Abstract
Early ripening in grape (Vitis vinifera L.) is a crucial agronomic trait. The fruits of the grape line ‘Summer Black’ (SBBM), which contains a bud mutation, can be harvested approximately one week earlier than the ‘Summer Black’ (SBC)control. To investigate the molecular mechanism of the bud mutation related to early ripening, we detected genome-wide genetic variations based on re-sequencing. In total, 3,692,777 single nucleotide polymorphisms (SNPs) and 81,223 structure variations (SVs) in the SBC genome and 3,823,464 SNPs and 85,801 SVs in the SBBM genome were detected compared with the reference grape sequence. Of these, 635 SBC-specific genes and 665 SBBM-specific genes were screened. Ripening and colour-associated unigenes with non-synonymous mutations (NS), SVs or frame-shift mutations (F) were analysed. The results showed that 90 unigenes in SBC, 76 unigenes in SBBM and 13 genes that mapped to large fragment indels were filtered. The expression patterns of eight genes were confirmed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR).The re-sequencing data showed that 635 SBC-specific genes and 665 SBBM-specific genes associated with early ripening were screened. Among these, NCED6 expression appears to be related to NCED1 and is involved in ABA biosynthesis in grape, which might play a role in the onset of anthocyanin accumulation. The SEP and ERF genes probably play roles in ethylene response.
Highlights
Grapevine (Vitis vinifera L.) is one of most important fruit crops worldwide, as it provides fruit used for both table grapes and wine
Phenotypic observation showed that the main difference between SBBM and Summer Black’ (SBC) was the ripening date, with SBBM ripening approximately one week earlier than SBC (Fig 1)
The several high- or low-density single nucleotide polymorphisms (SNPs) regions distributed on the SBC and SBBM chromosomes will be useful for further mapping, to identify markers that are closely linked to QTLs
Summary
Grapevine (Vitis vinifera L.) is one of most important fruit crops worldwide, as it provides fruit used for both table grapes and wine. The genome size of grapevine is about 475–500 Mb [1] and consists of 19 chromosomes (chr) with a high degree of heterozygosity [2]. Ripening is an attractive trait for producers, especially in areas when heavy rain occurs at the time of the year when the fruits are harvested. The mechanism of fruit ripening in grape is not clear.
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