A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations

Jiang N, Zhang F, Wu J, Chen Y, Hu X, Fang O, Leach L, Wang D, Luo Z (2016) Theoretical and Applied Genetics doi: 10.1007/s00122-016-2736-9 [pubmed]

Corresponding author Zewei Luo

Department of Biostatistics & Computational Biology, SKLG,

School of Life Sciences, Fudan University

zwluo@fudan.edu.cn

Advent of the new generation sequencing techniques motivates recent interest in developing sequence-based identification and genotyping of genome-wide genetic variants in large populations, with RAD-seq being a typical example. Without taking proper account for the fact that chloroplast and rRNA genes may occupy up to 60% of the resulting sequence reads, the current RAD-seq design could be very inefficient for plant and crop species. Based on the original RAD-seq idea, the new method presented here is thoroughly optimized by integrating an in silico guided selection of an optimal combination of restriction enzymes to shear the target genome into DNA segments with designed length, to remove the abundant and undesirable chloroplast and rRNA DNA from sequencing libraries and to guide selection of those DNA segments to be sequenced for predefined genome regions.

Fortran90_executable_and_guide_files.tar.gz

 

Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species

Corresponding author Zewei Luo

Chen J, Zhang F, Wang L, Leach L, and Luo Z (2017) Manuscript submitted.

School of BioSciences, University of Birmingham

z.luo@bham.ac.uk

Autotetraploids represent a critical form in the evolution of angiosperms and several economically important crops and aquaculture animals. The most prominent example is cultivated potato, the world’s 3rd most important food crop after rice and wheat. Although quantitative genetic analysis, the means for understanding the genetic architecture of quantitative traits, has been well established and routinely practiced in diploids, the research in autotetraploids is far behind due to the complexities of tetrasomic inheritance. The present study develops models and methods for linking together genes and their phenotypic effects and lays a rigorous scientific basis for quantitative genetic analysis in autotetraploids. Programs and data for statistical analyses presented in the paper are freely available from github here