Genome drafts of Pseudogracilibacillus spp. from soil and sediment of Mount Makiling, a dormant volcano in the Philippines.

We present the draft whole-genome sequences of Pseudogracilibacillus spp. isolated from the soils and sediments of Sipit Creek located at Mount Makiling, a dormant volcano in the southern part of Luzon Island, Philippines. This Pseudogracilibacillus spp. genome report extends the body of knowledge on a lesser-known genus of Bacillaceae.

Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species.

Introduction: Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. These viral elements, known as endogenous RTBV-like sequences (eRTBVLs), comprise five subfamilies, eRTBVL-A, -B, -C, -D, and -X. Four subfamilies (A, B, C, and X) are present to a limited degree in the genomes of the Asian cultivated rice Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon. Methods: The eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (Nipponbare) genome occur mostly at orthologous chromosomal positions in other AA-genome species. The eRTBVL-D sequences were inserted into the genomes just before speciation of the AA-genome species. Results and discussion: Ten eRTBVL-D segments are located at six loci, which were used for our evolutionary analyses during the speciation of the AA-genome species. The degree of genetic differentiation varied among the eRTBVL-D segments. Of the six loci, three showed phylogenetic trees consistent with the standard speciation pattern (SSP) of the AA-genome species (Type A), and the other three represented phylogenies different from the SSP (Type B). The atypical phylogenetic trees for the Type B loci revealed chromosome region-specific evolution among the AA-genome species that is associated with phylogenetic incongruences: complex genome rearrangements between eRTBVL-D segments, an introgression between the distant species, and low genetic diversity of a shared eRTBVL-D segment. Using eRTBVL-D as an indicator, this study revealed the phylogenetic incongruence of local chromosomal regions with different topologies that developed during speciation.

Screening for Resistance in Selected Tomato Varieties against the Root-Knot Nematode Meloidogyne incognita in the Philippines Using a Molecular Marker and Biochemical Analysis.

Tomato is a high-value vegetable crop widely cultivated in the Philippines, and its production is threatened by various stresses including infection by the root-knot nematode M. incognita. In this study, we checked for resistance to M. incognita in selected tomato germplasm collections and commercially available varieties using a bioassay method, the molecular marker Mi23 and biochemical analysis. Among the eight varieties tested, none showed a resistant reaction against M. incognita. Use of the molecular marker Mi23 yielded 430 bp in all the tomato varieties screened. Phylogenetic analysis using the neighbor-joining method revealed the clustering of consensus sequence of the varieties tested with the susceptible variety S. lycopersicum cv. M82-1-8 and a wild relative, S. pimpinellifolium isolate LA2184. The biochemical analysis showed varying responses among the varieties when they were inoculated with M. incognita. Increased levels of total antioxidant activity were observed in Diamante Max F1, Ilocos Red and Tm 2016 11-1, while total phenolic content was found to be elevated in Athena, Avatar TY F1 and Rosanna. Increased levels of ascorbic acid were observed in Athena and Avatar TY F1 even at 45 dpi. Even though these varieties showed elevated levels of the abovementioned biochemical parameters related to a resistance reaction, all of them showed highly susceptible reactions. Hence, this study showed that these tomato varieties have no resistance against M. incognita and that there is a need to identify other sources of resistance against M. incongita and produce resistant tomato cultivars adapted to local conditions.

Introgression of tsv1 improves tungro disease resistance of a rice variety BRRI dhan71.

