The Effect of Supplemental Lighting during the Late Gestation Period on Post-Partum Mechanical Properties of Mare and Foal Guard Hair.

This study investigates Thoroughbred mares exposed or not to supplemental blue light at the end of the gestation. Sixty mares and their 60 foals were selected for the investigation. Guard hair samples were collected from the shoulder just after (within 12 h) the parturition or birth. The foals of the light-treated mares developed significantly (p < 0.05) shorter hair than those of the control mares. A general effect of light treatment on basal hair diameter thinning could be demonstrated (p < 0.005). The maximum force of hair samples of light-treated mares and foals (0.098 and 0.085 N, respectively) was significantly lower than that of the control (0.272 and 0.178 N, respectively). The tensile strength (82.2 N/mm2) of the foal hair samples of the light-treated mares was significantly lower than that of the control foals (121.6 N/mm2). Although no significant difference was found in the elongation (ΔL), the hair of the control animals (mares and foals together) was more elastic than that of the treated animals (335 vs. 262 µm). In conclusion, the supplemental blue light treatment of the pregnant mares has a decreasing effect on both mares and their foals on the mechanical properties of the hair, making it shorter, thinner, and weaker.

SNP Based Trait Characterization Detects Genetically Important and Stable Multiple Stress Tolerance Rice Genotypes in Salt-Stress Environments.

Soil salinity is a major constraint to rice production in coastal areas around the globe, and modern high-yielding rice cultivars are more sensitive to high salt stress, which limits rice productivity. Traditional breeding programs find it challenging to develop stable salt-tolerant rice cultivars with other stress-tolerant for the saline environment in Bangladesh due to large yield variations caused by excessive salinity fluctuations during the dry (boro) season. We examined trait characterization of 18 advanced breeding lines using SNP genotyping and among them, we found line G6 (BR9621-B-1-2-11) (single breeding line with multiple-stress-tolerant QTL/genes) possessed 9 useful QTLs/genes, and two lines (G4:BR9620-2-7-1-1 and G14: IR 103854-8-3-AJY1) carried 7 QTLs/genes that control the desirable traits. To evaluate yield efficiency and stability of 18 rice breeding lines, two years of field experiment data were analyzed using AMMI (additive main effect and multiplicative interaction) and GGE (Genotype, Genotype Environment) biplot analysis. The AMMI analysis of variance demonstrated significant genotype, environment, and their interaction, accounting for 14.48%, 62.38%, and 19.70% of the total variation, respectively, and revealed that among the genotypes G1, G13, G14, G17, and G18 were shown to some extent promising. Genotype G13 (IR 104002-CMU 28-CMU 1-CMU 3) was the most stable yield based on the AMMI stability value. The GGE biplot analysis indicates 76% of the total variation (PC1 48.5% and PC2 27.5%) which is performed for revealing genotype × environment interactions. In the GGE biplot analysis, genotypes were checked thoroughly in two mega-environments (ME). Genotype G14 (IR103854-8-3-AJY1) was the winning genotype in ME I, whereas G1 (BR9627-1-3-1-10) in ME II. Because of the salinity and stability factors, as well as the highest averages of grain yield, the GGE and AMMI biplot model can explain that G1 and G13 are the best genotypes. These (G1, G6, G13, G14, G17, and G18) improved multiple-stress-tolerant breeding lines with stable grain yield could be included in the variety release system in Bangladesh and be used as elite donor parents for the future breeding program as well as for commercial purposes with sustainable production.

Strategies to Modulate Specialized Metabolism in Mediterranean Crops: From Molecular Aspects to Field.

Plant specialized metabolites (SMs) play an important role in the interaction with the environment and are part of the plant defense response. These natural products are volatile, semi-volatile and non-volatile compounds produced from common building blocks deriving from primary metabolic pathways and rapidly evolved to allow a better adaptation of plants to environmental cues. Specialized metabolites include terpenes, flavonoids, alkaloids, glucosinolates, tannins, resins, etc. that can be used as phytochemicals, food additives, flavoring agents and pharmaceutical compounds. This review will be focused on Mediterranean crop plants as a source of SMs, with a special attention on the strategies that can be used to modulate their production, including abiotic stresses, interaction with beneficial soil microorganisms and novel genetic approaches.

