The Comai lab regularly publishes peer-reviewed articles focused on our various areas of research, and as part of outreach efforts. See below for a short description of some of our published works.
For the most up-to-date list of publications, these buttons will take you to relevant Google Scholar pages.
2025
Clonal strains of the fresh-market potato cultivar Russet Norkotah changed the domestication gene CDF1
Plant Physiology, Volume 198, Issue 4, August 2025
Kirk Richard Amundson , Maria Isabel Vales , Isabelle Jocelyn DeMarco , Weier Guo , Isabelle Marie Henry , Luca Comai
Clonal selection is an established breeding method for crop improvement. Here, we report the characterization of clonal variants of tetraploid potato variety Russet Norkotah (RN). These variants were identified in the field by breeders and called “giant hills” or “bolters” because they displayed later maturity, higher vigor, and yields higher than RN. We demonstrate that these improvements are associated with the excision of a transposon from one of the alleles of the CDF1 gene, a domestication gene already known to involved in photoperiod-modulated tuberization and maturity in potatoes.
Velvet: An alternative high-yielding peppermint clone for oil production
Crop Science 2025
Nestor Kippes Darrin Culp Robert G. Wilson Eric Dowd Luca Comai and Isabelle M. Henry
Peppermint is mainly produced commercially by extraction from two main types of cultivars: Black Mitcham,a sterile polyploid and the backbone of peppermint oil production in the United States, and Arvensis (Mentha arvensis L.), the main cultivar used for peppermint oil extraction in India. Here, we present the identification of an accession called Velvet that is publicly available at the US National Plant Germplasm System and exhibits potential as an alternative peppermint-type oil producer.
Sterility and structural variation in an arabidopsis pedigree carrying a ring minichromosome
Chrom. Res. 2025
Benny Ordoñez, Weier Guo, Witsarut Chueakhunthod, Isabelle M. Henry & Luca Comai
2024
Chromosome-scale assembly of apple mint (Mentha suaveolens)
BMC Genomic Data (2024) 25:96
Alana Firl1,2, Meric C. Lieberman1, Nestor Kippes1,3, Helen Tsai1, Eric Dowd4, Luca Comai1 and Isabelle M. Henry1*
A k-mer-based bulked segregant analysis approach to map seed traits in unphased heterozygous potato genomes
G3, 2024
Pajaree Sonsungsan, Mwaura Livingstone Nganga, Meric C Lieberman, Kirk R Amundson, Victoria Stewart, Kitiporn Plaimas, Luca Comai, Isabelle M Henry
In this paper, we investigate the genetic determinants of seed size and seed color in potato. Identifying genes linked to agronomic traits in potatoes is challenging because potato genomes are complex and variable. Therefore, we used a bulk k-mer approach, which allowed us to identify regions of the potato genome associated with both traits.
2023
Establishment and inheritance of minichromosomes from Arabidopsis haploid induction
Chromosoma, 2023
Ek Han Tan, Benny Ordoñez, Tejas Thondehaalmath, Danelle K Seymour, Julin N Maloof, Ravi Maruthachalam, Luca Comai
Minichromosomes are small, sometimes circular, rearranged chromosomes consisting of one centromere and short chromosomal arms. They have the potential to serve as vectors to quickly move valuable genes across a wide range of germplasm, including into adapted crop varieties. Here we show that minichromosoms can be formed during CENH3-mediated genome elimination. Our findings document the formation of heritable, rearranged chromosomes, and we provide a method for convenient minichromosome production.
Chromoanagenesis in plants: triggers, mechanisms, and potential impact
Trends in Genetics, 2023
Weier Guo, Luca Comai, Isabelle M Henry
Chromoanagenesis is a single catastrophic event that involves, in most cases, localized chromosomal shattering and reorganization, resulting in a dramatically restructured chromosome. First discovered in cancer cells, it has since been observed in various other systems, including plants. We reviewed the origin, characteristics and potential mechanisms underlying chromoanagenesis in plants. This review was highlighted on the cover of the January 2023 Trends in Genetics Issue.
Chromoanagenesis in the asy1 meiotic mutant of Arabidopsis
G3 – Genes|Genomes|Genetics, 2023
Weier Guo, Luca Comai, Isabelle M Henry
Chromoanagenesis is a complex and catastrophic event that results in severely restructured chromosomes. It has been identified in cancer cells and in some plant samples, after specific triggering events. Here, we identified this kind of genome restructuring in a mutant that exhibits defective meiosis in the model plant system Arabidopsis thaliana. It is a remarkable case because of the high frequency of novel DNA junctions produced within a localized chromosomal region, which has never been observed in other genome rearrangement cases in plants. The event also demonstrates the potential for karyotypic innovation in connection to oogenesis.
