The Dawn of the Age of Multi-Parent MAGIC Populations in Plant Breeding: Novel Powerful Next-Generation Resources for Genetic Analysis and Selection of Recombinant Elite Material

The compelling need to increase global agricultural production requires new breeding approaches that facilitate exploiting the diversity available in the plant genetic resources. Multi-parent advanced generation inter-cross (MAGIC) populations are large sets of recombinant inbred lines (RILs) that are a genetic mosaic of multiple founder parents. MAGIC populations display emerging features over experimental bi-parental and germplasm populations in combining significant levels of genetic recombination, a lack of genetic structure, and high genetic and phenotypic diversity. The development of MAGIC populations can be performed using “funnel” or “diallel” cross-designs, which are of great relevance choosing appropriate parents and defining optimal population sizes. Significant advances in specific software development are facilitating the genetic analysis of the complex genetic constitutions of MAGIC populations. Despite the complexity and the resources required in their development, due to their potential and interest for breeding, the number of MAGIC populations available and under development is continuously growing, with 45 MAGIC populations in different crops being reported here. Though cereals are by far the crop group where more MAGIC populations have been developed, MAGIC populations have also started to become available in other crop groups. The results obtained so far demonstrate that MAGIC populations are a very powerful tool for the dissection of complex traits, as well as a resource for the selection of recombinant elite breeding material and cultivars. In addition, some new MAGIC approaches that can make significant contributions to breeding, such as the development of inter-specific MAGIC populations, the development of MAGIC-like populations in crops where pure lines are not available, and the establishment of strategies for the straightforward incorporation of MAGIC materials in breeding pipelines, have barely been explored. The evidence that is already available indicates that MAGIC populations will play a major role in the coming years in allowing for impressive gains in plant breeding for developing new generations of dramatically improved cultivars.

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Genetic analysis of complex traits via Bayesian variable selection: the utility of a mixture of uniform priors

Genetics Research ◽

10.1017/s0016672311000164 ◽

2011 ◽

Vol 93 (4) ◽

pp. 303-318 ◽

Cited By ~ 12

Author(s):

TIMO KNÜRR ◽

ESA LÄÄRÄ ◽

MIKKO J. SILLANPÄÄ

Keyword(s):

Genetic Analysis ◽

Variable Selection ◽

Complex Traits ◽

Bayesian Variable Selection ◽

Stochastic Search Variable Selection ◽

Indicator Variables ◽

Supplementary Material ◽

Selection Of ◽

Made In ◽

Search Variable

SummaryA new estimation-based Bayesian variable selection approach is presented for genetic analysis of complex traits based on linear or logistic regression. By assigning a mixture of uniform priors (MU) to genetic effects, the approach provides an intuitive way of specifying hyperparameters controlling the selection of multiple influential loci. It aims at avoiding the difficulty of interpreting assumptions made in the specifications of priors. The method is compared in two real datasets with two other approaches, stochastic search variable selection (SSVS) and a re-formulation of Bayes B utilizing indicator variables and adaptive Student's t-distributions (IAt). The Markov Chain Monte Carlo (MCMC) sampling performance of the three methods is evaluated using the publicly available software OpenBUGS (model scripts are provided in the Supplementary material). The sensitivity of MU to the specification of hyperparameters is assessed in one of the data examples.

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Formation and composition of training flax collection

Genetičnì resursi roslin (Plant Genetic Resources) ◽

10.36814/pgr.2020.26.06 ◽

2020 ◽

pp. 61-71

Author(s):

L.M. Kryvosheieva ◽

V.I. Chuchvaha ◽

N.M. Kandyba

Keyword(s):

