The ADH1B Arg47His polymorphism in East Asian populations and expansion of rice domestication in history

Background: The emergence of agriculture about 10,000 years ago marks a dramatic change in human evolutionary history. The diet shift in agriculture societies might have a great impact on the genetic makeup of Neolithic human populations. The regionally restricted enrichment of the class I alcohol dehydrogenase sequence polymorphism (ADH1BArg47His) in southern China and the adjacent areas suggests Darwinian positive selection on this genetic locus during Neolithic time though the driving force is yet to be disclosed. Results: We studied a total of 38 populations (2,275 individuals) including Han Chinese, Tibetan and other ethnic populations across China. The geographic distribution of the ADH1B*47His allele in these populations indicates a clear east-to-west cline, and it is dominant in south-eastern populations but rare in Tibetan populations. The molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10,000 similar to 7,000 years ago. Conclusion: We present genetic evidence of selection on the ADH1BArg47His polymorphism caused by the emergence and expansion of rice domestication in East Asia. The geographic distribution of the ADH1B*47His allele in East Asia is consistent with the unearthed culture relic sites of rice domestication in China. The estimated origin time of ADH1B*47His allele in those populations coincides with the time of origin and expansion of Neolithic agriculture in southern China.

Growth and yield of GIFT (Oreochromis niloticus) and Thai silver barb (Barbodes gonionotus Bleeker) in rice fields and their effects on the yield of rice

(GIFT) (Oreochromis niloticus) and Silver barb (Barbodes gonionotus) in rice fields and their effects on the yield of rice was carried out in nine experimental rice plots. Three treatments viz., treatment-1 with 0. niloticus (T1), treatment-2 with B. gonionotus (T2) and treatment- 3 was kept as control (T3, without fish) were used in this study. Fertilizers such as, Urea (178 kg ha-1), T.S.P (125 kg ha-1) and M.P. (67 kg ha-1) were applied in each treatment. The fishes were stocked @ 6250 ha·1 and the experiment was continued for a period of 107 days. The values of water quality parameters such as, water temperature, dissolved oxygen, pH and chlorophyll-a were found within suitable level. Between the two species, higher specific growth rate was recorded in 0. niloticus than that of B. gonionotus. But B. gonionotus showed much higher survival (72%) than that of 0. niloticus (35%). Similar to survival, higher production (244 kg ha-1) and income (Tk. 6399 ha-1) were recorded in B. gonionotus than those of 0. niloticus (142.8 kg ha'1 and Tk. 2137 ha-1). Significant differences (price grain and straw were observed between the treatments with fish and without fish.

Effect of farm made feeds on polyculture of shrimp (Penaeus monodon) and three brackishwater finfish species

A study was conducted to evaluate the effects of feed made from locally available ingredients on polyculture of shrimp and three brackishwater finfish species. Hatchery produced post-larvae (PL) of shrimp Penaeus monodon (0.005g) were stocked at the rate of 15,000 PLs/ha. Brackishwater finfish species Liza parsia, Mugil cephalus and Rhinomugil corsula of 0.63-1.4lg collected from local rivers were stocked at the rate 8,000, 1,000 and 2,000/ha, respectively in four treatments. Shrimp and finfishes were fed four different experimental diets composed of fish meal, mustard oil cake, rice bran, oyster shell power and vitamin premixes at the rate of 3-5% estimated crop/day for 195 days. Among four treatments, P. monodon showed comparative better growth in T4 and T3. Finfish L. parsia showed its better performance in treatment T2. Species M. cephalus and R. corsula showed insignificant production. P. monodon showed better growth with diet of fish meal and mustard oil cake@ 28.84 and 33.65%, respectively in T 3 and 19.22 and 43.27%, respectively in treatment T4.

