Resource management of a small-sized cyprinid population in an isolated small stream based on i

The indigenous cyprinid Rasbora rubrodorsalis is widely distributed in agricultural water masses (e.g., irrigation canals) of various Indochinese countries including Laos. This species is small-sized (max. ca. 30 mm), occurs abundantly in remote rural areas of hilly/mountainous regions, and is an important food resource in the area. In recent years, however, settlements and habitat expansion of invasive alien fishes as well as agricultural exploitation / urbanization in such areas are becoming a concern, possibly causing the decline in species diversity/stock level of indigenous fishes. This situation necessitates the acquisition of ecological information conducive to the species’ resource management.

The following ecological features and relevant findings were obtained in the present study.

1. ) The sex ratio of Rasbora rubrodorsalis is remarkably biased towards females (male : female = 0.43 : 1), and the females grow larger than males in size (figure omitted).
2. ) Mature female occurrence ratio increases with seasonal day-length extension (figure omitted), and breeding is more active during high-temperature period (March to October). However, mature females also occur even during low-temperature period (November to February), indicating that the species breed throughout the year (Fig. 2). Maturation sizes of females are > 20 mm SL and > 23 mm SL during high- and low-temperature periods, respectively (Fig. 2), and the maturation ages (in days) were estimated to be 50 and 80 days during high- and low-temperature periods, respectively (Fig. 3).
3. ) Longevities were estimated to be 150 days in females and 100 days in males (Fig. 3); therefore, plural generation alternations are considered to occur within a year.
4. ) Seasonal fishing control is considered not efficient for stock management of the species due to its short longevity. Although the upward migration of the species over the small waterfall located at the mid-stream is considered impossible because of limited swimming ability, stock provision from upstream to downstream areas is highly possible insofar as upstream breeding population is well conserved. Hence, continuous fishing in the downstream area concurrent with fishing prohibition in the upstream area is strongly recommended for the conservation of the breeding population and is contributory to both sustainable fisheries and species conservation (Fig. 4).

In addition to the above, environmental conservation is also indispensable for realizing the above-mentioned method for species conservation. Furthermore, considering the deterioration of genetic diversity as observed in the sympatric cyprinid Esomus metallicus and the ambassid Parambassis siamensis probably due to the geographical isolation, such deterioration may also be occurring in the Rasbora rubrodorsalis population. Genetic soundness, therefore, needs to be examined by micro-satellite DNA marker analysis.

(S. Morioka, N. Koizumi [National Institute of Rural Engineering], B. Vongvichith [Living Aquatic Resources Research Center])

Fig. 1. Laotian indigenous cyprinid Rasbora rubrodorsalis (adult, 24.3 mm SL)

Fig. 2. Relationship between standard length and gonad somatic index in female
Rasbora rubrodorsalis both in warmer and colder periods

Fig. 3. Growth models of female and male Rasbora rubrodorsalis （fitted by Gompertz growth curves)

Fig. 4. Schematic drawing of the stream investigated in this study and the suggested year-round no-fishing area and continual fishing area for Rasbora rubrodorsalis

For further details log on website :

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Economic benefits of various non-timber forestry products to Lao PDR’s farm economy (PDF A4:328KB A3:

Agriculture in Laos is primarily rain-dependent due to its tropical monsoon climate. Farmlands are often subjected to droughts and floods, rendering crop production unstable. Therefore, in addition to rice cultivation, Laotian farmers collect non-timber forestry products (NTFPs) in mountainous areas, thus providing a safety net to local residents in terms of livelihood support. To understand the actual utilization of NTFPs and its contribution to rural household economies, a study was conducted on all 140 households (104 valid responses) in a farming village in the northwestern part of Vientiane Province from July 2012 through June 2013, recording each day the types and quantities of NTFPs collected as well as their intended uses. To determine the economic values, a price table was created, with each NTFP's trade price multiplied by its trade value and then converted to a monetary amount.

