Impact of land‐use intensity on the relationships between vegetation indices,photosynthesis and biomass of intensively and extensively managed grassland fens

Vegetation indices are widely used as model inputs and for non‐destructive estimation of biomass and photosynthesis, but there have been few validation studies of the underlying relationships. To test their applicability on temperate fens and the impact of management intensity, we investigated the relationships between normalized difference vegetation index (NDVI), leaf area index (LAI), brown and green above‐ground biomass and photosynthesis potential (PP). Only the linear relationship between NDVI and PP was management independent (R² = 0·53). LAI to PP was described by a site‐specific and negative logarithmic function (R² = 0·07–0·68). The hyperbolic relationship of LAI versus NDVI showed a high residual standard error (s.e.) of 1·71–1·84 and differed between extensive and intensive meadows. Biomass and LAI correlated poorly (R² = 0·30), with high species‐specific variability. Intensive meadows had a higher ratio of LAI to biomass than extensive grasslands. The fraction of green to total biomass versus NDVI showed considerable noise (s.e. = 0·13). These relationships were relatively weak compared with results from other ecosystems. A likely explanation could be the high amount of standing litter, which was unevenly distributed within the vegetation canopy depending on the season and on the timing of cutting events. Our results show there is high uncertainty in the application of the relationships on temperate fen meadows. For reliable estimations, management intensity needs to be taken into account and several direct measurements throughout the year are required for site‐specific correction of the relationships, especially under extensive management. Using NDVI instead of LAI could reduce uncertainty in photosynthesis models.     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.

     

P0 protein of cotton leafroll dwarf virus-atypical isolate is a weak RNA silencing suppressor and the avirulence determinant that breaks the cotton Cbd gene-based resistance

Cotton blue disease (CBD) is the most important disease present in cotton crops in South America and cotton leafroll dwarf virus (CLRDV) is the causal agent. The disease has been controlled by sowing cotton varieties resistant to CLRDV. However, in the 2009/10 growing season, an outbreak due to an atypical CLRDV isolate (CLRDV-at) occurred in northwest Argentina. Although CLRDV and CLRDV-at genomes are very closely related, the symptoms they produce in cotton plants are quite different. P0 is the most divergent protein between the isolates and in CLRDV is a silencing suppressor protein. This work characterized the silencing suppressor activity of the P0 protein encoded by CLRDV-at (P0^CL-at) and evaluated its role in Cbd-resistance break in cotton plants. It was demonstrated that P0^CL-at, despite having a mutation in the consensus of the F-box-like motif, was able to suppress local RNA silencing, but displayed lower activity than P0^CL. P0^CL and P0^CL-at showed no differences in the interaction with Gossypium hirsutum SKP1 orthologue (GSK1) and Nicotiana benthamiana SKP1 and both P0 proteins triggered destabilization of ARGONAUTE1. However, when the ability to enhance PVX symptoms was evaluated, P0^CL-at was shown to be a weaker pathogenicity factor than P0^CL in N. benthamiana. Interestingly, trans-expressed P0^CL-at enabled CLRDV to systemically infect CBD-resistant plants, and a chimeric CLRDV-P0^CL-at infectious clone succeeded in establishing infection in CBD-resistant cotton varieties with symptoms resembling those produced by CLRDV-at. These results strongly suggest that P0^CL-at is the avirulence (Avr) determinant involved in breaking cotton Cbd gene-based resistance.     

Strategy to identify resistance to white mould associated with high yield for irrigated common bean in Brazil