Growth performance, recovery rate and fish yield of GIFT strain at various water depths under rice-fish culture systems

Effect of water depth on recovery rate, growth performance and fish yield of GIFT in the rice-fish production systems was studies in experimental plots of 123 m2 with a pond refuge of I meter deep which covered 10% of the total land area. Mortality rate of fish was very low ranging from 0.81-1.63%. However, at harvest, recovery rate ranged from 76.69-82.93% with the highest recovery at 11-15 em of water depth. Significantly the highest absolute growth (99.97) and specific growth rate (2.42%) were found at 21-25 cm water depth. The same treatment also produced significantly higher fish yield (909.76 kg/ha) although statistically similar to the fish yield (862.60 kg/ha) obtained at ll-15 em of water depth. Results also suggested that higher water depth can produce bigger fish but no significant effects of water depth was found on fish yield in the treatments 11-15 cm and 21-25 cm water depths of this experiment.

Performance of Amblypharyngodon mola with Barbodes gonionotus, Cyprinus carpio and Macrobrachium rosenbergii in rice-fish culture system

An experiment was conducted to assess the performance of mola (Amblyphmyngodon mola) in rice fish culture system with freshwater prawn Macrobrachium rosenbergii), Thai silver barb (Bm·bades ganianotus) and common carp (Cyprinus cmpia) for a period of 4 months at the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh, Bangladesh. Four treatments viz., treatment-I (T1) with A. mala and M. rosenbergii; treatmen t-II (T2) with A. mala, M. rosenbergii and B. gonianatus ; treatmentIII (T3) with A. mala, 1Vf. rosenbergii and C. cmpia, and treatment- IV (T4) as control (without fish) were used in triplicate. All treatments were equally fertilized with urea (200 kg/ha), TSP (150 kg/ha) and MP (75 kg/ha). The mean values of water quality parameters viz., temperature, dissolved oxygen, pH, nitrate-nitrogen showed a very small variations among different treatments, but phosphate-phosphorus and chlorophyll-a were relatively higher in T4 without fish (i.e., control). The fish production of 480.5 kg/ha in T3 was significantly higher than that of 355.6 kg/ha T2 and 223.8 kg/ha in T 1• The values of soil organic matter, total-nitrogen, phosphorus and potassium at harvest were significantly (P<0.05) higher in the treatments with fish than without fish, but pH did not show any significant differences. The yield of rice grain and straw was also obtained significantly (P<0.05) higher in the treatments with fish. The increase in grain was higher over the control by 11.81%, 9.41% and 14.76% and that in straw was by 9.83%, 4.77% and 13.29% in Tl> T2, and T3 respectively.

Culture of Amblypharyngodon mola in rice fields alone and in combination with Barbodes gonionotus and Cyprinus carpio

A rice-fish culture experiment with four treatments viz., T 1 with Amblyphmyngadan mala alone, T 2 with A. mala and Barbodes gonionotus, T3 with A. mala and Cyprinis carpio and T4 as control (without fish) was carried out in the rice fields during April through August1999. The recovery rate of A. mala were 42%, 37% and 42% in treatments 1, 2 and 3 respectively and the same recorded for B. gonionotus and C. cmpio were 62% and 55% respectively. Among the three species of fish, B. gonionotus showed much higher recovery rate than both of A. mala and C. carpio. The production of A. nwla was 12.50 kg/ha/3 months in monoculture, and 7.92 kglha/3 months and 8.86 kglha/3 months in combination with B. gonionotus and C. carpio, respectively. The production of B. gonionotus in T2 was 169.29 kg/ha/3 months and C. cmpio in T 3 was 252.92 kg/ha/3 months. The total fish production was 12.50 kg/ha/3 months, 175.21 kg/ha/3 months and 261.88 kg/ha/3 months in Tp T2 and T3, respectively. The highest yields of rice grain (5.78 ton/ha) and straw (7.83 ton/ha) were recorded in T3 and the lowest of the same was in T4 (grain 4.96 ton/ha and straw 6.62 ton/ha). Rice yield increased by about 12.10% in T1, 13.30% in T2 and 16.33% in T3 in context to T4, rice-alone culture. The results demonstrated that the culture of fish in rice fields had profound beneficial impact on the production of rice grain and straw.

