Luca Comai

University of California, Davis

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Isabelle Henry

University of California, Davis

Supachitra Chadchawan

Chulalongkorn University

Teerapong Buaboocha

Chulalongkorn University

Steven Henikoff

Fred Hutch Cancer Center

Helen Tsai

University of California, Davis

Kirk Amundson

University of California, Davis

Meric Lieberman

University of California, Davis

Brian P. Dilkes

Purdue University West Lafayette

Bradley J. Till

University of California, Davis

Ek Han Tan

University of Maine

Cooperative Institutions

University of California, Davis

154

University of Washington

Chulalongkorn University

Fred Hutch Cancer Center

Agricultural Research Service

Plant (United States)

Howard Hughes Medical Institute

United States Department of Agriculture

University of California, Berkeley

International Rice Research Institute

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Centromeric Localization and Adaptive Evolution of an Arabidopsis Histone H3 Variant

The Plant Cell (2002)

Paul B. Talbert Ricardo W. Masuelli Anand P. Tyagi Luca Comai Steven Henikoff

Centromeric H3-like histones, which replace histone H3 in the centromeric chromatin of animals and fungi, have not been reported in plants. We identified a histone H3 variant from Arabidopsis thaliana that encodes a centromere-identifying protein designated HTR12. By immunological detection, HTR12 localized at centromeres in both mitotic and meiotic cells. HTR12 signal revealed tissue- and stage-specific differences in centromere morphology, including a distended bead-like structure in interphase root tip cells. The anti-HTR12 antibody also detected spherical organelles in meiotic cells. Although the antibody does not label centromeres in the closely related species Arabidopsis arenosa, HTR12 signal was found on all centromeres in allopolyploids of these two species. Comparison of the HTR12 genes of A. thaliana and A. arenosa revealed striking adaptive evolution in the N-terminal tail of the protein, similar to the pattern seen in its counterpart in Drosophila. This finding suggests that the same evolutionary forces shape centromeric chromatin in both animals and plants.

Chromatin immunoprecipitation

Interphase

10.1105/tpc.010425

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Citations (395)

Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability

The Plant Cell (2021)

Kirk Amundson Benny Ordoñez Monica Santayana Mwaura Livingstone Nganga Isabelle Henry

In cultivated tetraploid potato (Solanum tuberosum), reduction to diploidy (dihaploidy) allows for hybridization to diploids and introgression breeding and may facilitate the production of inbreds. Pollination with haploid inducers (HIs) yields maternal dihaploids, as well as triploid and tetraploid hybrids. Dihaploids may result from parthenogenesis, entailing the development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and the loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of HI DNA in some dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three HIs: IVP35, IVP101, and PL-4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids, with karyotypes ranging from 2n = 2x - 1 = 23 to 2n = 2x + 3 = 27. Of the additional chromosomes in 74 aneuploids, 66 were from the non-inducer parent and 8 from the inducer parent. Overall, we detected full or partial chromosomes from the HI parent in 0.87% of the dihaploids, irrespective of parental genotypes. Chromosomal breaks commonly affected the paternal genome in the dihaploid and tetraploid progeny, but not in the triploid progeny, correlating instability to sperm ploidy and to haploid induction. The residual HI DNA discovered in the progeny is consistent with genome elimination as the mechanism of haploid induction.

Parthenogenesis

Chromosome instability

Polyploid

10.1093/plcell/koab100

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Citations (15)

Dataset_S2.tsvGenomic outcomes of haploid induction crosses in potato

Figshare (2019)

Luca Comai

List of parental SNP (homozygous and heterozygous haploid inducer genotypes included) used for segmental dosage analysis.

Doubled haploidy

10.6084/m9.figshare.10052354.v1

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Citations (0)

Tilling and Ecotilling for Crop Improvement

Springer eBooks (2007)

Bradley J. Till Luca Comai Steven Henikoff

TILLING

Reverse Genetics

10.1007/978-1-4020-6295-7_15

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Citations (51)

Multilayered epigenetic control of persistent and stage-specific imprinted genes in rice endosperm

Nature Plants (2024)

Kaoru Tonosaki Daichi Susaki Hatsune Morinaka A. Ono Hiroki Nagata

Genomic Imprinting

Imprinting (psychology)

DNA demethylation

Demethylase

10.1038/s41477-024-01754-4

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Chromoanagenesis in plants: triggers, mechanisms, and potential impact

Trends in Genetics (2022)

Weier Guo Luca Comai Isabelle Henry

Chromosome engineering

10.1016/j.tig.2022.08.003

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Citations (11)

EcoTILLING stress tolerance genes in cultivated and wild rice

Hehe Wang Ma. Elizabeth B. Naredo Giuseppe Carillo Bradley J. Till Elizabeth A. Greene

Source

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Variegation and silencing of the Heat Shock Cognate 80 gene are relieved by a bipartite downstream regulatory element

The Plant Journal (1996)

Anna Chinn Shannon R. Payne Luca Comai

Transgenes are important tools for plant molecular biologists. However, some aspects of their regulation are not completely understood. First, the contribution of elements separate from the promoter has been documented for several genes, but a general requirement for such elements is still unclear. Second, transgene expression can be subject to variability from chromosomal position effects and from epigenetic effects, often due to the presence of repeated sequences. While studying the regulation of the developmentally expressed Heat Shock Cognate 80 (HSC80) gene, several peculiarities were found which involve both of these questions. First, HSC80 transgenes are subject to silencing and variegation at a high frequency. Second, a bipartite element downstream of the transcriptional start is necessary to achieve efficient expression from the HSC80 promoter in stable transformants. Finally, this bipartite element is not required for expression in a transient system, where the promoter alone is sufficient. These results together support a role for chromatin structure in the regulation of HSC80 .

Variegation (histology)

Position effect

10.1046/j.1365-313x.1996.09030325.x

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Citations (15)

Differential mutation accumulation in plant meristematic layers

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Kirk Amundson Mohan P A Marimuthu Oanh Nguyen Konsam Sarika Isabelle J DeMarco

Abstract The upper plant body is formed by the continued growth of shoot apical meristems. In angiosperms, meristems are organized in three cell layers that tend to remain clonally isolated. Somatic variants emerge when mutant cells overtake part or all of a meristem. During sexual reproduction, only one layer, the L2, contributes to the next generation by forming gametes. The L2 is known to frequently invade and replace the L3, while L1-L2 separation is persistent. The role of different meristem layers in mutation accumulation is unknown. We discovered a potato periclinal chimera in which the L2 and L3, but not the L1, are marked by a chromosomal translocation. This enabled the identification of plants regenerated from leaf protoplasts originating from either the L1 or L2+L3. Leveraging these layer-specific clones, we identified and compared mutations that accumulated in the layers in the clonal parent for several decades. Here we show that the L1 accumulates mutations at 1.9 times the rate of the L2, indicating that plants might protect the germline by mechanisms that reduce the rate of mutation accumulation in the L2. In contrast to these layer-specific mutations, we found no evidence of somatic mutation fixation in all three meristem layers. Our findings highlight how periclinal chimeras are formed by independent mutational processes in which a mutation-prone epidermal layer could increase clonal variation.

Chimera (genetics)

Protoplast

10.1101/2023.09.25.559363

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Citations (6)

Human genetics: Human genetics discovering ourselves

Heredity (2007)

Luca Comai

Human genetics

Molecular Genetics

Human evolutionary genetics

Medical genetics

Statistical genetics

10.1038/sj.hdy.6801060

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Citations (1)