Development of common bean cultivars with partial white mould resistance through breeding techniques has been a challenge in Brazil. As yet, lines/cultivars from breeding programmes have not been investigated for resistance; therefore, this study screened 107 lines/cultivars for their reactions to white mould in 14 preliminary trials conducted under irrigation. Thirteen resistant lines/cultivars (three of Andean origin) and six Mesoamerican cultivars (three intermediately resistant and three susceptible) were selected for further investigation. These lines/cultivars and the resistant control A195 were evaluated in six advanced trials and two straw tests to assess the effectiveness of the screening procedure. In 11 preliminary trials, screenings were performed under moderate/high or higher disease pressure. These pressures occurred in two advanced trials in which, when yields were averaged across moderate/high and high pressures, 10 Mesoamerican lines/cultivars selected for resistance yielded 14%, 23%, and 38% more than intermediately resistant cultivars, A195, and susceptible cultivars, with median disease ratings (1–9 scale) of 4.5, 5.7, 5.7, and 6.7, respectively. In the straw test, three Andean lines/cultivars (A195 included) and two susceptible cultivars in the field were among those with the highest levels of physiological resistance. Thus, field rating under high disease pressure and greenhouse rating did not correlate significantly, suggesting that field trials are critical to evaluating resistance and to identifying high-yielding beans. Therefore, lines/cultivars from breeding programmes assessed in field trials may provide a low cost and fast way to identify high-yielding bean cultivars with partial resistance to white mould in the subtropical southern hemisphere.     

Surgical treatment of a mammary gland comedocarcinoma in an Arabian mare: Post-operative management,and histopathological and immunohistochemical features

A lactating 20-year-old, brown, Arabian mare, weighing about 300 kg, presented for bleeding from one teat and severe swelling of the entire mammary gland. The mare had untreated mastitis 10 months before. Consequently, a gangrenous teat developed after chronic bloody and purulent discharges. The teat was removed surgically by the field veterinarian. At that time, the mammary gland increased in size. Bloody and purulent discharges restarted 10 days previously. Under general anaesthesia, the entire mammary gland was removed. Comedocarcinoma was diagnosed by histopathological assessment. Immunohistochemical staining was performed for pan-cytokeratin and vimentin. Microscopic examination of immunohistochemical stained slides revealed expression of pan-cytokeratin. In conclusion, this report describes clinical, macroscopic, histopathological and immunohistochemical characteristics of comedocarcinoma that did not metastasise to regional lymph nodes. Reports in the field of equine oncology contribute to improved general knowledge in equine medicine, contributing to better diagnosis and treatment.     

Evaluating diverse systems of tobacco genetic resistance to Phytophthora nicotianae in Yunnan,China

Black shank, caused by the soilborne pathogen Phytophthora nicotianae, is one of the most devastating diseases affecting tobacco production in China. The most effective strategy for reducing economic loss from this pathogen is development and use of resistant tobacco varieties. Multiple sources and systems of resistance have been developed in the Western Hemisphere; however, populations of P. nicotianae are variable around the world, including the predominance of different races. Different P. nicotianae isolates may react differently on tobacco plants with different systems of resistance, a possibility that could complicate the breeding of cultivars with resistance that is effective in different tobacco production regions worldwide. The objective of this research was to evaluate an array of tobacco germplasm possessing different systems of genetic resistance to black shank disease in tobacco-growing regions of Yunnan, China. Resistance types included simply inherited resistance mechanisms introgressed from wild Nicotiana relatives and polygenic partial resistance systems of N. tabacum origin. The loci of Wz exhibited high level resistance to black shank in the five diverse disease environments in Yunnan, China. K326 Php/−Wz/− genotype and Beinhart 1000 exhibited the greatest levels of resistance in both 2015 and 2016. Field observed results for 13 tobacco genotypes were highly correlated with those tested in growth chamber evaluation. These findings suggest that both Wz− and Beinhart 1000-mediated resistance have important commercial value in flue-cured tobacco breeding programmes in China. Cultivars developed for black shank resistance in China may also have utility in other tobacco-growing areas.     

