Improving the phenotypic expression of rice genotypes:Rethinking “intensification” for production systems and selection practices for rice breeding

Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the management of rice plants, soil, water, and nutrients, reducing rather than increasing material inputs. Greater factor productivity can be achieved through the application of new knowledge and more skill, and(initially) more labor, as seen from the System of Rice Intensification(SRI), whose practices are used in various combinations by as many as 10 million farmers on about 4 million hectares in over 50 countries. The highest yields achieved with these management methods have come from hybrids and improved rice varieties, confirming the importance of making genetic improvements. However,unimproved varieties are also responsive to these changes, which induce better growth and functioning of rice root systems and more abundance, diversity, and activity of beneficial soil organisms. Some of these organisms as symbiotic endophytes can affect and enhance the expression of rice plants' genetic potential as well as their phenotypic resilience to multiple stresses, including those of climate change. SRI experience and data suggest that decades of plant breeding have been selecting for the best crop genetic endowments under suboptimal growing conditions, with crowding of plants that impedes their photosynthesis and growth, flooding of rice paddies that causes roots to degenerate and forgoes benefits derived from aerobic soil organisms, and overuse of agrochemicals that adversely affect these organisms as well as soil and human health. This review paper reports evidence from research in India and Indonesia that changes in crop and water management can improve the expression of rice plants' genetic potential, thereby creating more productive and robustphenotypes from given rice genotypes. Data indicate that increased plant density does not necessarily enhance crop yield potential, as classical breeding methods suggest. Developing cultivars that can achieve their higher productivity under a wide range of plant densities—breeding for density-neutral cultivars using alternative selection strategies—will enable more effective exploitation of available crop growth resources. Density-neutral cultivars that achieve high productivity under ample environmental growth resources can also achieve optimal productivity under limited resources, where lower densities can avert crop failure due to overcrowding. This will become more important to the extent that climatic and other factors become more adverse to crop production. Focusing more on which management practices can evoke the most productive and robust phenotypes from given genotypes is important for rice breeding and improvement programs since it is phenotypes that feed our human populations.     

Verification and evaluation of the “Three Optimums Theory”in rice breeding for maximum yield

Rice breeding for maximum yield is a hot topic today in the rice community of the world, and a hard nut to crack into the bargain. For many years, we have been devoted to the subject. In 1987 we discussed the subject in publications at home and abroad, in which we first introduced the general strategy of combining ideal plant morphology with the use of vigor. Afterward, drawing on the wisdoms of other researchers, we experimented with test materials featuring "rather short stalks" and "rather big panicles", but the results were not very satisfactory. Then, we switched from the "two rathers" to the "three optimums" (plant height, panicle size, and tillering ability). Three years' (1991-1993) verification, especially the demonstra     

Verification and evaluation of the ＂Three Optimums Theory＂ in rice breeding for maximum yield

Rice breeding for maximum yield is a hot topic today in the rice community of the world, and a hard out to crack into the bargain. For many years, we have been devoted to the subject. In 1987 we discussed the subject in publications at home and abroad,     

Genetic studies for breeding of rice cultivars with superior grain appearance and lodging resistance from the rice cultivar ‘Emi-no-kizuna’

ABSTRACT

We conducted a quantitative trait locus (QTL) analysis of grain appearance (GA) and agronomic traits of rice, using 128 recombinant inbred lines derived from ‘Emi-no-kizuna’ and ‘Tomohonami’. We detected two promising QTLs associated with GA: qGA4 on chromosome 4 and qGA8 on chromosome 8. qGA4 contributed highly to the greater percentage of perfect grains of the Emi-no-kizuna genotype. In the same region, we detected other QTLs associated with panicle number and spikelet number per panicle. In near-isogenic lines (NILs) in which Emi-no-kizuna alleles were introgressed in the genomic region of only the semi-dwarf 1 (sd1) locus (NIL_1) and both the sd1 locus and qGA8 (NIL_2), respectively, the percentage of perfect grains was significantly higher and the percentages of milky white, basal white, and white back grains were significantly lower than in Tomohonami; and the percentages of milky white and white back grains of NIL_2 were significantly lower than those of NIL_1. These results suggest that introgression in the sd1 region could improve GA, and that the addition of qGA8 could further improve GA. The culm lengths of the NILs were significantly shorter than that of Tomohonami, indicating improved lodging resistance. Grain weight of NIL_2 was significantly smaller than that of NIL_1, suggesting that the effect of qGA8 could be pleiotropic, or the gene that underlies qGA8 could be linked with genes associated with grain weight.

