SummaryRice tungro disease (RTD) is a serious constraint in rice production across tropical Asia. RTD is caused by the interaction between Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. RTSV resistance found in traditional cultivars has contributed to a reduction in the incidence of RTD in the field. Natural RTSV resistance is a recessive trait controlled by the translation initiation factor 4 gamma gene (eIF4G). The Y1059V1060V1061 residues of eIF4G are known to be associated with the reactions to RTSV. To develop new sources of resistance to RTD, mutations in eIF4G were generated using the CRISPR/Cas9 system in the RTSV‐susceptible variety IR64, widely grown across tropical Asia. The mutation rates ranged from 36.0% to 86.6%, depending on the target site, and the mutations were successfully transmitted to the next generations. Among various mutated eIF4G alleles examined, only those resulting in in‐frame mutations in SVLFPNLAGKS residues (mainly NL), adjacent to the YVV residues, conferred resistance. Furthermore, our data suggest that eIF4G is essential for normal development, as alleles resulting in truncated eIF4G could not be maintained in homozygous state. The final products with RTSV resistance and enhanced yield under glasshouse conditions were found to no longer contain the Cas9 sequence. Hence, the RTSV‐resistant plants with the novel eIF4G alleles represent a valuable material to develop more diverse RTSV‐resistant varieties.

A drought stress panel composed of diverse accessions selected from upland, aerobic, rainfed lowland and irrigated lowland environments, was assembled to serve as germplasm for aerobic adaptation breeding. Aerobic rice requires significant levels of tolerance to drought stress due to intermittent water deficit and high soil impedance caused by aerobic conditions. Genomic information may be utilized to investigate the nature of the panel to guide varietal improvement. Using 153 simple sequence repeat and 384 single nucleotide polymorphism markers, the aim of the study was to compare the allelic properties of the two marker types, infer population structure of the panel, and estimate kinship among the accessions. There was a general agreement between the results derived from the two marker types. Marker alleles were found to occur at low frequencies, as the panel was composed mostly of improved accessions with some landraces. The panel clustered into japonica (JA), aus (AU), upland-adapted indica (UL) and lowland-adapted indica (LL) subpopulations. The AU and JA subpopulations were more divergent from the rest of the subpopulations than were the LL and UL subpopulations. Average marker-based kinship for related accessions was less than 0.20, indicating a low degree of genetic relatedness in the panel. Within the LL and UL subpopulations, the low levels of kinship imply that there is still much genetic gain to be expected from utilizing the accessions in breeding. Thus, an understanding of the genetic variation in the panel suggests focusing on improving the mean in the short term, and tapping into the exotic alleles from the AU and JA subpopulations when genetic gain declines.

Oryza rufipogon Griff. or ‘Rufi’ is the wild progenitor of the cultivated rice, Oryza sativa L. In the Philippines, Rufi was previously known to be found only in Lake Apo, Bukidnon. However, a new population was identified in Lake Napalit in the same province. Based on previous morphological diversity assessment, both populations are unique for at least three characters, i.e., leaf, culm, and awn lengths. Environmental parameters such as rainfall and air temperature also differed between the two lakes. With these, an assessment of Rufi’s genetic diversity at the molecular level is beneficial to further ascertain its usefulness in rice breeding and gain insights on its conservation status. Thus, this study estimated the degree of genetic diversity and determined the population structure of 41 samples of natural Rufi populations in the Philippines using SSR markers. A total of 98 genome wide polymorphic SSR markers were selected to examine the genetic diversity and structure of Rufi populations, along with seven rice cultivars for comparison. Results showed that Philippine Rufi populations have lower genetic diversity compared to cultivated rice accessions and other Rufi populations in Southeast Asia and China. This low genetic diversity suggested that Rufi populations might be in a genetic bottleneck, perhaps due to observed unsustainable farming practices near their habitat and lack of awareness of their importance. A significant population structure and differentiation were determined using the STRUCTURE and phylogenetic analyses. Population differentiation might be due to geographic isolation which prevented gene flow between the two populations and the unique climatic conditions between the two lakes.

Oryza rufipogon Griff., or “Rufi” in the Philippines, was previously known to be found only in Lake Apo, Bukidnon. However, a new population was identified in Lake Napalit in the same province. A better understanding of the genetic diversity of both Rufi populations using molecular methods may be beneficial to further ascertain its usefulness in rice breeding and in the development of effective conservation strategies. Population genetic analysis was conducted to estimate the degree of genetic diversity and population structure of the two Philippine Rufi populations using 98 genome-wide simple sequence repeat (SSR) markers. Four Oryza sativa indica and three O. sativa japonica cultivars were added for comparison. Results indicate that both Rufi populations exhibit low genetic diversity but with significant population structure and differentiation. Low genetic diversity suggests that both populations might be in a genetic bottleneck, perhaps due to observed unsustainable farming practices near their habitat and lack of awareness among locals of their importance. Also, geographical isolation that prevented gene flow between the two populations, as well as the unique climatic conditions between the two lakes might have contributed to the significant population structuring and differentiation. Thus, in situ and ex situ conservation should be observed for both Rufi populations in the Philippines.