A Simple and Reliable Assay for Detecting Specific Nucleotide Sequences in Plants Using Optical Thin-film Biosensor Chips

Here we report the adaptation and optimization of an efficient, accurate and inexpensive assay that employs custom-designed silicon-based optical thin-film biosensor chips to detect unique transgenes in genetically modified （GM） crops and SN-P markers in model plant genomes. Briefly, aldehyde-attached sequence-specific singlestranded oligonucleotide probes are arrayed and covalently attached to a hydrazine-derivatized biosensor chip surface. Unique DNA sequences （or genes） are detected by hybridizing biotinylated PCR amplicons of the DNA sequences to probes on the chip surface. In the SN-P assay, target sequences （PCR amplicons） are hybridized in the presence of a mixture of biotinylated detector probes and a thermostable DNA ligase. Only perfect matches between the probe and target sequences, but not those with even a single nucleotide mismatch, can be covalently fixed on the chip surface. In both cases, the presence of specific target sequences is siL, nified by a color change on the chip surface （gold to blue/purple） after brief incubation with an anti-biotin IgG horseradish peroxidase （HRP） to generate a precipitable product from an HRP substrate.     

Seasonal Changes of Mineral Nutrients in Fruit and Leaves of ‘Newhall’ and ‘Skagg's Bonanza’ Navel Oranges

In southern Jiangxi province of China, ‘Newhall’(Citrus sinensis Osbeck) navel orange presented a conspicuous symptom of boron (B) deficiency in mature leaves, whereas B deficiency symptoms were not manifested on ‘Skagg's Bonanza’(C. sinensis Osbeck) navel orange. In this study, changes in concentrations of B, calcium (Ca), potassium (K), magnesium (Mg), manganese (Mn), and zinc (Zn) were comparatively investigated in the structural parts of the fruit (rind and pulp) and leaves (old leaves from last season and spring-flush leaves from current year) of ‘Newhall’ and ‘Skagg's Bonanza’ navel orange during the growing season. Two peaks of B concentrations were observed in the rind of the two cultivars during fruitlet growth and fruit enlargement, respectively. Boron concentrations were relatively high in the rind during fruitlet growth, and then decreased in both rind and pulp, whereas, during middle and late fruit enlargement significant increases were found for B in both rind and pulp of the two cultivars. Boron concentrations in old leaves of ‘Newhall’ decreased progressively and remained relatively low, whereas that of ‘Skagg's Bonanza’ was relatively high and changed slightly as the season progresses. Both Ca and K concentrations were above the critical threshold values, while their dynamics were reverse to that of B in fruit and leaves during certain times. Old leaf Mg concentrations of samples at 140 days after full bloom from the two cultivars and spring-flush leaves from ‘Newhall’ were below the threshold limit for sufficiency. In addition, Mg in old leaves was much lower from ‘Newhall’ than from ‘Skagg's Bonanza’. Spring-flush leaf concentrations of Mn and Zn and Mn concentrations in old leaves from ‘Newhall’ were relatively lacking during middle and late season, which accelerated the occurrence of B deficiency symptoms on mature leaves of ‘Newhall.’     

Impacts of soil erosion on organic carbon and nutrient dynamics in an alpine grassland soil

The impact of soil erosion on the nutrient dynamics in alpine grassland soils is still an essential problem. Selecting a grass-covered hillslope in eastern Tibet Plateau, the cesium-137 (¹³⁷Cs) technique was used to determine the impacts of soil erosion on soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), and total potassium (TK). The ¹³⁷Cs data revealed that there were distinct soil redistribution patterns in different hillslope positions because of the influences of slope runoff, plant coverage and grazing activity. For the upper slope, soil erosion first decreased downward, followed by soil deposition in its lower part. In contrast, for middle and toe slopes, there was an increasing soil erosion along a downslope transect. Across the lower slope, soil erosion showed an irregular variation. Influenced by the selective transport of water erosion, SOC, TN and TP storage decreased with increasing soil erosion in upper, middle and toe slopes. In contrast, SOC, TN and TP storage varied little with soil erosion in the lower slope. On the whole hillslope, TK storage also varied little with soil erosion due to the large amount of potassium elements derived from soil parent materials. Particularly noteworthy was the greatest storage of SOC, TN and TP in the lower slope where most obvious net soil erosion occurred, which is closely related to the humus accumulation combined with gravel separation as well as weathering and pedogenesis of parent rocks induced by soil freeze-thaw.     