Abbreviations: ANOVA: analysis of variance; AT20: mean air temperature in the 20 days after heading; BW: basal white grain; CL: culm length; DAH: days after heading; GA: grain appearance; GW: 1000-grain weight; LOD: logarithm of odds; MW: milky white grain; NIL: near-isogenic line; PG: perfect grain; PL: panicle length; PN: panicle number; PTSN: putative total spikelet number; PVE: percentage of phenotypic variation explained; QTL: quantitative trait locus; RIL: recombinant inbred line; SN: spikelet number per panicle; SNP: single nucleotide polymorphism; WB: white back grain     

Considerations for the use of neonicotinoid pesticides in management of Bactericera cockerelli (Šulk) (Hemiptera: Triozidae)

Bactericera cockerelli is a pest on multiple solanaceous crop plants and is the sole vector for the bacteria Candidatus Liberibacter psyllaurous. When the pathogen is present, feeding by these psyllids results in ‘vein greening’ disease in peppers and tomatoes, and “zebra chip” disease in potatoes. Currently, management is based entirely on the application of pesticides, including two neonicotinoid compounds. Populations of B. cockerelli collected in southern Texas in 2006 and 2012 were examined for reduced susceptibility and behavioral responses to imidacloprid.Tests comparing imidacloprid and thiamethoxam demonstrated that both can reduce nymph numbers in the field, but retention and effective periods vary among application methods and compounds. In addition, imidacloprid and thiamethoxam are both sensitive to the amount of water applied during irrigation. Collectedly, these results suggest that imidacloprid is unlikely to be effective in controlling B. cockerelli in south Texas. Moreover, its use needs to be carefully considered in other locations even where resistance has not yet been detected. Finally, thiamethoxam may be useful, but careful attention must be paid to irrigation and rainfall level, application method, and timing of application.     

STS dataset of major parents in current breeding programs of rice (O. saliva L. subsp. indica)

Many major genes of agricultural importanceand quantitative trait loci (QTL) controllingyield components in rice have been mappedwith molecular markers. The genetic distancesbetween some of the genes and the markers areless than 5cM and the markers are on both     

Evaluation of rice accessions for resistance to the whitebacked planthopper Sogatella furcifera (Horváth) (Homoptera: Delphacidae)

Rice, Oryza sativa L., and wild rice accessions from the world collection were evaluated for resistance to the whitebacked planthopper, Sogatella furcifera (Horváth). Of 48554 O. sativa accessions from 96 countries, 401 (0·8%) were selected for resistance and 351 (88%) of these were from Nepal, India, and Pakistan where S. furcifera is a serious pest. However, some resistant accessions originated from regions beyond the distribution of S. furcifera. Many of the wild rice accessions, consisting of 28 species primarily from the O. minuta Presl., O. nivara Sharma et Shastry and O. officinalis Wall groups, were resistant. Although no S. furcifera-resistant commercial cultivars have been released, advanced breeding lines with resistance to S. furcifera and other major insect pests have been developed.     

Utilization of nuclear magnetic resonance (NMR) in the determination of water status on rice seeds

The relation between seed viability and waterstatus in seed was studied. The experimentwas carried out at Zhongshan University.Seeds of hybrid rice Shanyou 63 were collectedfrom Guangdong Academy of Agriculture Sci-ences in 1993 and then stored for one year inopen air or with silica gel. Before and afterstorage, the relative content of free water and     

Insecticide-induced changes in the levels of resistance of rice cultivars to the whitebacked planthopper Sogatella furcifera (Horváth) (Homoptera: Delphacidae)

