Abstract Calophyllum soulattri Burm.f. is traditionally used to treat skin infections and reduce rheumatic pain, yet genetic and genomic studies are still limited. Here, we present the first complete mitochondrial genome of C. soulattri. It is 378,262 bp long with 43.97% GC content, containing 55 genes (30 protein-coding, 5 rRNA, and 20 tRNA). Repeat analysis of the mitochondrial genome revealed 194 SSRs, mostly mononucleotides, and 266 pairs of dispersed repeats ( $$\ge $$ ≥ 30 bp) that were predominantly palindromic. There were 23 homologous fragments found between the mitochondrial and plastome genomes. We also predicted 345 C-to-U RNA editing sites from 30 protein-coding genes (PCGs) of the C. soulatrii mitochondrial genome. These RNA editing events created the start codon of nad1 and the stop codon of ccmFc. Most PCGs of the C. soulattri mitochondrial genome underwent negative selection, but atp4 and ccmB experienced positive selection. Phylogenetic analyses showed C. soulattri is a sister taxon of Garcinia mangostana. This study has shed light on C. soulattri’s evolution and Malpighiales’ phylogeny. As the first complete mitochondrial genome in Calophyllaceae, it can be used as a reference genome for other medicinal plant species within the family for future genetic studies.

Abstract. Elec VH, Cadorna CAE, Tad-Awan BA, Basquial DA, Dumaslan MR, Rey JD. 2024. Genetic diversity and population structure of Philippine strawberry germplasm based on genome-wide simple sequence repeat markers. Biodiversitas 25: 2969-2979. Strawberry is a globally recognized fruit due to its health benefits and economic significance. Determining the level of genetic diversity and the relationship between germplasm resources involved in the breeding program is critical for effective crop improvement strategies. This study used 197 Simple Sequence Repeat (SSR) markers to assess the genetic diversity and population structure of 24 strawberry germplasm from the Benguet State University (BSU) collection. In this study, 70% of the markers used were polymorphic with reproducible fragments. A total of 792 alleles were detected, with an average of six per marker. The diversity indices indicated an intermediate level of diversity among the germplasm based on the Jaccard coefficient. Results from cluster analysis generated three groups, separating the Red Milky Way and Summer Princess cultivars from the rest of the germplasm evaluated, while a third cluster was further divided into six subgroups. Furthermore, identified clustering patterns of the evaluated genotypes showed independence from the region of origin, coinciding with Principal Component Analysis (PCA) and population structure analysis results. This study reveals the genetic diversity level and population structure of the strawberry cultivars in the Philippines using SSR markers, facilitating accurate identification and informed parental selection for breeding objectives.

Strawberry (Fragaria x ananassa Duchesne ex Rozier) is an economically important fruit crop grown commercially worldwide due to its known nutritional value. The demand for strawberries in the Philippines has been increasing but varietal development is slow due to the lack of genetic information on locally available germplasm. In addition, molecular marker resources for strawberries are limited. Here, we developed Simple Sequence Repeats (SSR) markers to characterize strawberries cultivated in tropical environments, particularly in the Philippines. In silico mining generated a total of 219,239 SSR markers, from which 160,025 unique markers were identified. Polymorphism scoring and the variation on the expected alleles resulting to the synthesis of the top 160 markers were validated using representative strawberry cultivars from the core collection. All 70 markers produced successful amplicons from all the genotypes, but only 67 markers displayed polymorphism. Using UPGMA, genetic similarities among the cultivars were calculated generating a dendrogram which categorized the strawberry cultivars into 3 groups. The grouping clearly showed the separation of the diploid Fragaria vesca from the octoploid F. x ananassa cultivars, considered as group 1. Furthermore, Groups 2 and 3 contained cultivars from different geographical origins (US, Japan, and North America). The eight novel markers developed and validated here can be added to the genetic marker resource for cultivar verification, assessment of genetic diversity, and most importantly, marker-assisted breeding.

Calophyllum soulattri Burm. f. (1768) is an evergreen tree native to Southeast Asia, Australia, and the Solomon Islands. It is known for its medicinal uses and has been utilized in traditional folk medicine. However, genomic resources for this species are still unavailable. In this study, we sequenced and assembled the first complete chloroplast genome of C. soulattri using next-generation sequencing data. The chloroplast genome of C. soulattri is 161,381 bp in length with a total GC content of 36.36%. The chloroplast genome contains a large single copy (LSC) region of 88,680 bp, a small single copy (SSC) region of 17,453 bp, and two inverted repeat (IR) regions of 27,624 bp each. Furthermore, the chloroplast genome has 131 genes, which include 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that C. soulattri is clustered in the same branch with C. inophyllum and is closely related to Mesua ferrea.

