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The area of dry-season rice (Oryza sativa L.) has rapidly increased in Cambodia owing to the large-scale development of irrigation infrastructure. But little is known of potential productivity and adaptive crop management. The objective of our study was to evaluate potential yield and nutrient requirements of dry-season rice in Cambodia, and the economic feasibility of soil-specific management recommended by the government. Field experiments were conducted on four soil types (Bakan, equivalent to Alfisol; Krakor, Inceptisol; Prateah Lang, Plinthustalfs; and Toul Samroung, Endoaqualfs) in four provinces (Battambang, Kampong Thom, Pursat, and Siem Reap) during the 2016 and 2017 dry seasons to compare 14 (2016) and 8 (2017) N-P-K combinations. Grain yield ranged from 1.0 to 5.5 t ha−1 in 2016 and from 1.3 to 6.7 t ha−1 in 2017. Potential yield from the experiments was 6–7 t ha−1 on Toul Samroung soil, 5–6 t ha−1 on Bakan soil, and 3–5 t ha−1 on Prateah Lang and Krakor soils. A rate of 140-60-60 kg ha−1 of N-P2O5-K2O was more than enough to achieve the best yields on any soil group. On the other hand, modest application rates in soil-specific management (44–78 kg ha−1 of N, 23–28 kg ha−1 of P2O5, 0–30 kg ha−1 of K2O) proved reasonable for resource-poor farmers in Cambodia, since the treatment always provided >75 % of the highest economic profit in high-input plots.

Rice is widely grown in rainfed lowlands during the wet season in the Mekong region. Limited nutrient availability is a common constraint on crop yield, and the optimal rate of fertilizer application depends on the soil type. The objective of our study was to evaluate rice productivity and the economic feasibility of various nutrient management regimes in Cambodia. We conducted field experiments on three soil types (Prey Khmer, Prateah Lang, and Toul Samroung, equivalent to Psamments, Plinthustalfs, and Endoaqualfs, respectively) in four provinces (Battambang, Kampong Thom, Pursat, and Siem Reap) during the 2016 and 2017 wet seasons to compare nine (2016) and seven (2017) N–P–K combinations. Grain yield ranged from 0.9 to 4.8 t ha−1 in 2016 and from 1.0 to 5.2 t ha−1 in 2017, depending on soil type and nutrient management. The Prey Khmer soil contained around 80% sand, and rice yield responded most weakly to nutrient management. The moderate fertilizer input in the current soil-specific recommendation was effective on this soil type. However, on more fertile soils with a higher clay content and a higher cation-exchange capacity (Toul Samroung and Prateah Lang), an additional 20 kg N ha−1 combined with adding 15 kg ha−1 of P2O5 or 20 kg ha−1 of K2O significantly increased yield and economic return. Although P and K use during Cambodia’s wet season is uncommon, our results demonstrate the importance of these nutrients in improving the country’s rice production.

Levels of gene expression underpin organismal phenotypes1,2, but the nature of selection that acts on gene expression and its role in adaptive evolution remain unknown1,2. Here we assayed gene expression in rice (Oryza sativa)3, and used phenotypic selection analysis to estimate the type and strength of selection on the levels of more than 15,000 transcripts4,5. Variation in most transcripts appears (nearly) neutral or under very weak stabilizing selection in wet paddy conditions (with median standardized selection differentials near zero), but selection is stronger under drought conditions. Overall, more transcripts are conditionally neutral (2.83%) than are antagonistically pleiotropic6 (0.04%), and transcripts that display lower levels of expression and stochastic noise7–9 and higher levels of plasticity9 are under stronger selection. Selection strength was further weakly negatively associated with levels of cis-regulation and network connectivity9. Our multivariate analysis suggests that selection acts on the expression of photosynthesis genes4,5, but that the efficacy of selection is genetically constrained under drought conditions10. Drought selected for earlier flowering11,12 and a higher expression of OsMADS18 (Os07g0605200), which encodes a MADS-box transcription factor and is a known regulator of early flowering13—marking this gene as a drought-escape gene11,12. The ability to estimate selection strengths provides insights into how selection can shape molecular traits at the core of gene action. Phenotypic selection analysis is used to estimate the type and strength of selection that acts on more than 15,000 transcripts in rice (Oryza sativa), which provides insight into the adaptive evolutionary role of selection on gene expression.