Over 400 diverse types of NTFPs, including 289 plant-type products (such as mushrooms) in addition to 124 animal-type products, were utilized. Excluding the types of NTFPs categorized as textiles, resins, and medicines, over 90 percent of NTFPs were used by the collecting households and mostly consumed as food. Out of 24 mushroom-type NTFPs, which are easily influenced by the forest environment, nine types accounted for 90% of collected amounts. Of these, five types are collected during rainy season, whereas one type, Lentinus polychrous (Lao name: Hed bot), is collected during dry season (Fig. 1). Mushrooms are, therefore, valuable sources of food that are collected throughout the year.

NTFPs categorized as textiles, resins, and medicines were collected for sale, and of these, approximately eight tons (dry weight) of textiles were collected (Fig. 1). The majority of these NTFPs were summer cypress, from which flower clusters are collected to make products such as brooms. Summer cypress appears in fallow land after slashing and burning and can be collected in great quantity for the first three years. It is also a valuable source of income between periods of farming.

The economic value was estimated at 5,480,000 kip (broken down into 3,820,000 kip from plant types and 1,660,000 kip from animal types) (Fig. 1). This equates to approximately 2.4 tons of glutinous rice, enough to feed 9.6 people (at 250 kg/person/year) and contributing greatly to the rural economy.

This study is important towards understanding the subsistence strategies of area residents in Laos over a full year. It can also be used as a basis for implementing safeguards, including the protection of indigenous peoples/ area residents and the maintenance of species diversity, by institutions that implement rural development programs and forest preservation programs such as participatory forest management. Lastly, it provides concrete data on NTFPs, as identified in forestry strategies by Laotian government organizations such as the Agriculture and Forestry Office and the Ministry of Natural Resources and Environment.

(K. Kimura, S. Kobayashi, R. Yoneda,
S. Xayalath [Forest Sciences Research Center], B. Khampumi [FSRC] )

Table 1. Number of NTFPs, amount, economic value, purpose of collection, and main products based on the attributes of NTFPs collected

Fig. 1. Monthly collection for each type of mushroom

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Identification of QTL for efficient root elongation under a wide range of nitrogen concentrations in a rice variety with an Indica-type genetic background (PDF A4:161KB A3:81 KB)

Because root is the sole organ for uptaking water and nutrients such as nitrogen from surrounding soils, improving root architecture and physiological functions are required for enhancing stability and production in rice. IR64, an elite Indica-type variety with high adaptability and high yield, has been widely accepted as a mega variety in rice production and breeding programs in many tropical regions. The International Rice Research Institute—Japan Collaborative Research Project has developed a total of 334 introgression lines (ILs) derived from ten high yielding donor varieties with the genetic background of IR64. Among them, a line designated as YTH183 showed stable and higher yield in tropical regions as well as in temperate regions compared with IR64. However, quantitative trait locus/loci (QTL) for the stable and higher yielding line have not been identified. Furthermore, QTL for root elongation efficiently under a wide range of nitrogen concentrations have not been identified in varieties with the genetic background of IR64. The aims of this study, therefore, were to map and characterize the QTL derived from YTH183 to understand the architecture and functions of roots in YTH183.

The longest root of YTH183 was significantly higher than that of IR64 seedlings hydroponically grown for 8 days in 5 μM NH₄Cl (Fig. 1). As a result, YTH183 had a QTL for root elongation, designated as qRL6.4-YP5. The longest root of near-isogenic line (NIL) for qRL6.4-YP5 with the genetic background of IR64 was significantly higher than that of IR64 (Fig. 1). The QTL qRL6.4-YP5 (R²=0.37) was identified in the flanked region between RM6395 and RM8242 on the long-arm region of chromosome 6 (Fig. 2). Further characterization of qRL6.4-YP5 was done using the NIL. Compared with IR64, total root length was always higher in the NIL and was enhanced in response to the increase in exogenous concentrations of nitrogen (Table 1). The length of the longest root was always higher in the NIL. It was enhanced under nitrogen concentrations of up to 50 μM NH₄Cl, but not in 500 μM NH₄Cl (Table 1). The effect of qRL6.4-YP5 on root number was not proven in these conditions (Table 1).