Plant Breeding ◽

Gene Pool ◽

Phenotypic Variability ◽

Plant Genetic Resources ◽

Field Measurements ◽

Educational Process ◽

Educational Institutions ◽

Economic Traits ◽

Wide Range ◽

History Of

Aim. Based on the results of multi-year research into the flax gene pool, to form a flax training collection to provide breeding scientific organizations and educational institutions with collection samples as well as with information about the bast crop gene pool. Results and Discussion. The studies were conducted in the crop rotation fields for breeding and seed production of the Institute of Bast Crops of the NAAS (Hlukhiv, Sumska Oblast) in 1992-2018. The field measurements and laboratory analyses were carried out in accordance with conventional methods of field and laboratory studies of collection flax samples.The article presents the results on the formation of a training collection of flax at the Institute of Bast Crops of the NAAS, which has 117 accessions (11 botanical species and three varieties) from 22 countries. In addition to species diversity, the collection includes accessions with different levels of expression of valuable economic and biological characteristics. It also includes accessions selected by phenotypic variability of individual characters or their combinations. The multi-year research into the flax collection accessions resulted in identification of sources of highly-expressed valuable economic traits, which are of interest for the plant breeding course. The history of flax breeding in Ukraine is shown, where breeding varieties that are most widespread or were significant breeding achievements in solving certain problems, are presented. The collection can be used as a visual aid for the plant breeding course in educational programs; in addition, it can provide starting material for scientific and educational institutions. The collection is registered with the National Center for Plant Genetic Resources of Ukraine (certificate No. 00273 dated 04/11/2019). Conclusions. The studies of accessions from the national flax collection allowed us to build up a training collection and register it with the NCPGRU. The collection represents a wide range of biological and economic features of the gene pool of this crop. The collection can be used in the educational process of educational agricultural and biological institutions. The multi-year research into the national flax collection resulted in identification of sources of highly-expressed valuable economic traits, which are of interest to the plant breeding course. The history of flax breeding in Ukraine got covered, and breeding varieties that are most widespread or were significant breeding achievements in solving certain problems are presented.

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Establishment and genetic analysis of complete diallel cross families of pearl oyster (Pinctada fucata)

JOURNAL OF FISHERIES OF CHINA ◽

10.3724/sp.j.1231.2010.06498 ◽

2010 ◽

Vol 34 (1) ◽

pp. 26-31

Author(s):

Long-chun GU ◽

Jin-bi LI ◽

Da-hui YU ◽

Gui-ju HUANG ◽

Jian-ye LIU

Keyword(s):

Genetic Analysis ◽

Diallel Cross ◽

Pearl Oyster ◽

Pinctada Fucata ◽

Complete Diallel Cross

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Evolution and Selection of Quantitative Traits

10.1093/oso/9780198830870.001.0001 ◽

2018 ◽

Cited By ~ 141

Author(s):

Bruce Walsh ◽

Michael Lynch

Keyword(s):

Mathematical Models ◽

Quantitative Genetics ◽

Complex Traits ◽

Evolutionary Biology ◽

Quantitative Traits ◽

Specific Gene ◽

Real World Data ◽

Holistic Treatment ◽

Genetics And Genomics ◽

Selection Of

Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences. This extensive work of reference is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of evolutionary biology, genetics, and genomics. It will also be of particular relevance and use to plant and animal breeders, human geneticists, and statisticians.

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THE SELECTION OF S. CEREVISIAE MUTANTS DEFECTIVE IN THE START EVENT OF CELL DIVISION

Genetics ◽

10.1093/genetics/95.3.561 ◽

1980 ◽

Vol 95 (3) ◽

pp. 561-577 ◽

Cited By ~ 4

Author(s):

Steven I Reed

Keyword(s):

Cell Division ◽

Genetic Analysis ◽

Linkage Map ◽

Nuclear Genes ◽

Temperature Sensitive ◽

Restrictive Temperature ◽

Mating Pheromone ◽

Preliminary Characterization ◽

Complementation Groups ◽

Selection Of

ABSTRACT Thirty-three temperature-sensitive mutations defective in the start event of the cell division cycle of Saccharomyces cereuisiae were isolated and subjected to preliminary characterization. Complementation studies assigned these mutations to four complementation groups, one of which, cdc28, has been described previously. Genetic analysis revealed that these complementation groups define single nuclear genes, unlinked to one another. One of the three newly identified genes, cdc37, has been located in the yeast linkage map on chromosome IV, two meiotic map units distal to hom2.—Each mutation produces stage-specific arrest of cell division at start, the same point where mating pheromone interrupts division. After synchronization at start by incubation at the restrictive temperature, the mutants retain the capacity to enlarge and to conjugate.

