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Basmati is a premium quality rice, famous for its aroma, fine grain, and excellent cooking qualities. However, it is highly susceptible to bacterial leaf blight (BLB). To develop BLB resistant Basmati rice varieties, we transferred three (03) BLB resistance genes namely Xa4, xa5, Xa21 from a coarse yet BLB-resistant variety, IRBB57, developed by International Rice Research Institute into fine-quality rice variety, Super Basmati, through marker-assisted breeding. The background parent genome was recovered performing several backcrosses using Super Basmati as a recurrent parent to restore the bona fide Basmati character. The introgression of BLB resistance genes was followed by foreground selection using DNA-markers tightly linked with BLB resistance genes. The recovery of the Basmati parent genome (Background Selection) was determined using two different marker systems. Simple Sequence Repeats and Single Nucleotide Polymorphism. Several Super Basmati Introgressed (SBIL) lines with the individual as well as different BLB resistance gene combinations were developed. The stable representative SBILs from single, double, and triple gene combinations showing > 90% parent genome recovery were further studied for different attributes particularly to determine their degree of tolerance to the bacterial blight that was studied at two different locations—Philippines and Pakistan. We observed that SBILs carrying a combination of xa5 + Xa21 and Xa4 + xa5 + Xa21 conferred broad-scale resistance against both the highly virulent Pakistani and Philippines Xanthomonas oryzae pv. oryzae strains. The marker-aided background selection coupled with stringent phenotypic selection as well as foreground selection using DNA markers tightly linked with grain quality ensured that SBILs possess the bona fide Basmati character. The performance of key agronomic traits in selected SBILs was comparable with the recurrent parent with no significant agronomic or yield penalty associated with incorporation of the resistance genes, confirming the linkage drag has been minimized. Therefore, in addition to sustaining Basmati rice yield against BLB, the SBILs developed in this study may represent a useful resource for transferring resistance to BLB-susceptible rice varieties. [ABSTRACT FROM AUTHOR]

This study examines the relationship between yields of modern rice varieties and warming temperatures. Data from a long‐running farm‐level survey in the Philippines, with rich information on planted rice varieties, allow us to estimate fixed effect econometric models of rice yields. We find that increases in temperature, especially minimum temperatures, have statistically significant negative impacts on rice yields. Point estimates of the marginal effect of higher temperatures on rice yields indicate that early modern varieties bred primarily for higher yields, pest resistance, and/or grain quality traits (i.e., not necessarily abiotic stress tolerance) tend to be more resilient to heat events than traditional rice varieties. Moreover, the marginal effect point estimates also suggest that more recent rice varieties bred for better tolerance to abiotic stresses are likely more resilient to warming than both traditional varieties and early modern varieties. Notwithstanding the heat resilience pattern suggested by these point estimates, we are unable to find statistically significant differences in the marginal yield response to warming across these three rice varietal groups. These results provide suggestive evidence that rice breeding efforts have improved resilience to warming temperatures and point to several interesting future research directions. [ABSTRACT FROM AUTHOR]

Background: Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating bacterial diseases of rice in temperate and tropical regions. Breeding and deployment of resistant cultivars carrying major resistance (R) genes has been the most effective approach for BB management. However, because of specific interaction of each R gene with the product of the corresponding pathogen avirulence or effector gene, new pathogen strains that can overcome the deployed resistance often emerge rapidly. To deal with ever-evolving Xoo, it is necessary to identify novel R genes and resistance quantitative trait loci (QTL). Results: BB resistance of a diverse panel of 340 accessions from the 3000 Rice Genomes Project (3 K RGP) was evaluated by artificial inoculation with four representative Xoo strains, namely Z173 (C4), GD1358 (C5), V from China and PXO339 (P9a) from Philippines. Using the 3 K RG 4.8mio filtered SNP Dataset, a total of 11 QTL associated with BB resistance on chromosomes 4, 5, 11 and 12 were identified through a genome-wide association study (GWAS). Among them, eight resistance loci, which were narrowed down to relatively small genomic intervals, coincided with previously reported QTL or R genes, e.g. xa5, xa25, xa44(t). The other three QTL were putative novel loci associated with BB resistance. Linear regression analysis showed a dependence of BB lesion length on the number of favorable alleles, suggesting that pyramiding QTL using marker-assisted selection would be an effective approach for improving resistance. In addition, the Hap2 allele of LOC_Os11g46250 underlying qC5–11.1 was validated as positively regulating resistance against strain C5. Conclusions: Our findings provide valuable information for the genetic improvement of BB resistance and application of germplasm resources in rice breeding programs. [ABSTRACT FROM AUTHOR]