Background Salinity has a significant impact on rice production in coastal, arid and semi-arid areas in many countries, including countries growing temperate rice, such as Kazakhstan. Recently, the complete genomes of 3000 rice accessions were sequenced through the 3 K rice genome project, and this set included 203 temperate japonica rice accessions. To identify salinity-tolerant germplasm and related genes for developing new salinity-tolerant breeding lines for the temperate japonica rice growing regions, we evaluated the seedling stage salinity tolerance of these sequenced temperate japonica rice accessions, and conducted genome-wide association studies (GWAS) for a series of salinity tolerance related traits. Results There were 27 accessions performed well (SES

Rice ( Oryza sativa L.) provides a life support system to millions of resource-poor farmers in rainfed environments; however, yields are very low because of various biotic and abiotic stresses. Submergence caused by typhoons and floods is one of the major reasons for production losses. Because of the complexity of these ecosystems, the breeding framework necessitates adequate feedback and a more in-depth understanding of the ecological and socioeconomic conditions in these flood-prone areas. Within this purview, this study validated the performance in farmers’ fields of lines with the SUB1 gene that confers tolerance of submergence for up to two weeks. The SUB1 gene was incorporated through marker-assisted backcrossing, MABC. The evaluation was conducted through participatory approaches to gain understanding of the risks as well as farmers’ preferences for these varieties. A baseline survey of 658 farm households accomplished during 2008, focus group discussions, key informant interviews, and adaptability trials were conducted, with focus on farmers commonly affected by submergence in four Southeast Asian countries: the Philippines, Lao PDR, Indonesia, and Southern Viet Nam. The study further examined farmers’ criteria in evaluating new varieties through the participatory varietal selection (PVS) process. Results showed that varying conditions of submergence can influence farmers’ criteria and preferences for rice cultivars. Depending on the timing of flood with respect to growth stage, shorter duration and shallow flashfloods can result in less than 10% production losses while deeper and stagnant water with two weeks’ duration and >100 cm depth can cause damage ranging from 40% to 77%. Major findings of PVS trials and preference analysis indicated that farmers prefer rice cultivars that are tolerant of submergence, have early to medium maturity relative to their commonly grown varieties, are resistant to pests and diseases, and are resistant to lodging, among other traits. To enhance adoption, male and female farmers should be involved in the evaluation process. The results of this study can contribute to enhancing breeding programs to develop appropriate varieties that reduce production losses, improve income, and ultimately reduce poverty incidence in submergence-prone areas.

†Background and Aims Flooding slows seed germination, imposes fatalities and delays seedling establishment in direct-seeded rice. This study describes responses of contrasting rice genotypes subjected to flooding or low oxygen stress during germination and discusses the basis of tolerance shown by certain cultivars. †Methods In one set of experiments, dry seeds were sown in soil and either watered normally or flooded with 10 cm of water. Seedling survival and shoot and root growth were assessed and seed portions of germinating seedlings were assayed for soluble sugars and starch concentrations. The whole germinating seedlings were assayed for amylase and peroxidase activities and for ethylene production. Activities of enzymes associated with anaerobic respiration were examined and gene expression was analysed separately with seeds germinating under different amounts of dissolved oxygen in dilute agar. †Key Results Flooding during germination reduced survival but to a lesser extent in tolerant genotypes. Starch concentration in germinating seeds decreased while sugar concentration increased under flooding, but more so in tolerant genotypes. Amylase activity correlated positively with elongation (r ¼ 0.85 for shoot and 0.83 for root length) and with plant survival (r ¼ 0.92). Tolerant genotypes had higher amylase activity and higher RAmy3D gene expression. Ethylene was not detected in seeds within 2 d after sowing, but increased thereafter, with a greater increase in tolerant genotypes starting 3 d after sowing. Peroxidase activity was higher in germinating seeds of sensitive genotypes and correlated negatively with survival. †Conclusions Under low oxygen stress, tolerant genotypes germinate, grow faster and more seedlings survive. They maintain their ability to use stored starch reserves through higher amylase activity and anaerobic respiration, have higher rates of ethylene production and lower peroxidase activity as germinating seeds and as seedlings. Relevance of these traits to tolerance of flooding during germination and early growth is discussed.