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RIL-StEp: epistasis analysis of rice recombinant inbred lines (RILs) reveals candidate interacting genes that control seed hull color and leaf chlorophyll content

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab130 ◽

2021 ◽

Author(s):

Toshiyuki Sakai ◽

Akira Abe ◽

Motoki Shimizu ◽

Ryohei Terauchi

Keyword(s):

Chlorophyll Content ◽

Recombinant Inbred ◽

Complex Traits ◽

Genetic Architecture ◽

Recombinant Inbred Lines ◽

Inbred Lines ◽

Gene Interactions ◽

Leaf Chlorophyll Content ◽

Leaf Chlorophyll ◽

Seed Hull

Abstract Characterizing epistatic gene interactions is fundamental for understanding the genetic architecture of complex traits. However, due to the large number of potential gene combinations, detecting epistatic gene interactions is computationally demanding. A simple, easy-to-perform method for sensitive detection of epistasis is required. Due to their homozygous nature, use of recombinant inbred lines (RILs) excludes the dominance effect of alleles and interactions involving heterozygous genotypes, thereby allowing detection of epistasis in a simple and interpretable model. Here, we present an approach called RIL-StEp (recombinant inbred lines stepwise epistasis detection) to detect epistasis using single nucleotide polymorphisms in the genome. We applied the method to reveal epistasis affecting rice (Oryza sativa) seed hull color and leaf chlorophyll content and successfully identified pairs of genomic regions that presumably control these phenotypes. This method has the potential to improve our understanding of the genetic architecture of various traits of crops and other organisms.

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Molecular and genetic analysis of the yeast early meiotic recombination genes REC102 and REC107/MER2.

Molecular and Cellular Biology ◽

10.1128/mcb.12.3.1248 ◽

1992 ◽

Vol 12 (3) ◽

pp. 1248-1256 ◽

Cited By ~ 23

Author(s):

M Cool ◽

R E Malone

Keyword(s):

Sequence Analysis ◽

Genetic Analysis ◽

Meiotic Recombination ◽

Genetic Recombination ◽

Recombination Process ◽

Genetic Complementation ◽

Rec Genes ◽

Reductional Division

By selecting for mutations which could rescue the meiotic lethality of a rad52 spo13 strain, we isolated several new Rec genes required relatively early in the meiotic recombination process. This paper presents data to confirm that two of them, REC102 and REC107, are general, meiosis-specific recombination genes that have no detectable role during mitosis. Sequence analysis and genetic complementation indicate that REC107 is identical to the MER2 gene. No sequences related to REC102 have been found in the GenBank or EMBL collections. REC102 is expressed only in meiosis, prior to the reductional division, at about the time that genetic recombination occurs. Examination of the REC102 sequence indicates the presence of several sequences which may play a role in the regulation of its expression; however, the URS1 sequence commonly found in genes expressed early in meiosis is not present.

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Modular evolution of phosphorylation-based signalling systems

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2012.0106 ◽

2012 ◽

Vol 367 (1602) ◽

pp. 2540-2555 ◽

Cited By ~ 91

Author(s):

Jing Jin ◽

Tony Pawson

Keyword(s):

Protein Kinases ◽

Genetic Recombination ◽

Cell Signalling ◽

Peptide Motifs ◽

Regulatory Processes ◽

Modular Evolution ◽

Interaction Domains ◽

Evolutionary Progression ◽

Signalling Systems ◽

Selection Of

Phosphorylation sites are formed by protein kinases (‘writers’), frequently exert their effects following recognition by phospho-binding proteins (‘readers’) and are removed by protein phosphatases (‘erasers’). This writer–reader–eraser toolkit allows phosphorylation events to control a broad range of regulatory processes, and has been pivotal in the evolution of new functions required for the development of multi-cellular animals. The proteins that comprise this system of protein kinases, phospho-binding targets and phosphatases are typically modular in organization, in the sense that they are composed of multiple globular domains and smaller peptide motifs with binding or catalytic properties. The linkage of these binding and catalytic modules in new ways through genetic recombination, and the selection of particular domain combinations, has promoted the evolution of novel, biologically useful processes. Conversely, the joining of domains in aberrant combinations can subvert cell signalling and be causative in diseases such as cancer. Major inventions such as phosphotyrosine (pTyr)-mediated signalling that flourished in the first multi-cellular animals and their immediate predecessors resulted from stepwise evolutionary progression. This involved changes in the binding properties of interaction domains such as SH2 and their linkage to new domain types, and alterations in the catalytic specificities of kinases and phosphatases. This review will focus on the modular aspects of signalling networks and the mechanism by which they may have evolved.

