Posts Tagged ‘genetics’

Quality control genotyping for assessment of genetic identity and purity in diverse tropical maize inbred lines

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics, 2012

Kassa Semagn, Yoseph Beyene, Dan Makumbi, Stephen Mugo, B. M. Prasanna, Cosmos Magorokosho and Gary Atlin

Quality control (QC) genotyping is an important component in breeding, but to our knowledge there are not well established protocols for its implementation in practical breeding programs. The objectives of our study were to (a) ascertain genetic identity among 2–4 seed sources of the same inbred line, (b) evaluate the extent of genetic homogeneity within inbred lines, and (c) identify a subset of highly informative single-nucleotide polymorphism (SNP) markers for routine and low-cost QC genotyping  and suggest guidelines for data interpretation. We used a total of 28 maize inbred lines to study genetic identity among different seed sources by genotyping them with 532 and 1,065 SNPs using the KASPar and GoldenGate platforms, respectively. An additional set of 544 inbred lines was used for studying genetic homogeneity. The proportion of alleles that differed between seed sources of the same inbred line varied from 0.1 to 42.3 %. Seed sources exhibiting high levels of genetic distance are mis-labeled, while those with lower levels of difference are contaminated or still segregating. Genetic homogeneity varied from 68.7 to 100 % with 71.3 % of the inbred lines considered to be homogenous. Based on the data sets obtained for a wide range of sample  sizes and diverse genetic backgrounds, we recommended a subset of 50–100 SNPs for routine and low-cost QC genotyping, verified them in a different set of double haploid and inbred lines, and outlined a protocol that could be used to minimize errors  in genetic analyses and breeding.

Genetic yield gains of the CIMMYT international semi-arid wheat yield trials from 1994 to 2010

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science  52 (4): 1543-1552, 2012

Y. Manès , H. F. Gomez, L. Puhl, M. Reynolds, H. J. Braun and R. Trethowan

Genetic progress for yield has been assessed globally in the semi-arid wheat yield trials (SAWYTs) of the International Maize and Wheat Improvement Center (CIMMYT) over a 17-yr period. Grain yield expressed as a percentage of the long-term check cultivar Dharwar Dry has increased at approximately 1% yr−1 between 1994 and 2010. In real terms, yield has been increased at a rate of 31 kg ha−1 yr−1. The rate of yield increase in high-yielding environments was twice that of low-yielding environments. The average yield of low-yielding sites are significantly correlated with the average yield of high-yielding sites (p < 0.001), and many of the highest-yielding lines of the various SAWYT performed well at both low- and high-yielding sites. The key parents Attila and Pastor were consistently high yielding in several of the early SAWYT. In later trials their derivatives were also high yielding. The line Vorobey, developed by crossing Pastor with a synthetic derivative, showed outstanding yield in SAWYT 11 and 12. The performance of CIMMYT lines compared to local check cultivars was relatively stable over time. A success rate was calculated as the ratio of the number of sites where a given line is superior to the local check divided by the total number of sites. On average, the success rate of the 10% best lines was 61% in low-yielding sites and 62% in high-yielding sites.

Genetic gains for grain yield in CIMMYT spring bread wheat across international environments

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science 52 (4): 1522-1533, 2012

R. C. Sharma, J. Crossa, G. Velu, J. Huerta-Espino, M. Vargas, T. S. Payne and R. P. Singh

The Global Wheat Program of the International Maize and Wheat Improvement Center (CIMMYT) develops and distributes improved germplasm targeted toward various wheat growing regions of developing world. The objective of our study was to quantify the genetic yield gains in CIMMYT’s spring bread wheat (Triticum aestivum L.) in the Elite Spring Wheat Yield Trial (ESWYT) distributed over the past 15 yr (1995–2009) as determined by the performance of entries across 919 environments in 69 countries. To determine the annual genetic gains, differences in mean yields of the five highest yielding entries from mean trial yield and mean yield of the widely grown international check ‘Attila’ were regressed over 15 yr of ESWYT testing. Across locations in all countries, mean yields of the five highest yielding entries showed an annual gain of 27.8 kg ha−1 (0.65%) compared to Attila. Annual yield gains in mega-environment 1 (ME1) (optimally irrigated), ME2 (high rainfall), Egypt, India, and Pakistan were 27.4 (0.55%), 21.4 (0.62%), 111.6 (1.13%), 32.5 (0.83%), and 18.5 kg ha−1 (0.5%), respectively. These results demonstrate continuous genetic yield gains in the elite spring bread wheat lines developed and distributed by CIMMYT and the positive outcomes achieved through breeding and the international exchange of elite spring wheat germplasm that have benefited national programs throughout the world.