†Background and Aims Submergence is a recurring problem in the rice-producing rainfed lowlands of south and south-east Asia. Developing rice cultivars with tolerance of submergence and with agronomic and quality traits acceptable to farmers is a feasible approach to address this problem. The objectives of this study were to (a) develop mega varieties with Sub1 introgression that are submergence tolerant, (b) assess the performance of Sub1 in different genetic backgrounds, (c) determine the roles of the Sub1A and Sub1C genes in conferring tolerance, and (d) assess the level of tolerance in F1 hybrids heterozygous for the Sub1A-1-tolerant allele. †Methods Tolerant varieties were developed by marker-assisted backcrossing through two or three backcrosses, and their performance was evaluated to determine the effect of Sub1 in different genetic backgrounds. The roles of Sub1A and Sub1C in conferring the tolerant phenotype were further investigated using recombinants identified within the Sub1 gene cluster based on survival and gene expression data. †Key Results All mega varieties with Sub1 introgression had a significantly higher survival rate than the original parents. An intolerant Sub1C allele combined with the tolerant Sub1A-1 allele did not significantly reduce the level of tolerance, and the Sub1C-1 expression appeared to be independent of the Sub1A allele; however, even when Sub1C-1 expression is completely turned off in the presence of Sub1A-2, plants remained intolerant. Survival rates and Sub1A expression were significantly lower in heterozygotes compared with the homozygous tolerant parent. †Conclusions Sub1 provided a substantial enhancement in the level of tolerance of all the sensitive mega varieties. Sub1A is confirmed as the primary contributor to tolerance, while Sub1C alleles do not seem important. Lack of dominance of Sub1 suggests that the Sub1A-1 allele should be carried by both parents for developing tolerant rice hybrids.

Submergence stress regularly affects 15 million hectares or more of rainfed lowland rice areas in South and Southeast Asia. A major QTL on chromosome 9, Sub1, has provided the opportunity to apply marker assisted backcrossing (MAB) to develop submergence tolerant versions of rice cultivars that are widely grown in the region. In the present study, molecular markers that were tightly linked with Sub1, flanking Sub1, and unlinked to Sub1 were used to apply foreground, recombinant, and background selection, respectively, in backcrosses between a submergence-tolerant donor and the widely grown recurrent parent Swarna. By the BC(2)F(2) generation a submergence tolerant plant was identified that possessed Swarna type simple sequence repeat (SSR) alleles on all fragments analyzed except the tip segment of rice chromosome 9 that possessed the Sub1 locus. A BC(3)F(2) double recombinant plant was identified that was homozygous for all Swarna type alleles except for an approximately 2.3-3.4 Mb region surrounding the Sub1 locus. The results showed that the mega variety Swarna could be efficiently converted to a submergence tolerant variety in three backcross generations, involving a time of two to three years. Polymorphic markers for foreground and recombinant selection were identified for four other mega varieties to develop a wider range of submergence tolerant varieties to meet the needs of farmers in the flood-prone regions. This approach demonstrates the effective use of marker assisted selection for a major QTL in a molecular breeding program.

Bentgrasses (Agrostis spp.) are widely occurring temperate grasses with more than 220 species that represent a vast resource for genetic improvement of turfgrass cultivars. Bentgrasses are normally outcrossing species and exhibit many ploidy levels. Difficulties in morphological characterization, which are largely subjected to environmental influences, have resulted in many synonymous species and uncertainties in phylogenetic relationships. To study the genetic diversity and relationships between bentgrass species, 40 accessions from the USDA's germplasm collection representing 14 species of Agrostis from twenty countries were investigated by fluorescence-labeled amplified fragment length polymorphism (AFLP) analysis. Four hundred AFLP markers from five chosen primer combinations were used to differentiate between bentgrass accessions of a bulk of 25 genotypes per accession. Genetic similarities between accessions ranged from 0.62 to 0.98 showing no duplication in the collection and a high level of diversity in Agrostis. Both principal component analysis and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram clearly distinguished seven groups. Genetic relationships between diploids and other polyploids were revealed in the cluster groupings.

