once-fruiting phenotypes are highlighted in pale green. On the left of the grey vertical bar are calculations that assume the presence of a second locus with a completely dominant allele (STOP) conferring epistatic suppression of the mapped locus when homozygous (STOP STOP) or heterozygous (STOP stop), and a recessive allele (stop) that does not affect the mapped locus). On the right of the grey vertical bar are calculations that assume the presence of a second locus with a recessive allele (stop) conferring epistatic suppression of (or failure to support) the mapped locus when homozygous (stop stop), and a completely dominant allele (STOP) that does not change the phenotype conferred by the mapped locus. Horizontal grey and purple bars separate different genotypic parental-combination possibilities for similar phenotypic possibilities. Resulting progeny phenotypes are characterized as repeat-fruiting (RB) or once-fruiting (jb) similar to the mapped locus. Expected resulting segregation ratios are highlighted in bright yellow boxes. (XLSX 235 kb)