IR2035-117-3 (highly resistant), ARC 10239 (resistant), and TN1 (susceptible) rice plants received one application at 40 days after transplanting (DT) or three spray applications (20, 30, and 40DT) of monocrotophos, diazinon or deltamethrin. When these plants were exposed to S. furcifera adults, either 24 hours after the single application, or 15 days after the third of the spray applications, the deltamethrin-treated were most preferred. The percentage of S. furcifera that alighted on the three varieties decreased correspondingly with an increase in the level of varietal resistance. Differences in S. furcifera population growth, nymphal survival, nymphal duration, growth index and feeding rate between IR2035-117-3 and TN1 were significant. Foliar application of deltamethrin caused a significant increase in population growth on IR2035-117-3, ARC 10239, and TN1 and an increase in the nymphal survival and growth index on TN1.     

Changing Phenology of Potato and of the Treatment for its Major Pest (Colorado Potato Beetle) – A Long-term Analysis

Potato Solanum tuberosum is one of the world’s four most important crops. Its cultivation is steadily increasing in response to the need to feed a growing world population. The yield of potato is influenced inter alia by both climate and pests. The main defoliator pest of potato is Colorado potato beetle Leptinotarsa decemlineata. Using data from a long-term experiment (1958–2013) in western Poland, we show that increasing temperature has affected the trophic relationship between potato and Colorado potato beetle. The planting, leafing, flowering and harvest dates for potato were advanced, after controlling for different cultivars, by 2.00 days, 3.04 days, 3.80 days and 3.42 days respectively for every 1 °C increase in temperature. In contrast, first treatment against Colorado potato beetle advanced by 4.66 days for every 1 °C increase in temperature, and, furthermore, the number of treatments against the beetle increased by 0.204 per 1 °C increase in temperature. This suggests that the beetle responds faster to increasing temperature than the plant does, but both parts of the system are probably greatly modified by farming practices.     

Effect of intermittent irrigation following the system of rice intensification (SRI) on rice yield in a farmer’s paddy fields in Indonesia

System of rice intensification (SRI) has been disseminated in many countries because of its high yield, although the mechanism of yield increase has yet to be fully understood. The aims of this study were to clarify the actual water management of a skilled SRI farmer in irrigated paddy field of Indonesia and to examine the effect of intermittent water management on rice growth and yield. Yield and yield components were compared in the field experiments in the farmer’s fields under intermittent (SRI) or flooded (FL) irrigation for 4 years from 2013 to 2016. The daily mean water depth of SRI plots during 0–40 days after transplanting showed very shallow (ca. 2 cm) or little lower than soil surface and continued to be lower than soil surface during reproductive stage when panicles were formed. The yield of SRI significantly exceeded that of FL for 4 years by 13% (P?=?0.0004), so did the panicle numbers per area (P?=?0.036). The yield increase in SRI was associated with the increased number of panicles, which should have resulted from enhanced tiller development under shallow water level during the vegetative stage. The increased number of panicles was, however, counteracted by the reduced number of spikelets per panicle and resulted in nonsignificant increase in the spikelet density, defined as number of spikelets per unit area of crop. This dampening change in spikelet number per panicle could have been caused by limited supply of either nitrogen or carbohydrate during the panicle development stage under the intermittent water supply. A greater yield increase by SRI could be expected by improving nutrient or water management during the reproductive stage.     

Mechanism of rice variety resistance to the yellow stem borer,Scirpophaga incertulas (Walker)

Yellow stem borer (YSB) , Scir-pophaga incertulas (Walker) has become the main rice insect pest once again along the Changjiang River since 1990s. Unfortunately, no rice variety with resistance to YSB has been reported so far. Japonica Zhen-dao 2 with moderate resistance to YSB was found. In 10 rice varieties with different resistance levels, YSB individuals showed distinct developmental rates, and the asynchronous development even occurred in the same rice variety. In this     

Mapping of QTL for salt tolerance in rice (Oryza sativa L. ) via molecular markers

A recombination inbred (RI) population wasdeveloped by single seed decent from a combi-     