To our knowledge, qRL6.4-YP5 is the first promising QTL for efficient root elongation under a wide range of nitrogen concentrations in rice varieties with the genetic background of IR64. These achievements should help improve root architecture of rice for a stable and high yielding production system in tropical developing countries.

(M.Obara, T. Ishimaru, T. Abiko [Kyushu University], D. Fujita[Kyushu University], N. Kobayashi[NARO-NICS], S. Yanagihara, Y. Fukuta)

Fig. 1. Typical phenotypes of seedlings grown for 8 days in 5 μM NH₄Cl. YTH183 and NIL have positive allele of qRL6.4-YP5. Scale bar in individual pictures indicates 50 mm.

Fig. 2. Physical position of qRL6.4-YP5 on the long-arm region of chromosome 6. Closed vertical column indicates candidate region for qRL6.4-YP5. Closed triangle indicates the position of the peak F score.

Table 1. Elongation and development of roots in NIL for qRL6.4-YP5 under a wide range of nitrogen concentrations

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Variation at the Pup1 locus within the genus Oryza predates domestication (PDF A4:248KB A3:255 KB)

The deficiency of phosphorus (P) in soil is a worldwide problem, and though there are many approaches to tackle this problem, the development of rice cultivars with enhanced P efficiency would represent a sustainable strategy to improve the livelihood of resource-poor farmers. Recently, the Pup1 locus (Fig. 1), a major QTL for tolerance to P deficiency, was successfully narrowed down to a single-candidate gene, the protein kinase: P starvation tolerance (OsPSTOL1). The aim of this study was to search for novel OsPSTOL1 alleles and to survey Pup1 locus variation in Asian (O. sativa)- and African (O. glaberrima)-cultivated rice and their wild progenitors. This information would help in designing a suitable strategy for marker-assisted introgression of Pup1/PSTOL1 into rice megavarieties.

A novel OsPSTOL1 allele was detected in O. glaberrima. This allele has 35 base-pair changes (when aligned to Kasalath allele), but none of the functional domains were affected and it is expressed. Allele-specific markers were then developed for single PCR and/or duplex PCR system, which produce a band pattern clearly distinguishable on agarose gels (Fig. 2), and are therefore suitable for most marker laboratories throughout the world. Using these markers to survey allelic distribution of PSTOL1 across the genus Oryza showed that the novel allele is common in accessions belonging to O. glaberrima and its ancestor O. bartii, but is not restricted to African rice as O. sativa, O. rufipogon, and O. nivara accessions do carry the glaberrima allele at low frequency (Fig. 1).

Using additional allele-specific markers across the entire Pup1 locus revealed two main patterns in the Africa rice (O. glaberrima and O. barthii): the more typical ‘Africa pattern’ characterized by the novel PSTOL1 allele and partial presence of the Pup1-specific INDEL region, but general absence of 90 kb of a region upstream of PSTOL1 (pattern G, Fig. 1); and the less common pattern (K) with Kasalath alleles across most of Pup1. Within O. sativa, the Kasalath (K) and Nipponbare (N) patterns could be distinguished as described earlier, but in addition a mixed pattern (m) with partial presence of Kasalath, O. glaberrima, and novel alleles was detected. These three patterns were already present in O. rufipogon and O. nivara, the wild ancestors of O. sativa. Results suggested that Pup1 locus variation was already a common feature within wild ancestors of cultivated Asian and African rice. Thus, divergence at Pup1 appears to predate domestication of rice.

Since the function of other genes within the Pup1 locus remains unclear, it would be desirable to transfer the entire Pup1 region from Kasalath into recipient varieties during marker-assisted selection. Thus, we propose using two foreground markers (K46-K and K20-K) in breeding programs aimed at introgressing Pup1.

(M. Wissuwa, J.Pariasca-Tanaka, JH. Chin [IRRI], NK. Drame [Africa Rice])

Fig. 1. Characterization of the Pup1 locus in Nipponbare and Kasalath, and cultivated and wild rice genotypes. A main difference is the absence of a 90 kb INDEL region in Nipponbare containing OsPSTOL1 and 20 other Kasalath-specific genes.

