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Dissection of chilling requirement and bloom date QTLs in peach using a whole genome sequencing of sibling trees from an F2 mapping population

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Abstract

Chilling requirement (CR) for floral bud dormancy release is one of the major limiting factors for geographical adaptation of fruiting trees. Using a whole genome sequencing approach (Illumina platform), we explored polymorphism underlying phenotypic differences among individuals in a peach F2 cross segregating for chilling requirement and bloom date. Allelic configuration of individuals, which represented phenotypic extremes in the cross (300 vs. 1,100 chill hours) allowed reconstruction of low- and high-chill haplotypes within three most significant quantitative trait locus (QTL) intervals on the Prunus G1, G4, and G7. We detected single nucleotide polymorphic sites (SNPs), small deletions and insertions (DIPs), and large structural variants (SVs) associated with low-chill haplotypes and created a prioritized list of candidate genes based on functionally characterized homologs from Arabidopsis thaliana. Two dormancy associated genes PpeDAM5 and PpeDAM6 are the strongest candidate genes for the major QTL signal at the lower end of G1. Also, key functional genes involved in the Polycomb repressive mechanism, cell cycle progression, and hormone regulation were evident as strong candidate genes underlying QTL intervals in this peach cross.

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Acknowledgments

The study was carried out with financial support from the Robert and Lois Coker Trustees Chair in Molecular Genetics at the Department of Genetics and Biochemistry, Clemson University. We also are thankful to Kathy Brock for maintaining plants used in this study and Dr. Mike Wang at the David H. Murdock Research Institution (Kannapolis, NC) for guidance with Illumina Sequencing applications.

Data Archiving Statement

We followed standard Tree Genetics and Genomes policy. The GDR accession number for QTL data is tfGDR1004. Sequences submitted to GenBank have accession numbers KF218189–KF218196 which are also listed in the Supplemental File S7.

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Authors and Affiliations

  1. Department of Genetics and Biochemistry, Robert F. Poole Agricultural Center, Clemson University, Room 154, Clemson, SC, 29634-0318, USA

    Tatyana N. Zhebentyayeva, Anirudh Chandra & Albert G. Abbott

  2. JC Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC, 29646, USA

    Shenghua Fan

  3. School of Agricultural, Forest, and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA

    Douglas G. Bielenberg & Gregory L. Reighard

  4. Southeastern Fruit and Tree Nut Research Laboratory, ARS-USDA, Byron, GA, 31008, USA

    William R. Okie

  5. UMR BFP1332–INRA–Universite Bordeaux II, Villenave d’Ornon, France

    Albert G. Abbott

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  1. Tatyana N. Zhebentyayeva
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  2. Shenghua Fan
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  3. Anirudh Chandra
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  4. Douglas G. Bielenberg
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  6. William R. Okie
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  7. Albert G. Abbott
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Corresponding authors

Correspondence to Tatyana N. Zhebentyayeva or Albert G. Abbott.

Additional information

Communicated by D. Neale

Supplementary material

Below is the link to the electronic supplementary material.

Supplemental Fig. S1

Size distribution of the paired-end reads in the “4ind” assembly (DOCX 132 kb)

Supplemental Table S1

The SSR haplotypes of the C × Fla individuals A209, A318, A323 and A340 within QTL intervals on G1, G4 and G7 (DOCX 18 kb)

Supplemental Table S2

Gene targeted SSRs used for saturation QTL intervals in the C × Fla cross (XLSX 15 kb)

Supplemental Table S3

List of primers used for SNP/DIP verification in peach germplasm (XLSX 15 kb)

Supplemental Table S4

List of the PcG homologs in peach genome (XLSX 14 kb)

Supplemental Table S5

SNP/DIP validation in peach germplasm. Chilling requirement in hours is shown (XLS 43 kb)

Supplemental Table S6

The SNP/DIP polymorphic sites within annotated gene models underlying 3 strongest CR/BD QTLs on G1, G4 and G7 in the C × Fla cross (XLSX 255 kb)

Supplemental File S7

Verification of the low-chill polymorphic sites resolved using Sanger sequencing (DOCX 18 kb)

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Zhebentyayeva, T.N., Fan, S., Chandra, A. et al. Dissection of chilling requirement and bloom date QTLs in peach using a whole genome sequencing of sibling trees from an F2 mapping population. Tree Genetics & Genomes 10, 35–51 (2014). https://doi.org/10.1007/s11295-013-0660-6

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  • DOI: https://doi.org/10.1007/s11295-013-0660-6

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