Genome Editing of Rice by CRISPR-Cas: End-to-End Pipeline for Crop Improvement.

CRISPR-Cas resonates a revolutionary genome editing technology applicable through a horizon spreading across microbial organism to higher plant and animal. This technology can be harnessed with ease to understand the basic genetics of a living system by altering sequence of individual genes and characterizing their functions. The precision of this technology is unparallel. It allows very precise and targeted base pair level edits in the genome. Here, in the current chapter, we have provided end-to-end process outline on how to generate genome edited plants in crops like rice to evaluate for agronomic traits associated with yield, disease resistance and abiotic stress tolerance, etc. Genome editing process includes designing of gene editing strategy, vector construction, plant transformation, molecular screening, and phenotyping under control environment conditions. Furthermore, its application for development of commercial crop product may require additional processes, including field trials in the target geography for evaluation of product efficacy. Evaluation of genome edited lines in controlled greenhouse/net house or open field condition requires few generations for outcrossing with wild-type parent to eliminate and/or reduce any potential pleiotropic effect in the edited genome which may arise during the process. The genome edited plant selected for advancement shall harbor the genome with only the intended changes, which can be analyzed by various molecular techniques, advanced sequencing methods, and genomic data analysis tools. CRISPR-Cas-based genome editing has opened a plethora of opportunities in agriculture as well as human health.

Maize transformation: history, progress, and perspectives.

Maize functional genomics research and genetic improvement strategies have been greatly accelerated and refined through the development and utilization of genetic transformation systems. Maize transformation is a composite technology based on decades' efforts in optimizing multiple factors involving microbiology and physical/biochemical DNA delivery, as well as cellular and molecular biology. This review provides a historical reflection on the development of maize transformation technology including the early failures and successful milestones. It also provides a current perspective on the understanding of tissue culture responses and their impact on plant regeneration, the pros and cons of different DNA delivery methods, the identification of a palette of selectable/screenable markers, and most recently the development of growth-stimulating or morphogenic genes to improve efficiencies and extend the range of transformable genotypes. Steady research progress in these interdependent components has been punctuated by benchmark reports celebrating the progress in maize transformation, which invariably relied on a large volume of supporting research that contributed to each step and to the current state of the art. The recent explosive use of CRISPR/Cas9-mediated genome editing has heightened the demand for higher transformation efficiencies, especially for important inbreds, to support increasingly sophisticated and complicated genomic modifications, in a manner that is widely accessible. These trends place an urgent demand on taking maize transformation to the next level, presaging a new generation of improvements on the horizon. Once realized, we anticipate a near-future where readily accessible, genotype-independent maize transformation, together with advanced genomics, genome editing, and accelerated breeding, will contribute to world agriculture and global food security.

Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs.

BACKGROUND: The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). RESULTS: Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. CONCLUSION: Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.

Data describing Upland cotton cultivars and advanced breeding lines used in Colombia.

In the last century, more than a hundred of cultivars were used in the cotton production system in Colombia. Breeding for cultivars adapted to tropical environments had been the main purpose of the Colombian agricultural research institutions dedicated to cotton. Data describing yield and fiber quality traits of these cultivars (and the introduced ones mainly from USA) is scattered across grey literature which reduces chances of discovering, accessing and assessing this information.This data article contains databases describing i) Colombian and introduced Upland cotton cultivars used in Colombia and ii) ramulosis-resistance scores of lines developed by the Colombian breeding program. The first database was constructed from data extracted from grey literature mainly produced by ICA and CORPOICA (rebranded today as AGROSAVIA), the Colombian agricultural research agencies. The second one describes the Cereté lines (LCER) database. These advanced breeding lines were developed for improved yield performance in tropical environments, specifically monsoon and savanna climates. The LCER dataset also describes the ramulosis field resistance of these cultivars. Ramulosis is an endemic disease in South America caused by Colletotrichum gossypii var. cephalosporioides. The data in this article supports and augments information presented in the research articles [1]: and [3].

Edit at will: Genotype independent plant transformation in the era of advanced genomics and genome editing.