Fig. 2. Amplification of OsPSTOL1 alleles using allele-specific markers for Kasalath and CG14 in single PCR (A), and duplex PCR system to detect both alleles in one reaction (B).
(1: CG14, 2: IRAT, 3: NERICA16, 4: WAB56-50, 5: NERICA1, 6: NERICA10, 7: WAB181-18, 8: IDSA,
9: IR12979, 10: WAB56-104, 11: IAC165, 12: Nipponbare, 13: Kasalath)

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Low night temperature inhibits fertilization and consequently reduces fruit set in ‘Mon

Durian flowers mainly in January in Chanthaburi, the main production area in Thailand. Chanthaburi’s average minimum temperature for January is 20.7°C (10-year average); however, in 2014, the daily minimum temperature dropped to lower than 15°C for the first time in five years, with record-low temperatures (below 17°C) lasting about a week. Usually, durian trees set fruits at 15-30%; however, the fruit set was quite poor that year especially for ‘Monthong’, the leading cultivar in Thailand. Empirical observations have shown that ‘low temperature’ during anthesis reduces fruit set, but the effect of low temperatures on the development of fruit set in durian is not fully understood because the trees grow very high in the fields where environmental factors, such as temperature, are difficult to control.

In this study, we developed a temperature controller that can be used in the orchard, and we examined the effect of night temperature on fruit set. Morphological development of ovules was also observed and its influence on fruit set was evaluated.

A polystyrene foam box equipped with Peltier devices was attached to a bearing branch to enclose one cluster (Fig. 1). The temperature inside the box was fixed at 15°C or 25°C during nighttime (2000 to 0800h) for 7 days after pollination (DAP). The box was detached after the 7th day. At 25°C, about 30% of the flowers set fruits at 28 DAP, whereas all flowers abscised by 21 DAP at 15°C (Fig. 2). Pollen tubes elongated within the styles in both 15°C and 25°C. However, at 15°C, 14.7% of ovules remained at the mature stage (Fig. 3A, Table1), which is the normal stage before accepting pollen-tube nucleus. No mature ovules were found at 25°C. On the other hand, 22.7% of ovules proceeded to the endosperm nuclei division stage at 25°C (Fig. 3B, Table 1). No endosperm-nuclei-division ovules were found at 15°C. Endosperm nuclei are the result of fertilization; therefore, it was considered that fertilization occurred at 25°C but did not occur at 15°C. The average length of the ovule at 15°C was considerably shorter than the one at 25°C (Table 1).

These findings suggest that night temperature of 15°C inhibits fertilization and consequently causes poor fruit set in ‘Monthong’ durian. ‘Monthong’ is the most important cultivar in Thailand; however, the fruit set is easily affected by night temperatures. To avoid risk caused by low temperature, planting other cultivars besides ‘Monthong’ or applying plant growth regulators to extend the flowering period is recommended. Adaptation of other cultivars that set fruits at low temperature conditions is also an effectual way for the stable production of durian. In this regard, the temperature controller we have developed can be a useful tool for examining cultivars that set fruit even at low-temperature conditions.

(N. Kozai, T. Ogata, O. Chusri [Chanthaburi Horticultural Research Center]
S. Tongtao [Chanthaburi Horticultural Research Center])

Fig. 1. Temperature controller set on a flower cluster.
A: A polystyrene foam box equipped with Peltier devices was used as controller.
B: Inside the controller (The lid was left open during daytime).

Fig. 2. Percentages of flowers or fruits remaining after pollination. Asterisks (* and **) indicate significant differences between the treatments based on Fisher’s exact test at P<0.05 and P<0.01, respectively. NS indicates a non-significant difference. Arrow shows the duration of temperature treatment.

Fig. 3. Micrographs showing the morphological development of ovules at 7 days after pollination (DAP).
A: Ovule at the mature stage containing an embryo sac with a fused polar nucleus (15°C).
B: Ovule at the endosperm nuclei division stage (25°C). White arrows indicate endosperm nuclei.

