Association mapping in rice: basic concepts and perspectives for molecular breeding

In the last decade, association mapping (AM) has become a well-established method to detect genes and quantitative trait loci (QTLs) associated with agronomically important traits. The identification of a large number of single nucleotide polymorphisms (SNPs) from genome sequencing and concurrent development of high-throughput genotyping platforms has led to AM being widely used for a range of crops. These technologies have been used in rice (Oryza sativa) to explore the abundant diversity and there is enormous potential to identify novel QTLs for traits of interest. Due to the availability of cost-effective high-throughput SNP genotyping methods and rapid developments in rice genomics, it is inevitable that these AM approaches will become more popular in the future, especially in the context of genome-wide association studies (GWASs). In this paper, we review the fundamental concepts, critical considerations and limitations of AM focusing on rice, and reiterate the importance of accurate phenotypic data. We also include a section about connecting GWAS to molecular breeding, covering practical consideration for breeders, which is required to use GWAS results in actual rice molecular breeding programs and which has not received adequate attention in the scientific literature.     

Albendazole Resistance in Gastrointestinal Nematode Parasites of Cattle in Bangladesh

Tropical Animal Health and Production -     

Assessment of the pest status of Pratylenchus curvicauda and ultrastructural changes in roots of infected wheat and barley

Pratylenchus curvicauda, which was first described in metropolitan Perth in 1991, was recently identified in grain-growing areas in Western Australia. The biology of this root-lesion nematode, and especially its pest status, is unknown. We investigated its life cycle and interaction with host plants, because such information is essential for its management. The life cycle took 45 days to complete in a wheat cultivar maintained at 23°C. Over 10 weeks, the nematode multiplied in 26 of 61 genotypes; these host plants were all cereals and included widely grown cultivars of wheat and barley. Eighteen other cereal genotypes and 13 cultivars including canola, chickpea, ryegrass, lupin, soybean, and tomato, sustained the nematodes to different degrees without multiplication. Four cover crops were not suitable hosts. The patterns of attraction of the nematodes and penetration into roots of the host and tolerant plants were similar. The nonhosts attracted fewer nematodes, none of which penetrated the roots. Browning of infected roots was atypical—it occurred late in some roots, 55 days after inoculation, and in the presence of a fungus. The nematodes were confined to, and fed from, cortical cells. The ultrastructure of infected wheat and barley cells showed typical signs of damage caused by Pratylenchus spp. and included cell disorganization and lack of membrane integrity, disintegration of cytoplasm, hypertrophy of some nuclei, and deposition of tannin-like granules. This detailed characterization of P. curvicauda–host interaction indicates the nematode is likely to be a pest of major crops, and attention should be given to its management.     

Household Animal and Human Medicine Use and Animal Husbandry Practices in Rural Bangladesh: Risk Factors for Emerging Zoonotic Disease and Antibiotic Resistance

Animal antimicrobial use and husbandry practices increase risk of emerging zoonotic disease and antibiotic resistance. We surveyed 700 households to elicit information on human and animal medicine use and husbandry practices. Households that owned livestock (n = 265/459, 57.7%) reported using animal treatments 630 times during the previous 6 months; 57.6% obtained medicines, including antibiotics, from drug sellers. Government animal healthcare providers were rarely visited (9.7%), and respondents more often sought animal health care from pharmacies and village doctors (70.6% and 11.9%, respectively), citing the latter two as less costly and more successful based on past performance. Animal husbandry practices that could promote the transmission of microbes from animals to humans included the following: the proximity of chickens to humans (50.1% of households reported that the chickens slept in the bedroom); the shared use of natural bodies of water for human and animal bathing (78.3%); the use of livestock waste as fertilizer (60.9%); and gender roles that dictate that females are the primary caretakers of poultry and children (62.8%). In the absence of an effective animal healthcare system, villagers must depend on informal healthcare providers for treatment of their animals. Suboptimal use of antimicrobials coupled with unhygienic animal husbandry practices is an important risk factor for emerging zoonotic disease and resistant pathogens.     

Production risk,technical efficiency,and input use nexus: Lessons from Bangladesh aquaculture

The optimal use of resources in aquaculture is important, especially in developing countries, to obtain the highest possible outcome from the production process to support food security and poverty alleviation. Thus, within this study, the risk, efficiency, and input‐use variation in aquaculture farms in Bangladesh is investigated using a flexible stochastic frontier model with a risk and an inefficiency function. The results reveal that feed, labor, and capital have positive and significant impacts on production. In addition, an increased fingerling density and a larger farm increase the risk, whereas the use of feed and the capital invested have the opposite effect. Access to extension services has a positive effect and increases farm efficiency. An investigation of the farm size–productivity inverse relationship reveals that this phenomenon is not applicable to Bangladesh aquaculture. In general, efficient farmers are large‐scale farmers, who use a lower stocking density but a higher feeding intensity, resulting in a higher yield. On average, farmers use less labor and feed than what is optimal. To increase efficiency and reduce risk, it is recommended that more technical knowledge on optimal input use, extension service, and capital is made available to aquaculture farmers.     