Gene expression profile during seed development of Bixa orellana accessions varying in bixin pigment
Frontiers in Plant Science, 2023
Yair Cárdenas-Conejo, José Alberto Narváez-Zapata, Víctor Manuel Carballo-Uicab, Margarita Aguilar-Espinosa, Rosa Us-Camas, Pedro Escobar-Turriza, Luca Comai, Renata Rivera-Madrid
Diverse morphological, cellular and physiological changes occur during seed maturation in Bixa orellana when the seed tissues form specialized cell glands that produce reddish latex with high bixin amounts. Transcriptomic profiling during seed development in three B. orellana accessions with contrasting morphologic characteristics showed enrichment in pathways of triterpenes, sesquiterpenes, and cuticular wax biosynthesis. Our results will help understand the metabolic context for bixin production in this important crop.
Accurate Direct PCR with Arabidopsis and Rice
Plant and Cell Physiology, 2023
Peter G Lynagh, Paul Osuna-Kleist, Bohai Wang, Edgar Malagon, Maria Ximena Anleu Gil, Luca Comai
In direct polymerase chain reaction (PCR), impure DNA is directly transferred from the plant to the PCR reaction, simplifying the procedure. Direct PCR using tissue collected in different ways has not been widely adopted even though it works for many plant species. Here we show a direct-PCR approach that involves using fishing line to harvest DNA in a fast and non-invasive manner. We also show that the accuracy, ease and speed of Line PCR enable quick, cost-effective and reliable genotyping.
The Arabidopsis Hop1 homolog ASY1 mediates cross-over assurance and interference
PNAS nexus, 2023
Gaetan Pochon, Isabelle M Henry, Chao Yang, Niels Lory, Nadia Fernández-Jiménez, Franziska Böwer, Bingyan Hu, Lena Carstens, Helen T Tsai, Monica Pradillo, Luca Comai, Arp Schnittger
The regulation of the number and placement of cross-overs (COs) during meiosis is critical to ensure meiotic fidelity and promote new genetic combinations. Here, we investigated the function of ASY1, which resides on the chromosome axis and plays a key role in CO formation. Our results show that COs in asy1 mutants are positioned closer to each other than in the wildtype and that, despite a roughly similar number of COs, not every chromosome receives a CO. With this, our results shed light on the mechanisms regulating two important but still poorly understood aspects of meiosis: CO assurance, which safeguards at least one CO per chromosome pair, and CO interference, which prevents two COs from occurring close to each other.
2022
The United States Potato Genebank Holding of cv. Desiree is a Somatic Mutant of cv. Urgenta
American Journal of Potato Research, 2022
Kirk R Amundson, Isabelle M Henry, Luca Comai
Genome-wide markers enable routine confirmation of whether varieties are true-to-type, and when they are not, to infer their identity. The objective of this study was to determine the basis of a previously described chromosome translocation, tr8-7, which was apparently polymorphic among holdings of the tetraploid potato (Solanum tuberosum L.) cultivar Desiree. Through analysis of publicly available genotype data from North American and European tetraploid potato germplasm, we resolved a longstanding mistaken identity of the United States Potato Genebank holding of Desiree, which is actually a somatic mutant of its maternal parent, cv. Urgenta. Comparison of multiple holdings revealed that tr8-7 was a somatic mutation that occurred at least 25 years ago and was maintained in isolated lineages.
2021
Diploid mint (M. longifolia) can produce spearmint type oil with a high yield potential
Scientific Reports, 2021
Nestor Kippes, Helen Tsai, Meric Lieberman, Darrin Culp, Brian McCormack, Rob G Wilson, Eric Dowd, Luca Comai, Isabelle M Henry
Mint oil is a key source of natural flavors with wide industrial applications. Two unbalanced polyploid cultivars are the main producers of spearmint type oil, which is characterized by high levels of the monoterpenes (−)-carvone and (−)-limonene. Here we show that sexual breeding at the diploid level can be leveraged to develop new varieties that produce spearmint type oil, along with the improvement of other important traits. Using field trials and GC-FID oil analysis we characterized plant materials from a public germplasm repository and identified a diploid accession that exhibited 89.5% increase in oil yield, compared to the industry standard, and another that produces spearmint type oil. Spearmint-type oil was present at high frequency in a segregating F2 population (32/160) produced from these two accessions. Field-testing showed segregation for oil yield and confirmed the production of spearmint-type oil profiles. These results demonstrate that spearmint-type oil can be produced in a diploid background with high yield potential, providing a simpler genetic system for the development of improved spearmint varieties.