Table 1. Average length of the ovules and the developmental stages at 7 DAP
 

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Four AREB/ABF transcription factors function downstream of three SnRK2 protein kina

Global climate change has increased the frequency and severity of drought, resulting in significant yield losses in staple crops worldwide. Drought is one of the major abiotic stresses that adversely affect plant growth, survival, distribution, and productivity. Under drought conditions, many genes involved in drought stress response are induced in a wide range of plant species. The plant hormone abscisic acid (ABA) plays a crucial role in coordinating the responses to reduced water availability as well as in multiple developmental processes. Endogenous ABA levels in plant cells are increased in response to drought stress, leading to expression of stress-responsive genes. In a model plant Arabidopsis, under drought stress conditions, ABA controls stress-responsive gene expression mainly through three bZIP transcription factors (TFs) -- AREB1/ABF2, AREB2/ABF4 and ABF3 -- which are activated by SNF1-related kinase 2s (SnRK2s) such as SRK2D/SnRK2.2, SRK2E/SnRK2.6/OST1, and SRK2I/SnRK2.3 (SRK2D/E/I). However, as the three AREB/ABFs are required, but not exclusive, for the SnRK2-mediated gene expression, transcriptional pathways regulated by SRK2D/E/I remain unknown.

In this report, we show that a Clade A bZIP transcription factor, ABF1, function as a homolog of AREB1/ABF2, AREB2/ABF4, and ABF3 in ABA-dependent gene expression in Arabidopsis. In spite of lower expression levels of ABF1 than those of the three AREB/ABFs, the areb1 areb2 abf3 abf1 quadruple knockout mutant plants exhibited enhanced sensitivity to drought and reduced sensitivity to ABA in primary root growth compared with the areb1 areb2 abf3 triple knockout mutant. Large-scale transcriptome analyses uncovered that expression of downstream genes of SRK2D/E/I, which include many functional genes in drought stress responses and tolerance such as TFs and LEA proteins, was mostly impaired in the quadruple mutant. These results indicate that the four AREB/ABFs are the predominant TFs downstream of SRK2D/E/I in ABA signaling in response to drought stress during vegetative growth.

Considering that many findings strengthen the view that ABA signaling has contributed to land colonization and adaptation to various environmental changes, the manipulation of genes involved in ABA signaling has the potential to improve crop productivity and quality under drought stress conditions. AREB/ABFs, which are key players in drought stress response, are well conserved in land plants, so that the four AREB/ABFs can be good candidates to engineer enhanced drought tolerance. Thus, engineering ABA signaling through manipulation of SnRK2-AREB/ABF-mediated transcriptional regulation would create a new path to face climate change through improvement of crop production.

(T. Yoshida [Max-Planck-Institute, The University of Tokyo], Y. Fujita, K. Maruyama, J. Mogami [The University of Tokyo], D. Todaka [The University of Tokyo], Kazuo Shinozaki [RIKEN], Kazuko Yamaguchi-Shinozaki [The University of Tokyo])

Fig. 1. The areb1 areb2 abf3 abf1 quadruple knockout mutant displays enhanced sensitivity to drought compared with the areb1 areb2 abf3 triple knockout mutant. Watering was withheld from 4-week-old plants for 11–12 d, and then the plants were re-watered for 1 week before the photograph was taken. Circles and crosses indicate survival and dead plants, respectively. Wild-type (WT) and two kinds of mutant plants (n = 5 each) were grown in soil in a 9 cm pot. Survival rates were shown in the central column and calculated from the results from eight independent experiments (n=40). Representative result is shown. **P < 0.01（Student’s t-test, based on comparison with WT）

Fig. 2. Model showing the AREB/ABF-SnRK2 pathway that controls ABA-mediated transcriptional regulation in responses to drought stress in plants

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Integrated analysis of the effects of dehydration and cold on rice metabolites, phytohorm

Land plants must mount suitable responses to overcome the adverse effects of water stress caused by either drought or low-temperature conditions. Among external stresses, water stress is one of the most important limitations to crop productivity. Discoveries of useful genes for molecular breeding using metabolomics and transcriptomics promise to facilitate the improvement of crop yields under water stress conditions. It is important to identify plant metabolites and transcripts that respond to water stress to determine the essential steps in molecular processes related to the effective adaptation of plants to stress conditions. Metabolomic and transcriptomic data have provided much information on the metabolite, phytohormone, and transcript networks that control plant growth and development. Rice is important not only as a major crop but also as a model monocot.

