Summary 1. Neonicotinoids are now the most widely used insecticides in the world. They act systemically, travelling through plant tissues and protecting all parts of the crop, and are widely applied as seed dressings. As neurotoxins with high toxicity to most arthropods, they provide effective pest control and have numerous uses in arable farming and horticulture. 2. However, the prophylactic use of broad-spectrum pesticides goes against the long-established principles of integrated pest management (IPM), leading to environmental concerns. 3. It has recently emerged that neonicotinoids can persist and accumulate in soils. They are water soluble and prone to leaching into waterways. Being systemic, they are found in nectar and pollen of treated crops. Reported levels in soils, waterways, field margin plants and floral resources overlap substantially with concentrations that are sufficient to control pests in crops, and commonly exceed the LC50 (the concentration which kills 50% of individuals) for beneficial organisms. Concentrations in nectar and pollen in crops are sufficient to impact substantially on colony reproduction in bumblebees. 4. Although vertebrates are less susceptible than arthropods, consumption of small numbers of dressed seeds offers a route to direct mortality in birds and mammals. 5. Synthesis and applications. Major knowledge gaps remain, but current use of neonicotinoids is likely to be impacting on a broad range of non-target taxa including pollinators and soil and aquatic invertebrates and hence threatens a range of ecosystem services.

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REVIEW: An overview of the environmental risks posed by neonicotinoid insecticides

Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers. Herein we describe a bioinformatics pipeline, tassel-gbs, designed for the efficient processing of raw GBS sequence data into SNP genotypes. The tassel-gbs pipeline successfully fulfills the following key design criteria: (1) Ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8–16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished “pseudo-reference” consisting of numerous contigs. We describe the tassel-gbs pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (Zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based SNP filters. Overall, the GBS assay and the tassel-gbs pipeline provide robust tools for studying genomic diversity.

/pdf/tassel-gbs-a-high-capacity-genotyping-by-sequencing-analysis-48u7fd4437.pdf

TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline

In the coming decades, continued population growth, rising meat and dairy consumption and expanding biofuel use will dramatically increase the pressure on global agriculture. Even as we face these future burdens, there have been scattered reports of yield stagnation in the world's major cereal crops, including maize, rice and wheat. Here we study data from ∼2.5 million census observations across the globe extending over the period 1961-2008. We examined the trends in crop yields for four key global crops: maize, rice, wheat and soybeans. Although yields continue to increase in many areas, we find that across 24-39% of maize-, rice-, wheat- and soybean-growing areas, yields either never improve, stagnate or collapse. This result underscores the challenge of meeting increasing global agricultural demands. New investments in underperforming regions, as well as strategies to continue increasing yields in the high-performing areas, are required.

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Recent patterns of crop yield growth and stagnation

High-throughput techniques based on restriction site-associated DNA sequencing (RADseq) are enabling the low-cost discovery and genotyping of thousands of genetic markers for any species, including non-model organisms, which is revolutionizing ecological, evolutionary and conservation genetics. Technical differences among these methods lead to important considerations for all steps of genomics studies, from the specific scientific questions that can be addressed, and the costs of library preparation and sequencing, to the types of bias and error inherent in the resulting data. In this Review, we provide a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.

/pdf/harnessing-the-power-of-radseq-for-ecological-and-1ienyx5mk2.pdf

Harnessing the power of RADseq for ecological and evolutionary genomics

Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.

/pdf/evolution-of-gene-duplication-in-plants-rtuaqmb3s9.pdf

Evolution of Gene Duplication in Plants.

Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS) and genomic selection (GS). All of the 840 individuals were then genotyped using genotyping by sequencing (GBS), generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid) species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP) discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK). Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L.) P. Beauv.), two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics of switchgrass.