Recent advances in rice breeding in tropical Asia led to the release of high-yielding drought-tolerant cultivars. Together with the use of these cultivars, improved nutrient management under drought should further increase rice productivity in rainfed lowland ecosystems. The objectives of this study were to evaluate cultivar differences in the responses of plant growth and grain yield to fertilizer application regimes. We compared 13 drought-tolerant rice cultivars with two irrigated rice cultivars under three nutrient management conditions in irrigated and rainfed lowlands in the Philippines during the wet seasons of 2014 and 2015. Drought stress was mild in both years, with a yield reduction of 11 to 12%, and there was no significant cultivar × nutrient management interaction in yield. The drought-tolerant cultivar NSIC Rc282 proved fertilizer-responsive, and had similar yield to those of the popular high-yielding cultivar NSIC Rc222 under all conditions. An ancillary experiment in 2016 confirmed that NSIC Rc282 was more drought-adapted than NSIC Rc222, with 11% to 37% higher yield under stress. In order to maximize the yield, NSIC Rc282 required N application only when the drought ended, whereas NSIC Rc222 required additional N during the drought. This shows that the details of drought-adaptive nutrient management differ between irrigated and drought-tolerant rice cultivars. We suggest that the introduction of high-yielding drought-tolerant rice cultivars will both improve productivity and increase the nutrient-use efficiency in rainfed environments. [ABSTRACT FROM AUTHOR]

The enhancement of heat stress tolerance at anthesis is an important strategy to achieve sustainable rice production in the context of predicted global warming. In this study, we genetically analysed spikelet fertility under high temperature treatment (38°C) at anthesis using the three rice varieties, namely, Koshihikari and Takanari, which were developed in Japan, and IR64, which was developed in the Philippines. Genetic analysis of the F2 population between Takanari and IR64 revealed a quantitative trait locus (QTL) on chromosome 4 that increased spikelet fertility with the Takanari allele and that was likely qHTSF4.1, a previously fine-mapped major QTL. Genetic analysis using chromosome segment substitution lines (CSSLs) carrying Koshihikari chromosome segments in the IR64 genetic background did not show any QTLs. In contrast, genetic analysis using CSSLs carrying Koshihikari chromosome segments in the Takanari genetic background revealed some QTLs, including chromosomes 4 and 9. These results suggest that the expression of QTLs may depend on genetic background. The two CSSLs, SL1313 and SL1330, which carried the QTLs on chromosomes 4 and 9, respectively, exhibited a spikelet fertility of over 80% and relatively large anther dehiscence compared with Takanari. These results suggest that the Koshihikari allele of QTLs may be related to improved anther dehiscence, which may lead to successful pollination and ultimately increased spikelet fertility under heat stress conditions. The findings in the present study should be useful to enhance heat stress tolerance at anthesis in rice in future breeding programs. [ABSTRACT FROM AUTHOR]

Genetic diversity is necessary to safeguard potentially vital traits for adaptation to environmental stresses and a proximate defense against a resurgence of pests and diseases amid climate change. The hybridization core germplasm of the Philippine Rice Research Institute (PhilRice) comprises local and foreign landraces, varieties, and elite breeding lines, which are various sources for diversification and creation of superior rice varieties. The objective of the study is to investigate the level of genetic diversity and population structure across 472 parental germplasm using 17 polymorphic simple sequence repeat (SSR) markers as assistance for rice breeders in the selection of unique parents for hybridization. Germplasm accessions showed high genetic diversity (71%) and formed a structure delineating indica, temperate japonica, and tropical japonica - with 32.8% admixtures identified through the distance-based neighbor-joining (NJ) method, model-based Bayesian structure, and discriminant analysis of principal components (DAPC). Analysis of molecular variance (AMOVA) revealed that the majority of the variation (87.0%) was attributed to accession differences within a population, indicating regular seed movement limited to each subgroup rather than between population (8.7%), wherein the highest fixation index (FST) was observed between tropical and temperate japonica (FST = 0.13). The study established a PhilRice parental germplasm collection containing 306 genetically pure accessions retaining the majority of genetic diversity from the first collection, which offers a promising aid in generating favorable genetic gain through careful genotypic selection in rice breeding programs. [ABSTRACT FROM AUTHOR]

