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High-density linkage maps and loci for berry color and flower sex in muscadine grape (Vitis rotundifolia)

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Abstract

Key message

Linkage maps of muscadine grape generated using genotyping-by-sequencing (GBS) provide insight into genome collinearity between Muscadinia and Euvitis subgenera and genetic control of flower sex and berry color.

Abstract

The muscadine grape, Vitis rotundifolia, is a specialty crop native to the southeastern USA. Muscadine vines can be male, female, or perfect-flowered, and berry color ranges from bronze to black. Genetic linkage maps were constructed using genotyping-by-sequencing in two F1 populations segregating for flower sex and berry color. The linkage maps consisted of 1244 and 2069 markers assigned to 20 linkage groups (LG) for the ‘Black Beauty’ × ‘Nesbitt’ and ‘Supreme’ × ‘Nesbitt’ populations, respectively. Data from both populations were used to generate a consensus map with 2346 markers across 20 LGs. A high degree of collinearity was observed between the genetic maps and the Vitis vinifera physical map. The higher chromosome number in muscadine (2n = 40) compared to V. vinifera (2n = 38) was accounted for by the behavior of V. vinifera chromosome 7 as two independently segregating LGs in muscadine. The muscadine sex locus mapped to an interval that aligned to 4.64–5.09 Mb on V. vinifera chromosome 2, a region which includes the previously described V. vinifera subsp. sylvestris sex locus. While the MYB transcription factor genes controlling fruit color in V. vinifera are located on chromosome 2, the muscadine berry color locus mapped to an interval aligning to 11.09–11.88 Mb on V. vinifera chromosome 4, suggesting that a mutation in a different gene in the anthocyanin biosynthesis pathway determines berry color in muscadine. These linkage maps lay the groundwork for marker-assisted breeding in muscadine and provide insight into the evolution of Vitis species.

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Acknowledgements

We thank the staff of the University of Arkansas System Division of Agriculture Fruit Research Station for planting and maintaining the mapping populations. The authors also acknowledge the USDA-ARS Grape Genetics Research Unit, the Cornell University Biotechnology Resource Center, and the Institute of Genomic Diversity, Cornell University, for their contributions to data generation.

Funding

This research was supported by a grant from the Southern Region Small Fruit Consortium, SRSFC Project # 2012-02.

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  1. Christopher L. Owens

    Present address: IFG, 8224 Espresso Dr. Suite 200, Bakersfield, CA, 93312, USA

Authors and Affiliations

  1. Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA

    Jennifer Lewter, Margaret L. Worthington, John R. Clark, Aruna V. Varanasi & Lacy Nelson

  2. USDA-ARS Grape Genetics Research Unit, Cornell University, 630 W. North St., Geneva, NY, 14456, USA

    Christopher L. Owens

  3. Department of Horticulture, University of Georgia, 4604 Research Way, Tifton, GA, 31793, USA

    Patrick Conner & Gunawati Gunawan

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Supplementary Fig.

 1 Pedigrees of ‘Black Beauty,’ ‘Supreme,’ and ‘Nesbitt’ based on breeders’ records as documented in Clark (1997), Conner (2013), and Goldy and Nesbitt (1985). Lines connecting female and male parents to offspring are colored red and blue, respectively. Bronze- and black-fruited cultivars and breeding selections are colored yellow and purple, respectively. Breeding selections with unknown berry color are indicated in white (JPEG 2522 kb)

Supplementary Fig.

 2 High-density genetic linkage map of the ‘Black Beauty’ × ‘Nesbitt’ mapping population. Markers segregating in only the female parent (lm × ll), the male parent (nn × np), and both parents (hk × hk) are colored red, blue, and black, respectively. The VR006 and VR009 muscadine sex markers developed by Conner et al. (2017) are colored orange, the sex locus is colored green, and the color locus is colored pink. Marker positions are expressed in centimorgans (PDF 253 kb)

Supplementary Fig.

 3 High-density genetic linkage map of the ‘Supreme’ × ‘Nesbitt’ mapping population. Markers segregating in only the female parent (lm × ll), the male parent (nn × np), and both parents (hk × hk) are colored red, blue, and black, respectively. The VR006 and VR009 muscadine sex markers developed by Conner et al. (2017) are colored orange, the sex locus is colored green, and the color locus is colored pink. Marker positions are expressed in centimorgans (PDF 308 kb)

Supplementary Fig.

 4 High-density consensus linkage map of muscadine grape created from ‘Black Beauty’ × ‘Nesbitt’ (BB × N) and ‘Supreme’ × ‘Nesbitt’ (S × N) F1 populations. Markers present in only the BB × N linkage map and segregating in only the female parent (lm × ll), the male parent (nn × np), and both parents (hk × hk) are colored orange, aqua, and forest green, respectively. Markers present in only the S × N linkage map and segregating in only the female parent (lm × ll), the male parent (nn × np), and both parents (hk × hk) are colored red, blue, and neon green, respectively. Markers present in both linkage maps and segregating in only the female parents (lm × ll), the male parent (nn × np), and all three parents (hk × hk) are colored pink, dark blue, and black, respectively. The VR006 and VR009 muscadine sex markers developed by Conner et al. (2017), sex locus, and color locus are all colored yellow. Marker positions are expressed in centimorgans (PDF 328 kb)

Supplementary Table

 1 Marker positions in the ‘Black Beauty’ × ‘Nesbitt’ linkage map, physical positions on the V. vinifera reference genome, deviations from the expected segregation ratios, and genotype scores in the progeny (XLSX 894 kb)

Supplementary Table

 2 Marker positions in the ‘Supreme’ × ‘Nesbitt’ linkage map, physical positions on the V. vinifera reference genome, deviations from the expected segregation ratios, and genotype scores in the progeny. (XLSX 1504 kb)

Supplementary Table

 3 Marker positions in the muscadine consensus map, physical positions on the V. vinifera reference genome, and marker positions and classes in the ‘Supreme’ × ‘Nesbitt’ and ‘Black Beauty’ × ‘Nesbitt’ F1 linkage maps. (XLSX 195 kb)

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Lewter, J., Worthington, M.L., Clark, J.R. et al. High-density linkage maps and loci for berry color and flower sex in muscadine grape (Vitis rotundifolia). Theor Appl Genet 132, 1571–1585 (2019). https://doi.org/10.1007/s00122-019-03302-7

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