Optimal Compost Rates for Organic Crop Production Based on a Decay Series

One of the more challenging aspects of organic farming is the development of an appropriate fertility plan, which may include crop rotation, cover crops, and/or soil amendments. When fertility is maintained by applying manure and/or compost, a pressing question is how much should be used. A framework was developed to address this question based on the idea of a decay series, which is a sequence of numbers quantifying the effects of compost on crop yield over a multi-year period. Prior research has focused on decay series expressed in nitrogen fertilizer equivalents. Given this information, I show how to calculate what manure/compost rates are needed to meet the nitrogen targets in a multi-crop rotation. Analogous results are presented for when the objective is profit rather than yield maximization. The planning framework is then generalized to include decay series where the carryover effects of manure/compost are measured, not against nitrogen fertilizer, but against new applications of the amendment. This change of basis, from nitrogen fertilizer equivalents to manure/compost equivalents, allows for field research on organically certified land and quantifies non-nutritive effects in a more meaningful way. Two case studies are presented to illustrate how this new type of decay series may be estimated and used to optimize crop production. By using data from a continuous corn (Zea mays L.) system amended with cattle manure slurry, the case study in estimation explores the methodological challenges that arise when the yield response to nitrogen fertilizer is not available as a benchmark. The case study in optimization looks at profit-maximizing compost rates for dryland, organic wheat (Triticum aestivum L.) in northern Utah

Structure-Guided Recombination Creates an Artificial Family of Cytochromes P450

Creating artificial protein families affords new opportunities to explore the determinants of structure and biological function free from many of the constraints of natural selection. We have created an artificial family comprising ~3,000 P450 heme proteins that correctly fold and incorporate a heme cofactor by recombining three cytochromes P450 at seven crossover locations chosen to minimize structural disruption. Members of this protein family differ from any known sequence at an average of 72 and by as many as 109 amino acids. Most (>73%) of the properly folded chimeric P450 heme proteins are catalytically active peroxygenases; some are more thermostable than the parent proteins. A multiple sequence alignment of 955 chimeras, including both folded and not, is a valuable resource for sequence-structure-function studies. Logistic regression analysis of the multiple sequence alignment identifies key structural contributions to cytochrome P450 heme incorporation and peroxygenase activity and suggests possible structural differences between parents CYP102A1 and CYP102A2

Compost Carryover: Nitrogen Phosphorous and FT-IR Analysis of Soil Organic Matter

Compost plays a central role in organic soil fertility plans but is bulky and costly to apply. Determining compost carryover is therefore important for cost-effective soil fertility planning. This study investigated two aspects of nutritive carryover [nitrogen and phosphorus (P)], and an indicator of non-nutritive carryover [soil organic matter (SOM)] to determine the residual effect of a one-time compost application applied at four rates in a corn-squash rotation. Crop yield was measured as an integrated carryover indicator of nutritive and non-nutritive effects. Functional groups of compost and SOM were investigated using FT-IR spectroscopy and soil organic carbon (SOC). While year to year variability was great, compost had a persistent positive effect on crop yields, evident 3 years after application with no reduction in magnitude over time. Soil nitrate was low, and additions of compost at any rate generally did not increase levels beyond the year of application, with the exception of year four. Olsen P was also low, yet was higher in amended soils than in non-amended soils 3 years after application. Pronounced polysaccharide peaks, evident in compost spectra and absent in control soil, were apparent in compost-amended soils 3 years after compost treatment and SOC was greater 2 years afterwards. Compost carryover was most pronounced in year four following the incorporation of a nitrogen-fixing cover crop. These results show that compost can influence nutritive and non-nutritive soil properties many years after incorporation, thereby reinforcing the importance of including compost in organic fertility plans despite the unpredictability of year-to-year response

Clonal diploid and autopolyploid breeding strategies to harness heterosis: insights from stochastic simulation