Socioeconomic assessment of shrimp farming in relation to local livelihoods in the south-west coastal Bangladesh

Nine different categories of stakeholders in shrimp farming industry ·were assessed to show the socioeconomic impact of shrimp farming in south-west Bangladesh. Among all the stakeholders the shrimp farmer's average own land was 4 ha whereas the seed collectors and faria's had lowest amount of average land, 0.1 and 0.5 ha respectively. The shrimp farming positively impacted to the livelihood of stakeholders. Income of the coastal people, sanitation, working facilities of women, employment, health condition and the literacy rate increased due to shrimp farming. On the other hand shrimp farming had negative impact on the rice production, livestock, drinking water supply, and social conflict and violence had increased due to shrimp farming. There were internal conflicts between different stakeholders; the farias conflict with the depot owners and shrimp farmers, marginal farmers' conflict with the rich shrimp farmers about leasing lands and saline water control, the rice farmers conflicts with the shrimp farmers about agricultural crop production.

Input-output relationship and economics of pangas monoculture and carp-pangas polyculture in two districts of Bangladesh

An attempt was made to study the input-output relationships and economics of pangas monoculture and carp-pangas polyculture in Bangladesh. By analyzing the data collected from 50 pangas farms and 55 carp-pangas farms, the study has investigated the production systems of two technologies and the effects of fingerling stocking and applications of feed and fertilizer on fisheries income. The data were collected from the fishermen of Trishal and Bhaluka of Mymensingh district, and Kahaloo and Adamdighee of Bogra district during 2001-02. For pangas monoculture, the stocking density was 31,561 per ha while it was 55,017 per ha in carp-pangas polyculture. Most of the farmers used urea, TSP and lime before stocking. Rice and wheat bran happened to be the most common feed ingredients for both types of culture in general. Other important ingredients used were mustard oil-cakes, rice polish, wheat flour, fish meal, bone meal, soybean meal and poultry litter. In terms of quantities, rice bran and wheat bran dominated the farmers list. Rice and wheat bran together constituted about 60% of all studied feeds. Feed cost constituted 59.13% of total costs for pangas monoculture and 67.44% for carp-pangas polyculture. Per ha productions of pangas and carp-pangas in a single culture cycle were 15,508 kg and 19,745 kg, respectively. Per ha gross profits were estimated to be Tk 310,311 and Tk 464,418 for pangas monoculture and carp-pangas polyculture, respectively. Net profit appeared to be Tk 264,216 per ha for pangas monoculture and Tk 416,509 per ha for carp-pangas polyculture. The BCRs calculated were 1.46 and 1.68 for monoculture and polyculture, respectively. The break-even costs per kg of fish were estimated at Tk 36.93 for pangas and Tk 30.93 for mixed species which was much lower than the prices the producers received. Break-even productions were estimated at 10,702 kg per ha for pangas monoculture and 11,784 kg per ha for carp-pangas polyculture. Fingerling and feed cost, and pond size significantly explained the variation of income from pangas monoculture. These factors have significantly influenced the income from the crop. Functional analysis shows that 1% increase in the feed cost might increase 0.51% of pangas income and 0.41% in carp-pangas income. No other inputs had shown this much of responses to increasing income from a fish.

