Seed longevity phenotyping: recommendations on research methodology.

The length of time for which seed lots maintain their viability and vigour in storage has become a trait of interest for rice and other crop and model species. However, different research groups have taken different approaches to measuring this trait, including storing seeds under 'natural ageing', accelerated ageing, and controlled deterioration test conditions. There has also been a tendency to use only a single germination test result to assess the relative longevity of different genotypes. Here, we explain why we have taken a different approach in a genome-wide association study of seed longevity in Oryza sativa (Indica Group), and offer suggestions as to how, in the future, this trait should be assessed to make it possible to develop varieties with improved seed longevity, depending on the target storage environment.

Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits.

Breeding staple crops with increased micronutrient concentration is a sustainable approach to address micronutrient malnutrition. We carried out Multi-Cross QTL analysis and Inclusive Composite Interval Mapping for 11 agronomic, yield and biofortification traits using four connected RILs populations of rice. Overall, MC-156 QTLs were detected for agronomic (115) and biofortification (41) traits, which were higher in number but smaller in effects compared to single population analysis. The MC-QTL analysis was able to detect important QTLs viz: qZn5.2, qFe7.1, qGY10.1, qDF7.1, qPH1.1, qNT4.1, qPT4.1, qPL1.2, qTGW5.1, qGL3.1 , and qGW6.1 , which can be used in rice genomics assisted breeding. A major QTL (qZn5.2 ) for grain Zn concentration has been detected on chromosome 5 that accounted for 13% of R2. In all, 26 QTL clusters were identified on different chromosomes. qPH6.1 epistatically interacted with qZn5.1 and qGY6.2 . Most of QTLs were co-located with functionally related candidate genes indicating the accuracy of QTL mapping. The genomic region of qZn5.2 was co-located with putative genes such as OsZIP5, OsZIP9, and LOC_OS05G40490 that are involved in Zn uptake. These genes included polymorphic functional SNPs, and their promoter regions were enriched with cis-regulatory elements involved in plant growth and development, and biotic and abiotic stress tolerance. Major effect QTL identified for biofortification and agronomic traits can be utilized in breeding for Zn biofortified rice varieties.

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.

Responses of AG1 and AG2 QTL introgression lines and seed pre-treatment on growth and physiological processes during anaerobic germination of rice under flooding.

Rice seeds germinating in flooded soils encounter hypoxia or even anoxia leading to poor seed germination and crop establishment. Introgression of AG1 and AG2 QTLs associated with tolerance of flooding during germination, together with seed pre-treatment via hydro-priming or presoaking can enhance germination and seedling growth in anaerobic soils. This study assessed the performance of elite lines incorporating AG1, AG2 and their combination when directly seeded in flooded soils using dry seeds. The QTLs were in the background of two popular varieties PSB Rc82 and Ciherang-Sub1, evaluated along with the donors Kho Hlan On (AG1) and Ma-Zhan Red (AG2) and recipient parents PSB Rc82 and Ciherang-Sub1. In one set of experiments conducted in the greenhouse, seedling emergence, growth, and carbohydrate mobilization from seeds were assessed. Metabolites associated with reactive oxygen species (ROS) scavenging including malondialdehyde (MDA) as a measure of lipid peroxidation, ascorbate, total phenolic concentration (TPC), and activities of ROS scavenging enzymes were quantified in seeds germinating under control (saturated) and flooded (10 cm) soils. In another set of experiments conducted in a natural field with 3-5 cm flooding depths, control and pretreated seeds of Ciherang-Sub1 introgression lines and checks were used. Flooding reduced seedling emergence of all genotypes, though emergence of AG1 + AG2 introgression lines was greater than the other AG lines. Soluble sugars increased, while starch concentration decreased gradually under flooding especially in the tolerant checks and in AG1 + AG2 introgression lines. Less lipid peroxidation and higher α-amylase activity, higher ascorbate (RAsA) and TPC were observed in the tolerant checks and in the AG1 + AG2 introgression lines. Lipid peroxidation correlated negatively with ascorbate, TPC, and with ROS scavengers. Seed hydro-priming or pre-soaking increased emergence by 7-10% over that of dry seeds. Introgression of AG2 and AG1 + AG2 QTLs with seed pretreatment showed 101-153% higher emergence over dry seeds of intolerant genotypes in the field. Lines carrying AG1 + AG2 QTLs showed higher α-amylase activity, leading to rapid starch degradation and increase in soluble sugars, ascorbate, and TPC, together leading to higher germination and seedling growth in flooded soils. Seed hydro-priming or pre-soaking for 24 h also improved traits associated with flooding tolerance. Combining tolerance with seed management could therefore, improve crop establishment in flooded soils and encourage large-scale adoption of direct seeded rice system.