Efficient construction of a linkage map and haplotypes for Mentha suaveolens using sequence capture
G3 Genes|Genomes|Genetics 2021
Helen Tsai, Nestor Kippes, Alana Firl, Meric Lieberman, Luca Comai, Isabelle M Henry
Efficient application of modern breeding requires high-density linkage maps that are integrated into a highly contiguous reference genome. Here, we present a rapid method for deriving haplotypes and developing linkage maps, and its application to Mentha suaveolens, one of the diploid progenitors of cultivated mints. Using sequence-capture via DNA hybridization to target single nucleotide polymorphisms (SNPs), we successfully genotyped ∼5000 SNPs within the genome of >400 individuals derived from a self cross. After stringent quality control, and identification of nonredundant SNPs, 1919 informative SNPs were retained for linkage map construction. The resulting linkage map defined 12 linkage groups, which are in good agreement with pseudomolecules from our preliminary genome assembly. We discuss the advantages of this method for the rapid creation of linkage maps.
Epigenetically mismatched parental centromeres trigger genome elimination in hybrids
Science Advances, 2021
Mohan PA Marimuthu, Ravi Maruthachalam, Ramesh Bondada, Sundaram Kuppu, Ek Han Tan, Anne Britt, Simon WL Chan, Luca Comai
Wide crosses result in postzygotic elimination of one parental chromosome set, but the mechanisms that result in such differential fate are poorly understood. Here, we show that alterations of centromeric histone H3 (CENH3) lead to its selective removal from centromeres of mature Arabidopsis eggs and early zygotes, while wild-type CENH3 persists. In the hybrid zygotes and embryos, CENH3 and essential centromere proteins load preferentially on the CENH3-rich centromeres of the wild-type parent, while CENH3-depleted centromeres fail to reconstitute new CENH3-chromatin and the kinetochore and are frequently lost. Genome elimination is opposed by E3 ubiquitin ligase VIM1. We propose a model based on cooperative binding of CENH3 to chromatin to explain the differential CENH3 loading rates. Thus, parental CENH3 polymorphisms result in epigenetically distinct centromeres that instantiate a strong mating barrier and produce haploids.
LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci
Genetics, 2021
Luca Comai, Kirk R Amundson, Benny Ordonez, Xin Zhao, Guilherme Tomaz Braz, Jiming Jiang, Isabelle M Henry
Large-scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1 Mb bin, we tested independence, effectively an apparent linkage disequilibrium (LD), with other variable bins. In potato, we found evidence for translocation affecting euchromatic arms. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, while apparent LD between pericentromeric regions suggested the effect of repeats. This method, LD-CNV, should be useful in species where translocations are suspected because it tests linkage without the need for genotyping.
PL-4 (CIP596131.4): an Improved Potato Haploid Inducer
American Journal of Potato Research, 2021
Benny Julissa Ordonez Aquino, Monica Santayana, Mariela Aponte, Isabelle M. Henry, Luca Comai, Raúl Eyzaguirre, Hannele Lindqvist-Kreuze & Merideth Bonierbale
In the pursuit of simplifying genetic manipulation, the production of dihaploids (2x) from tetraploid cultivars has gained traction in potato breeding. Within this realm, an efficient haploid inducer (HI) plays a pivotal role as a true game-changer. PL-4, stands out among its HI counterparts, outperforming them in terms of dihaploid production and haploid induction rate. Additionally, PL-4’s ability to render a reduced proportion of hybrid seeds streamlines the screening process, further enhancing its value. As an enhanced HI, PL-4 serves as a gateway to accelerated progress for potato breeding.
Chromoanagenesis from radiation-induced genome damage in Populus
Plos Genetics, 2021
Weier Guo, Luca Comai, Isabelle M. Henry
We studied a population of poplar trees produced by gamma irradiation of pollen, and asked what kind of DNA changes were associated with this variation. We found many changes, most often in the form of added (insertions) or removed (deletions) pieces of DNA. We also found two lines with much more drastic changes. In those lines, we observed massive reorganization. We characterized these two lines in detail and found that catastrophic pulverization and random reassembly only occurred on a single chromosome. This type of rearrangement is commonly observed in human cancer cells, but has rarely been observed in plants. We demonstrated here that they can be induced by gamma irradiation, indicating this type of event might be more widespread than we expected. Characterizing such genome restructuring instances helps to understand how genome instability can remodel chromosomes and affect genome function.
2020
The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants
Plos Genetics, 2020
Takashi Akagi , Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle M. Henry
We developed a reference genome for Diospyros lotus (diploid persimmon) to further investigate the evolutionary steps that lead to dioecy in this system. Using this new genome assembly, we were able to identify a species-specific whole-genome duplication (WGD) event, as well as add to our understanding of the sex determination system in persimmon (published previously here in Science), by identifying a third homolog of MeGI and OGI, called Sister-of-MeGI (SiMeGI), originating from a local duplication event. Our data suggests that this WGD event initiated the evolution of the current sex determination system and further highlights the role of gene duplications on the transition between sexual systems.