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Candidate gene selection and detailed morphological evaluations of fs8.1, a quantitative trait locus controlling tomato fruit shape.

Sun L, Rodriguez GR, Clevenger JP, Illa-Berenguer E, Lin J, Blakeslee JJ, Liu W, Fei Z, Wijeratne A, Meulia T, van der Knaap E - J. Exp. Bot. (2015)

Bottom Line: Of the 122 annotated genes found in the fs8.1 region, 51 were expressed during floral development and six were differentially expressed in anthesis-stage ovaries in fs8.1 and wild-type (WT) lines.This led to the identification of 158 single-nucleotide polymorphisms (SNPs) and five small indels in the fs8.1 interval, including 31 that could be associated with changes in gene expression or function.Fruit weight was also increased in fs8.1 compared with WT, which was predominantly attributed to the increased fruit length.

View Article: PubMed Central - PubMed

Affiliation: Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH 44691, USA.

No MeSH data available.


Genome sequence variations between M82 (fs8.1 allele) and Yellow Pear (WT allele) at the fs8.1 locus. Black arrows represent expressed genes. Vertical lines represent SNPs or small indels. The number above each SNP/small indel indicates the distance of the SNP/small indel from the nearest gene. Bold font with underlining indicates differentially expressed genes in anthesis-stage ovaries of fs8.1 backcrossed lines. Black dots indicate high likely candidate genes. –, deletion; ex, exon; *, the SNP was not confirmed in the additional datasets.
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Figure 4: Genome sequence variations between M82 (fs8.1 allele) and Yellow Pear (WT allele) at the fs8.1 locus. Black arrows represent expressed genes. Vertical lines represent SNPs or small indels. The number above each SNP/small indel indicates the distance of the SNP/small indel from the nearest gene. Bold font with underlining indicates differentially expressed genes in anthesis-stage ovaries of fs8.1 backcrossed lines. Black dots indicate high likely candidate genes. –, deletion; ex, exon; *, the SNP was not confirmed in the additional datasets.

Mentions: To evaluate whether other cultivars carry fs8.1, an F2 population was generated from a cross between Yellow Pear and LA1589, the latter carrying the WT allele at the locus. As no association of fruit shape with the alleles of fs8.1 was observed in a population derived from these two parents (Supplementary Table S6, available at JXB online), we concluded that the tomato cultivar Yellow Pear carried the WT allele of the fs8.1 locus. Previously, M82 has been shown to carry the mutant allele of fs8.1 (Grandillo et al., 1996; Grandillo and Tanksley, 1996; Ku et al., 2000) and therefore M82 and Yellow Pear should differ in the causative nucleotide sequence polymorphism underlying the locus. By aligning the DNA sequences of these two accessions, 158 SNPs and five small indels were identified in the 3.03Mb region spanning the fs8.1 locus (Supplementary Table S4). Of these, 19 SNPs were located within 10kb upstream of the transcription start point of 14 expressed genes, five SNPs and one small indel were located in 10kb downstream of four expressed genes, and lastly, three SNPs were located in introns of three expressed genes and three other SNPs were located in the exons of three expressed genes (Solyc08g061850, Solyc08g061910, and Solyc08g062200) (Fig. 4, Supplementary Table S4). The three exonic SNPs resulted in a non-synonymous change (N253D), a premature stop codon, and addition of 190 aa, respectively (Fig. 4, Supplementary Table S4). The mutation in Solyc08g061910 leading to the premature stop codon probably resulted in a mutation. The high level of genome sequence read depth of 50- to 52-fold and the inclusion of two M82 and Yellow Pear SNP datasets (http://solgenomics.net/jbrowse/JBrowse-1.11.4/?data=data/json/tomato_variants; Lin et al., 2014; E. van der Knaap, unpublished) suggested that these polymorphisms were most likely correct. However, despite the knowledge that structural variation often underlies phenotypic diversity (van der Knaap et al, 2014), large indels, inversions, translocations, and copy number variants were not analysed due to the characteristics of the sequence data.