Rice Tungro disease poses a threat to rice production in Asia. Marker assisted backcross breeding is the most feasible approach to address the tungro disease. We targeted to introgress tungro resistance locus tsv1 from Matatag 1 into a popular but tungro susceptible rice variety of Bangladesh, BRRI dhan71. The tsv1 locus was traced using two tightly linked markers RM336 and RM21801, and background genotyping was carried out using 7 K SNPs. A series of three back crosses followed by selfing resulted in identification of plants similar to BRRI dhan71. The background recovery varied at 91-95% with most of the lines having 95%. The disease screening of the lines showed moderate to high level of tungro resistance with a disease index score of ≤ 5. Introgression Lines (ILs) had medium slender grain type, and head rice recovery (59.2%), amylose content (20.1%), gel consistency (40.1 mm) and gelatinization temperature were within the acceptable range. AMMI and Kang's stability analysis based on multi-location data revealed that multiple selected ILs outperformed BRRI dhan71 across the locations. IR144480-2-2-5, IR144483-1-2-4, IR144484-1-2-2 and IR144484-1-2-5 are the most promising lines. These lines will be further evaluated and nominated for varietal testing in Bangladesh.

Genomics-Based Diagnostic Marker Development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola.

A computational genomics pipeline was used to compare sequenced genomes of Xanthomonas spp. and to rapidly identify unique regions for development of highly specific diagnostic markers. A suite of diagnostic primers was selected to monitor diverse loci and to distinguish the rice bacterial blight and bacterial leaf streak pathogens, Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola, respectively. A subset of these primers was combined into a multiplex polymerase chain reaction set that accurately distinguished the two rice pathogens in a survey of a geographically diverse collection of X. oryzae pv. oryzae, X. oryzae pv. oryzicola, other xanthomonads, and several genera of plant-pathogenic and plant- or seed-associated bacteria. This computational approach for identification of unique loci through whole-genome comparisons is a powerful tool that can be applied to other plant pathogens to expedite development of diagnostic primers.

Identification of quantitative trait loci governing early germination and seedling vigor traits related to weed competitive ability in rice.

Weed competitive ability (WCA) is vital for the improvement of grain yield under direct-seeded and aerobic rice ecosystems where weeds are a major limiting factor. Early seed germination (ESG) and early seedling vigor (ESV) are the crucial traits for WCA. This study attempted to map the quantitative trait loci (QTLs) and hotspot regions governing ESG and ESV traits. A total of 167 BC1F5 selective introgression lines developed from an early backcross population involving Weed Tolerant Rice 1 (WTR-1) as the recipient parent and Y-134 as the donor parent were phenotyped for ESG and ESV traits. Analysis of variance revealed significant differences in ESG-related traits except for root length and in ESV-related traits except for plant height at 7 days after sowing. A total of 677-high quality single nucleotide polymorphism (SNP) markers were used to analyze the marker-trait association from a 6 K SNP genotyping array. Forty-three QTLs were identified on all chromosomes, except on chromosomes 4 and 8. Thirty QTLs were contributed by a desirable allele from Y-134, whereas 13 QTLs were from WTR-1. Twenty-eight of the identified genetic loci associated with ESG and ESV traits were novel. Two QTL hotspot regions were mapped on chromosomes 11 and 12. The genomic regions of QTL hotspots were fine-tuned and a total of 13 putative candidate genes were discovered on chromosomes 11 and 12 collectively. The mapped QTLs will be useful in advancing the marker aided-selection schemes and breeding programs for the development of rice cultivars with WCA traits.

Draft Genome Sequence of Bacillus lehensis M136, Isolated from the Manleluag Hyperalkaline Spring in Pangasinan, Philippines.

Here, we report the draft whole-genome sequence of Bacillus lehensis M136, isolated from a hyperalkaline spring located in Pangasinan, Philippines. From 24 scaffolds, the total genome assembly length is 3,985,437 bp. Industrially important genes like cyclodextrin glycosyltransferase (CGTase) and proteases were detected in this draft genome.

DNA fingerprinting at farm level maps rice biodiversity across Bangladesh and reveals regional varietal preferences.