Rice tungro is one of the most economically damaging virus diseases in the Philippines, which is caused jointly by Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). The disease causes a significant effect on rice propagation and cultivation. This study aimed to determine the level of genetic diversity of RTBV coat protein gene sequences collected from tungro-hotspot areas in the Philippines and infer their phylogenetic relationships. A total of 144 RTBV coat protein gene sequences were analyzed from six provinces with 21 municipalities representing Luzon, Visayas, and Mindanao. The highest percentage of RTBV detected was in Camarines Sur at 78% while Nueva Ecija had the least at 45%. Among the provinces, nucleotide diversity and number of segregating sites of RTBV were highest in Camarines Sur (π = 0.010797, S = 145) and lowest in Laguna (π = 0.006233, S = 67). Phylogenetic analysis revealed six divergent groups but did not completely reflect geographical origin while principal coordinate analysis (PCoA) resulted in three major groups: Laguna, Negros Occidental, and Nueva Ecija (Luzon and Visayas); and Camarines Sur and North Cotabato plus Isabela (Luzon and Mindanao). These results could infer genetic differentiation is relevant that disease severity variation could be observed including some breaking in resistance in some areas. There is a need to re-design breeding such as locationspecific breeding for RTBV-resistant rice varieties that would consider genetic variation within and between location. Other molecular approaches such as the use of next-generation sequencing could be recommended to support the findings from this study. [ABSTRACT FROM AUTHOR]

Plant breeders evaluate large numbers of breeding lines/accessions and measure various traits in the field in order to identify and select elite genotypes with high yield. Therefore, information on highly correlated yield-related traits and simple high-throughput methods to predict grain yield would be useful for rice breeders. The objective of this study was to examine the usefulness of various traits as indirect selection criteria for high yield in tropical rice breeding, with an emphasis on rapid and non-destructive measurements. We evaluated a wide range of germplasm, including popular varieties, elite genotypes, and donor parents, in the irrigated rice breeding program at the International Rice Research Institute, in the Philippines, during the 2015 wet season and 2016 dry season. We measured the normalized-difference vegetation index (NDVI), leaf chlorophyll content (SPAD value), agronomic traits, and grain yield. Harvest index, NDVI at the heading and late grain-filling stages, and SPAD value at the late grain-filling stage were significantly correlated with yield during the wet season, whereas plant height, panicle length, and NDVI from panicle initiation to the booting stage during the dry season. Our results indicate that pre-harvest analysis of primary and secondary traits such as NDVI has potential for selecting high-yielding accessions in tropical rice breeding programs. By using low-cost portable equipment, NDVI measurements could be incorporated into breeding programs. Trait associations with yield differed between the dry and wet seasons, which has important implications for breeding new varieties and germplasm evaluation in different seasons. [ABSTRACT FROM AUTHOR]

The breeding strategy implemented by the Philippine Rice Research Institute (PhilRice) is anchored in Agriculture 4.0 that aims to revolutionize the variety development system of the Philippines, thereby addressing the grand challenges the rice industry facing at present and in the future, considering the struggles of a sustainable agriculture in the face of global warming. It advocates a stronger and more cohesive variety development structure to keep up with the need of the times as well as climate change. Our breeders are challenged to produce a variety that will double the yield at the same time, climate and pest resistant with good eating quality and nutritious. Strategies implemented by PhilRice include the use of advanced methodologies in biotechnology and molecular biology as tools in developing rice varieties to hasten crop improvement, thereby addressing the grand challenges the rice industry facing at present and in the future. [ABSTRACT FROM AUTHOR]

A statistical analysis of 9,771 non-glutinous rice in breeding line germplasm collected from Korea (2,836), China (2,136), Japan (1,219), and the Philippines (1,213) was conducted using normal distribution, variability index value (VIV), analysis of variation (ANOVA) and Ducan’s multiple range test (DMRT) based on the data obtained from NIRS analysis. According to the normal distribution, the average protein content was 7.9%, and non-glutinous rice ranging over 10% amylose had 23.6% average content. Most resources were between 5.3 and 10.5% in protein content, and 15.7 and 31.5% in amylose content. The VIV was 0.54 for protein, and 0.83 for amylose. The average amylose content was 25.18%, 24.54%, 22.08%, and 21.47% in Filipino, Chinese, Korean, and Japanese resources, respectively, wheereas the average protein content was found to be 8.19%, 7.79%, 7.58%, and 7.42% in Filipino, Chinese, Korean, and Japanese resources, respectively. The ANOVA of amylose and protein content showed significant differences at the level of 0.01. The F-test value was 412.2 for amylose content, and 108.4 for protein when compared with the critical value of 3.78. The DMRT of amylose and protein content showed significant differences (p<0.01) among resources from different countries. The Filipino resources had the highest level of amylose and protein content, whereas; the lowest level of amylose and protein content were found in Japanese when compared with resources of other origins. These results are recommended as helpful materials in the field of breeding. [ABSTRACT FROM AUTHOR]

