scholarly journals Haplotype Structure of the Stigmatic Self-Incompatibility Gene in Natural Populations of Arabidopsis lyrata

2003 ◽  
Vol 20 (11) ◽  
pp. 1741-1753 ◽  
Author(s):  
D. Charlesworth
Keyword(s):  
Natural Populations ◽  
Haplotype Structure ◽  
Self Incompatibility ◽  
Arabidopsis Lyrata

Subdivision and haplotype structure in natural populations of Arabidopsis lyrata

2003 ◽  
Vol 12 (5) ◽  
pp. 1247-1263 ◽  
Author(s):  
Stephen I. Wright ◽  
Beatrice Lauga ◽  
Deborah Charlesworth
Keyword(s):  
Natural Populations ◽  
Haplotype Structure ◽  
Arabidopsis Lyrata

scholarly journals Diversity and Linkage of Genes in the Self-Incompatibility Gene Family inArabidopsis lyrata

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1519-1535 ◽  
Author(s):  
Deborah Charlesworth ◽  
Barbara K Mable ◽  
Mikkel H Schierup ◽  
Carolina Bartolomé ◽  
Philip Awadalla
Keyword(s):  
Gene Family ◽  
Balancing Selection ◽  
Natural Populations ◽  
The Self ◽  
Self Incompatibility ◽  
Arabidopsis Lyrata ◽  
Hypervariable Regions ◽  
Synonymous Polymorphism ◽  
Protein Locus ◽  
Linkage Of Genes

AbstractWe report studies of seven members of the S-domain gene family in Arabidopsis lyrata, a member of the Brassicaceae that has a sporophytic self-incompatibility (SI) system. Orthologs for five loci are identifiable in the self-compatible relative A. thaliana. Like the Brassica stigmatic incompatibility protein locus (SRK), some of these genes have kinase domains. We show that several of these genes are unlinked to the putative A. lyrata SRK, Aly13. These genes have much lower nonsynonymous and synonymous polymorphism than Aly13 in the S-domains within natural populations, and differentiation between populations is higher, consistent with balancing selection at the Aly13 locus. One gene (Aly8) is linked to Aly13 and has high diversity. No departures from neutrality were detected for any of the loci. Comparing different loci within A. lyrata, sites corresponding to hypervariable regions in the Brassica S-loci (SLG and SRK) and in comparable regions of Aly13 have greater replacement site divergence than the rest of the S-domain. This suggests that the high polymorphism in these regions of incompatibility loci is due to balancing selection acting on sites within or near these regions, combined with low selective constraints.

scholarly journals Homology-Based Interactions between Small RNAs and Their Targets Control Dominance Hierarchy of Male Determinant Alleles of Self-Incompatibility in Arabidopsis lyrata

2021 ◽  
Vol 22 (13) ◽  
pp. 6990
Author(s):  
Shinsuke Yasuda ◽  
Risa Kobayashi ◽  
Toshiro Ito ◽  
Yuko Wada ◽  
Seiji Takayama
Keyword(s):  
Dominance Hierarchy ◽  
Male Dominance ◽  
Self Incompatibility ◽  
Arabidopsis Halleri ◽  
Plant Family ◽  
Arabidopsis Lyrata ◽  
Multiple Networks ◽  
Target Sites ◽  
Gains And Losses ◽  
Linear Dominance Hierarchy

Self-incompatibility (SI) is conserved among members of the Brassicaceae plant family. This trait is controlled epigenetically by the dominance hierarchy of the male determinant alleles. We previously demonstrated that a single small RNA (sRNA) gene is sufficient to control the linear dominance hierarchy in Brassica rapa and proposed a model in which a homology-based interaction between sRNAs and target sites controls the complicated dominance hierarchy of male SI determinants. In Arabidopsis halleri, male dominance hierarchy is reported to have arisen from multiple networks of sRNA target gains and losses. Despite these findings, it remains unknown whether the molecular mechanism underlying the dominance hierarchy is conserved among Brassicaceae. Here, we identified sRNAs and their target sites that can explain the linear dominance hierarchy of Arabidopsis lyrata, a species closely related to A. halleri. We tested the model that we established in Brassica to explain the linear dominance hierarchy in A. lyrata. Our results suggest that the dominance hierarchy of A. lyrata is also controlled by a homology-based interaction between sRNAs and their targets.

