Revisiting rice breeding methods – evaluating the use of rapid generation advance (RGA) for routine rice breeding

Rice production needs to increase in the future in order to meet increasing demands. The development of new improved and higher yielding varieties more quickly will be needed to meet this demand. However, most rice breeding programmes in the world have not changed in several decades. In this article, we revisit the evidence in favour of using rapid generation advance (RGA) as a routine breeding method. We describe preliminary activities at the International Rice Research Institute (IRRI) to re-establish RGA on a large scale as the main breeding method for irrigated rice breeding. We also describe experiences from the early adoption at the Bangladesh Rice Research Institute. Evaluation of RGA breeding lines at IRRI for yield, flowering time and plant height indicated transgressive segregation for all traits. Some RGA lines were also higher yielding than the check varieties. The cost advantages of using RGA compared to the pedigree method were also empirically determined by performing an economic analysis. This indicated that RGA is several times more cost effective and advantages will be realized after 1 year even if facilities need to be built. Based on our experience, and previous independent research empirically testing the RGA method in rice, we recommend that this method should be implemented for routine rice breeding in order to improve breeding efficiency.     

Changes in phosphorus fractions in three tropical soils amended with corn cob and rice husk biochars

ABSTRACT

The formation of phosphorus (P) compounds including iron-P, aluminum-P and calcium-P in highly weathered tropical soils can be altered upon biochar addition. We investigated the effect of corn cob biochar (CC) and rice husk biochar (RH) pyrolyzed at three temperatures (300°C, 450°C and 650°C) on phosphorus (P) fractions of three contrasting soils. A 90d incubation study was conducted by mixing biochar with soil at a rate of 1% w/w and at 70% field capacity. Sequential P fraction was performed on biochar, soil and soil-biochar mixtures. Increase in most labile P (resin-P_i, NaHCO₃-P_i) and organic P fraction (NaHCO₃-P_o + NaOH-P_o) in CC and RH biochars were inversely related to increasing temperature. HCl-P_i and residual P increased with increasing temperature. Interaction of CC and RH with soils resulted in an increase in most labile P as well as moderately labile P (NaOH-P_i) fractions in the soils. CC increased most labile P in the soils more than RH. The increase in most labile P fraction in soils was more significant at relatively lower temperatures (300°C and 450°C) than 650°C. However, the increase in HCl-P_i and residual P of the soils was more predominant at high temperature (650°C). The study suggested that biochar pyrolyzed at 300–450°C could be used to increase P bioavailability in tropical soils.     

Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases

Abscisic acid (ABA) is an essential hormone for plants to survive environmental stresses. At the center of the ABA signaling network is a subfamily of type 2C protein phosphatases (PP2Cs), which form exclusive interactions with ABA receptors and subfamily 2 Snfl-related kinase (SnRK2s). Here, we report a SnRK2-PP2C complex structure, which reveals marked similarity in PP2C recognition by SnRK2 and ABA receptors. In the complex, the kinase activation loop docks into the active site of PP2C, while the conserved ABA-sensing tryptophan of PP2C inserts into the kinase catalytic cleft, thus mimicking receptor-PP2C interactions. These structural results provide a simple mechanism that directly couples ABA binding to SnRK2 kinase activation and highlight a new paradigm of kinase-phosphatase regulation through mutual packing of their catalytic sites.     

Multiple watershed alterations influence fish community structure in Great Plains prairie streams

Stream fish distributions are commonly linked to environmental disturbances affecting terrestrial landscapes. In Great Plains prairie streams, the independent and interactive effects of watershed impoundments and land cover changes remain poorly understood despite their prevalence and assumed contribution to declining stream fish diversity. We used structural equation models and fish community samples from third‐order streams in the Kansas River and Arkansas River basins of Kansas, USA to test the simultaneous effects of geographic location, terrestrial landscape alteration, watershed impoundments and local habitat on species richness for stream‐associated and impoundment‐associated habitat guilds. Watershed impoundment density increased from west to east in both basins, while per cent altered terrestrial landscape (urbanisation + row‐crop agriculture) averaged ~50% in the west, declined throughout the Flint Hills ecoregion and increased (Kansas River basin ~80%) or decreased (Arkansas River basin ~30%) to the east. Geographic location had the strongest effect on richness for both guilds across basins, supporting known zoogeography patterns. In addition to location, impoundment species richness was positively correlated with local habitat in both basins; whereas stream‐species richness was negatively correlated with landscape alterations (Kansas River basin) or landscape alterations and watershed impoundments (Arkansas River basin). These findings suggest that convergences in the relative proportions of impoundment and stream species (i.e., community structure) in the eastern extent of both basins are related to positive effects of increased habitat opportunities for impoundment species and negative effects caused by landscape alterations (Kansas River basin) or landscape alterations plus watershed impoundments (Arkansas River basin) for stream species.     

