Fine Scale Genomic Signals of Admixture and Alien Introgression among Asian Rice Landraces.

Authors:
Dmytro Chebotarov
Dmytro Chebotarov
T.T.Chang Genetic Resources Center
Kenneth L McNally
Kenneth L McNally
International Rice Research Institute
Philippines
Claire Billot
Claire Billot
Institute for Tropical Medicine
Belgium

Genome Biol Evol 2019 May;11(5):1358-1373

UMR AGAP, CIRAD, Montpellier, France.

Modern rice cultivars are adapted to a range of environmental conditions and human preferences. At the root of this diversity is a marked genetic structure, owing to multiple foundation events. Admixture and recurrent introgression from wild sources have played upon this base to produce the myriad adaptations existing today. Genome-wide studies bring support to this idea, but understanding the history and nature of particular genetic adaptations requires the identification of specific patterns of genetic exchange. In this study, we explore the patterns of haplotype similarity along the genomes of a subset of rice cultivars available in the 3,000 Rice Genomes data set. We begin by establishing a custom method of classification based on a combination of dimensionality reduction and kernel density estimation. Through simulations, the behavior of this classifier is studied under scenarios of varying genetic divergence, admixture, and alien introgression. Finally, the method is applied to local haplotypes along the genome of a Core set of Asian Landraces. Taking the Japonica, Indica, and cAus groups as references, we find evidence of reciprocal introgressions covering 2.6% of reference genomes on average. Structured signals of introgression among reference accessions are discussed. We extend the analysis to elucidate the genetic structure of the group circum-Basmati: we delimit regions of Japonica, cAus, and Indica origin, as well as regions outlier to these groups (13% on average). Finally, the approach used highlights regions of partial to complete loss of structure that can be attributed to selective pressures during domestication.

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Source
https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe
Publisher Site
http://dx.doi.org/10.1093/gbe/evz084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499253PMC
May 2019
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