scholarly journals Testing for Effects of Recombination Rate on Nucleotide Diversity in Natural Populations of Arabidopsis lyrata

Genetics ◽  
2006 ◽  
Vol 174 (3) ◽  
pp. 1421-1430 ◽  
Author(s):  
Stephen I. Wright ◽  
John Paul Foxe ◽  
Leah DeRose-Wilson ◽  
Akira Kawabe ◽  
Mark Looseley ◽  
...  
Keyword(s):  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Natural Populations ◽  
Arabidopsis Lyrata

BREAKDOWN OF SELF-INCOMPATIBILITY IN THE PERENNIAL ARABIDOPSIS LYRATA (BRASSICACEAE) AND ITS GENETIC CONSEQUENCES

Evolution ◽  
2005 ◽  
Vol 59 (7) ◽  
pp. 1437 ◽  
Author(s):  
Barbara K. Mable ◽  
Alexander V. Robertson ◽  
Sara Dart ◽  
Christina Di Berardo ◽  
Laura Witham
Keyword(s):  
Self Incompatibility ◽  
Arabidopsis Lyrata

Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata

2006 ◽  
Vol 0 (0) ◽  
pp. 061222052703001-??? ◽  
Author(s):  
MAARIT KIVIMÄKI ◽  
KATRI KÄRKKÄINEN ◽  
MYRIAM GAUDEUL ◽  
GEIR LØE ◽  
JON ÅGREN
Keyword(s):  
Natural Populations ◽  
Arabidopsis Lyrata ◽  
Resistance To Herbivory ◽  
And Function

scholarly journals Genotyping and De Novo Discovery of Allelic Variants at the Brassicaceae Self-Incompatibility Locus from Short-Read Sequencing Data

2019 ◽  
Vol 37 (4) ◽  
pp. 1193-1201 ◽  
Author(s):  
Mathieu Genete ◽  
Vincent Castric ◽  
Xavier Vekemans
Keyword(s):  
De Novo ◽  
Balancing Selection ◽  
Methodological Approach ◽  
Natural Populations ◽  
Sequence Divergence ◽  
Reference Database ◽  
Self Incompatibility ◽  
Sequencing Data ◽  
Allelic Series ◽  
S Alleles

Abstract Plant self-incompatibility (SI) is a genetic system that prevents selfing and enforces outcrossing. Because of strong balancing selection, the genes encoding SI are predicted to maintain extraordinarily high levels of polymorphism, both in terms of the number of functionally distinct S-alleles that segregate in SI species and in terms of their nucleotide sequence divergence. However, because of these two combined features, documenting polymorphism of these genes also presents important methodological challenges that have so far largely prevented the comprehensive analysis of complete allelic series in natural populations, and also precluded the obtention of complete genic sequences for many S-alleles. Here, we develop a powerful methodological approach based on a computationally optimized comparison of short Illumina sequencing reads from genomic DNA to a database of known nucleotide sequences of the extracellular domain of SRK (eSRK). By examining mapping patterns along the reference sequences, we obtain highly reliable predictions of S-genotypes from individuals collected from natural populations of Arabidopsis halleri. Furthermore, using a de novo assembly approach of the filtered short reads, we obtain full-length sequences of eSRK even when the initial sequence in the database was only partial, and we discover putative new SRK alleles that were not initially present in the database. When including those new alleles in the reference database, we were able to resolve the complete diploid SI genotypes of all individuals. Beyond the specific case of Brassicaceae S-alleles, our approach can be readily applied to other polymorphic loci, given reference allelic sequences are available.

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