AlphaSim: Software for Breeding Program Simulation

This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree; (ii) drop haplotypes into the base generation of the pedigree and select single-nucleotide polymorphism (SNP) and quantitative trait nucleotide (QTN); (iii) assign QTN effects, calculate genetic values, and simulate phenotypes; (iv) drop haplotypes into the burn-in generations; and (v) perform selection and simulate new generations. The program is flexible in terms of historical population structure and diversity, recent pedigree structure, trait architecture, and selection strategy. It integrates biotechnologies such as doubled-haploids (DHs) and gene editing and allows the user to simulate multiple traits and multiple environments, specify recombination hot spots and cold spots, specify gene jungles and deserts, perform genomic predictions, and apply optimal contribution selection. AlphaSim also includes restart functionalities, which increase its flexibility by allowing the simulation process to be paused so that the parameters can be changed or to import an externally created pedigree, trial design, or results of an analysis of previously simulated data. By combining the options, a user can simulate simple or complex breeding programs with several generations, variable population structures and variable breeding decisions over time. In conclusion, AlphaSim is a flexible and computationally efficient software package to simulate biotechnology enhanced breeding programs with the aim of performing rapid, low-cost, and objective in silico comparison of breeding technologies

Redesigning crop varieties to win the race between climate change and food security

Climate change poses daunting challenges to agricultural production and food security. Rising temperatures, shifting weather patterns, and more frequent extreme events have already demonstrated their effects on local, regional, and global agricultural systems. Crop varieties that withstand climate-related stresses and are suitable for cultivation in innovative cropping systems will be crucial to maximize risk avoidance, productivity, and profitability under climate-changed environments. We surveyed 588 expert stakeholders to predict current and novel traits that may be essential for future pearl millet, sorghum, maize, groundnut, cowpea, and common bean varieties, particularly in sub-Saharan Africa. We then review the current progress and prospects for breeding three prioritized future-essential traits for each of these crops. Experts predict that most current breeding priorities will remain important, but that rates of genetic gain must increase to keep pace with climate challenges and consumer demands. Importantly, the predicted future-essential traits include innovative breeding targets that must also be prioritized; for example, (1) optimized rhizosphere microbiome, with benefits for P, N, and water use efficiency, (2) optimized performance across or in specific cropping systems, (3) lower nighttime respiration, (4) improved stover quality, and (5) increased early vigor. We further discuss cutting-edge tools and approaches to discover, validate, and incorporate novel genetic diversity from exotic germplasm into breeding populations with unprecedented precision, accuracy, and speed. We conclude that the greatest challenge to developing crop varieties to win the race between climate change and food security might be our innovativeness in defining and boldness to breed for the traits of tomorrow

Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations

BACKGROUND: The limited genetic diversity of elite maize germplasms raises concerns about the potential to breed for new challenges. Initiatives have been formed over the years to identify and utilize useful diversity from landraces to overcome this issue. The aim of this study was to evaluate the proposed designs to initiate a pre-breeding program within the Seeds of Discovery (SeeD) initiative with emphasis on harnessing polygenic variation from landraces using genomic selection. We evaluated these designs with stochastic simulation to provide decision support about the effect of several design factors on the quality of resulting (pre-bridging) germplasm. The evaluated design factors were: i) the approach to initiate a pre-breeding program from the selected landraces, doubled haploids of the selected landraces, or testcrosses of the elite hybrid and selected landraces, ii) the genetic parameters of landraces and phenotypes, and iii) logistical factors related to the size and management of a pre-breeding program. RESULTS: The results suggest a pre-breeding program should be initiated directly from landraces. Initiating from testcrosses leads to a rapid reconstruction of the elite donor genome during further improvement of the pre-bridging germplasm. The analysis of accuracy of genomic predictions across the various design factors indicate the power of genomic selection for pre-breeding programs with large genetic diversity and constrained resources for data recording. The joint effect of design factors was summarized with decision trees with easy to follow guidelines to optimize pre-breeding efforts of SeeD and similar initiatives. CONCLUSIONS: Results of this study provide guidelines for SeeD and similar initiatives on how to initiate pre-breeding programs that aim to harness polygenic variation from landraces. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2345-z) contains supplementary material, which is available to authorized users

Stimulating a Canadian narrative for climate

ABSTRACT: This perspective documents current thinking around climate actions in Canada by synthesizing scholarly proposals made by Sustainable Canada Dialogues (SCD), an informal network of scholars from all 10 provinces, and by reviewing responses from civil society representatives to the scholars' proposals. Motivated by Canada's recent history of repeatedly missing its emissions reduction targets and failing to produce a coherent plan to address climate change, SCD mobilized more than 60 scholars to identify possible pathways towards a low-carbon economy and sustainable society and invited civil society to comment on the proposed solutions. This perspective illustrates a range of Canadian ideas coming from many sectors of society and a wealth of existing inspiring initiatives. Solutions discussed include climate change governance, low-carbon transition, energy production, and consumption. This process of knowledge synthesis/creation is novel and important because it provides a working model for making connections across academic fields as well as between academia and civil society. The process produces a holistic set of insights and recommendations for climate change actions and a unique model of engagement. The different voices reported here enrich the scope of possible solutions, showing that Canada is brimming with ideas, possibilities, and the will to act

Table_Samples_Information

This file contains all information regarding the RNAseq libraries/samples

Annotation_transcripts_containing_outliers

Annotated transcripts with outliers in S. hermonthica growing in Sorghum vs Maize

Biofunctionalization of zirconia based materials by immobilization of alp in tissue engineering applications

The aim of this project is to modify Zirconia surface to perform as a bioactive material in contact with biological tissue with high stability and activity. Alumina was also modified in order to compare the properties with Zirconia in the same laboratory condition. The protein used in this test is alkaline phosphatase (ALP) which improves mineralization and creation of hydroxyapatite in bone formation process. Adsorption and covalent bonding immobilization were investigated on both ceramics. The modified ceramic surfaces also tested in contact with and without human body cells, in biological condition in vitro. This project contains laboratory tests for powders and planar surfaces. Characterizations of zirconia powder, such as IEP (isoelectric point) were investigated after ALP immobilization. In addition, ALP functionalized planar surface and its behaviour was studied in vitro in simulated body conditions with and without presence of osteoblast-like cells. Main results of these studies supported that high mineralization accomplished by ALP functionalized zirconia in compare with non-functionalized zirconia in in vitro. In summary, the results of this research indicate the successful immobilization and surface modification of zirconia. In addition, zirconia powder silanized by APTES, as the initial step of surface modification, showed acceptable stability in room temperature during 28 days. In case of comparison between physical adsorption and covalent bonding methods, it can be observed that physical adsorption represents higher enzyme attachment. However, these attachments do not show suitable stability. In all the experiments regarding modification of the particle surface, Zirconia powder illustrates higher potential for protein (ALP) immobilization compare to Alumina