ArticleGenome biology and evolution2019
Fine Scale Genomic Signals of Admixture and Alien Introgression among Asian Rice Landraces.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic bases of resistance to the rice hoja blanca disease deciphered by a quantitative trait locus approach.G3 (Bethesda, Md.) · 2023Pooled it
- Deciphering the mosaic genome of sugarcane cultivars through polyploid admixture inference with AdmixPoly.Genome biology · 2026Article
- A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination.Nature communications · 2024Article
- Article
- Historical Routes for Diversification of Domesticated Chickpea Inferred from Landrace Genomics.Molecular biology and evolution · 2023Article
- Traces of Introgression from cAus into Tropical Japonica Observed in African Upland Rice Varieties.Rice (New York, N.Y.) · 2023Article
- Choosing the right tool: Leveraging of plant genetic resources in wheat (Triticum aestivum L.) benefits from selection of a suitable genomic prediction model.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Genetic introgression between different groups reveals the differential process of Asian cultivated rice.Scientific reports · 2022Article
- GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics.Database : the journal of biological databases and curation · 2022Article
- Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars.Plant communications · 2022Article
- Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas.Frontiers in plant science · 2022Article
- Anchoring alien chromosome segment substitutions bearing gene(s) for resistance to mustard aphid in Brassica juncea-B. fruticulosa introgression lines and their possible disruption through gamma irradiation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- A new comprehensive annotation of leucine-rich repeat-containing receptors in rice.The Plant journal : for cell and molecular biology · 2021Article
- Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species.Scientific reports · 2021Article
- On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo.PLoS computational biology · 2021Article
- Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.Rice (New York, N.Y.) · 2021Article
- Evolutionary Processes Involved in the Emergence and Expansion of an Atypical O. sativa Group in Madagascar.Rice (New York, N.Y.) · 2021Article
- Three founding ancestral genomes involved in the origin of sugarcane.Annals of botany · 2021Article
- Chromosome reciprocal translocations have accompanied subspecies evolution in bananas.The Plant journal : for cell and molecular biology · 2020Article
- Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice.Genome biology · 2020Article
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7 authors.
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Abstract
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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