Assessment of different methods of rice (Oryza sativa. L) cultivation affecting growth parameters, soil chemical, biological, and microbiological properties, water saving, and grain yield in rice–rice system

Field experiments were conducted at DRR farm located at ICRISAT, Patancheru, in sandy clay loam soils during four seasons, Kharif 2008, Rabi 2008–2009, Kharif 2009 and Rabi 2009–2010, to investigate growth parameters, water-saving potential, root characteristics, chemical, biological, and microbial properties of rhizosphere soil, and grain yield of rice (Oryza sativa L.) by comparing the plants grown with system of rice intensification (SRI) methods, with organic or organic + inorganic fertilization, against current recommended best management practices (BMP). All the growth parameters including plant height, effective tillers (10–45 %), panicle length, dry matter, root dry weight (24–57 %), and root volume (10–66 %) were found to be significantly higher with in SRI-organic + inorganic over BMP. With SRI-organic fertilization, growth parameters showed inconsistent results; however, root dry weight (3–77 %) and root volume (31–162 %) were found significantly superior compared to BMP. Grain yield was found significantly higher in SRI-organic + inorganic (12–23 and 4–35 % in the Kharif and Rabi seasons, respectively), while with SRI-organic management, yield was found higher (4–34 %) only in the Rabi seasons compared to BMP. An average of 31 and 37 % of irrigation water were saved during Kharif and Rabi seasons, respectively, with both SRI methods of rice cultivation compared to BMP. Further, total nitrogen, organic carbon%, soil dehydrogenase, microbial biomass carbon, total bacteria, fungi, and actinomycetes were found higher in the two SRI plots in comparison to BMP. It is concluded that SRI practices create favorable conditions for beneficial soil microbes to prosper, save irrigation water, and increase grain yield.     

Genetic expression and effects of the rolled leaf gene Rl(t) in hybrid rice (Oryza sativa L.)

We constructed a nearisogenic line of rolled leaf gene Rl(t), which ex-pressed incompletely dondnance for the character of rolled leaf(RL), with ge-netic background of Zhenshan 97B. Using RL Zhenshan 97B and the originalZhenshan 97B as the female parents, and Minghui 63 and Yanhui 559 as themale parents, crosses of RL Shanyu 63 (RS63) and Shanyu 63(S63), RLShanyou 559 (RS559) and Shanyou 559 (S559) were made. Inheritance andeffects of Rl(t) in hybrid rice were studied at the flowering and at the 20 d afterflowering, respectively. Results were as follow:     

Effect of day length and temperature on the pollen fertility in photo(thermo)-sensitive genic male-sterile rice

The effect of day length and temperature on the pollen fertility of five photoperiod-sensitive genic male-sterile japonica rice lines (PGMSR) and three temperature-sensitive genic malesterile indica rice lines (TGMSR) were investigated in phytotron. The light source used for illumination was xenon lamp, and the light intensity which plant accepted on the leaf surface was 300—350μmol photons m~(-2)s~(-1). The results indicated that pollens of PGMSR 7001S and E47S aborted completely whereas a little part of 31116S pollens appeared normal under long day photoperiod (LD,25℃,15h) (Table 1). High temperature (HT, 30℃, 12h) and lower temperature (LT,     

Ultrastructure and AcPase ultracytochemical localization of the abortive functional megaspores in intersubspecific F_1 hybrid rice(Oryza sativa)

Exploitation of the high yield potential intersubspecific heterosis has so far been hampered due to primarily the existence of high femalesterility. We have offered a cytological explanation for this abortion, such as the absence of embryo sacs or the occurrence of empty embryo sacs. Here we report the ultrastructural changes and ultracytochemical localization of acid phosphatase(AcPase) in the abortive functional megaspores. The F_1 hybrid was derived from a cross, Liaoqiu 5 (japonica)×Zhenjinzhen (indica), which showed high seed sterility in F_1 plants. The tissue prepared for enzyme ultracytochemicl study was fixed in 2.5% glutaraldehyde and 4% paraformaldehyde, incubated at 20℃ in the complete reaction medium of Barka-Anderson for 2h, post-fixed in 1% OsO_4 before ethanol-dehydration, infiltration and embedding in Epon 812. The sections, cut on. LKB-2088V ultramicrotome, were viewed and photographed, either unstained (in the case of AcPase localization) or double-stained with urayl acetate and lea     

