Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches

Claudia Muñoz-Espinoza, Alex Di Genova, Alicia Sánchez, José Correa, Alonso Espinoza, Claudio Meneses, Alejandro Maass, Ariel Orellana, Patricio Hinrichsen

Research output: Contribution to journalArticlepeer-review

16 Citations (Scopus)


BACKGROUND: Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds. RESULTS: Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotype-phenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed. CONCLUSIONS: We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.

Original languageEnglish
Article number365
Pages (from-to)365
Number of pages1
JournalBMC Plant Biology
Issue number1
Publication statusPublished - 3 Aug 2020


  • Berry size
  • InDel
  • Marker-assisted selection
  • Plant breeding
  • RNA-Seq
  • SNP
  • Vitis vinifera

ASJC Scopus subject areas

  • Plant Science


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