/pdf/switchgrass-genomic-diversity-ploidy-and-evolution-novel-3nvt6ye73f.pdf

Switchgrass genomic diversity, ploidy, and evolution: Novel insights from a network-based SNP discovery protocol

Some growers in northern latitudes plant soybean [Glycine max (L.) Merr.] with a row crop planter in 0.38 m rows, but an economic analysis concluded that drilled soybean in rows <0.25 m was optimum in the North-Central United States. We planted two varieties in 0.19, 0.38, and 0.76 m rows at 321,000; 371,000; 420,000; and 469,000 seeds ha -1 in New York in 2008 and 2009 to evaluate how soybean compensates to wide rows or low seeding rates in the Northeast United States. Soybean had limited compensation in biomass, pods, and seeds plant -1 at wider rows so row spacing had linear responses for biomass accumulation (598, 554, and 497 g m -2 in 0.19, 0.38. and 0.76 m rows, respectively) and leaf area index (LAI, 3.64, 3.47, and 3.16) at seed initiation; pod (1012, 935, and 875 pods m -2 ) and seed density (2272, 2230, and 2072 seeds m -2 , respectively) at harvest; and yield (3.37, 3.12, and 2.86 Mg ha -1 , respectively). Compensation in biomass, pods, and seeds plant -1 at lower seeding rates resulted in similar biomass accumulation (528-570 g m -2 ), LAI (3.38-3.46), pod (921-965 pods m -2 ), and seed densities (2123 to 2234 seeds m-2 ) across seeding rates. Nevertheless, yield showed a quadratic response to seeding rate (3.04, 3.25, and 3.12 Mg ha -1 at 321,000; 420,000; and 469,000 seeds ha -1 , respectively) with no row spacing interaction. Soybean compensated more at lower seeding rates than at wider rows, but field-scale studies are being conducted to evaluate the economics of both practices.

Growth and Yield Responses of Soybean to Row Spacing and Seeding Rate

Yield Components, Plant Morphology, and Forage Quality of Alfalfa as Influenced by Plant Population1

Future of grass and dairy cattle breeding cool season grasses breeding tropical and subtropical grasses management of cool season grasses' management of tropical and subtropical grasses potassium management nitrogen management and sustainability phosphorus management and sustainability grass silage grass baleage principles of grass growth and pasture utilization grazing management systems for dairy cattle supplementation of grass forage for dairy cattle modelling grass utilization by dairy cattle economics of grass for dairy cattle.

http://www.jsava.co.za/index.php/jsava/article/download/778/751

Grass for Dairy Cattle

Corn (Zea mays L.) hybrids may show different silage quality responses to harvest date and cutting height because hybrids differ in neutral detergent fiber (NDF) digestibility. A brown midrib, leafy, and dual-purpose hybrid were harvested at early [280 g kg -1 dry matter (DM) content], medium (350 g kg -1 ), and late (420 g kg -1 ) harvest dates at 15-, 30-, and 46-cm cutting heights in 2001 and 2002 to determine optimum harvest management for each hybrid type. Most forage quality characteristics had hybrid × harvest date interactions as indicated by the 73 g kg -1 decrease in NDF digestibility of the brown midrib compared with 20 g kg -1 decreases of the other hybrids between the early and late harvest date. Milk per megagram, a forage quality index, declined (1523, 1487, and 1417 kg Mg -1 ), but DM yields increased (13.2, 13.6, and 14.1 Mg ha -1 ), so calculated milk yields were similar (20 333, 20 200, and 20 233 kg ha -1 ) at early, medium, and late harvest dates, respectively, suggesting a broad optimum DM content for harvest. The sharp decline in NDF digestibility, however, raises concern about harvesting the brown midrib hybrid above 350 g kg -1 DM content. Calculated milk yield had a hybrid × cutting height interaction, as indicated by no change in the leafy hybrid and a 13% decrease in the brown midrib hybrid as cutting height increased from 15 to 46 cm. This suggests that an increase in cutting height may be a good management practice for the leafy hybrid but not for the brown midrib hybrid.

Jerome H. Cherney

Papers

Switchgrass genomic diversity, ploidy, and evolution: Novel insights from a network-based SNP discovery protocol

Growth and Yield Responses of Soybean to Row Spacing and Seeding Rate

Yield Components, Plant Morphology, and Forage Quality of Alfalfa as Influenced by Plant Population1

Grass for Dairy Cattle

Hybrid, Maturity, and Cutting Height Interactions on Corn Forage Yield and Quality