In this study, we performed an integrated analysis of the metabolites, phytohormones, and gene transcripts in rice plants subjected to dehydration or cold treatments. Our aim was to comprehensively survey the molecular responses of rice to dehydration or cold stimuli. We used three types of MS systems: gas chromatography coupled with time-of-flight MS (GC-TOF-MS), capillary electrophoresis coupled with MS (CE-MS), and liquid chromatography coupled with MS (LC-MS). We identified and characterized representative dehydration-responsive and cold-responsive metabolites and phytohormones. We also performed a transcriptome analysis using a rice oligonucleotide microarray. We analyzed metabolite–gene and phytohormone–gene correlations and identified several genes encoding metabolic enzymes that might play key roles in the responses of rice plants to dehydration or cold. We compared the roles of the identified rice genes with those of their counterparts in Arabidopsis under dehydration or cold conditions.

An integrated analysis of metabolites and gene expression indicated that several genes encoding enzymes involved in starch degradation, sucrose metabolism, and the glyoxylate cycle are upregulated in rice plants exposed to dehydration or cold, and that these changes are correlated with the accumulation of glucose, fructose, and sucrose (Fig.1). In particular, high expression levels of genes encoding isocitrate lyase and malate synthase in the glyoxylate cycle correlate with increased glucose levels in rice, but not in Arabidopsis, under dehydration conditions, indicating that the regulation of the glyoxylate cycle may be involved in glucose accumulation under dehydration conditions in rice, but not in Arabidopsis. An integrated analysis of phytohormones and gene transcripts revealed an inverse relationship between abscisic acid (ABA)-signaling and cytokinin-signaling under cold and dehydration stresses; these stresses increase ABA signaling and decrease cytokinin signaling (Fig. 2). High levels of OsNCED transcripts correlate with ABA accumulation, and low levels of CYP735A transcripts correlate with decreased levels of a cytokinin precursor in rice. This reduced expression of CYP735As occurs in rice, but not in Arabidopsis. Therefore, transcriptional regulation of CYP735As might be involved in regulating cytokinin levels under dehydration and cold conditions in rice, but not in Arabidopsis.

(K. Maruyama and K. Yamaguchi-Shinozaki [The University of Tokyo])

Fig. 1. Carbohydrate and amino acid metabolic pathways. (A) Starch degradation; (B) Sucrose metabolism; (C) Glyoxylate cycle: BAMY, β-amylase; A/N-invs, alkaline/neutral invertase; ICL, isocitrate lyase.

Fig. 2. Pathways for ABA and CK biosyntheses. (A) ABA biosynthesis; (B) CK biosynthesis. NCED, 9-cis-epoxycarotenoid dioxygenase.

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A flexible high-throughput marker system to distinguish African rice (Oryza glaberrima) from Asia

The African rice Oryza glaberrima is an important reservoir of genes for abiotic stress tolerance. To discover such tolerance genes and to exploit them in rice improvement, a flexible, high-throughput marker system is needed. Single nucleotide polymorphism (SNP) sites, where the genome sequence of two or more individuals differs by a single base, are increasingly becoming the marker of choice. Although the number of discovered SNPs has increased significantly over the past few years, most of these efforts have focused on variations within the Asian rice Oryza sativa.The aim of the present study was to detect a set of SNPs that differentiate between O. sativa and O. glaberrima, and to use a representative subset to develop a high-throughput PCR-based genotyping panel.

