Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map.

Dilmini Alahakoon,Anna Katharine Mansfield,Qi Sun,David Manns,Lance Cadle-Davidson,Cheng Zou,Avinash Karn,Gavin Sacks,Anne Fennell,Bruce I Reisch,Jason P Londo,Zachary Helget,Terry Bates

doi:10.3390/plants11050696

Dilmini Alahakoon, Anna Katharine Mansfield + Show 11 more

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https://doi.org/10.3390/plants11050696

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Abstract

Increased map density and transferability of markers are essential for the genetic analysis of fruit quality and stress tolerance in interspecific grapevine populations. We used 1449 GBS and 2000 rhAmpSeq markers to develop a dense map for an interspecific F2 population (VRS-F2) that was derived by selfing a single F1 from a Vitis riparia x ‘Seyval blanc’ cross. The resultant map contained 2519 markers spanning 1131.3 cM and was highly collinear with the Vitis vinifera ‘PN40024’ genome. Quantitative trait loci (QTL) for berry skin color and flower type were used to validate the map. Four rhAmpSeq transferable markers were identified that can be used in pairs (one pistillate and one hermaphroditic) to predict pistillate and hermaphrodite flower type with ≥99.7% accuracy. Total and individual anthocyanin diglucoside QTL mapped to chromosome 9 near a 5-O-GLUCOSYLTRANSFERASE candidate gene. Malic acid QTL were observed on chromosome 1 and 6 with two MALATE DEHYRDROGENASE CYTOPLASMIC 1 and ALUMINUM-ACTIVATED MALATE TRANSPORTER 2-LIKE (ALMT) candidate genes, respectively. Modeling malic acid identified a potential QTL on chromosome 8 with peak position in proximity of another ALMT. A first-ever reported QTL for the grassy smelling volatile (E)-2-hexenal was found on chromosome 2 with a PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE candidate gene near peak markers.

Highlights

IntroductionGrapevine [Vitis sp.] is a perennial woody fruit crop species with high economic and nutritional value [1]
Genotype frequency plots for markers in the linkage map showed deviation from an expected 1:2:1 ratio for many markers associated with chromosomes 5, 7, 11, and 15 (Figures 1 and S1)
The addition of some of the distorted markers did not show any effect on marker order or recombination percentage, suggesting that marker segregation distortion is natural in these chromosomal regions for this F2 grapevine population [39,40]

Summary

Introduction

Grapevine [Vitis sp.] is a perennial woody fruit crop species with high economic and nutritional value [1]. Typical grapevine primary breeding objectives include greater yield and higher quality, tolerance to biotic and abiotic stresses, and desirable plant growth habits [1]. The heterozygosity and long generation cycle of Vitis present a breeding challenge [1–3]. Molecular mapping with transferable markers provides the opportunity to reduce the time needed to study interspecific populations by facilitating quantitative trait loci (QTL) identification, marker assisted selection, and candidate gene discovery [1,3,4]

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