Inhibition of postharvest senescence of green leafy vegetables by exogenous D-cysteine and L-cysteine as precursors of hydrogen sulphide

Hydrogen sulphide (H₂S) inhibits senescence in harvested fruit and vegetables but presents logistical, safety and regulatory issues to become a commercial treatment. D-cysteine and L-cysteine are semi-essential amino acids that are metabolised to hydrogen sulphide by plant tissues albeit by different pathways. This paper examines the effect of cysteine on postharvest senescence of three green leafy vegetables. Spraying pak choy leaves with 10 mmol D-cysteine, L-cysteine or DL-cysteine inhibited leaf senescence through a delayed loss of green colour expressed as market life, reduced respiration rate and reduced ethylene production. The beneficial effects of cysteine were similar to those achieved by fumigation with hydrogen sulphide. L-cysteine sprays on parsley and peppermint leaves also showed reduced leaf colour loss and respiration compared to untreated leaves. Cysteine, either as the racemate or individual enantiomers, is considered to have commercial potential for green leafy vegetables as it provides the beneficial effect of hydrogen sulphide but should be easier to register for commercial use due to the GRAS status of L-cysteine.     

Emergence of Edwardsiella piscicida in Farmed Channel ♀, Ictalurus punctatus × Blue ♂, Ictalurus furcatus,Hybrid Catfish Cultured in Mississippi

There is a trend toward the increased incidence and prevalence of Edwardsiella piscicida septicemia in US catfish aquaculture, particularly in channel ♀, Ictalurus punctatus, × blue ♂, I. furcatus, hybrid catfish. From 2013 to 2017, a total of 3242 disease case submissions were made to the Aquatic Research and Diagnostic Laboratory (ARDL) at the Thad Cochran National Warmwater Aquaculture Center in Stoneville, MS. Of these, 1400 (43.2%) were hybrids. E. piscicida was suspected in 138 (4.3%) of cases, the majority of which (89.1%) were from hybrid catfish. A molecular survey of these isolates confirmed the majority (92.0%) to be E. piscicida. Furthermore, cases of E. piscicida from hybrids submitted to the ARDL and the Aquatic Diagnostic Laboratory of the Mississippi State University College of Veterinary Medicine in Starkville, MS, were documented for gross lesions and histological analysis. Grossly, E. piscicida presents with small dermal ulcerations, a raised fluid‐filled cranial midline lesion that is frequently ulcerated, hemorrhage in the gills, exophthalmia, and abdominal distension. Internally, lesions include splenomegaly, straw‐colored ascites, renomegaly, and occasionally hemorrhagic intestines. Histopathological examination is in agreement with gross observations, and infected fish repeatedly demonstrate a mononuclear meningoencephalitis, hemorrhagic branchitis, splenitis, ulcerative dermatitis, granulomatous interstitial nephritis, and hepatitis coupled with a hemorrhagic enteritis.     

Secondary Stress Responses in Juvenile Brazilian Flounder,Paralichthys orbignyanus,throughout and after Exposure to Sublethal Levels of Ammonia and Nitrite

This study investigated the secondary stress responses of Paralichthys orbignyanus exposed to ammonia and nitrite and after recovery. Fish were exposed to 0.12, 0.28, and 0.57 mg NH₃‐N/L, or 5.72, 10.43, and 15.27 mg NO₂‐N/L for 10 d followed by the same time length for recovery. Ammonia‐ and nitrite‐free water was used as a control treatment. Blood samples were collected after 1, 5, and 10 d of exposure and after recovery. Fish exposed to ammonia presented lower and higher glucose levels after 10 d of exposure and recovery, respectively. Ammonia induced initial and transient ionic disturbances and metabolic alkalosis. Nitrite exposure caused hyperglycemia, increased plasma K⁺ levels, and respiratory alkalosis, whereas metabolic acidosis was observed after recovery. Increased proportion of monocytes and/or granulocytes and reduced number of lymphocytes were demonstrated in fish exposed to 0.28 mg NH₃‐N/L (Day 1) and 10.43 mg NO₂‐N/L (Day 5) and after recovery in the 0.28 and 0.57 mg NH₃‐N/L treatments. Exposure to ammonia decreased the proportion of granulocytes on Day 5. In conclusion, exposure to concentrations at 0.12 mg NH₃‐N/L and 5.72 mg NO₂‐N/L provoked physiological disorders in Brazilian flounder. Nonetheless, fish exposed to 5.72 mg NO₂‐N/L following a 10‐d recovery period showed complete resumption of homeostasis.