Genetic control of juvenile growth and botanical architecture in an ornamental woody plant, Prunus mume Sieb. et Zucc. as revealed by a high-density linkage map

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Abstract

Mei, Prunus mume Sieb. et Zucc., is an ornamental plant popular in East Asia and, as an important member of genus Prunus, has played a pivotal role in systematic studies of the Rosaceae. However, the genetic architecture of botanical traits in this species remains elusive. This paper represents the first genome-wide mapping study of quantitative trait loci (QTLs) that affect stem growth and form, leaf morphology and leaf anatomy in an intraspecific cross derived from two different mei cultivars. Genetic mapping based on a high-density linkage map constricted from 120 SSRs and 1,484 SNPs led to the detection of multiple QTLs for each trait, some of which exert pleiotropic effects on correlative traits. Each QTL explains 3-12% of the phenotypic variance. Several leaf size traits were found to share common QTLs, whereas growth-related traits and plant form traits might be controlled by a different set of QTLs. Our findings provide unique insights into the genetic control of tree growth and architecture in mei and help to develop an efficient breeding program for selecting superior mei cultivars.

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Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers.

D Grattapaglia, R. Sederoff (1994)

We have used a "two-way pseudo-testcross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F1 progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, theta = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support > or = 1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organisms. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the paradigm of a species index map to the heterodox proposal of constructing several maps for individual trees of a population, therefore mitigating the problem of linkage equilibrium between marker and trait loci for the application of marker assisted strategies in tree breeding.

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Functional mapping - how to map and study the genetic architecture of dynamic complex traits.

Rongling Wu, Min Lin (2006)

The development of any organism is a complex dynamic process that is controlled by a network of genes as well as by environmental factors. Traditional mapping approaches for analysing phenotypic data measured at a single time point are too simple to reveal the genetic control of developmental processes. A general statistical mapping framework, called functional mapping, has been proposed to characterize, in a single step, the quantitative trait loci (QTLs) or nucleotides (QTNs) that underlie a complex dynamic trait. Functional mapping estimates mathematical parameters that describe the developmental mechanisms of trait formation and expression for each QTL or QTN. The approach provides a useful quantitative and testable framework for assessing the interplay between gene actions or interactions and developmental changes.

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The Bayesian lasso for genome-wide association studies.

Jiahan Li, Kiranmoy Das, Guifang Fu … (2011)

Despite their success in identifying genes that affect complex disease or traits, current genome-wide association studies (GWASs) based on a single SNP analysis are too simple to elucidate a comprehensive picture of the genetic architecture of phenotypes. A simultaneous analysis of a large number of SNPs, although statistically challenging, especially with a small number of samples, is crucial for genetic modeling. We propose a two-stage procedure for multi-SNP modeling and analysis in GWASs, by first producing a 'preconditioned' response variable using a supervised principle component analysis and then formulating Bayesian lasso to select a subset of significant SNPs. The Bayesian lasso is implemented with a hierarchical model, in which scale mixtures of normal are used as prior distributions for the genetic effects and exponential priors are considered for their variances, and then solved by using the Markov chain Monte Carlo (MCMC) algorithm. Our approach obviates the choice of the lasso parameter by imposing a diffuse hyperprior on it and estimating it along with other parameters and is particularly powerful for selecting the most relevant SNPs for GWASs, where the number of predictors exceeds the number of observations. The new approach was examined through a simulation study. By using the approach to analyze a real dataset from the Framingham Heart Study, we detected several significant genes that are associated with body mass index (BMI). Our findings support the previous results about BMI-related SNPs and, meanwhile, gain new insights into the genetic control of this trait. The computer code for the approach developed is available at Penn State Center for Statistical Genetics web site, http://statgen.psu.edu.

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Author and article information

Contributors

Lidan Sun

Yaqun Wang

Xiaolan Yan

Tangren Cheng

Kaifeng Ma

Weiru Yang

Huitang Pan

Chengfei Zheng

Xuli Zhu

Jia Wang

Rongling Wu

Qixiang Zhang

Conference

Journal ID (nlm-ta): BMC Genet

Journal ID (iso-abbrev): BMC Genet

Title: BMC Genetics

Publisher: BioMed Central

ISSN (Electronic): 1471-2156

Publication date Collection: 2014

Publication date (Electronic): 20 June 2014

Volume: 15

Issue: Suppl 1

Page: S1

Affiliations

[1 ]Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China

[2 ]Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA

[3 ]Mei Research Center of China, Wuhan 430074, China

[4 ]Center for Computational Biology, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China

Article

Publisher ID: 1471-2156-15-S1-S1

DOI: 10.1186/1471-2156-15-S1-S1

PMC ID: 4118613

PubMed ID: 25078672

SO-VID: 1ea2a534-38e9-4f71-9fba-758d49fb6244

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Conference name: International Symposium on Quantitative Genetics and Genomics of Woody Plants

Genetic control of juvenile growth and botanical architecture in an ornamental woody plant, Prunus mume Sieb. et Zucc. as revealed by a high-density linkage map

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Most cited references 21

Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers.

Functional mapping - how to map and study the genetic architecture of dynamic complex traits.

The Bayesian lasso for genome-wide association studies.

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