Candidate gene selection and detailed morphological evaluations of fs8.1, a quantitative trait locus controlling tomato fruit shape.

Sun L, Rodriguez GR, Clevenger JP, Illa-Berenguer E, Lin J, Blakeslee JJ, Liu W, Fei Z, Wijeratne A, Meulia T, van der Knaap E - J. Exp. Bot. (2015)

Genome sequence variations between M82 (fs8.1 allele) and Yellow Pear (WT allele) at the fs8.1 locus. Black arrows represent expressed genes. Vertical lines represent SNPs or small indels. The number above each SNP/small indel indicates the distance of the SNP/small indel from the nearest gene. Bold font with underlining indicates differentially expressed genes in anthesis-stage ovaries of fs8.1 backcrossed lines. Black dots indicate high likely candidate genes. –, deletion; ex, exon; *, the SNP was not confirmed in the additional datasets.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
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Figure 4: Genome sequence variations between M82 (fs8.1 allele) and Yellow Pear (WT allele) at the fs8.1 locus. Black arrows represent expressed genes. Vertical lines represent SNPs or small indels. The number above each SNP/small indel indicates the distance of the SNP/small indel from the nearest gene. Bold font with underlining indicates differentially expressed genes in anthesis-stage ovaries of fs8.1 backcrossed lines. Black dots indicate high likely candidate genes. –, deletion; ex, exon; *, the SNP was not confirmed in the additional datasets.
Mentions: To evaluate whether other cultivars carry fs8.1, an F2 population was generated from a cross between Yellow Pear and LA1589, the latter carrying the WT allele at the locus. As no association of fruit shape with the alleles of fs8.1 was observed in a population derived from these two parents (Supplementary Table S6, available at JXB online), we concluded that the tomato cultivar Yellow Pear carried the WT allele of the fs8.1 locus. Previously, M82 has been shown to carry the mutant allele of fs8.1 (Grandillo et al., 1996; Grandillo and Tanksley, 1996; Ku et al., 2000) and therefore M82 and Yellow Pear should differ in the causative nucleotide sequence polymorphism underlying the locus. By aligning the DNA sequences of these two accessions, 158 SNPs and five small indels were identified in the 3.03Mb region spanning the fs8.1 locus (Supplementary Table S4). Of these, 19 SNPs were located within 10kb upstream of the transcription start point of 14 expressed genes, five SNPs and one small indel were located in 10kb downstream of four expressed genes, and lastly, three SNPs were located in introns of three expressed genes and three other SNPs were located in the exons of three expressed genes (Solyc08g061850, Solyc08g061910, and Solyc08g062200) (Fig. 4, Supplementary Table S4). The three exonic SNPs resulted in a non-synonymous change (N253D), a premature stop codon, and addition of 190 aa, respectively (Fig. 4, Supplementary Table S4). The mutation in Solyc08g061910 leading to the premature stop codon probably resulted in a mutation. The high level of genome sequence read depth of 50- to 52-fold and the inclusion of two M82 and Yellow Pear SNP datasets (http://solgenomics.net/jbrowse/JBrowse-1.11.4/?data=data/json/tomato_variants; Lin et al., 2014; E. van der Knaap, unpublished) suggested that these polymorphisms were most likely correct. However, despite the knowledge that structural variation often underlies phenotypic diversity (van der Knaap et al, 2014), large indels, inversions, translocations, and copy number variants were not analysed due to the characteristics of the sequence data.

Bottom Line: Of the 122 annotated genes found in the fs8.1 region, 51 were expressed during floral development and six were differentially expressed in anthesis-stage ovaries in fs8.1 and wild-type (WT) lines.This led to the identification of 158 single-nucleotide polymorphisms (SNPs) and five small indels in the fs8.1 interval, including 31 that could be associated with changes in gene expression or function.Fruit weight was also increased in fs8.1 compared with WT, which was predominantly attributed to the increased fruit length.

View Article: PubMed Central - PubMed

Affiliation: Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH 44691, USA.

No MeSH data available.