We examined intrahousehold decision making with respect to household investment in portfolios of future rice varietal trait improvements (VTIs) to increase farm households' livelihoods in Nueva Ecija, Philippines. Investment decisions were elicited using an experimental methodology based on investment games. In the investment game, couples from rice farming households were given the opportunity to invest in public rice breeding. They selected, first individually, and then jointly, a replacement rice variety to improve upon and were then asked to allocate a research endowment fund to a portfolio of VTIs. We developed a novel indicator of women's intrahousehold decision-making power (WIDMP) based on the relative Euclidean distances between the individual and joint VTI portfolios. We found that WIDMP is normally distributed; and that, on average, women had almost equal (48%) decision-making power as men (52%), revealing almost perfect gender equity in investment decision making in rice breeding. Women were slightly more empowered if they were engaged in off-farm employment and were less experienced in farming. More empowered women had a higher discount factor and based their investment decisions on anticipated future trends, rather than current or past experience. The findings not only highlight the importance of considering gender roles in technology design, adoption and extension programs, but also have broader implications in terms of women empowerment programs. Consistent with the Sustainable Development Goals (SDGs), our evidence suggests that education and training programs need to be paired with investments generating off-farm employment opportunities to effectively increase women's bargaining power in the household. • We develop a novel indicator of women's intrahousehold decision-making power. • Filipino rice farms exhibit high gender equity in investment decision making in rice breeding. • Off-farm employment empowers women in investment decision making in rice breeding. • More empowered women base their investment decisions on anticipated future trends. [ABSTRACT FROM AUTHOR]

The Magnaporthe oryzae avirulence gene AvrPib is required for the resistance mediated by its cognate resistance gene Pib, which has been intensively used in indica rice breeding programs in many Asian countries. However, the sequence diversity of AvrPib among geographically distinct M. oryzae populations was recently shown to be increasing. Here, we selected a field population consisting of 248 rice blast isolates collected from a disease hotspot in Philippine for the analysis of AvrPib haplotypes and their pathogenicity against Pib. We found that all of the isolates were virulent to Pib and each of them contained an insertion of Pot3 transposon in AvrPib. Moreover, Pot3 insertion was detected in different genomic positions, resulting in three different AvrPib haplotypes, designated avrPib-Hl to H3. We further conducted a genome-wide Pot2 fingerprinting analysis by repetitive element palindromic polymerase chain reaction (PCR) and identified seven different lineages out of 47 representative isolates. The isolates belonging to the same lineage often had the same AvrPib haplotype. In contrast, the isolates having the same AvrPib haplotypes did not always belong to the same lineages. Both mating types MAT1-1 and MAT1-2 were identified in the population in Bohol and the latter appeared dominant. On the host side, we found that 32 of 52 released rice varieties in the Philippines contained Pib diagnosed by PCR gene-specific primers and DNA sequencing of gene amplicons, suggesting that it was widely incorporated in different rice varieties. Our study highlights the genetic dynamics of rice blast population at both the AvrPib locus and the genome-wide levels, providing insight into the mechanisms of the mutations in AvrPib leading to the breakdown of Pi/j-mediated resistance in rice. [ABSTRACT FROM AUTHOR]

Rice plants are Si accumulators and the uptake of Si can significantly improve their growth and stress tolerance. The Si that is taken up polymerises in above-ground plant tissues and forms amorphous silicon bodies called phytoliths. When rice straw is left on rice fields this biogenic Si pool may be an important source of plant-available Si, especially in old, highly weathered soils. Reports on the bioavailability of phytoliths are, however, sparse and sometimes contradictory. To study the in-situ dissolution of phytoliths over time in the field requires the extraction of phytoliths from rice straw. Several different extraction methods have been proposed but their impact on the morphology and surface chemistry (and consequently the solubility) of the phytoliths is not well studied. We have tested four different extraction methods: (i) oxidation with H2O2, (ii) wet ashing, (iii) dry ashing, and (iv) microwave treatment to extract phytoliths from Si-rich rice straw (Oryza sativa L. cv. NSIC Rc222) from the Philippines. The effect of the extraction methods on the morphology of the phytoliths was analysed using confocal laser scanning microscopy, while changes in particle size and specific surface area were determined by dynamic light scattering and N2 gas adsorption at 77 K, respectively. Surface chemistry was analysed with X-ray photoelectron spectroscopy (XPS); bulk element composition was determined using inductive-coupled plasma‒optical emmission spectrometry after microwave digestion. Dissolution experiments in mini reactors were carried out for assessing the solubility of phytoliths under conditions similar to those in the field. Data analysis is currently underway. First results using XPS suggest that dry ashing resulted in very clean SiO2 surfaces suitable for tracking of surface transformations of phytoliths in soil. [ABSTRACT FROM AUTHOR]