Movement patterns of Brook Trout in a restored coastal stream system in southern Massachusetts

Coastal Brook Trout (Salvelinus fontinalis) populations are found from northern Canada to New England. The extent of anadromy generally decreases with latitude, but the ecology and movements of more southern populations are poorly understood. We conducted a 33‐month acoustic telemetry study of Brook Trout in Red Brook, MA, and adjacent Buttermilk Bay (marine system) using 16 fixed acoustic receivers and surgically implanting acoustic transmitters in 84 individuals. Tagged Brook Trout used the stream, estuary (50% of individuals) and bay (10% of individuals). Movements into full sea water were brief when occurring. GAMM models revealed that transitions between habitat areas occurred most often in spring and fall. Environmental data suggest that use of the saline environment is limited by summer temperatures in the bay. Movements may also be related to moon phase. Compared to more northern coastal populations of Brook Trout, the Red Brook population appears to be less anadromous overall, yet the estuarine segment of the system may have considerable ecological importance as a food resource.     

Dispersal and tributary immigration by juvenile coho salmon contribute to spatial expansion during colonisation

Anadromous fishes are frequently restricted by artificial barriers to movement such as dams and culverts, so measuring dispersal helps identify sites where improved connectivity could promote range expansion and population viability. We used a combination of DNA‐based parentage analysis and mark–recapture techniques to evaluate dispersal by juvenile coho salmon (Oncorhynchus kisutch) in a population in the initial stages of colonisation following installation of fish passage structures at a previously impassable dam on the Cedar River, WA, USA. The spatial distribution of individuals within maternal families revealed that dispersal was common. Among the offspring of radio‐tagged mothers, 28% were collected outside the spawning reach and dispersed up to 6.3 km (median = 1.5 km). Most juveniles captured in a tributary (Rock Creek, where few adults spawned) had immigrated from the Cedar River and represented many different families. Juvenile dispersal therefore provided a secondary phase of spatial expansion following initial colonisation by adults. Consistent with the condition‐dependent dispersal hypothesis, juveniles that dispersed farther upstream in the tributary were larger than fish collected near the tributary mouth. Overall, the results demonstrated widespread dispersal in a system with low coho salmon densities, and this might increase the rate of population growth if it reduces the effects of local density dependence. By implication, juveniles can take advantage of rearing habitats reconnected through barrier removal, even when such areas are located several kilometres from adult breeding grounds.     

Atypical parasitic migration and necrotizing sacral myelitis due to Serratospiculoides amaculata in a prairie falcon (Falco mexicanus)

An adult, wild-caught, female prairie falcon (Falco mexicanus) was presented with the chief complaint of anorexia. Radiographic findings included increased densities within the air sacs, and coelomic endoscopy revealed numerous slender worms within the air sacs and on the serosal surfaces of the ovary, oviduct, liver, proventriculus, and ventriculus. The bird seemed to improve for a short period of time with antiparasitic therapy (ivermectin and fenbendazole) and supportive care. Twenty-one days after initial presentation, the bird became recumbent with increasing pelvic limb neurologic deficits and was euthanized. On histopathologic examination, mature nematodes and larvated eggs identified as Serratospiculoides amaculata were found within the subdural space of the distal thoracolumbar and synsacral spinal cord and within the coelomic cavity. This case suggests that S. amaculata can cause clinically significant lesions in its falconiform host with potentially fatal results.     

Binding of ciprofloxacin labelled with technetium Tc 99m versus 99mTc-pertechnetate to a live and killed equine isolate of Escherichia coli

This paper describes a simple methodology for evaluating the bacterial binding of ciprofloxacin labelled with technetium Tc 99m. Using this methodology, the binding of 99mTc-ciprofloxacin by live Escherichia coli was compared with the binding of 99mTc-ciprofloxacin by killed E. coli and the binding of 99mTc-pertechnetate (99mTcO4-) by live E. coli. The antimicrobial effect of 99mTc-ciprofloxacin on E. coli was evaluated. Four groups were defined: live E. coli with 99mTc-ciprofloxacin, live E. coli with 99mTcO4 , killed E. coli with 99mTc-ciprofloxacin, and killed E. coli with 99mTcO4-. After 0, 2, and 4 h of incubation of 1 x 10(8) colony-forming units of E. coli suspended in 5 mL of sterile distilled water with 1.85 MBq of 99mTc-ciprofloxacin or 99mTcO4, 1 mL from each sample was centrifuged. The radioactivity of the bacterial pellet and that of the supernatant were measured separately, and the percentage of sample radioactivity attributable to bacterial binding was calculated. Of the 99mTc-ciprofloxacin, 3.6% to 5.9% was bound to live or killed E. coli; only 0.1% to 0.2% of the 99mTcO4- was bound to live E. coli (P < 0.0001). No significant difference in 99mTc-ciprofloxacin binding was found between live and killed E. coli (P = 0.887). An antimicrobial effect on E. coli was seen with 99mTc-ciprofloxacin: colony counts were reduced after 4 h. The small amount of 99mTc-ciprofloxacin binding and the lack of difference in binding between live and killed E. coli may limit the utility of this methodology in evaluating the presence of E. coli infection.     

Rapid clonal propagation of rhubarb by in vitro culture of shoot-tips

In vitro culture of shoot-tips of rhubarb (Rheum rhaponticum L.) on the medium of Murashige and Skoog (1962), containing 1 mg/l of 6 benzylaminopurine and 1 mg/l of 3-indolebutyric acid, induced the development of axillary buds. Rooting was easily attained in 4–5 days by omitting the cytokinin from the basal medium. The temperature was 25 ± 1° C during the 16-h photoperiod and 20 ± 1° C during the 8-h dark period. The rooted plantlets were transplanted to soil medium with 70% success. The method described gives a multiplication rate of 5 per month.