A genome-wide 44,000 SNP genotyping array identified a set of 9523 SNPs polymorphic between O. glaberrima and O. sativa subspecies indica, and 7444 SNPs between O. glaberrimaand O. sativa subspecies japonica （Figure 1A）. From the above set, a subset of 1540 SNPs was selected in collaboration with partners within the Generation Challenge Program (GCP) for conversion into PCR-based markers, using the KASP (competitive-allele PCR) technology. A final set of 2015 SNPs were successfully converted to KASP markers, which are evenly distributed in the genome, with the exception of small gaps in chromosomes 4 and 10 (Figure 1B). The panel was validated in the ‘New Rice for Africa’ (NERICA) parents. Of the 2015 markers tested, 745 markers were polymorphs between CG14 and WAB56-104 (upland NERICA parents) and 752 between TOG5681 and IR64 (lowland NERICA parents) (Figure 2). Several subsets of these markers have been used successfully to map O. glaberrima introgressions in NERICA rice varieties and interspecific breeding lines.

This new genotyping panel is a cost-effective, gel-free genotyping platform that allows maximum flexibility for ‘pick-and-choose’ markers according to individual breeder’s needs. Presently, it is fully outsourced to service companies that can perform all steps, from DNA extraction to genotyping, which would extend the capacity of low-resource laboratories to perform molecular breeding using local rice varieties. In addition, the information for each SNP is publicly available allowing the rice breeding community to complement the set with their own subset of markers. JIRCAS is expanding its collaborative rice breeding network with applications ranging from parental surveys, development of QTL mapping populations, and marker-assisted introgressions of major stress tolerance genes like OsPSTOL1.

(M. Wissuwa, J. Pariasca-Tanaka, M. Lorieux [CIAT], C. He [GCP], S. McCouch [Cornell University], MJ. Thomson [IRRI])

Fig. 1. Flow chart indicating the selection of polymorphic SNPs between O. glaberrima vs O. sativa ssp japonica and indica for conversion into PCR-based markers (A). Distribution of SNP markers along the rice genome. Color represents the number of markers per 1 Mb (B).

Fig. 2. Distribution of polymorphic SNP markers for crosses of O. glaberrima vs O. sativa. There are 745 and 751 polymorphic markers for upland and lowland NERICA varieties, respectively.

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Manual of soil fertility improvement technologies in lowland rice ecologies of Ghana (PDF A4:535KB A3: 134KB)

The impact of fertilizer application on crop production in Sub-Saharan Africa (SSA) is considered enormous as the region is very low in soil fertility. However, access to chemical fertilizers is difficult especially for small-scale SSA farmers who do not have sufficient financial resources in a market-oriented economy. This crucial issue underscores the urgent need for the farmers to increase agricultural productivity, which can be achieved through inexpensive and cost-effective techniques of improving soil fertility in rural areas.

With financial support from the Ministry of Agriculture, Forestry and Fisheries (MAFF) of Japan, JIRCAS carried out a study on technology development for improved soil fertility using indigenous resources that are accessible and acceptable to local farmers. The study, with rice being the target crop, is aimed at contributing to the goal of the Coalition for African Rice Development (CARD) to double rice production in SSA by 2018. Ghana was selected as the country of implementation because it has two major rice ecologies (rainfed lowland and irrigated lowland) and has good research counterpart institutions.

As one of the products of the study, a technical handbook, titled “Manual of soil fertility improvement technologies in lowland rice ecologies of Ghana,” was published. Written in English, this manual would greatly benefit extension workers and assist them in disseminating the technologies to rice farmers. A summary of the manual’s features is listed below.

1. The manual describes the application of indigenous organic matter as well as their composting and charring technologies, the application of phosphate rocks from neighboring Burkina Faso and its solubilizing technologies, and the enhancement of early rice growth using a minimum quantity of chemical fertilizer (Table 1).
2. The technologies mentioned in the manual were developed in consideration of available materials in each rice ecology and corresponding region. The technologies were evaluated for effectiveness and affordability to the rural communities in on-farm participatory studies.
3. Government officers as well as counterpart researchers in Ghana were actively involved in the editorial process, enhancing their sense of ownership of the manual and technologies. The foreword was written by the deputy minister of the Food and Agriculture (MoFA), Ghana.
4. This manual is compact enough to be carried around. It is printed on A5 size paper and contains only 44 pages, with visually descriptive text and plenty of visuals (photographs and illustrations).
5. The technologies adopted in the manual may be extended to other SSA countries having the same rice ecologies.