The development, dissemination, and adoption of improved rice varieties are imperative for global food and nutritional security. Knowledge of the crop's distribution across agro-ecologies is important for impact assessment studies, varietal replacement strategies, and the development and implementation of agricultural policies. Bangladesh is the world's 4th largest rice producer. Though traditional varieties (TVs) are abundant and valued throughout Bangladesh, population growth and vulnerability to climate change, necessitate efficient deployment of high-yielding stress-tolerant modern varieties (MVs). To aid agricultural policy and strategy this study aimed to accurately assess the distribution of MVs and TVs across Bangladesh during the rainfed rice-growing season. Information derived from a survey of rice production areas were compared and combined with DNA fingerprinting information from the same locations. Biodiversity of Bangladesh rice remained high. While TVs and first generation MVs of Bangladeshi and Indian origin were still commonly grown, recently released stress-tolerant MVs were adopted in large proportions in several districts. Although farmers successfully distinguished TVs from MVs grown in their fields, a considerable lack of authenticity among MVs was observed, pinpointing shortcomings in the seed supply chain. This study identifies focal points for extension work and validates DNA fingerprinting as reliable method for impact assessment studies.

Performance of Newly Developed Weed-Competitive Rice Cultivars under Lowland and Upland Weedy Conditions.

Four early-generation backcross populations (BC1F2) derived from one common recipient parental background, Weed Tolerant Rice 1 ('WTR1'), and four different donor parents ('Y134', 'Zhong 143', 'Khazar', and 'Cheng Hui-448') were tested to identify suitable donor and recipient parents for weed competitiveness and to standardize evaluation of the weed-competitive ability in rice. 'GSR IR2-6' (G-6) derived from a backcross of WTR1/Y134//WTR1 was selected as the best population and was advanced for phenotypic experiments in the 2014 dry season. The introgression lines (ILs) derived from the G-6 population were evaluated for seed germination and seedling vigor in greenhouse conditions and for weed-competitive ability under field conditions (upland weed-free, upland weedy, and lowland weedy). Parents and checks were included for comparison. Selection pressure for weed competitiveness was relatively stronger in upland conditions than in lowland conditions. After three rounds of selection and based on their relative grain yield performances across conditions, a total of 21 most-promising introgression fixed lines showing superior traits and weed-competitive ability were identified. G-6-L2-WL-3, G-6-RF6-WL-3, G-6-L15-WU-1,G-6-Y16-WL-2, and G-6-L6-WU-3 were the top ILs in lowland weedy conditions, whereas G-6-Y7-WL-3, G-6-Y6-WU-3, G-6-Y3-WL-3, and G-6-Y8-WU-1 were the highest yielding in upland weedy conditions. The use of weed-competitive rice cultivars in African and Asian countries will be a highly effective strategy to reduce production costs and provide alternative solutions to the unavailability of herbicides. Competitive rice varieties will also significantly improve grain yields in aerobic rice systems and can become an important strategy for successful upland rice production. Nomenclature: Rice, Oryza sativa L.

Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm.

BACKGROUND: A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines. Rice diversity panels can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. This study was conducted to identify loci associated to BB resistance, new genetic donors and useful molecular markers for marker-assisted breeding. RESULTS: A genome-wide association study (GWAS) of BB resistance using a diverse panel of 285 rice accessions was performed to identify loci that are associated with resistance to nine Xoo strains from the Philippines, representative of eight global races. Single nucleotide polymorphisms (SNPs) associated with differential resistance were identified in the diverse panel and a subset of 198 indica accessions. Strong associations were found for novel SNPs linked with known bacterial blight resistance Xa genes, from which high utility markers for tracking and selection of resistance genes in breeding programs were designed. Furthermore, significant associations of SNPs in chromosomes 6, 9, 11, and 12 did not overlap with known resistance loci and hence might prove to be novel sources of resistance. Detailed analysis revealed haplotypes that correlated with resistance and analysis of putative resistance alleles identified resistant genotypes as potential donors of new resistance genes. CONCLUSIONS: The results of the GWAS validated known genes underlying resistance and identified novel loci that provide useful targets for further investigation. SNP markers and genetic donors identified in this study will help plant breeders in improving and diversifying resistance to BB.