Comparative population genomics dissects the genetic basis of seven domestication traits in jujube.

Horticulture Research
Mingxin GuoXusheng Zhao

Abstract

Jujube (Ziziphus jujuba Mill.) is an important perennial fruit tree with a range of interesting horticultural traits. It was domesticated from wild jujube (Ziziphus acidojujuba), but the genomic variation dynamics and genetic changes underlying its horticultural traits during domestication are poorly understood. Here, we report a comprehensive genome variation map based on the resequencing of 350 accessions, including wild, semi-wild and cultivated jujube plants, at a >15× depth. Using the combination of a genome-wide association study (GWAS) and selective sweep analysis, we identified several candidate genes potentially involved in regulating seven domestication traits in jujube. For fruit shape and kernel shape, we integrated the GWAS approach with transcriptome profiling data, expression analysis and the transgenic validation of a candidate gene to identify a causal gene, ZjFS3, which encodes an ethylene-responsive transcription factor. Similarly, we identified a candidate gene for bearing-shoot length and the number of leaves per bearing shoot and two candidate genes for the seed-setting rate using GWAS. In the selective sweep analysis, we also discovered several putative genes for the presence of prickles on bearing shoots...Continue Reading

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Datasets Mentioned

BETA
SRX1518656
SRX691539
KT381859

Methods Mentioned

BETA
transgenic
PCR
PCA
RNA-seq

Software Mentioned

Cufflinks
HISAT
Genetic type 1 Error Calculator ( GEC )
Haploview
CLR
vcftools
SAMtools
BWA ( Burrows - Wheeler Aligner )
TreeBest
GEMMA

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