title: Genome-Wide Detection of SNP and SV Variations to Reveal Early Ripening-Related Genes in Grape.
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.
authors: College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, P. R. China.|Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, No.50 Zhongling Street, Nanjing, 210014, P.R. China.
authors: Yanshuai
authors: Y
authors: Xu
authors: College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, P. R. China.
authors: Zhihong
authors: Z
authors: Gao
authors: College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, P. R. China.
authors: Jianmin
authors: J
authors: Tao
authors: Agricultural Bureau & Forestry Workstation, Wujin District, Changzhou, 213000, P. R. China.
authors: Weihua
authors: W
authors: Jiang
authors: College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, P. R. China.
authors: Shijie
authors: S
authors: Zhang
authors: Agricultural Bureau & Forestry Workstation, Wujin District, Changzhou, 213000, P. R. China.
authors: Qiunan
authors: Q
authors: Wang
authors: College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, P. R. China.
authors: Shenchun
authors: S
authors: Qu
mesh_terms: D032461:Chromosomes, Plant; D019295:Computational Biology / Q000379:methods; D016368:Frameshift Mutation; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D054643:INDEL Mutation; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010641:Phenotype; D010937:Plant Growth Regulators / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D014158:Transcription, Genetic; D027843:Vitis / Q000235:genetics* / Q000378:metabolism
chemical_list: D010937:Plant Growth Regulators