Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial.

KEY MESSAGE: We find evidence of selection for local adaptation and extensive genotype-by-environment interaction in the potato National Chip Processing Trial (NCPT). We present a novel method for dissecting the interplay between selection, local adaptation and environmental response in plant breeding schemes. Balancing local adaptation and the desire for widely adapted cultivars is challenging for plant breeders and makes genotype-by-environment interactions (GxE) an important target of selection. Selecting for GxE requires plant breeders to evaluate plants across multiple environments. One way breeders have accomplished this is to test advanced materials across many locations. Public potato breeders test advanced breeding material in the National Chip Processing Trial (NCPT), a public-private partnership where breeders from ten institutions submit advanced chip lines to be evaluated in up to ten locations across the country. These clones are genotyped and phenotyped for important agronomic traits. We used these data to interrogate the NCPT for GxE. Further, because breeders submitting clones to the NCPT select in a relatively small geographic range for the first 3 years of selection, we examined these data for evidence of incidental selection for local adaptation, and the alleles underlying it, using an environmental genome-wide association study (envGWAS). We found genomic regions associated with continuous environmental variables and discrete breeding programs, as well as regions of the genome potentially underlying GxE for yield.

Evaluating the impact of modeling the family effect for clonal selection in potato-breeding programs.

Because of its wide distribution, high yield potential, and short cycle, the potato has become essential for global food security. However, the complexity of tetrasomic inheritance, the high level of heterozygosity of the parents, the low multiplication rate of tubers, and the genotype-by-environment interactions impose severe challenges on tetraploid potato-breeding programs. The initial stages of selection take place in experiments with low selection accuracy for many of the quantitative traits of interest, for example, tuber yield. The goal of this study was to investigate the contribution of incorporating a family effect in the estimation of the total genotypic effect and selection of clones in the initial stage of a potato-breeding program. The evaluation included single trials (STs) and multi-environment trials (METs). A total of 1,280 clones from 67 full-sib families from the potato-breeding program at Universidade Federal de Lavras were evaluated for the traits total tuber yield and specific gravity. These clones were distributed in six evaluated trials that varied according to the heat stress level: without heat stress, moderate heat stress, and high heat stress. To verify the importance of the family effect, models with and without the family effect were compared for the analysis of ST and MET data for both traits. The models that included the family effect were better adjusted in the ST and MET data analyses for both traits, except when the family effect was not significant. Furthermore, the inclusion of the family effect increased the selective efficiency of clones in both ST and MET analyses via an increase in the accuracy of the total genotypic value. These same models also allowed the prediction of clone effects more realistically, as the variance components associated with family and clone effects within a family were not confounded. Thus, clonal selection based on the total genotypic value, combining the effects of family and clones within a family, proved to be a good alternative for potato-breeding programs that can accommodate the logistic and data tracking required in the breeding program.

Enhanced Agronomic Efficiency Using a New Controlled-Released, Polymeric-Coated Nitrogen Fertilizer in Rice.

Fertilizer-use efficiency is one of the most critical concerns in rice cultivation to reduce N losses, increase yields, and improve crop management. The effects of a new polymeric-coated controlled-release fertilizer (CRF) were compared to those of other slow-release and traditional fertilizers in a microscale experiment, which was carried out in cuvettes under partly controlled ambient conditions, and a large-scale field experiment. To evaluate the fertilizer's efficiency, nitrogen and water-use efficiency were calculated using the measurement of different photosynthetic and crop yield parameters. Improved responses regarding some of the analyzed physiological and growth parameters were observed for those plants fertilized with the new CRF. In the microscale experiment, significantly increased yields (ca. 35%) were produced in the plants treated with CRF as compared to traditional fertilizer. These results were in accordance with ca. 24% significant increased levels of N in leaves of CRF-treated plants, besides increased P, Fe, Mn, and cytokinin contents. At the field scale, similar yields were obtained with the slow-release or traditional fertilizers and CRF at a 20% reduced N dose. The new controlled-release fertilizer is a urea-based fertilizer coated with lignosulfonates, which is cheaply produced from the waste of pulp and wood industries, containing humic acids as biostimulants. In conclusion, CRF is recommended to facilitate rice crop management and to reduce contamination, as it can be formulated with lower N doses and because it is ecological manufacturing.

