skip to main content

Explore Research Products in the NSF-PAR

  • NSF Public Access
  • Search Results
  • Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence
Title: Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence
Abstract Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single-molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildews. A genome browser, annotation, and Blast tool for Trayshed are available at www.grapegenomics.com.  more » « less
Award ID(s):
1741627
NSF-PAR ID:
10320847
Author(s) / Creator(s):
; ; ; ; ;
Editor(s):
Morrell, P
Date Published:
Journal Name:
G3 Genes|Genomes|Genetics
Volume:
11
Issue:
4
ISSN:
2160-1836
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; ; ; ; et al ( , Nature Communications)
    Abstract

    It remains a major challenge to identify the genes and mutations that lead to plant sexual differentiation. Here, we study the structure and evolution of the sex-determining region (SDR) inVitisspecies. We report an improved, chromosome-scale Cabernet Sauvignon genome sequence and the phased assembly of nine wild and cultivated grape genomes. By resolving twentyVitisSDR haplotypes, we compare male, female, and hermaphrodite haplotype structures and identify sex-linked regions. Coupled with gene expression data, we identify a candidate male-sterility mutation in theVviINP1gene and potential female-sterility function associated with the transcription factorVviYABBY3. Our data suggest that dioecy has been lost during domestication through a rare recombination event between male and female haplotypes. This work significantly advances the understanding of the genetic basis of sex determination inVitisand provides the information necessary to rapidly identify sex types in grape breeding programs.

     
    more » « less
  2. ; ; ; ; ; ; ; ; ; ; et al ( , Phytopathology®)

    The U.S. wine and grape industry loses $3B annually due to viral diseases including grapevine leafroll-associated virus complex 3 (GLRaV-3). Current detection methods are labor-intensive and expensive. GLRaV-3 has a latent period in which the vines are infected but do not display visible symptoms, making it an ideal model to evaluate the scalability of imaging spectroscopy-based disease detection. The NASA Airborne Visible and Infrared Imaging Spectrometer Next Generation was deployed to detect GLRaV-3 in Cabernet Sauvignon grapevines in Lodi, CA in September 2020. Foliage was removed from the vines as part of mechanical harvest soon after image acquisition. In September of both 2020 and 2021, industry collaborators scouted 317 hectares on a vine-by-vine basis for visible viral symptoms and collected a subset for molecular confirmation testing. Symptomatic grapevines identified in 2021 were assumed to have been latently infected at the time of image acquisition. Random forest models were trained on a spectroscopic signal of noninfected and GLRaV-3 infected grapevines balanced with synthetic minority oversampling of noninfected and GLRaV-3 infected grapevines. The models were able to differentiate between noninfected and GLRaV-3 infected vines both pre- and postsymptomatically at 1 to 5 m resolution. The best-performing models had 87% accuracy distinguishing between noninfected and asymptomatic vines, and 85% accuracy distinguishing between noninfected and asymptomatic + symptomatic vines. The importance of nonvisible wavelengths suggests that this capacity is driven by disease-induced changes to plant physiology. The results lay a foundation for using the forthcoming hyperspectral satellite Surface Biology and Geology for regional disease monitoring in grapevine and other crop species.

