Genetic Analyses for Leaf Variegation in Hybrid Grape Populations (Vitis spp.) Reveals Two Loci, Lvar1 and Lvar2

Olson, Jack; Zou, Cheng; Karn, Avinash; Reisch, Bruce I.; Cadle‐Davidson, Lance; Sun, Qi; Clark, Matthew D.

doi:10.21273/hortsci16763-22

Cited by 3 publications

(2 citation statements)

References 29 publications

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“…In grapevine, Reisch and Watson (1984) were the first to propose the expression of a nuclear recessive gene var to account for the leaf variegation. Further studies in grapevines developed by Olson et al (2022) demonstrated that the variegated phenotype was related to the expression of two nuclear recessive genes Lvar1 and Lvar2. It is possible that the variegation observed in 'Variegada' could be related to the expression of a recessive gene.…”

Section: Results Results Resultsmentioning

confidence: 99%

Meiotic behavior of two grapevine somatic mutants with ornamental potential

Pierozzi

Moura

2023

Not Bot Horti Agrobo

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‘Niagara Steck’ and ‘Niagara Variegada’ are two grapevine varieties that arose spontaneously as somatic mutants of ‘Niagara Rosada’. Berries characterize ‘Niagara Steck’ at young stages exhibiting a remarkable brown reticulated structure on the epidermis which develops into a brown-bronze russet-like structure as the berries ripe. The mature berries have strongly acidic flesh. ‘Niagara Variegada’ shows notable variegation in leaves and berries. Meiotic studies were carried out to ascertain if the mutant phenotypes could be related to any change in chromosome number, structure or other irregularity. Floral buds of both varieties at different developmental stages were collected and fixed for cytological analyses. Chromosome counts at diakinesis/metaphase I showed n=19 bivalents for both varieties. Univalent, trivalent, tetravalent chromosomes or chain configuration were not recorded ruling out the possibility of any alteration in the chromosome number or structure in both mutant varieties. However, low percentages of meiotic irregularities were recorded such as chromosome stickiness, laggards, non-oriented chromosomes, precocious chromosome segregation, tetrads with one microcyte, microspore fusion, and tetrad degeneration. The total percentage of abnormalities was higher in ‘Niagara Variegada’ (19.68%) than in ‘Niagara Steck’ (14.40%) which may have contributed to a lower percentage of pollen fertility (79.80%) when compared to ‘Steck’ (90.74%). The aforementioned varieties can be propagated by hardwood cuttings and constitute an interesting option for ornamentation of home backyards, patios, and gardens with the advantage that ‘Niagara Variegada’ bearing sweet edible berries.

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Section: Results Results Resultsmentioning

confidence: 99%

Meiotic behavior of two grapevine somatic mutants with ornamental potential

Pierozzi

Moura

2023

Not Bot Horti Agrobo

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“…Especially the experimental work on variegation mutants in Arabidopsis thaliana helped us better understand the underlying mechanisms [ 1 , 5 – 22 ]. Other leaf variegation studies were carried out on tomato [ 23 – 33 ], and studies on Arum italicum [ 34 ], barley [ 35 ], Brassica napus [ 36 ], Camellia sinensis [ 37 , 38 ]; Grapevine [ 39 ], Ilex X altaclerensis [ 20 , 21 ], Lotus japonicus [ 20 ], Epipremnum aureum [ 40 ], tobacco [ 41 ], Hedera helix [ 42 ], Vigna radiata [ 43 ] and Zea mays [ 44 ].…”

Section: Introductionmentioning

confidence: 99%

Mutation mapping of a variegated EMS tomato reveals an FtsH-like protein precursor potentially causing patches of four phenotype classes in the leaves with distinctive internal morphology