New insights into the genetics of in vivo induction of maternal haploids, the backbone of doubled haploid technology in maize

Posted by Carelia Juarez on , in Journal Articles

Published in Genetics, 2011

Vanessa Prigge, Xiaowei Xu, Liang Li,  Raman Babu, Shaojiang Chen,  Gary N. Atlin  and  Albrecht E. Melchinger

Haploids and doubled haploid (DH) inbred lines have become an invaluable tool for maize genetic research and hybrid breeding, but the genetic basis of in vivo induction of maternal haploids is still unknown. This is the first study reporting comparative quantitative trait locus (QTL) analyses of this trait in maize. We determined haploid induction rates (HIR) in testcrosses of a total of 1061 progenies of four segregating populations involving two temperate haploid inducers, UH400 (HIR=8%) and CAUHOI (HIR=2%), one temperate and two tropical inbreds with HIR=0%, and up to three generations per population. Mean HIR of the populations ranged from 0.6 to 5.2% and strongly deviated from the mid-parent values. One QTL (qhir1) explaining up to p^ = 66% of the genetic variance was detected in bin 1.04 in the three populations involving a non-inducer parent and the HIR-enhancing allele was contributed by UH400. Segregation ratios of loci in bin 1.04 were highly distorted against the UH400 allele in these three populations, suggesting that transmission failure of the inducer gamete and haploid induction ability are related phenomena. In the CAUHOIxUH400 population, seven QTL were identified on five chromosomes, with qhir8 on chromosome having p^ > 20% in three generations of this cross. The large-effect QTL qhir1 and qhir8 will likely become fixed quickly during inducer development due to strong selection pressure applied for high HIR. Hence, marker-based pyramiding of small-effect and/or modifier QTL influencing qhir1 and qhir8 may help to further increase HIR in maize. We propose a conceptual genetic framework for inheritance of haploid induction ability, which is also applicable to other dichotomous traits requiring progeny testing, and discuss the implications of our results for haploid inducer development.


Genetics and mapping of resistance to spore inoculum and culture filtrate of Phaeosphaeria nodorum in spring wheat line

Posted by on , in Journal Articles

Published in Crop Protection 30(2): 2011

Genetics and mapping of resistance to spore inoculum and culture filtrate of Phaeosphaeria nodorum in spring wheat line ND 735

P.K. Singh; M. Mergoum; T.B. Adhikari; F. Ghavami; and S.F. Kianian

Stagonospora nodorum blotch (SNB), caused by Phaeosphaeria nodorum, is one of the most devastating foliar diseases on wheat (Triticum aestivum L.) in the northern Great Plains of North America. This study was conducted, under controlled environmental conditions, to elucidate the genetics and map the resistance to SNB caused by spore inoculum and culture filtrate of P. nodorum isolate Sn2000. A hard red spring wheat population was developed from a cross between the susceptible cultivar Steele-ND and the resistant line ND 735 for this study. Two-leaf seedlings of the parents, F1 and F2 generations, and F2:6 recombinant-inbred lines (RILs) were inoculated with spore suspensions while independent two week old seedlings of segregating generations were infiltrated with culture filtrate. Disease reaction was assessed 8 days after inoculation based on a lesion-type scale while plants were evaluated for culture filtrate response four days after infiltration for the presence or absence of necrosis. Genetic analysis revealed that a single recessive gene, Tsn1, in ND 735 confers resistance to both spore suspension and culture filtrate of P. nodorum isolate Sn2000. Mapping analysis using Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) markers indicates the gene, Tsn1, is located on the long arm of chromosome 5B and is flanked by the DArt markers wPt-8285 and wPt-3049 at a distance of 7.0 cM and 2.9 cM, respectively. This gene also controls resistance to tan spot caused by Pyrenophora tritici-repentis race 2. Results of this study reveal that wheat-P. nodorum interaction follows the toxin model of gene-for-gene hypothesis. Additionally, the finding of single gene control in the line ND 735 for both tan spot and SNB enhances the utility of the line ND 735 in wheat breeding program as a source of multiple disease resistance.

NEW BOOK IN THE LIBRARY: Applied Statistical Genetics with R: for Population-based Association Studies

Posted by Jose Juan Caballero on , in New Acquisitions

Andrea S. Foulkes

Applied Statistical Genetics with R: For Population-based Association Studies (Use R)

ISBN: 978-0-387-89553-6

Product Description
Statistical genetics has become a core course in many graduate programs in public health and medicine. This book presents fundamental concepts and principles in this emerging field at a level that is accessible to students and researchers with a first course in biostatistics. Extensive examples are provided using publicly available data and the open source, statistical computing environment, R.

NEW BOOK IN THE LIBRARY: Plant Biotechnology – Current and future applications of genetically modified crops

Posted by Jose Juan Caballero on , in New Acquisitions

Nigel Halford

ISBN: 13-978-0-470-02181-1

Plant Biotechnology: Current and future applications of genetically modified crops

Product Description

Plant Biotechnology: Current and Future Uses of Genetically Modified Crops covers in detail the development, use and regulation of GM crops. Split into three sections, Part 1 introduces GM crops and describes the GM crops that are used commercially. Part 2 looks at new developments and methodologies in areas including potential applications of GM crops for the production of vaccines, enhanced nutritional value of GM food, and engineering resistance to fungal pathogens. Part 3 concludes by considering the key issues of safety and legislation, including allergenicity, environmental impacts, risk assessment and labelling.


