So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

To feed the several billion people living on this planet, the production of high-quality food must increase with reduced inputs, but this accomplishment will be particularly challenging in the face of global environmental change. Plant breeders need to focus on traits with the greatest potential to increase yield. Hence, new technologies must be developed to accelerate breeding through improving genotyping and phenotyping methods and by increasing the available genetic diversity in breeding germplasm. The most gain will come from delivering these technologies in developing countries, but the technologies will have to be economically accessible and readily disseminated. Crop improvement through breeding brings immense value relative to investment and offers an effective approach to improving food security.

https://science.sciencemag.org/content/sci/327/5967/818.full.pdf

Breeding Technologies to Increase Crop Production in a Changing World

The present invention provides for soybean plant and seed comprising transformation event MON89788 and DNA molecules unique to these events. The invention also provides methods for detecting the presence of these DNA molecules in a sample.

Soybean event MON89788 and methods for detection thereof

Knowledge about germplasm diversity and genetic relationships among breeding materials could be an invaluable aid in crop improvement strategies. A number of methods are currently available for analysis of genetic diversity in germplasm accessions, breeding lines, and populations. These methods have relied on pedigree data, morphological data, agronomic performance data, biochemical data, and more recently molecular (DNA-based) data. For reasonably accurate and unbiased estimates of genetic diversity, adequate attention has to be devoted to (i) sampling strategies; (ii) utilization of various data sets on the basis of the understanding of their strengths and constraints; (iii) choice of genetic distance measure(s), clustering procedures, and other multivariate methods in analyses of data; and (iv) objective determination of genetic relationships. Judicious combination and utilization of statistical tools and techniques, such as bootstrapping, is vital for addressing complex issues related to data analysis and interpretation of results from different types of data sets, particularly through clustering procedures. This review focuses on application of statistical tools and techniques in analysis of genetic diversity at the intraspecific level in crop plants.

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Analysis of Genetic Diversity in Crop Plants—Salient Statistical Tools and Considerations

The fundamental discoveries of Darwin and Mendel established the scientific basis for plant breeding and genetics at the turn of the 20th century. Similarly, the recent integration of advances in biotechnology, genomic research, and molecular marker applications with conventional plant breeding

/pdf/molecular-plant-breeding-as-the-foundation-for-21st-century-4wu0zq6rzj.pdf

Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement

Methods and compositions relating to glyphosate resistant maize plants, including the GA21, GG25, GJ11 and FI117 transformation events, are disclosed. Also disclosed are methods of using herbicide resistance transformation events in plant breeding procedures. The invention further includes methods of ensuring plant seed purity.

Glyphosate resistant maize lines

Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.

/pdf/incomplete-dominance-of-deleterious-alleles-contributes-s86yjlejw5.pdf

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize.

A broad range of U.S. maize (Zea mays L.) germplasm was evaluated for plant density tolerance (PDT) to identify potential sources of favorable alleles and to obtain a better understanding the underlying genetics involved. Thirty-two hybrids created using a set of inbreds representing parentage of key heterotic subgroups were evaluated at plant densities ranging from 47,000 (19,000 plants per acre [ppA]) to 133,000 plants ha-1 (54,000 ppA). Forty-eight phenotypic traits from five categories (photosynthetic capability, plant architecture, growth responses, source– sink relationship, and general stress tolerance) as well as grain yield were evaluated in three environments that differed for levels of soil moisture availability. The relationship between plant density and grain yield was assessed for each hybrid, with a wide range of responses observed. Five hybrids showed substantial tolerance to plant densities ≥116,000 plants ha-1 based on grain yield performance. Phenotypic trait correlations revealed a subset of traits associated with grain yield across plant densities, with all five categories of traits implicated directly; the subset included leaf angle, upper stem diameter, leaf area required to produce a gram of grain, kernel rows per ear, days to canopy closure, barrenness, kernels per plant, kernel length, leaf number, upper leaf area, staygreen, zipper effect, kernels per row, and anthesis–silking interval. Analysis of gene action for grain yield across plant densities emphasized the prominence of additivity, the increasing importance of nonadditivity as plant density and environmental stress levels increased, and genotype by environment interaction. This work paves the way for further characterization of PDT through quantitative trait locus mapping and candidate gene approaches. Department of Crop Sciences and the Illinois Plant Breeding Center, University of Illinois at Urbana-Champaign,1102 S. Goodwin Ave., Urbana, IL 61801; B.D. Mansfield, present address: Northwestern Illinois Agricultural Research and Education Center, 321 210th Ave., Monmouth, IL 61462. This work was funded in part by USDA National Institute of Food and Agriculture, grant award 2010-85117-20532. B.D. Mansfield was supported in part in his graduate studies through the William B. and Nancy L. Ambrose Fellowship in Crop Sciences. Received 17 Apr. 2013. *Corresponding author (ritamumm@illinois.edu). Abbreviations: ASI, anthesis–silking interval; b1, slope; bu/A, bushels per acre; E, environment; Env1, Environment 1; Env2, Environment 2; Env3, Environment 3; GCA, general combining ability; H2, broadsense heritability; h2, narrow-sense heritability; HA, alternate hypothesis; MINN13, Minnesota13; NSS, non-Stiff Stalk Synthetic; QTL, quantitative trait locus; PDT, pant density tolerance; ppA, plants per acre; PVP, Plant Variety Protection; SCA, specific combining ability; SSS, Stiff Stalk Synthetic. Published in Crop Sci. 54:157–173 (2014). doi: 10.2135/cropsci2013.04.0252 © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.

https://www.digital-workshop.com/ASTA/chicago_11/posters/mansfield_mumm.pdf

Survey of Plant Density Tolerance in U.S. Maize Germplasm

Methods and compositions relating to glyphosate resistant maize plants, including the GA21, GG25, GJ11 and FI117 transformation events, are disclosed Also disclosed are methods of using herbicide resistance transformation events in plant breeding procedures The invention further includes methods of ensuring plant seed purity

Rita H. Mumm

Papers

Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement

Glyphosate resistant maize lines

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize.

Survey of Plant Density Tolerance in U.S. Maize Germplasm

Method of breeding glyphosate resistant plants