Simulating site-specific impacts of climate change on soil erosion and surface hydrology in southern Loess Plateau of China

Proper spatial and temporal treatments of climate change scenarios projected by General Circulation Models (GCMs) are critical to accurate assessment of climatic impacts on natural resources and ecosystems. The objective of this study was to evaluate the site-specific impacts of climate change on soil erosion and surface hydrology at the Changwu station of Shaanxi, China using a new spatiotemporal downscaling method. The Water Erosion Prediction Project (WEPP) model and climate change scenarios projected by the U.K. Hadley Centre's GCM (HadCM3) under the A2, B2, and GGa emissions scenarios were used in this study. The monthly precipitation and temperature projections were downloaded for the periods of 1900–1999 and 2010–2039 for the grid box containing the Changwu station. Univariate transfer functions were derived by matching probability distributions between station-measured and GCM-projected monthly precipitation and temperature for the 1950–1999 period. The derived functions were used to spatially downscale the GCM monthly projections of 2010–2039 in the grid box to the Changwu station. The downscaled monthly data were further disaggregated to daily weather series using a stochastic weather generator (CLIGEN). The HadCM3 projected that average annual precipitation during 2010–2039 would increase by 4 to 18% at Changwu and that frequency and intensity of large storms would also increase. Under the conventional tillage, simulated percent increases during 2010–2039, compared with the present climate, would be 49–112% for runoff and 31–167% for soil loss. However, simulated soil losses under the conservation tillage during 2010–2039 would be reduced by 39–51% compared with those under the conventional tillage in the present climate. The considerable reduction in soil loss in the conservation tillage indicates the importance of adopting conservation tillage in the region to control soil erosion under climate change.     

The Optimization for Crop Planning and Some Advances for Water-Saving Crop Planning in the Semiarid Loess Plateau of China

The establishment of water-saving crop planning is an inevitable choice of the water-saving agriculture for the water-deficiency region in the arid and semiarid Loess Plateau of China and the world. The water-saving crop planning refers to the planting structure that centres the adjustment of the crop's adaptation to water, the optimization of temporal and spatial layout for crops, the local natural resources, marketing resources, human resources and financial input to enable region or basin with limited water resources to achieve the maximum economic, social and ecological benefits of planting industry under certain technology and economy. After the analysis on the research progress of optimization theory, optimization goals, optimization methods of water-saving cultivation structure and macro-control measures, it is pointed out that the main deficiencies of the current research of water-saving cultivation pattern optimization are lacking of a strong theoretical basis, and the immaturity of optimization technologies. The future crucial research direction will focus on five aspects such as the special optimization theory system, the division methods by studying the watershed unit and using 3S technology, optimization model based on multi-objective evolutionary algorithm, evaluation of rationality and macro-control measures on the basis of the public participation.     

The genetic relationship between popping expansion volume and two yield components in popcorn using unconditional and conditional QTL analysis

Popping expansion volume (PEV) is the most important quality trait in popcorn, while its germplasm is inferior to normal dent/flint corn in yield. In this study, 259 F_2:3 families, developed from the cross between a dent corn inbred Dan232 and a popcorn inbred N04, were evaluated for their PEV, grain weight per plant (GWP) and 100-grain weight (100 GW) in two environments. The genetic relationship between PEV and GWP, and 100 GW on individual gene loci were evaluated using unconditional and conditional QTL mapping methods. In total, five, one and three unconditional QTL were identified for PEV, GWP, and 100 GW, respectively. The positive alleles of all QTL for PEV were from N04, while positive alleles of all QTL for GWP and 100 GW were from Dan232. In conditional mapping, one and two QTL failed to be detected, and all four additional QTL were detected. Nevertheless, three QTL were identified, which controlled PEV independently from GWP/100 GW. They seemed to be potential candidates in popcorn breeding to increase PEV without decreasing GWP/100 GW. The results suggested that for significantly correlated traits, the conditional QTL mapping method could be used to dissect the genetic interrelationship between traits at the level of individual QTL, as well as reveal additional QTL that were undetectable by unconditional mapping.     

Effects of plastic film mulch and tillage on maize productivity and soil parameters

