TY - JOUR
T1 - Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus
AU - Zou, Cheng
AU - Karn, Avinash
AU - Reisch, Bruce
AU - Nguyen, Allen
AU - Sun, Yongming
AU - Bao, Yun
AU - Campbell, Michael S.
AU - Church, Deanna
AU - Williams, Stephen
AU - Xu, Xia
AU - Ledbetter, Craig A.
AU - Patel, Sagar
AU - Fennell, Anne
AU - Glaubitz, Jeffrey C.
AU - Clark, Matthew
AU - Ware, Doreen
AU - Londo, Jason P.
AU - Sun, Qi
AU - Cadle-Davidson, Lance
N1 - Publisher Copyright:
© 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.
PY - 2020/12/1
Y1 - 2020/12/1
N2 - 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 linked-read 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.
AB - 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 linked-read 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.
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U2 - 10.1038/s41467-019-14280-1
DO - 10.1038/s41467-019-14280-1
M3 - Article
C2 - 31964885
AN - SCOPUS:85078186320
SN - 2041-1723
VL - 11
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 413
ER -