Economic feasibility of Pabda and stinging catfish culture in recirculating aquaculture systems (RAS) in Bangladesh

Recirculating aquaculture system (RAS) is a unique approach that offers total control to culture a wide variety of aquatic species. As capital investment is higher for setting up RAS, it is necessary to conduct an economic feasibility analysis based on real data. A structured questionnaire was used to collect all economic and technical data on two catfish species, viz., Pabda (Ompok pabda) and Shing (Heteropneustes fossilis), cultured in an RAS farm. The ultimate objective was to estimate net cash flow, net present value (NPV), profitability index (PI), payback period, discounted payback period, internal rate of return (IRR), and sensitivity analysis to find out the best profitability indicators. The analysis revealed that the IRR were 4% and 16% for Pabda and Shing production, respectively. However, for Pabda and Shing productions, the payback periods were 15 years and 4 months and 6 years and 2 months, respectively. The NPV value was positive for Shing production and negative for Pabda. On the other hand, the PI was lower than one for Pabda production and higher than one for Shing production. Therefore, the results showed that the Shing production in the RAS facility could be economically feasible; however, Pabda production may not be viable in RAS due to lower production and longer culture period. This study may suggest that by increasing the production capacity of the farm and market price of the product through the proper supply chain and by decreasing the initial investment, cost of fingerlings and feed, profitability can be achieved in RAS in Bangladesh.

     

Emergence of physiological rhythmicity in term and preterm neonates in a neonatal intensive care unit

Background  

Biological rhythmicity, particularly circadian rhythmicity, is considered to be a key mechanism in the maintenance of physiological function. Very little is known, however, about biological rhythmicity pattern in preterm and term neonates in neonatal intensive care units (NICU). In this study, we investigated whether term and preterm neonates admitted to NICU exhibit biological rhythmicity during the neonatal period.     

Comparison of structural diversity of tree-crop associations in Peripheral and Buffer zones of Gachabari Sal forest area, Bangladesh

The original version of this article unfortunately contained three mistakes.
（1） The spelling of the [A. Nishad＇] name was incorrect. The corrected spelling is given below.     

Variation in soil organic carbon stock in different land uses and altitudes in Bagrot Valley,Northern Karakoram

Soil organic carbon tends to respond more sensitively to climate change and land use intensification in ecologically fragile and economically marginal regions of mountainous areas. This study aims to evaluate the soil organic carbon stock dynamic across various land uses at different altitudes in the Bagrot valley, Northern Karakoram, Gilgit-Baltistan, Pakistan. Soil samples from 0–20, 20–40 and 40–60 cm depth were collected from three land uses: pasture, forest, and adjacently located arable land at different altitude (ranging from 2100–4163 m). The variables investigated were soil bulk density (BD), soil organic carbon concentration (SOC), soil organic carbon stock (SOCS) and pH. A significant variation in all tested variables were found across the land uses and altitudes. Likewise, soil under forest had significantly higher values of SOCS (59.35?Mg ha^?1) than pasture (42.48?Mg ha^?1) and arable land (23.63?Mg ha^?1). Similarly, SOCS increased with increasing altitude and decreased with soil depth in all land uses. In addition, SOCS had a negative relationship with BD and pH. Overall results indicated that the land use intensification and climate change (increase in temperature and decrease in precipitation) were associated with declining SOCS. These results suggest restoration of degraded agricultural land to the forest, especially at higher altitude, and decrease in intensity of land use could increase SOCS in the study area as well as other similar mountainous regions.     

Effect of dietary saponin rich soapnut (Sapindus mukorossi) shell powder on growth performance,immunity, serum biochemistry and gut health of broiler chickens

This study was conducted to evaluate the effects of dietary soapnut (Sapindus mukorossi) shell powder (SSP), a cheap source of saponins, on growth performance, immunity, serum biochemistry and gut health of broiler chickens. The experimental design was 4×2, employing four saponin levels (0, 100, 150 and 200 mg/kg diet), each provided for two time durations (0–42 day and 21–42 day) resulting into eight dietary treatments. Results revealed no significant effect of dietary saponins on body weight gain, feed intake and feed conversion ratio of birds. The abdominal fat percentage, heterophil to lymphocyte ratio, serum cholesterol and triglyceride levels, faecal total plate count, coliform count and E. coli count decreased (p < .05) progressively with increasing saponin levels and lower values were observed at 150 mg and 200 mg saponin levels. Significant improvement of cell‐mediated and humoral immune response was observed in birds fed 150 mg and 200 mg saponin compared to control. The serum glucose concentration was significantly (p < .05) higher in control group compared to other groups. No significant effects of dietary saponin were observed on carcass characteristics, faecal Lactobacillus count, intestinal histomorphometry and cost economics of broiler chicken production. Thus, dietary saponins at 150 mg/kg diet as SSP for three weeks (21–42 days) was optimum for better immunity and welfare of birds without adverse effects on the growth performance.