Cocos nucifera (coconut) is an economically important crop in the Philippines. Coconut is the only species in the genus Cocos of the family Arecaceae and is widely cultivated for its extensive use in agriculture and industry. The SHELL gene has already been characterized in oil palm which is responsible for its coconut-like shell and various fruit forms. However, this gene has not yet been isolated and characterized in coconut. In this study, the CnSHELL gene region was successfully amplified across 22 coconut cultivars originating from different regions and amplicon size ranges at about 450-550 bp. Based on BLAST analysis, this gene is homologous with Elaeis guineesis shell-specific gene. The isolated gene can also be mapped on the whole genome sequences of coconut deposited in NCBI. Sequence analysis of the CnSHELL gene revealed low level of genetic diversity (Hd = 0.039394, = 0.00131) which indicates that the amplified region is highly conserved. Nevertheless, phylogenetic analysis using the CnSHELL gene region showed two groups of coconut, which is consistent with previous reports on separate domestication origins of coconut. Indeed, this is the first report of SHELL gene region isolated from 22 Cocos nucifera tall cultivars.

Solanum lycopersicum var. cerasiforme (tomato) is an economically important commodity in the Philippine fresh vegetable market and is also considered as a model system for fruit development studies. This study was conducted to establish baseline data on the effect of electrical conductivity (EC) on the physical, biochemical, and nutritional quality of the fruits at different developmental stages using two cherry tomato hybrids, namely Sweet Princess (SP) and Cutie Pie (CP), grown in Simple Nutrient Addition Program (SNAP) hydroponics system. A replicated experiment with three EC treatments using NaCl (1.2 dS m(-1), 1.5 dS m(-1), and 2.0 dS m(-1)) was established while total soluble solids (TSS), vitamin C content, titratable acidity (TA), yield or weight of the fruits were measured at different fruit development stages namely, green, turner and red. Results showed that EC of nutrient solution affected the total soluble solids, vitamin C content, and titratable acidity of two cherry tomato hybrids, SP and CP. Our study establishes the significant effect of EC 1.5 on TSS, which is increased at turner stage, on TA and Vitamin C at red stage for SP and subsequent decrease in fruit weight and TA, while that of CP hybrid, EC 1.5 significantly decreases TSS, TA and fruit weight, but increases Vitamin C content at turner stage. EC 2.0 has significant increase on TSS, TA and fruit weight of SP hybrid only. These results are initial reports for the Philippine cherry tomato hybrids grown in hydroponics system. Further studies with larger population size to further minimize the variations between replication and to conduct more technical replications in the assays is recommended.

More than two billion people are micronutrient deficient. Polished grains of popular rice varieties have concentration of approximately 2 μg g−1 iron (Fe) and 16 μg g−1 zinc (Zn). The HarvestPlus breeding programs for biofortified rice target 13 μg g−1 Fe and 28 μg g−1 Zn to reach approximately 30% of the estimated average requirement (EAR). Reports on engineering Fe content in rice have shown an increase up to 18 μg g−1 in glasshouse settings; in contrast, under field conditions, 4 μg g−1 was the highest reported concentration. Here, we report on selected transgenic events, field evaluated in two countries, showing 15 μg g−1 Fe and 45.7 μg g−1 Zn in polished grain. Rigorous selection was applied to 1,689 IR64 transgenic events for insert cleanliness and, trait and agronomic performances. Event NASFer-274 containing rice nicotianamine synthase (OsNAS2) and soybean ferritin (SferH-1) genes showed a single locus insertion without a yield penalty or altered grain quality. Endosperm Fe and Zn enrichment was visualized by X-ray fluorescence imaging. The Caco-2 cell assay indicated that Fe is bioavailable. No harmful heavy metals were detected in the grain. The trait remained stable in different genotype backgrounds.

Multiplexed single nucleotide polymorphism (SNP) markers have the potential to increase the speed and cost-effectiveness of genotyping, provided that an optimal SNP density is used for each application. To test the efficiency of multiplexed SNP genotyping for diversity, mapping and breeding applications in rice (Oryza sativa L.), we designed seven GoldenGate VeraCode oligo pool assay (OPA) sets for the Illumina BeadXpress Reader. Validated markers from existing 1536 Illumina SNPs and 44 K Affymetrix SNP chips developed at Cornell University were used to select subsets of informative SNPs for different germplasm groups with even distribution across the genome. A 96-plex OPA was developed for quality control purposes and for assigning a sample into one of the five O. sativa population subgroups. Six 384-plex OPAs were designed for genetic diversity analysis, DNA fingerprinting, and to have evenly-spaced polymorphic markers for quantitative trait locus (QTL) mapping and background selection for crosses between different germplasm pools in rice: Indica/Indica, Indica/Japonica, Japonica/Japonica, Indica/O. rufipogon, and Japonica/O. rufipogon. After testing on a diverse set of rice varieties, two of the SNP sets were re-designed by replacing poor-performing SNPs. Pilot studies were successfully performed for diversity analysis, QTL mapping, marker-assisted backcrossing, and developing specialized genetic stocks, demonstrating that 384-plex SNP genotyping on the BeadXpress platform is a robust and efficient method for marker genotyping in rice.