Breeding can change the dominance as well as additive genetic value of populations, thus utilizing heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability. However, the relative performances of RRS and other breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths, but these are sometimes outweighed by its ability to harness heterosis due to dominance. Here, we used stochastic simulation to compare genetic gain per unit cost of RRS, terminal crossing, recurrent selection on breeding value, and recurrent selection on cross performance considering different amounts of population heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid-cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. Diploid RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity and time horizon decreased. The optimal strategy depended on selection intensity, a proxy for inbreeding rate. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically did not outperform one-pool strategies regardless of the initial population heterosis

New algorithm improves fine structure of the barley consensus SNP map

<p>Abstract</p> <p>Background</p> <p>The need to integrate information from multiple linkage maps is a long-standing problem in genetics. One way to visualize the complex ordinal relationships is with a directed graph, where each vertex in the graph is a bin of markers. When there are no ordering conflicts between the linkage maps, the result is a directed acyclic graph, or DAG, which can then be linearized to produce a consensus map.</p> <p>Results</p> <p>New algorithms for the simplification and linearization of consensus graphs have been implemented as a package for the R computing environment called DAGGER. The simplified consensus graphs produced by DAGGER exactly capture the ordinal relationships present in a series of linkage maps. Using either linear or quadratic programming, DAGGER generates a consensus map with minimum error relative to the linkage maps while remaining ordinally consistent with them. Both linearization methods produce consensus maps that are compressed relative to the mean of the linkage maps. After rescaling, however, the consensus maps had higher accuracy (and higher marker density) than the individual linkage maps in genetic simulations. When applied to four barley linkage maps genotyped at nearly 3000 SNP markers, DAGGER produced a consensus map with improved fine structure compared to the existing barley consensus SNP map. The root-mean-squared error between the linkage maps and the DAGGER map was 0.82 cM per marker interval compared to 2.28 cM for the existing consensus map. Examination of the barley hardness locus at the 5HS telomere, for which there is a physical map, confirmed that the DAGGER output was more accurate for fine structure analysis.</p> <p>Conclusions</p> <p>The R package DAGGER is an effective, freely available resource for integrating the information from a set of consistent linkage maps.</p

The USDA Barley Core Collection: Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies

New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define ‘mini-core’ sets of accessions capturing the majority of the allelic diversity present in the core collection. These ‘mini-core’ sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of ‘hull cover’, ‘spike row number’, and ‘heading date’ demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections

Acrylamide-Forming Potential and Agronomic Properties of Elite US Potato Germplasm from the National Fry Processing Trial

Processed potato (Solanum tuberosum L.) products, such as chips and French fries, contribute to the dietary intake of acrylamide, a suspected human carcinogen. One of the most promising approaches for reducing its consumption is to develop and commercialize new potato varieties with low acrylamide-forming potential. To facilitate this effort, a National Fry Processing Trial (NFPT) was conducted from 2011 to 2013 in five states. More than 140 advanced breeding lines were evaluated for tuber agronomic traits and biochemical properties from harvest through 8 mo of storage. Thirty-eight and 29 entries had significantly less acrylamide in French fries than standard varieties Russet Burbank and Ranger Russet, with reductions in excess of 50%, after one and 8 mo of storage, respectively. As in previous studies, the glucose content of raw tubers was predictive of acrylamide in finished French fries (R² = 0.64–0.77). Despite its role in acrylamide formation, tuber free asparagine was not significant, potentially because it showed relatively little variation in the NFPT population. Even when glucose was included in the model as a covariate, genotype was highly significant (p = 0.001) for predicting acrylamide, indicating there may be yet-unidentified genetic loci to target in breeding. The NFPT has demonstrated that there exist many elite US breeding lines with low acrylamide-forming potential. Our ongoing challenge is to combine this trait with complex quality attributes required by the fry processing industry.This is the publisher’s final pdf. The published article is copyrighted by the Crop Science Society of America and can be found at: https://dl.sciencesocieties.org/publications/c