Zinc and Iron Nutrition Status in the Philippines Population and Local Soils.

The Philippines is one of the major rice-producing and rice-consuming countries of Asia. A large portion of its population depends on rice for their daily caloric intake and nutritional needs. The lack of dietary diversity among poor communities has led to nutritional consequences, particularly micronutrient deficiencies. Iron-deficiency anemia (IDA) and zinc deficiency (ZnD) are two serious nutritional problems that affect the health and economic sector of the country. Since rice dominates the Filipino diet by default, biofortification of rice will help improve the micronutrient status. The Philippine government has proactively initiated various programs and policies to address micronutrient deficiencies, particularly through fortification of basic food commodities. Biofortification, the fortification of rice with micronutrients through breeding, is considered the most sustainable and cost-effective strategy that can benefit large vulnerable populations. However, developing promising genotypes with micronutrient-enriched grains should be coupled with improving micronutrient bioavailability in the soil in order to optimize biofortification. This review documents the prevailing soil Zn-deficiency problems in the major rice production areas in the Philippines that may influence the Zn nutritional status of the population. The article also reports on the biofortification efforts that have resulted in the development of two biofortified varieties approved for commercial release in the Philippines. As nutritional security is increasingly recognized as a priority area, greater efforts are required to develop biofortified rice varieties that suit both farmers' and consumers' preferences, and that can address these critical needs for human health in a sustainable and cost-effective manner.

Atmospheric CO2 concentration effects on rice water use and biomass production.

Numerous studies have addressed effects of rising atmospheric CO2 concentration on rice biomass production and yield but effects on crop water use are less well understood. Irrigated rice evapotranspiration (ET) is composed of floodwater evaporation and canopy transpiration. Crop coefficient Kc (ET over potential ET, or ETo) is crop specific according to FAO, but may decrease as CO2 concentration rises. A sunlit growth chamber experiment was conducted in the Philippines, exposing 1.44-m2 canopies of IR72 rice to four constant CO2 levels (195, 390, 780 and 1560 ppmv). Crop geometry and management emulated field conditions. In two wet (WS) and two dry (DS) seasons, final aboveground dry weight (agdw) was measured. At 390 ppmv [CO2] (current ambient level), agdw averaged 1744 g m-2, similar to field although solar radiation was only 61% of ambient. Reduction to 195 ppmv [CO2] reduced agdw to 56±5% (SE), increase to 780 ppmv increased agdw to 128±8%, and 1560 ppmv increased agdw to 142±5%. In 2013WS, crop ET was measured by weighing the water extracted daily from the chambers by the air conditioners controlling air humidity. Chamber ETo was calculated according to FAO and empirically corrected via observed pan evaporation in chamber vs. field. For 390 ppmv [CO2], Kc was about 1 during crop establishment but increased to about 3 at flowering. 195 ppmv CO2 reduced Kc, 780 ppmv increased it, but at 1560 ppmv it declined. Whole-season crop water use was 564 mm (195 ppmv), 719 mm (390 ppmv), 928 mm (780 ppmv) and 803 mm (1560 ppmv). With increasing [CO2], crop water use efficiency (WUE) gradually increased from 1.59 g kg-1 (195 ppmv) to 2.88 g kg-1 (1560 ppmv). Transpiration efficiency (TE) measured on flag leaves responded more strongly to [CO2] than WUE. Responses of some morphological traits are also reported. In conclusion, increased CO2 promotes biomass more than water use of irrigated rice, causing increased WUE, but it does not help saving water. Comparability with field conditions is discussed. The results will be used to train crop models.