Direct seeding is replacing transplanting in rice. Early flooding suppresses weeds but selective action is compromised by the sharing of flood-tolerance traits. Understanding adaptive traits in both species is therefore a prerequisite for developing direct seeding systems that control weeds while leaving rice seedlings relatively unharmed., Background and aims Direct seeding of rice is being adopted in rainfed and irrigated lowland ecosystems because it reduces labour costs in addition to other benefits. However, early flooding due to uneven fields or rainfall slows down seed germination and hinders crop establishment. Conversely, early flooding helps suppress weeds and reduces the costs of manual weeding and/or dependence on herbicides; however, numerous weed species are adapted to lowlands and present challenges for the use of flooding to control weeds. Advancing knowledge on the mechanisms of tolerance of flooding during germination and early growth in rice and weeds could facilitate the development of improved rice varieties and effective weed management practices for direct-seeded rice. Principal results Rice genotypes with a greater ability to germinate and establish in flooded soils were identified, providing opportunities to develop varieties suitable for direct seeding in flooded soils. Tolerance of flooding in these genotypes was mostly attributed to traits associated with better ability to mobilize stored carbohydrates and anaerobic metabolism. Limited studies were undertaken in weeds associated with lowland rice systems. Remaining studies compared rice and weeds and related weed species such as Echinochloa crus-galli and E. colona or compared ecotypes of the same species of Cyperus rotundus adapted to either aerobic or flooded soils. Conclusions Tolerant weeds and rice genotypes mostly developed similar adaptive traits that allow them to establish in flooded fields, including the ability to germinate and elongate faster under hypoxia, mobilize stored starch reserves and generate energy through fermentation pathways. Remarkably, some weeds developed additional traits such as larger storage tubers that enlarge further in deeper flooded soils (C. rotundus). Unravelling the mechanisms involved in adaptation to flooding will help design management options that will allow tolerant rice genotypes to adequately establish in flooded soils while simultaneously suppressing weeds.

Randomly amplified polymorphic DNA (RAPD) markers were used to assess the genetic diversity of isolates of grey snow mould ('gray snow mold'), Typhula incarnata, taken from infected turfgrasses from 40 different locations in the northern USA. Data from 115 markers using 37 RAPD primers showed 48 % polymorphism. The distance coefficients between isolates indicate the wide genetic diversity of T. incarnata across the sample area. Dendrograms generated using neighbour-joining (NJ) bootstrap analyses showed three clades and suggest possible recent colonization from common founder groups. Partitioning of the genetic variance using analysis of molecular variance (AMOVA) of four groups based on geographic locations (Michigan, lower and upper peninsula; Minnesota; Wisconsin) showed that genetic variation attributable among groups and within groups was 12.67 and 87.33 %, respectively. No correlation was found between geographic distance and pairwise genetic distance of the groups. High outcrossing and sexual recombination of T. incarnata may well be key factors explaining the genetic variability as shown with the low Fixation index (FST) and high average of genetic diversity per locus within groups.

The turf industry in the last decade has seen doubling in number of new creeping bentgrass [Agrostis stolonifera var. palustris (Huds.) Farw. and A. stolonifera var. stolonifera Huds.] cultivars, many with unknown variability and lineage. Understanding the genetic diversity of putative parental and wild stocks would be useful in plant breeding programs. Amplified fragment length polymorphism (AFLP) analysis was conducted to investigate genetic variability among old and new cultivars of creeping bentgrasses, redtop bentgrasses (Agrostis gigantea Roth), plant introductions, and selected creeping bentgrass genotypes with resistance to gray snow mold (Typhula incarnata Lasch). Seven chosen primer combinations resulting in 355 polymorphic markers were used to differentiate the bentgrasses. Three groups were extracted by principal component analysis (PCA). With unweighted pair group method with the arithmetic mean (UPGMA) analysis, mean similarity coefficients of creeping bentgrass genotypes found in the first group was 0.78. Creeping bentgrasses in the USA were clustered as a subgroup and separated from European plant introductions, indicating that most selection and genetic exchanges in the last fifty years have evolved locally. Redtop bentgrasses were the most diverse and were found in different groups. Selected lines from northern Michigan, MI 20104, MI 20215, and MI 203164, were well differentiated from the other cultivars and would be advantageous to use as sources of disease-resistant traits and for development of populations for future gene mapping.