Nuclear and chloroplast diversity and phenotypic distribution of rice (Oryza sativa L.) germplasm from the democratic people’s republic of Korea (DPRK; North Korea)

Background

Rice accounts for 43% of staple food production in the Democratic People’s Republic of Korea (DPRK). The most widely planted rice varieties were developed from a limited number of ancestral lines that were repeatedly used as parents in breeding programs. However, detailed pedigrees are not publicly available and little is known about the genetic, phenotypic, and geographical variation of DPRK varieties.

Results

We evaluated 80 O. sativa accessions from the DPRK, consisting of 67 improved varieties and 13 landraces. Based on nuclear SSR analysis, we divide the varieties into two genetic groups: Group 1 corresponds to the temperate japonica subpopulation and represents 78.75% of the accessions, while Group 2 shares recent ancestry with indica varieties. Interestingly, members of Group 1 are less diverse than Group 2 at the nuclear level, but are more diverse at the chloroplast level. All Group 2 varieties share a single Japonica maternal-haplotype, while Group 1 varieties trace maternal ancestry to both Japonica and Indica. Phenotypically, members of Group 1 have shorter grains than Group 2, and varieties from breeding programs have thicker and wider grains than landraces. Improved varieties in Group 1 also show similar and/or better levels of cold tolerance for most traits, except for spikelet number per panicle. Finally, geographic analysis demonstrates that the majority of genetic variation is located within regions that have the most intensive rice cultivation, including the Western territories near the capital city Pyungyang. This is consistent with the conscious and highly centralized role of human selection in determining local dispersion patterns of rice in the DPRK.

Conclusions

Diversity studies of DPRK rice germplasm revealed two genetic groups. The most widely planted group has a narrow genetic base and would benefit from the introduction of new genetic variation from cold tolerant landraces, wild accessions, and/or cultivated gene pools to enhance yield potential and performance.     

Chemical changes during the fermentation of African locust-bean (Parkia filicoidea Welw) seeds for production of ‘Daddawa’

African locust-bean (Parkia filicoidea Welw) seeds were allowed to ferment under natural conditions and the chemical changes occurring during the fermentation were studied. Chemical analysis of fermented and unfermented beans showed a marked decrease in the total sugar content; crude and true protein levels all increased. The results of the chemical analyses indicate that fermentation resulted in protein enrichment of the fermented locust bean (daddaw). Fermentation also imparts a characteristic flavour and odour to the beans.     

Interpreting the Possible Ecological Role(s) of Cyanotoxins: Compounds for Competitive Advantage and/or Physiological Aide?

To date, most research on freshwater cyanotoxin(s) has focused on understanding the dynamics of toxin production and decomposition, as well as evaluating the environmental conditions that trigger toxin production, all with the objective of informing management strategies and options for risk reduction. Comparatively few research studies have considered how this information can be used to understand the broader ecological role of cyanotoxin(s), and the possible applications of this knowledge to the management of toxic blooms. This paper explores the ecological, toxicological, and genetic evidence for cyanotoxin production in natural environments. The possible evolutionary advantages of toxin production are grouped into two main themes: That of “competitive advantage” or “physiological aide”. The first grouping illustrates how compounds produced by cyanobacteria may have originated from the need for a cellular defence mechanism, in response to grazing pressure and/or resource competition. The second grouping considers the contribution that secondary metabolites make to improved cellular physiology, through benefits to homeostasis, photosynthetic efficiencies, and accelerated growth rates. The discussion also includes other factors in the debate about possible evolutionary roles for toxins, such as different modes of exposures and effects on non-target (i.e., non-competitive) species. The paper demonstrates that complex and multiple factors are at play in driving evolutionary processes in aquatic environments. This information may provide a fresh perspective on managing toxic blooms, including the need to use a “systems approach” to understand how physico-chemical conditions, as well biological stressors, interact to trigger toxin production.