Influence of Environmental Factors, Cultural Practices, and Herbicide Application on Seed Germination and Emergence Ecology of Ischaemum rugosum Salisb.

Ischaemum rugosum Salisb. (Saramolla grass) is a noxious weed of rice that is difficult to control by chemical or mechanical means once established. A study was conducted to determine the effect of light, temperature, salt, drought, flooding, rice residue mulch, burial depth, and pre-emergence herbicides on seed germination and emergence of I. rugosum. Germination was stimulated by light and inhibited under complete darkness. Optimum temperature for germination was 30/20°C (97.5% germination). Germination reduced from 31 to 3.5% when the osmotic potential of the growing medium decreased from -0.1 to -0.6 MPa and no germination occurred at -0.8 MPa. Germination was 18 and 0.5% at 50 and 100 mM NaCl concentrations, respectively, but was completely inhibited at 150 mM or higher. Residue application at 1-6 t ha-1 reduced weed emergence by 35-88% and shoot biomass by 55-95%. The efficacy of pre-emergence herbicides increased with increasing application rates and decreased with increasing rice residue mulching. The efficacy of herbicides was in the order of oxadiazon> pendimethalin> pretilachlor. At 6 t ha-1, all herbicides, regardless of rates, did not differ from the control treatment. I. rugosum seeds buried at 2 cm or deeper did not emerge; however, they emerged by 4.5 and 0.5% at 0.5 and 1 cm depths, respectively, compared to the 39% germination for soil surface seeding. Flooding at 4 DAS or earlier reduced seedling emergence and shoot biomass while flooding at 8 DAS reduced only seedling emergence. The depth and timing of flooding independently reduced root biomass. Flooding at 4 and 6 cm depths reduced the root biomass. Relative to flooding on the day of sowing, flooding at 8 DAS increased root biomass by 89%. Similarly, flooding on the day of sowing and at 2 DAS reduced the root-shoot biomass ratio. Under the no-flood treatment, increasing rates of pretilachlor from 0.075 to 0.3 kg ai ha-1 reduced weed emergence by 61-79%. At the flooding depth of 2-4 cm, pretilachlor reduced weed emergence and shoot and root biomass, but the differences across rates were non-significant. Information generated in this study will be helpful in developing integrated weed management strategies for managing this weed.

Influence of environmental factors on the germination of Urena lobata L. and its response to herbicides.

Urena lobata is becoming a noxious and invasive weed in rangelands, pastures, and undisturbed areas in the Philippines. This study determined the effects of seed scarification, light, salt and water stress, amount of rice residue, and seed burial depth on seed germination and emergence of U. lobata; and evaluated the weed's response to post-emergence herbicides. Germination was stimulated by both mechanical and chemical seed scarifications. The combination of the two scarification methods provided maximum (99%) seed germination. Germination was slightly stimulated when seeds were placed in light (65%) compared with when seeds were kept in the dark (46%). Sodium chloride concentrations ranging from 0 to 200 mM and osmotic potential ranging from 0 to -1.6 MPa affected the germination of U. lobata seeds significantly. The osmotic potential required for 50% inhibition of the maximum germination was -0.1 MPa; however, some seeds germinated at -0.8 MPa, but none germinated at -1.6 MPa. Seedling emergence and biomass increased with increase in rice residue amount up to 4 t ha(-1), but declined beyond this amount. Soil surface placement of weed seeds resulted in the highest seedling emergence (84%), which declined with increase in burial depth. The burial depth required for 50% inhibition of maximum emergence was 2 cm; emergence was greatly reduced (93%) at burial depth of 4 cm or more. Weed seedling biomass also decreased with increase in burial depth. Bispyribac-sodium, a commonly used herbicide in rice, sprayed at the 4-leaf stage of the weed, provided 100% control, which did not differ much with 2,4-D (98%), glyphosate (97%), and thiobencarb + 2,4-D (98%). These herbicides reduced shoot and root biomass by 99-100%.