Selenium impedes cadmium and arsenic toxicity in potato by modulating carbohydrate and nitrogen metabolism.

Past studies have already determined that selenium (Se) is very effective in alleviating cell oxidative damage caused by various abiotic stresses in plants. Past studies have also indicated other physiological pathways by which Se may benefit plants. In order to better understand the full array of potential applications for Se in agriculture, this study investigated the influence of Se on carbohydrate and nitrogen (N) metabolism in potato plants (Solanum tuberosum L. cv. Sante) grown under cadmium (Cd) and/or arsenic (As) toxicity. Potato plants were grown in a growth chamber and fertigated with Hoagland nutrient solution with or without Se (9 µM). After 48-d of growth under Cd (40 µM) and/or As (40 µM) stress, carbohydrate and N metabolism in leaves, roots and stolons were measured. For carbohydrate metabolism, various sugars-i.e., sucrose, starch, glucose, fructose, and total soluble sugar contents (TSSC)-and the activities of enzymes associated with sucrose metabolism and glycolysis-i.e., acid invertase (AI), neutral invertase (NI), sucrose-synthetase (SS), sucrose phosphatesynthetase (SPS), fructokinase (FK), hexokinase (HK), phosphofructokinase (PFK), and pyruvatekinase (PK)-were measured. For N metabolism, NO3-, NO2- and NH4+ contents along with the enzymatic activities of nitrate reductase (NRA), nitrite reductase (NiRA), glutamine-synthetase (GS), and glutamate-synthetase (GOGAT) were measured. Overall, Cd and/or As treatments had reduced plant growth relative to those plants grown without heavy metal toxicity, due to hindered photosynthesis and alterations in N metabolism and glycolysis. Regarding N metabolism, heavy metal toxicity caused a reduction in NO3- and NO2- content and NRA and NiRA enzymatic activity and enhanced NH4+ content and GDH activity in leaves, roots and stolons. Regarding glycolysis, the activity of enzymes of glycolysis-i.e., FK, HK, PFK, and PK-were also reduced. In the C metabolism study, plants combatted Cd and As toxicity naturally by an adaptation mechanism which caused an increase in soluble sugars (fructose, glucose, sucrose) by increasing NI, SS and SSP enzymatic activity. Supplementation with Se in the Cd and/or As treatments in the carbohydrate and N metabolism studies improved plant growth. Selenium supplementation in the Cd and As treatments decreased Cd and/or As content in the plant tissue and alleviating the Cd- and/or As-induced toxicity by enhancing the C-metabolism adaptation mechanism. Applying Se to Cd and As treatments also decreased nitrogen losses by hindering Cd- and As-induced changes in the N-metabolism. Se also limited Cd and As accumulation in the plant tissue by the antagonistic effect between Cd/Se and As/Se in the roots. The results of this study indicate that in the presence of Cd and/or As. soil toxicity, Se may be a powerful tool for promoting plant growth.

Monitoring of nitrate leaching in sandy soils: comparison of three methods.

Proper N fertilizer and irrigation management can reduce nitrate leaching while maintaining crop yield, which is critical to enhance the sustainability of vegetable production on soils with poor water and nutrient-holding capacities. This study evaluated different methods to measure nitrate leaching in mulched drip-irrigated zucchini, pepper, and tomato production systems. Fertigation rates were 145 and 217 kg N ha(-1) for zucchini; 192 and 288 kg N ha(-1) for pepper; and 208 and 312 kg N ha(-1) for tomato. Irrigation was either applied at a fixed daily rate or based on threshold values of soil moisture sensors placed in production beds. Ceramic suction cup lysimeters, subsurface drainage lysimeters and soil cores were used to access the interactive effects of N rate and irrigation management on N leaching. Irrigation treatments and N rate interaction effects on N leaching were significant for all crops. Applying N rates in excess of standard recommendations increased N leaching by 64, 59, and 32%, respectively, for pepper, tomato, and zucchini crops. Independent of the irrigation treatment or nitrogen rate, N leaching values measured from the ceramic cup lysimeter-based N leaching values were lower than the values from the drainage lysimeter and soil coring methods. However, overall nitrate concentration patterns were similar for all methods when the nitrate concentration and leached volume were relatively low.