New Book in the Library: Genetics and Analysis of Quantitative Traits

Posted by Jose Juan Caballero on , in New Acquisitions

Genetics and Analysis of Quantitative Traits

 Michael Lynch; Bruce Walsh

ISBN-13: 978-0878934812

Genetics and Analysis of Quantitative Traits brings together the diverse array of theoretical and empirical applications of quantitative genetics under one cover, in a way that is both comprehensive and accessible to anyone with a rudimentary understanding of statistics and genetics. What was originally envisioned as a single text has now become two, with the focus of this first book being on the basic biology and methods of analysis of quantitative characters. (The second book, Evolution and Selection of Quantitative Traits, will address the basic principles that govern the evolutionary dynamics of quantitative characters under the forces of mutation, random genetic drift, and natural and/or artificial selection, integrating the theory of evolution of such characters with existing empirical data from natural and domesticated plant and animal populations.) Written as a general text in quantitative genetics, the book will also be useful as a basic reference for the seasoned professional. Throughout, central theoretical concepts are developed from first principles. To aid the less statistically sophisticated reader, several chapters and appendices focus on the basic statistical tools needed to digest the book. Wherever possible, theoretical and analytical concepts are illustrated with empirical examples from diverse settings. Three major features of Genetics and Analysis of Quantitative Traits distinguish it from earlier work. First, it reflects the explosive influx over the past few years of quantitative-genetic thinking into evolutionary biology. Second, in animal breeding, enormous strides have been made in the development of new techniques for estimating breeding values (for the purposes of identifying elite individuals in selection programs) and for estimating variance components from samples of complex pedigrees. In this text’s last two chapters, the authors outline the basic principles of complex pedigree analysis, without getting bogged down in technical details. Third, Genetics and Analysis of Quantitative Traits provides a broad overview of the newly emerging array of techniques for quantitative-trait loci (QTL) analysis, currently one of the most active fields of quantitative-genetic research. Genetics and Analysis of Quantitative Traits contains numerous fully-worked examples and illustrations of theoretical concepts, as well as over 2,000 references with indices by subject, author, and organism. In addition, the authors maintain a World Wide Web site featuring up-to-date lists of computer programs and on-line resources, and added information on various topics presented in the text.

Predicting quantitative Traits With Regression Models for dense molecular markers and pedigree

Posted by on , in Journal Articles

Published in Genetics 182: 375-385, 2009

Predicting quantitative Traits With Regression Models for dense molecular markers and pedigree

Gustavo de los Campos, Hugo Naya, Daniel Gianola, José Crossa, Andrés Legarra, Eduardo Manfredi, Kent Weigel and José Miguel Cotes

The availability of genomewide dense markers brings opportunities and challenges to breeding programs. An important question concerns the ways in which dense markers and pedigrees, together with phenotypic records, should be used to arrive at predictions of genetic values for complex traits. If a large number of markers are included in a regression model, marker-specific shrinkage of regression coefficients may be needed. For this reason, the Bayesian least absolute shrinkage and selection operator (LASSO) (BL) appears to be an interesting approach for fitting marker effects in a regression model. This article adapts the BL to arrive at a regression model where markers, pedigrees, and covariates other than markers are considered jointly. Connections between BL and other marker-based regression models are discussed, and the sensitivity of BL with respect to the choice of prior distributions assigned to key parameters is evaluated using simulation. The proposed model was fitted to two data sets from wheat and mouse populations, and evaluated using cross-validation methods. Results indicate that inclusion of markers in the regression further improved the predictive ability of models. An R program that implements the proposed model is freely available.

New book in the library: Principles of Plant Genetics and Breeding

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Principles of Plant Genetics and Breeding. George Acquaah.
This book introduces both classical and molecular tools for plant breeding,  topics such as biotechnology in plant breeding, intellectual property, risks, emerging concepts (decentralized breeding, organic breeding), and more are addressed in this state of the art text. The final 8 chapters provide a useful reference on breeding the largest and most common crops. In addition, over 25 plant breeders share their professional experiences while illustrating concepts in the text.  Contents:

Part I: Underlying Science and Methods of Plant Breeding
  • Historical Perspectives and Importance of Plant Breeding.
  • General Biological Concepts.
  • Germplasm Issues.
  • Genetic Analysis in Plant Breeding.
  • Tools in Plant Breeding.
  • Classic Methods of Plant Breeding.
  • Selected Breeding Objectives.
  • Cultivar Release and Commercial Seed Production.
  • Part II: Breeding Selected Crops.