Adoption, productivity and profitability of rice-fish and fingerling culture in three selected districts of Bangladesh

The study aimed to investigate the productivity and profitability of rice-fish farming. It also determined the factors affecting rice-fish and fingerling production in Bangladesh. Among the total respondents about 55% were involved in rice-fish farming, 37% in pond fish culture and rest 9% in fish nursery. Integrated rice-fish farming contributed about 83% of the annual farm income in Comilla while it was about 20% in both Kishoregonj and Chandpur districts. Among the different farming systems integrated rice-fish culture and rearing fingerlings in the nursery pond were more profitable at the farm level. Farmers earned a net return of Tk. 49,714/ha from integrated fish culture with boro rice while the net return of boro rice-alone was only Tk. 11,179/ha. This indicated that farmer could earn 218% higher net return from integrated rice-fish farming than that of boro rice only farming. Moreover, integrated rice-fish culture also reduced pesticides cost to about 77% and weeding cost to about 51% in boro season. Fingerling nursing earned highest net returns among the three technologies.

A characterization of community fish refuge typologies in rice field fisheries ecosystems

In rural Cambodia, fish is a source of food and income to millions of people. However, there has been a real threat to fish populations in natural wetlands due to the degradation of aquatic biodiversity and habitat, illegal fishing, increase of population and demand for fish, and the use of harmful pesticides for agriculture. The Rice Field Fisheries Enhancement Project (RFFEP) seeks to rebuild and protect the fish populations through innovative methods. The project works with communities to sustainably strengthen the rice field fisheries near their villages by improving protected habitats called "community fish refuges". This handbook characterizes rice field fisheries that are connected to community fish refuges. Community fish refuges are designated fish conservation areas promoted by the Fisheries Administration of the Royal Cambodian Government. It also examines the characteristics of rain-fed rice field ecosystems that are connected to community fish refuges in order to further refine descriptive criteria and better understand potential benefits and management strategies.

Rapid evolution in a pair of recent duplicate segments of rice

Gene duplication has been considered the most important way of generating genetic novelties. The subsequent evolution right after gene duplication is critical for new function to occur. Here we analyzed the evolutionary pattern for a recently duplicated s

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

Effect of stocking density on growth and yield of GIFT tilapia under rice-fish production system

The study was conducted at the Central Experimental Station, Philippine Rice Research Institute, Maligaya, Science City of Munoz, Nueva Ecija, Philippines during the wet season to determine the suitable stocking density(s) for better growth and yield of fish under rice-fish production systems. Recovery rate of GIFT tilapia in different stocking densities ranged from 75.74 to 83.47%. Among different treatments, rice +5,000 fingerlings/ha and rice +10,000 fingerlings/ha resulted in the highest recovery rate of 83.33% and 83.47%, respectively. The lowest recovery rate of 75.75% was obtained from rice +20,000 fingerlings/ha, but similar to that was obtained (78.56%) from rice +15,000 fingerlings/ha. Significantly higher rate of gain in body weight and that of specific growth rate were recorded in the treatment from rice +5,000 fingerlings/ha, while other treatments resulted in similar absolute and specific growth rate. Fish yield increased significantly with relatively higher stocking densities, but higher densities produced maximum number of smaller fishes and also lower recovery rate.

Impact of common carp, Cyprinus carpio (L.) and Nile tilapia, Oreochromis niloticus (L.) on arthropods population, zoobenthos and weeds in rice-fish culture

An experiment was carried out in the fields of the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh, Bangladesh to determine the impact of common carp (Cyprinus carpio) and tilapia (Oreochromis niloticus) culture on arthropod population, zoobenthos and weeds of rice field. The treatments were: (1) rice combined with mono sex tilapia, (2) rice combined with common carp, (3) rice combined with a mixed culture of mono sex tilapia and common carp and (4) rice alone. It was observed that tilapia significantly reduced the number of arthropods, green leafhoppers and white leafhoppers in the rice-fish production systems. Benthos analysis revealed significant effects of fish culture on the abundance of molluscs, oligochaete worms and chironomid larvae. Lowest number of benthos was obtained in the treatments with common carp and significant reduction of the weed biomass was observed, especially in the tilapia containing plots. Based on the results of the study it can be suggested that common carp may play an important role in controlling of benthic organisms, while tilapia might be more effective to control terrestrial arthropods and weeds.