(Satoshi Tobita, Satoshi Nakamura, Monrawee Fukuda, Fujio Nagumo)

Table 1.Technology options adopted in the soil fertility manual

Fig. 1. Charring of saw dust (Kumasi City)

Fig. 2. Demonstration in an on-farm field (at Ziong Village, a suburb of Tamale City)

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Sorgoleone release determines the hydrophobic-BNI capacity in sorghum root systems (PDF A4:128K

Nitrification and denitrification are the two most important processes that contribute to greenhouse gas emissions and the inefficient use of nitrogen. Suppressing soil nitrification through the release of nitrification inhibitors from roots is a plant function, termed ‘Biological Nitrification Inhibition (BNI)’. Sorghum releases two categories of nitrification inhibitors from roots: hydrophilic BNIs and hydrophobic BNIs. Our earlier published work on sorghum mostly focused on characterizing hydrophilic BNI release. Here we report the characterization of hydrophobic-BNI release in sorghum. The functional role and contribution of sorgoleone release to hydrophobic-BNI function and the existence of genotypic variability for sorgoleone release is the focus of this investigation. Three sorghum genotypes (Hybridsorgo, IS 41245 and GDLP 35-5-5-3) were evaluated for their capacity to release sorgoleone in hydroponic, in soil culture, and under field environments. Sorgoleone released from roots is measured using a high performance liquid chromatograph (HPLC) and BNI activity is determined using a luminescent recombinant Nitrosomonas europaea assay.

Sorgoleone was found to be the dominant and major component of hydrophobic-BNI activity released from sorghum roots, and there were significant genotypic differences for sorgoleone release (Fig. 1). Sorgoleone release and BNI-activity release in sorghum roots are closely associated, i.e., 1 μg of sorgoleone released is equivalent to 1 ATU activity in the bioassay (Fig. 2). Sorgoleone genotypes release varying quantities of sorgoleone. GDLP 34-5-5-3 and Hybridsorgo have higher capacity for both sorgoleone release and BNI activity than IS41245. In soil culture, GDLP 34-5-5-3 released significantly higher quantities of sorgoleone into the rhizosphere, had higher BNI activity, and suppressed soil nitrification better than IS41245 (Fig. 3). Purified sorgoleone inhibited Nitrosomonas activity in the bioassay; when amended to soil, sorgoleone suppressed nitrification, improved NH₄⁺ availability, and reduced NO₃^- formation in soils during a 60-day incubation study (Fig. 4). These results demonstrate genetic differences for sorgoleone release and its functional link to hydrophobic-BNI release and BNI capacity in sorghum.

Sorgoleone release contributes significantly to BNI capacity in sorghum. The significant genetic differences for sorgoleone release from sorghum roots suggest that there is potential for genetic improvement to improve sorgoleone release and BNI capacity in sorghum. Higher BNI capacity is critical to the development of low-nitrifying sorghum production systems and the results presented here suggest the feasibility of this approach.

(T. Tesfamariam, H. Yoshinaga, S. P. Deshpande. [International Crops Research Institute for Semi-Arid Tropics (ICRISAT)], P. Srinivasa Rao [ICRISAT], K. L. Sahrawat [ICRISAT], Y. Ando, K. Nakahara, C.T. Hash [ICRISAT], G. V. Subbarao)

Fig. 1. Chemical structural formula of sorgoleone

Fig. 2. The relationship between total sorgoleone concentration (μg) and BNI activity (ATU) in root–DCM wash of three sorghum genotypes

Fig. 3. Nitrification rate at 30-day incubation period along with NH4+ inoculation of rhizosphere soil collected from two sorghum genotypes (IS1245 and GDLP 34-5-5-3) grown up to heading stage in potted soil. Control pots were included with bare soil without plants but handled the same way like pots with plants. As positive control, soils taken from control treatments were also incubated with DCD addition at 25 ppm (a known synthetic inhibitor) as a reference.

Fig. 4. Concentration of inorganic N (NO3− and NH4+) in soil samples incubated after adding different concentrations of sorgoleone (0, 10, 20, 30, 40, and 100 μg g−1 soil) for 60 days

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