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Genetic Analysis of Half Diallel Matting with Different Methods and their Comparisons for Yield and its Associated Traits in Sunflower under Saline Soil Stress Conditions

Helia ◽

10.1515/helia-2017-0001 ◽

2017 ◽

Vol 40 (66) ◽

Cited By ~ 1

Author(s):

Mohamed Ali Abd El-Satar

Keyword(s):

Genetic Analysis ◽

Agricultural Research ◽

Saline Soil ◽

Block Design ◽

Diallel Cross ◽

Head Diameter ◽

Physiological Maturity ◽

Randomized Complete Block Design ◽

Soil Stress ◽

Half Diallel

AbstractA half diallel cross between five divergent sunflower genotypes was evaluated under two contrast locations of Kafr El-Hamam (fovourable soil as a control) and Tag Al-Ezz (as salt affected soil) Agricultural Research Stations using randomized complete block design with three replications. High significance variation among genotypes and their components was detected for all studied traits at both and combined locations. Selection in early generations would be effective at both locations for improving days to 50 % flowering, days to physiological maturity, plant height, head diameter, No. of green leaves plant

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Access to plant genetic resources for genomic research for the poor: from global policies to target-oriented rules

Plant Genetic Resources ◽

10.1079/pgr2006112 ◽

2006 ◽

Vol 4 (1) ◽

pp. 54-63 ◽

Cited By ~ 3

Author(s):

Niels P. Louwaars ◽

Eva Thörn ◽

José Esquinas-Alcázar ◽

Shumin Wang ◽

Abebe Demissie ◽

...

Keyword(s):

Plant Breeding ◽

Genetic Resources ◽

Plant Genetic Resources ◽

Green Revolution ◽

Building Blocks ◽

Genomic Research ◽

Benefit Sharing ◽

Food And Agriculture ◽

The Poor ◽

Multilateral System

Applied genetics combined with practical plant breeding is a powerful tool in agricultural development and for food security. The Green Revolution spurred the world's potential to meet its food, feed and fibre needs at a time when vast regions were notoriously food-insecure. Subsequent adaptations of such strategies, from the late 1980s onwards, in order to develop new plant varieties in a more participatory way, have strengthened the focus on applying technology to farmers' diverse needs, feeding research results into a variety of seed systems. During these developments, there were no major legal impediments to the acquisition of either local or formal knowledge or of the building blocks of plant breeding: genetic resources. The emergence of molecular biology in plant science is creating a wealth of opportunities, both to understand better the limitations of crop production and to use a much wider array of genetic diversity in crop improvement. This ‘Gene Revolution’ needs to incorporate the lessons from the Green Revolution in order to reach its target groups. However, the policy environment has changed. Access to technologies is complicated by the spread of private rights (intellectual property rights), and access to genetic resources by new national access laws. Policies on access to genetic resources have changed from the concept of the ‘Heritage of Mankind’ for use for the benefit of all mankind to ‘National Sovereignty’, based on the Convention on Biological Diversity, for negotiated benefit-sharing between a provider and a user. The Generation Challenge Programme intends to use genomic techniques to identify and use characteristics that are of value to the resource-poor, and is looking for ways to promote freedom-to-operate for plant breeding technologies and materials. Biodiversity provides the basis for the effective use of these genomic techniques. National access regulations usually apply to all biodiversity indiscriminately and may cause obstacles or delays in the use of genetic resources in agriculture. Different policies are being developed in different regions. Some emphasize benefit-sharing, and limit access in order to implement this (the ‘African Model Law’), while others, in recognition of countries' interdependence, provide for facilitated access to all genetic resources under the jurisdiction of countries in the region (the Nordic Region). There are good reasons why the use of agricultural biodiversity needs to be regulated differently from industrial uses of biodiversity. The International Treaty on Plant Genetic Resources for Food and Agriculture, which entered into force in 2004, provides for facilitated access to agricultural genetic resources, at least for the crops that are included in the Treaty's ‘Multilateral System of Access and Benefit-sharing’. Ratification of the Treaty is proceeding apace, and negotiations have entered a critical stage in the development of practical instruments for its implementation. Although the scope of the Treaty is all plant genetic resources for food and agriculture, there are important crops that are not covered by its Multilateral System. Humanitarian licences are being used to provide access for the poor to protected technologies: countries may need to create such a general humanitarian access regime, to ensure the poor have the access they need to agricultural genetic resources.

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