Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

GGE biplot analysis of multi-environment yield trials of rice produced in a temperate climate

Low temperature is one of the main environmental constraints for rice ( Oryza sativa L.) grain production yield. It is known that multi-environment studies play a critical role in the sustainability of rice production across diverse environments. However, there are few studies based on multi-environment studies of rice in temperate climates. The aim was to study the performance of rice plants in cold environments. Four experimental lines and six cultivars were evaluated at three locations during three seasons. The grain yield data were analyzed with ANOVA, mixed models based on the best linear unbiased predictors (BLUPs), and genotype plus Genotype × Environment interaction (GGE) biplot. High genotype contribution (> 25%) was observed in grain yield and the interaction between genotype and locations was not very important. Results also showed that ‘Quila 241319’ was the best experimental line with the highest grain yield (11.3 t ha-1) and grain yield stability across the environments; commercial cultivars were classified as medium grain yield genotypes.

Effects of trunk-shaker harvester and ethephon on plant water status, leaf gas exchange, and yield of citrus cultivated under Mediterranean conditions

This work was aimed to study whether the application of ethephon as an abscission agent and mechanical harvest using a trunk shaker have any effect on plant water status, leaf gas exchange, and yield of mandarin and orange trees cultivated under Mediterranean conditions. The experiment was performed from 2008 to 2011 in five commercial orchards where parameters related to the plant water status and leaf gas exchange were measured before the application of ethephon, at harvest time and at different occasions after harvest. In addition, the effects of ethephon dose on yield in the current and subsequent seasons were also evaluated. Results showed that ethephon applications and mechanical harvest did not detrimentally affect plant water status in any of the cultivars studied. Furthermore, either had no effect or had a short temporal decrease effect on leaf gas exchange depending on the cultivar studied although with no consequences for the fruit yield obtained during the current season. Increasing ethephon doses led to fruit yield reductions in the mandarin ‘Orogrande’ trees in subsequent seasons. When trunk-shaker and ethephon applications were combined, however, yields from the late-maturing orange significantly decline in subsequent seasons. Overall, results show that using a trunk shaker is a viable technique to mechanically harvest citrus trees destined to both fresh and industry market and can be considered as an alternative to the traditional manual harvest usually performed under Mediterranean conditions. However, its use cannot be recommended for late-maturing oranges, such as the ‘Navel Lane Late’ in which mature fruit and fruitlets coexist in the tree at the time of harvest.

Evaluation of water use, yield and water productivity of a high-density orchard (cv. Cobrançosa) subjected to different irrigation regimes – An account of four years

The impact of different irrigation scheduling regimes on the water use, yield and water productivity from a high-density olive grove cv. Cobrançosa in southern Portugal was assessed during the irrigation seasons of 2011, 2012, 2013 and 2014. The experiments were conducted in a commercial olive orchard at the Herdade Álamo de Cima, near Évora (38o 29' 49.44'' N, 7o 45' 8.83'' W; alt. 75 m) in southern Alentejo, Portugal. The orchard was established with 10-year old Cobrançosa trees in grids of 8.0 x 4.2 m (300 trees ha-1) in the E-W direction, and experiments conducted on a shallow sandy loam Regosoil Haplic soil. From mid-May to the end of September the orchard was irrigated and three plots were subjected to one of two irrigation treatments: a control treatment A, irrigated to replace 100% ETc, a moderate deficit irrigation treatment B irrigated to 70% of ETc, and a more severe deficit irrigation treatment C that provided for approximately 50% of ETc. Daily tree transpiration rates were obtained by continuously monitoring of sap flow in representative trees per treatment. Among the irrigated treatments, water use efficiency (WUE, ratio of water used to irrigation- water applied) of treatment C was the highest, with a value of 0.89, being treatment B slightly lower, with a WUE of 0.76. Olive harvest for 2012 was an exceptional “on year”. Bearing yields showed contrasting differences within years where an “on year” was followed by an “off year”. In 2011 and 2012 treatment B yields were 41 and 50% higher than treatment C, respectively. In 2013 treatment B yield was 45% higher than yield of the fully irrigated treatment A, and treatment C showed practically the same yield than treatment A. In the “on year” of 2014 treatment B averaged 48% higher yield than treatment C. Treatment B farm irrigation water productivity (WPI-Farm, ratio of yield to water applied) was the highest among all treatments. Treatment A showed the lowest conversion efficiency of all treatments, indicating treatment B as the adequate deficit irrigation treatment for our Cobrançosa orchard

Adaptability and phenotypic stability of soybean cultivars for grain yield and oil content.

ABSTRACT. The aim of this study was to verify the adaptability and stability of soybean cultivars with regards to yield and oil content. Data of soybean yield and oil content were used from experiments set up in six environments in the 2011/12 and 2012/13 crop seasons in the municipalities of Patos de Minas, Uberaba, Lavras, and São Gotardo, Minas Gerais, Brazil, testing 36 commercial soybean cultivars of both conventional and transgenic varieties. The Wricke method and GGE biplot analysis were used to evaluate adaptability and stability of these cultivars. Large variations were observed in grain yield in relation to the different environments studied, showing that these materials are adaptable. The cultivars exhibited significant differences in oil content. The cultivars BRSGO204 (Goiânia) and BRSMG (Garantia) exhibited the greatest average grain yield in the different environments studied, and the cultivar BRSMG 760 SRR had the greatest oil content among the cultivars evaluated. Ecovalence was adopted to identify the most stable cultivars, and the estimates were nearly uniform both for grain yield and oil content, showing a variation of 0.07 and 0.01%, respectively. The GGE biplot was efficient at identifying cultivars with high adaptability and phenotype stability.

Winter cover crops on weed infestation and maize yield.

The establishment of commercial crops in succession to winter cover crops that leaves a dense straw layer provides significantly suppression of weeds. The objective of this work was to evaluate the suppressive potential of winter cover crops on weed infestation in maize and its effect on the yield of the maize sown in succession.