    [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

     
    more » « less
  3. ; ; ; ; ( , Scientific Data)
    Abstract Cultivated grapevines are commonly grafted on closely related species to cope with specific biotic and abiotic stress conditions. The three North American Vitis species V. riparia , V. rupestris , and V. berlandieri , are the main species used for breeding grape rootstocks. Here, we report the diploid chromosome-scale assembly of three widely used rootstocks derived from these species: Richter 110 (110R), Kober 5BB, and 101–14 Millardet et de Grasset (Mgt). Draft genomes of the three hybrids were assembled using PacBio HiFi sequences at an average coverage of 53.1 X-fold. Using the tool suite HaploSync, we reconstructed the two sets of nineteen chromosome-scale pseudomolecules for each genome with an average haploid genome size of 494.5 Mbp. Residual haplotype switches were resolved using shared-haplotype information. These three reference genomes represent a valuable resource for studying the genetic basis of grape adaption to biotic and abiotic stresses, and designing trait-associated markers for rootstock breeding programs. 
    more » « less
  4. ; ; ; ; ; ; ; ; ; ; et al ( , Frontiers in Plant Science)
    Breeding of agricultural crops adapted to climate change and resistant to diseases and pests is hindered by a limited gene pool because of domestication and thousands of years of human selection. One way to increase genetic variation is chromosome-mediated gene transfer from wild relatives by cross hybridization. In the case of wheat ( Triticum aestivum ), the species of genus Aegilops are a particularly attractive source of new genes and alleles. However, during the evolution of the Aegilops and Triticum genera, diversification of the D-genome lineage resulted in the formation of diploid C, M, and U genomes of Aegilops . The extent of structural genome alterations, which accompanied their evolution and speciation, and the shortage of molecular tools to detect Aegilops chromatin hamper gene transfer into wheat. To investigate the chromosome structure and help develop molecular markers with a known physical position that could improve the efficiency of the selection of desired introgressions, we developed single-gene fluorescence in situ hybridization (FISH) maps for M- and U-genome progenitors, Aegilops comosa and Aegilops umbellulata , respectively. Forty-three ortholog genes were located on 47 loci in Ae. comosa and on 52 loci in Ae. umbellulata using wheat cDNA probes. The results obtained showed that M-genome chromosomes preserved collinearity with those of wheat, excluding 2 and 6M containing an intrachromosomal rearrangement and paracentric inversion of 6ML, respectively. While Ae. umbellulata chromosomes 1, 3, and 5U maintained collinearity with wheat, structural reorganizations in 2, 4, 6, and 7U suggested a similarity with the C genome of Aegilops markgrafii . To develop molecular markers with exact physical positions on chromosomes of Aegilops , the single-gene FISH data were validated in silico using DNA sequence assemblies from flow-sorted M- and U-genome chromosomes. The sequence similarity search of cDNA sequences confirmed 44 out of the 47 single-gene loci in Ae. comosa and 40 of the 52 map positions in Ae. umbellulata . Polymorphic regions, thus, identified enabled the development of molecular markers, which were PCR validated using wheat- Aegilops disomic chromosome addition lines. The single-gene FISH-based approach allowed the development of PCR markers specific for cytogenetically mapped positions on Aegilops chromosomes, substituting as yet unavailable segregating map. The new knowledge and resources will support the efforts for the introgression of Aegilops genes into wheat and their cloning. 
    more » « less
  5. ; ; ; ; ; ( , Scientific Reports)
    Abstract The prevalent mode of reproduction among ants is arrhenotokous parthenogenesis where unfertilized eggs give rise to haploid males and fertilized eggs develop into diploid females. Some ant species are capable of thelytokous parthenogenesis, a type of asexual reproduction where females develop from unfertilized diploid eggs. Thelytoky is well-documented in more than 20 ant species. Cytogenetic data are available for six species demonstrating that some thelytokous ant species are capable of producing males occasionally as well as maintaining their chromosome numbers and proper chromosome pairings. Mycocepurus smithii is a thelytokous fungus-growing ant species that inhabits large parts of Central and South America. Cytogenetic data are unavailable for M. smithii and male individuals were never documented for this species, although the presence of males is expected because genetic recombination was observed in a few sexually reproducing populations in Brazil and haploid sperm was documented from the spermathecae of M. smithii queens. This study aims at comparatively studying asexual and sexual populations of M. smithii using classical and molecular cytogenetic methods to test whether karyotype configuration is modified according to the mode of reproduction in M. smithii . Moreover, we report the discovery of M. smithii males from a sexually reproducing population in the Brazilian state Pará, diagnose the male of M. smithii , and morphologically characterize their spermatozoa. Karyotypic variation was observed within the asexual population (2n = 9, 10, or 11), whereas the chromosome number was fixed in the sexual population (2n = 14, n = 7). Identical karyotypes were maintained within individual M. smithii colonies and karyotype variation was only observed between colonies. In asexual individuals, the karyomorphs showed a decay of homologous chromosome pairs, especially in individuals with the karyomorph 2n = 11, which is potentially caused by relaxed natural selection on proper chromosome pairing. In contrast, females in the sexual population showed proper homologous chromosome pairings. In individuals of both asexual and sexual populations, we find that heterochromatin was localized in centromeric regions and on the short arms of the chromosomes, GC-rich regions were associated with heterochromatic regions, and 18S rDNA genes were located on the largest chromosome pair. This comparative cytogenetic analysis contributes to our understanding about the cytological mechanisms associated with thelytokous parthenogenesis in ants and suggests the decay of chromosome structure in the absence of meiosis and genetic recombination. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email