This paper determined the effects of mulching time for double furrows and ridges using plastic film on soil water status, grain yield of maize, soil quality, and economic benefits. The study was conducted in a typical semiarid area during two growing seasons of 2006–2007 with the following three treatments: (i) plastic film mulching at maize sowing with conventional tillage, and the film was removed at harvest (CK); (ii) mulching applied 30 d before sowing with conventional tillage, and the film was removed at harvest (T1); and (iii) mulching at sowing with no-tillage, and the film left on the field after harvest in the first season and used for mulching in the second season (T2). The T1 in both years and T2 in the second year (2007) improved soil water content (in the 0–60 cm layer) and temperature (10 cm) at sowing compared with CK. After the two seasons, the soil water content was significantly higher in the 0–80 cm soil layer in CK and T1, and in the 0–120 cm soil layer in T2; however, it decreased significantly in 140–200 cm soil layer in CK and T1, compared to their initial values at sowing in April 2006, and there was no significant change in T2. The rainfall storage in the 0–200 cm soil layer during the non-growing season (late September 2006 to late April 2007) was 18.2 mm in CK, 34.0 mm in T1, and 59.7 mm in T2, and the rainfall storage in 100–200 cm soil layer was 16.5 and 18.6 mm higher in T2 than in CK and T1, respectively. In 2006, there were no significant differences in yield and water use efficiency (WUE) in all treatments. In 2007, the yield in T1 was significantly higher than in T2, but yields in T2 and CK were not significantly different, and there was no significant difference in WUE among treatments. Soil organic carbon (SOC) (0–20 cm) decreased in CK and T1, but increased (by 2.7%) in T2 at harvesting in September 2007 from the initial value of sowing in April 2006. The ratio of output to input was 1.32:1 for CK, 1.40:1 for T1, and 1.67:1 for T2 averaged across the two seasons. Therefore, T2 was a more sustainable model for increasing water storage, producing greater economic benefit and maintaining SOC balance for maize production in semiarid area.     

Assessment of partial resistance to powdery mildew in Chinese wheat varieties

Field trials in two cropping seasons and two locations in central China were conducted on 60 Chinese autumn‐sown wheat varieties to assess their partial resistance to powdery mildew. Mean levels of disease severity ranged from close to 0 to more than 90%. The method of inoculation and the location in which trials were conducted affected the relative performance of the varieties, but these effects were much smaller than the main effect of variety. The area under the disease progress curve was highly correlated with final disease severity, but both were poorly correlated with apparent infection rate. Disease severity was regressed against frequencies of virulence in the Blumeria graminis (syn. Erysiphe graminis) f sp. tritici populations in the trial plots. A vertical distance (D) from the mean mildew severity to the fitted line was calculated for each variety and was used to quantify partial resistance. Five of the 60 varieties, ‘Hx8541’, ‘E28547’, ‘Chuan1066’, ‘Zhe88pin6’ and ‘Lin5064’, consistently expressed relatively low levels of disease despite high frequencies of virulence in the pathogen and had consistently high D‐values. They may therefore have good levels of partial resistance.     

Genetic mapping of loci determining long glumes in the genus Triticum

Elongated glumes are present in thetetraploid wheat species T.polonicum, T. turanicum, T.durum convar. falcatum and in thehexaploid species T. petropavlovskyi.Inheritance of glume length was studiedwith the aim to map the respective lociusing wheat microsatellite markers. In T. polonicum and T. petropavlovskyiloci conferring long glume were mapped nearthe centromere on chromosome 7A. These twoloci are designated P-A ^pol 1 andP-A ^pet 1, respectively. It isshown that both are probably homoeoallelicto each other and to the P gene ofT. ispahanicum on chromosome 7B. The loci determining elongated glumes in T. turanicum and T. durum conv. falcatum are not homoeologous to the P loci in the centromeric region of thegroup 7 chromosomes.     

A SCAR marker linked to the N gene for resistance to root knot nematodes (Meloidogyne spp.) in pepper (Capsicum annuum L.)

The root-knot nematodes (Meloidogyne spp.) are important nematode pests and cause serious diseases in pepper in the world. No molecular markers linked to the nematodes resistance N gene have been reported. In this paper, ‘Carolina Wonder’ (Capsicum annuum L.), a sweet pepper line resistant to root-knot nematode with N gene, ‘20080-5-29’ (C. annuum L.), an inbred line susceptible to root-knot nematode with good horticultural characteristics, and their F₂ progeny with 320 individuals were used as materials. Evaluation of resistance and susceptibility of parental lines, F₁ and F₂ progeny inoculated with root-knot nematodes (Meloidogyne incognita) were carried out. ‘Bulked segregant analysis’ method was used to search for polymorphic markers from 512 pairs of AFLP primers. Based on the assessment of resistance and susceptibility and polymorphism of the AFLP marker in F₂ population, the genetic linkage distance between the AFLP marker and the N gene was estimated. One AFLP marker E39/M41-339 was obtained and transferred to a SCAR marker amplifying a 315 bp DNA fragment linked to the N resistant allele and a 331 bp fragment linked to the N⁺ susceptible allele. The distance between the molecular marker and the nematodes resistance N gene is 6.3 cM. This research delivered a valuable tool for the marker assisted selection of nematodes resistance in pepper.