Biology subjects

Cutti, L.

Publications and source records attributed to Cutti, L..

5 recordsLinked to original sources

bioRxiv2025

Subgenome dominance of ALS target site mutations impacts herbicide resistance in allohexaploid Echinochloa crus-galli

Herbicide target site resistance in polyploid species is more complex than diploids due to potential subgenome interactions and gene dosage of mutations. The objective of this study was to identify the level of resistance and cross-resistance patterns of ALS mutations located in the different subgenomes of allohexaploid Echinochloa crus-galli. E. crus-galli populations were screened and dose-response curves were performed with ALS-inhibitors from different chemical groups. The ALS genes of each subgenome (A, B, and C) were sequenced. Copy number variation, global relative expression, and the specific relative expression of ALS gene from each subgenome were performed. Out of 100 populations, 32% were resistant only to imazethapyr, and 48% were cross-resistant to all ALS-inhibitors. The mutations Ala122Thr, Ala205Asn, and Ser653Asn confer resistance only to imazethapyr, while Trp574Leu confers resistance to all four herbicides tested. ALS mutations were most frequent in subgenome A, but ALS from subgenome C had the highest expression. The biotype SAOJER-01 had Trp574Leu mutation in subgenome C and was 22 times more resistant to imazethapyr and penoxsulam than CAMAQ-01, which had the same Trp574Leu mutation in subgenome A with no differences in herbicide metabolism rate. The ALS genes from subgenomes A and C contribute approximately 13% and 50% respectively to the total ALS transcripts. The higher contribution of subgenome C to the total ALS transcripts pool combined with the Trp574Leu resistance mutation makes the biotype SAOJER-01 more resistant to herbicides than CAMAQ-01. This is the first study showing the effect of subgenome gene expression level on the herbicide resistance level in a polyploid weed species. In addition, while imazethapyr did not control any biotype with an ALS mutation, the other ALS-inhibitor herbicides were able to control biotypes carrying Ala122Thr, Ala205Asn, and Ser653Asn, which reinforces the utility of these herbicides in weed and resistance management.

genetics↗

bioRxiv2024

A Novel Genomic Rearrangement in the Amaranthus palmeri Extrachromosomal Circular DNA Provides Dual Herbicide Resistance to Glyphosate and Glufosinate

Amplification of chloroplastic glutamine synthetase (GS2) has been characterized as one of the resistance mechanisms in glufosinate-resistant Amaranthus palmeri accession (MSR2). Previously, the overamplification of the glyphosate-resistance gene, 5-enolpyruvylshikimate-3-phosphate (EPSPS), in A. palmeri was determined to be driven by an extrachromosomal circular DNA (eccDNA). Here, a novel eccDNA is described that carries both glyphosate and glufosinate-ammonium target site due to co-duplication of their chromosomic native region, conferring resistance. Besides EPSPS, the novel replicon has a region replaced by a fragment carrying the GS2 isoforms (GS2.1 and GS2.2) and other genes. The co-existence of eccDNA carrying only EPSPS was confirmed in MSR2 samples harboring dual targeting eccDNA. The genomic structure of GS2 and EPSPS amplification was also assessed in a different glufosinate-resistant A. palmeri accession (MSR1) along with MSR2. The accessions showed distinct GS2.1 and GS2.2 amplification patterns suggesting the existence of diverse replicons that were not assembled here. The EPSPS was amplified in both accessions, and a correlation was observed with the GS2 isoforms in MSR2, further supporting the co-existence of these genes in the same replicon. These findings shed light on the complexity of eccDNA formation in plant systems, with the collection and accumulation of extra pieces of DNA.

genomics↗

bioRxiv2024

Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region

Amaranthus palmeri (Palmer amaranth), A. retroflexus (redroot pigweed), and A. hybridus (smooth pigweed) are troublesome weeds that are economically damaging to several cropping systems. Collectively referred to as pigweeds, these species are incredibly adaptive and have become successful competitors in diverse agricultural settings. Development of genomic resources for these species promises to facilitate the elucidation of the genetic basis of traits such as biotic and abiotic stress tolerance (e.g., herbicide resistance) and sex determination. Here, we sequenced and assembled chromosome-level genomes of these three pigweed weed species. By combining the haplotype-resolved assembly of A. palmeri with existing restriction site-associated DNA sequencing data, we identified a [~]2.84 Mb region on chromosome 3 of Hap1 that is male-specific and contains 37 genes. Transcriptomic analysis revealed two genes within the male-specific region, RESTORER OF FERTILITY 1 (Rf1) and TLC DOMAIN-CONTAINING PROTEIN (TLC), were upregulated in male individuals across the shoot apical meristem, the floral meristem, and mature flowers, indicating their potential involvement in sex determination in A. palmeri. In addition, we rigorously classified cytochrome P450 genes in all three pigweeds due to their involvement in non-target site herbicide resistance. Finally, we identified contiguous extrachromosomal circular DNA (eccDNA) in A. palmeri, a critical component of glyphosate resistance in this species. The findings of this study advance our understanding of sex determination in A. palmeri and provide genomic resources for elucidating the genetic basis and evolutionary origins of adaptive traits within the genus.

genomics↗

bioRxiv2024

A phased chromosome-level genome assembly provides insights into the evolution of sex chromosomes in Amaranthus tuberculatus

O_LIAmaranthus tuberculatus (waterhemp) is a troublesome weed species of agronomic importance that is dioecious with an XY sex-determination system. The evolution of sex chromosomes, the contiguity of sex-determining region (SDR) and the expression pattern of genes within the SDR remain poorly understood. C_LIO_LIWe assembled the genome of a male A. tuberculatus, phased the genome into two chromosome-level haplotypes, and performed restriction site-associated DNA genome- wide association (RAD-GWA) analysis, comparative genomics, adaptive evolution analysis, and, with existing data, transcriptomic profiling to characterize the species sex chromosomes. C_LIO_LIComparative analysis enabled the identification of a [~]32.8 Mb SDR on chromosome 1 that is gene-poor, abundant in long terminal repeat (LTR) retrotransposons, and harbors two inversions. Synteny analysis revealed that chromosome 1 likely originated from the fusion of two ancestral chromosomes, and mRNA data indicated 93 genes out of the 531 protein-coding genes within the SDR of haplome 2 were differentially expressed between mature male and female flowers, with several of the genes enriched for Gene Ontology (GO) terms involved in floral development. C_LIO_LIBeyond adding to our understanding of sex chromosome evolution, the genomic resource provided here will be valuable for addressing further questions on adaptive trait evolution in Amaranthus. C_LI

genomics↗

bioRxiv2023

The International Weed Genomics Consortium: Community Resources for Weed Genomics Research

The International Weed Genomics Consortium is a collaborative group of researchers focused on developing genomic resources for the study of weedy plants. Weeds are attractive systems for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Our goal is to use genomic information to develop sustainable and effective weed control methods and to provide insights about biotic and abiotic stress tolerance to assist crop breeding. Here, we outline resources under development by the consortium and highlight areas of research that will be impacted by these enabling resources.

genomics↗