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Identification of favorable SNP alleles and candidate genes for seedlessness in Vitis vinifera L. using genome-wide association mapping

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Abstract

This study investigated the genetics of seedlessness in grape (Vitis vinifera L.) by the application of specific locus amplified fragment sequencing (SLAF-seq) and genome-wide association mapping. SLAF-seq was used to provide dense genome-wide marker coverage for the 199 grape accessions to screen for genetic controls over seedlessness. After comparison of genome sequences with the reference genome, single nucleotide polymorphisms (SNPs) were developed. A phylogenetic tree of the 199 accessions was then constructed and investigated using principal component analysis (PCA). Linkage disequilibrium between the SNPs was estimated and a genome wide association study (GWAS) was performed to detect trait loci and candidate genes associated with seedlessness. In total, 414,223 SNPs were identified, and were used for the fine mapping of seed development genes. The r2 decay to half of its initial value was 11.57 kb. The phylogenetic tree showed that the 199 accessions were clustered into 12 branches; PCA indicated that most grape accessions were clustered. Analysis using a general linear model identified 294 SNPs significant correlation with seedlessness, while the compressed mixed linear model identified 82 SNPs. Candidate genes involved in seed development were identified at loci near the significant SNPs. These candidates included ubiquitin protein, abscisic aldehyde oxidase, ethylene responsive transcription factor, zinc finger protein, somatic embryogenesis receptor, and MADs-box genes. This study demonstrates that integrating SLAF-seq and GWAS are powerful complementary approaches for dissecting complex traits in the grape.

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Abbreviations

SDI:

Seed development inhibitor

QTL:

Quantitative trait locus

GWAS:

Genome-wide association study

SLAF:

Specific-locus amplified fragment sequencing

SNPs:

Single nucleotide polymorphisms

OIV:

International Organisation of Vine and Wine

MAF:

Minor allele frequencies

LD:

Linkage disequilibrium

GLM:

General linear model

MLM:

Compressed mixed linear model

SSR:

Simple sequence repeat

GBS:

Genotyping by sequencing

2b-RAD:

IIB restriction site associated DNA

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Acknowledgements

This research was supported by a grant from Agricultural Science and Technology Innovation Program of CAAS (ASTIP, Project#CAAS-ASTIP-2015-ZFRI); China Agriculture Research System (Project#CARS-30-yz-1); Crop Resources Protection Program of China Ministry of Agriculture (Project#2130135-34); The National Key Technology R&D Program of the Ministry of Science and Technology of China (Grant No. 2013BAD01B04-20). We thank Bioinformatics Division, Biomarker Technologies Corporation by help in bioinformatics and technical support.

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  1. Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China

    Heng Zhang, Xiucai Fan, Ying Zhang, Jianfu Jiang & Chonghuai Liu

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  1. Heng Zhang
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  2. Xiucai Fan
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  3. Ying Zhang
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Correspondence to Chonghuai Liu.

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Zhang, H., Fan, X., Zhang, Y. et al. Identification of favorable SNP alleles and candidate genes for seedlessness in Vitis vinifera L. using genome-wide association mapping. Euphytica 213, 136 (2017). https://doi.org/10.1007/s10681-017-1919-z

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