Dechkrong,

Srima,

Sukkhaeng

et al. 2024

BMC Plant Biol

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Background Leaf variegation is an intriguing phenomenon observed in many plant species. However, questions remain on its mechanisms causing patterns of different colours. In this study, we describe a tomato plant detected in an M2 population of EMS mutagenised seeds, showing variegated leaves with sectors of dark green (DG), medium green (MG), light green (LG) hues, and white (WH). Cells and tissues of these classes, along with wild-type tomato plants, were studied by light, fluorescence, and transmission electron microscopy. We also measured chlorophyll a/b and carotene and quantified the variegation patterns with a machine-learning image analysis tool. We compared the genomes of pooled plants with wild-type-like and mutant phenotypes in a segregating F2 population to reveal candidate genes responsible for the variegation. Results A genetic test demonstrated a recessive nuclear mutation caused the variegated phenotype. Cross-sections displayed distinct anatomy of four-leaf phenotypes, suggesting a stepwise mesophyll degradation. DG sectors showed large spongy layers, MG presented intercellular spaces in palisade layers, and LG displayed deformed palisade cells. Electron photomicrographs of those mesophyll cells demonstrated a gradual breakdown of the chloroplasts. Chlorophyll a/b and carotene were proportionally reduced in the sectors with reduced green pigments, whereas white sectors have hardly any of these pigments. The colour segmentation system based on machine-learning image analysis was able to convert leaf variegation patterns into binary images for quantitative measurements. The bulk segregant analysis of pooled wild-type-like and variegated progeny enabled the identification of SNP and InDels via bioinformatic analysis. The mutation mapping bioinformatic pipeline revealed a region with three candidate genes in chromosome 4, of which the FtsH-like protein precursor (LOC100037730) carries an SNP that we consider the causal variegated phenotype mutation. Phylogenetic analysis shows the candidate is evolutionary closest to the Arabidopsis VAR1. The synonymous mutation created by the SNP generated a miRNA binding site, potentially disrupting the photoprotection mechanism and thylakoid development, resulting in leaf variegation. Conclusion We described the histology, anatomy, physiology, and image analysis of four classes of cell layers and chloroplast degradation in a tomato plant with a variegated phenotype. The genomics and bioinformatics pipeline revealed a VAR1-related FtsH mutant, the first of its kind in tomato variegation phenotypes. The miRNA binding site of the mutated SNP opens the way to future studies on its epigenetic mechanism underlying the variegation.

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A multitiered haplotype strategy to enhance phased assembly and fine mapping of a disease resistance locus

Zou,

Sapkota,

Figueroa-Balderas

et al. 2023

Plant Physiology

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Fine mapping of quantitative trait loci (QTL) to dissect the genetic basis of traits of interest is essential to modern breeding practice. Here, we employed a multi-tiered haplotypic marker system to increase fine mapping accuracy by constructing a chromosome-level, haplotype-resolved parental genome, accurate detection of recombination sites, and allele-specific characterization of the transcriptome. In the first tier of this system, we applied the preexisting panel of 2000 rhAmpSeq core genome markers that is transferable across the entire Vitis genus and provides a genomic resolution of 200 kb to 1 Mb. The second tier consisted of high-density haplotypic markers generated from Illumina skim sequencing data for samples enriched for relevant recombinations, increasing the potential resolution to hundreds of base pairs. We used this approach to dissect a novel Resistance to Plasmopara viticola-33 (RPV33) locus conferring resistance to grapevine downy mildew, narrowing the candidate region to only 0.46 Mb. In the third tier, we used allele-specific RNA-seq analysis to identify a cluster of three putative disease resistance RPP13-like protein 2 genes located tandemly in a non-syntenic insertion as candidates for the disease resistance trait. In addition, combining the rhAmpSeq core genome haplotype markers and skim sequencing-derived high-density haplotype markers enabled chromosomal-level scaffolding and phasing of the grape Vitis × doaniana ‘PI 588149’ assembly, initially built solely from PacBio HiFi reads, leading to the correction of 16 large-scale phasing errors. Our mapping strategy integrates high-density, phased genetic information with individual reference genomes to pinpoint the genetic basis of QTLs, and will likely be widely adopted in highly heterozygous species.

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Genetic Analyses for Leaf Variegation in Hybrid Grape Populations (Vitis spp.) Reveals Two Loci, Lvar1 and Lvar2

Cited by 3 publications

References 29 publications

Meiotic behavior of two grapevine somatic mutants with ornamental potential

Meiotic behavior of two grapevine somatic mutants with ornamental potential

Mutation mapping of a variegated EMS tomato reveals an FtsH-like protein precursor potentially causing patches of four phenotype classes in the leaves with distinctive internal morphology

A multitiered haplotype strategy to enhance phased assembly and fine mapping of a disease resistance locus

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