The combination of advanced genomics, genome editing and plant transformation biology presents a powerful platform for basic plant research and crop improvement. Together these advances provide the tools to identify genes as targets for direct editing as single base pair changes, deletions, insertions and site specific homologous recombination. Recent breakthrough technologies using morphogenic regulators in plant transformation creates the ability to introduce reagents specific toward their identified targets and recover stably transformed and/or edited plants which are genotype independent. These technologies enable the possibility to alter a trait in any variety, without genetic disruption which would require subsequent extensive breeding, but rather to deliver the same variety with one trait changed. Regulatory issues regarding this technology will predicate how broadly these technologies will be implemented. In addition, education will play a crucial role for positive public acceptance. Taken together these technologies comprise a platform for advanced breeding which is an imperative for future world food security.

The State of "Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization.

Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. "Omics" based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species. While the culture of penaeid shrimp has increased markedly, the industry continues to be impeded in many regards by disease, reproductive dysfunction, and a poor understanding of production traits. Extensive effort has been, and continues to be, applied to develop critical genomic resources for many commercially important penaeids. However, the industry application of these genomic resources, and the translation of the knowledge derived from "omics" studies has not yet been completely realized. Integration between the multiple "omics" resources now available (i.e., genome assemblies, transcriptomes, linkage maps, optical maps, and proteomes) will prove critical to unlocking the full utility of these otherwise independently developed and isolated resources. Furthermore, emerging "omics" based techniques are now available to address longstanding issues with completing keystone genome assemblies (e.g., through long-read sequencing), and can provide cost-effective industrial scale genotyping tools (e.g., through low density SNP chips and genotype-by-sequencing) to undertake advanced selective breeding programs (i.e., genomic selection) and powerful genome-wide association studies. In particular, this review highlights the status, utility and suggested path forward for continued development, and improved use of "omics" resources in penaeid aquaculture.

Use of CRISPR/Cas9 for Crop Improvement in Maize and Soybean.

CRISPR/Cas enables precise improvement of commercially relevant crop species by transgenic and nontransgenic methodologies. We have used CRISPR/Cas with or without DNA repair template in both corn and soybean for a range of applications including enhancing drought tolerance, improving seed oil composition, and endowing herbicide tolerance. Importantly, by pairing CRISPR/Cas technology with recent advances in plant tissue culture, these changes can be introduced directly into commercially relevant genotypes. This powerful combination of technologies enables advanced breeding techniques for introducing natural genetic variations directly into product relevant lines with improved speed and quality compared with traditional breeding methods. Variation generated through such CRISPR/Cas enabled advanced breeding approaches can be indistinguishable from naturally occurring variation and therefore should be readily accessible for commercialization. The precision, reach, and flexibility afforded by CRISPR/Cas promise an important role for genome editing in future crop improvement efforts.

Effect of Host Plant Resistance and Reduced Rates and Frequencies of Fungicide Application to Control Potato Late Blight.

Field experiments were conducted during 1998 to 2000 to determine the response of commercial potato cultivars and advanced breeding lines (ABL) differing in susceptibility to foliar late blight (caused by Phytophthora infestans) to reduced rates and frequencies of residual, contact fungicide applications. When environmental conditions were most favorable for the development of late blight, the lowest application rate of the fungicides chlorothalonil or fluazinam (33% of the manufacturers' recommended application rate [MRAR]) gave unsatisfactory control of potato late blight. Under conditions moderately conducive for late blight development, effective control was achieved with 33 to 66% MRAR with either fungicide. The Michigan State University advanced selection, MSG274-3, was the least susceptible ABL tested and, during 1998 to 2000, late blight was effectively managed using reduced rates of fungicides. Application rates of chlorothalonil (33 to 100% MRAR) significantly reduced late blight in the cultivar Snowden (5-day application interval) compared with the nontreated control; whereas, late blight was not effectively controlled in Snowden even at 100% MRAR of chlorothalonil at either 10- or 15-day application intervals in 1999 or 2000. The ABL MSG274-3 was the least susceptible of all cultivars and ABL used in this study, and required minimal chemical protection against late blight. The study demonstrates that ABL with reduced susceptibility to late blight can be managed with reduced fungicide rates and longer application intervals, thus offering more economical control of this disease.