Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

Abstract

Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linkedread de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those~20 million years divergent.

Challenges of viticulture adaptation to global change: tackling the issue from the roots

“…Gloire de Montpellier (Girollet et al 2019). Amplicon sequencing (AmpSeq) is an approach that proved useful for the development of Vitis inter-specific marker panels (Zou et al 2020), a convenient feature for the transferability of core genome markers to inter-specific germplasm and hybrids that rootstock breeding has to deal with. Irrespective of how markers are identified, they are basic to the identification of genetic loci controlling traits of interest by genetic approaches such as QTL mapping or genome-wide association studies (Delrot et al 2020).…”

On the origin and dispersal of cultivated spinach (Spinacia oleracea L.)

“…The prefixes EAST and WEST correspond to the, respectively, Eastern and Western group of accessions observed in the phylogenetic tree (Fig. 2) due to mismatches in primer binding sites is commonly observed when primers designed for a species are used in another species, and the effect generally reduces with increasing genetic relatedness between the species (Housley et al 2006;Zou et al 2020). The closer genetic relationship between S. oleracea and S. turkestanica was also shown by their similar degree of polymorphism and level of heterozygosity, which contrasted with the substantially lower extent of variation detected in S. tetrandra.…”

Stable QTL for malate levels in ripe fruit and their transferability acrossVitisspecies

“…To expedite and improve grape breeding, considerable efforts have been made in recent years to develop appropriate markers to permit marker assisted selection (MAS) [17][18][19][20] for desirable traits, and in the past decade over a dozen quantitative trait loci (QTL)-mapping studies have been performed in grape on acidity-related traits including malate (e.g. [21][22][23][24] ).…”

“…In the final year of the study, the separate contribution of accumulation, degradation, and dilution to malate in ripe fruit was used to understand the physiological basis of the identified QTL. A novel system of genetic markers targeting the core genome and reported to be transferable across the Vitis genus 20 was utilized on an additional family with close genetic relatedness, to assess their use as a tool to improve QTL consistency across families. Our results were integrated with the accumulated literature to report on the most stable and conserved loci associated with malate concentration in ripe grape berries.…”