Fig 1.
(A) The fw11.3 locus was mapped to the EP2028-EP2032 interval on tomato chromosome 11. The fw11.3 locus was further narrowed down to EP2030-EP2032 interval including two and a half open reading frames. Numbers above the chromosome indicate number of recombinant plants in the respective interval that were progeny tested. The black region delineates the fine mapped locus on the genome. The three candidate genes are shown in red, green and blue. (B) The DNA polymorphisms at the fw11.3 locus among LA1589 and Howard German/Rio Grande (upper) or Yellow Pear and Gold Ball Livingston (lower) segregating populations. Bold numbers above the chromosome indicate polymorphisms in the coding region; non-bold numbers indicate polymorphisms in the non-coding region. EP2030, EP2030, HP61, HP32 and HP31 denote markers. Δ: deletion or insertion. (C) Association mapping results of fruit weight with markers HP61, HP32 and HP31. The years used to collect the data are shown as FW2007, FW2008 and FW2010. (D) Transgenic complementation tests. Average fruit weight of 10 to 13 plants from T1 generation transgenic and non-transgenic sib plants cultivated under the same growing conditions are shown. Error bar: standard deviation. HF, Howard German background and 9F/CF, VIR347 background. Data collected during the 2013 field season is denoted with an “a”. Data collected during the 2014 field season is denoted with a “b”. Significance determined by paired t-tests and transgenic (transgenically carrying the CSR-D allele) plants were compared to their non-transgenic (CSR-WT) sibs. *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001.
Fig 2.
Fruit and cellular structure of fw11.3 NILs in the Howard German background.
(A) Medio-lateral section of fw11.3-WT fruit. Size bar = 1 cm. The pericarp, columella and placenta tissues are shown. (B) Medio-lateral section of fw11.3-D fruit. Size bar = 1 cm. (C) Hand cut section of a fw11.3-WT pericarp from a representative mature green fruit stained with toluidine blue. Size bar = 1 mm. (D) Hand cut section of a fw11.3-D pericarp from a representative mature green fruit stained in toluidine blue. Size bar = 1 mm. The inner epidermis is denoted as “en” whereas the outer epidermis is denoted as “ex”. The mesocarp are represented by the cells between the inner and outer epidermis.
Table 1.
Fruit structure analyses in medio-lateral sections of the fw11.3 NILs.
Table 2.
Cell size and cell number comparisons in the pericarp of fw11.3 NILs and VIR347 transgenic lines.
Fig 3.
Phylogenic and motif analysis of FAF domain-containing proteins.
(A) Phylogenic tree of tomato and Arabidopsis proteins, using FAF domain sequences in the tree construction. Motif structure is based on full length protein sequences. (B) Phylogenic tree and motif analysis of CSR-like proteins found in different plant species: Solanum lycopersicum (Sl), Solanum tuberosum (St), Solanum melongena (Sm), Capsicum annuum (Ca), Coffea canephora (Cc), Sesamum indicum (Si), Mimulus guttatus (Mg), Arabidopsis thaliana (At), Fragaria vesca (Fv), Prunus persica (Pp), Populus trichocarpa (Pt), Citrullus lanatus (Cl), Cucumis sativus (Cs), Vitis vinifera (Vv), and Selaginella moellendorffii (Smo). Selaginella moellendorfii (Smo) is used as outgroup. The same colored dots or triangles represent same subclade. Scale bar: 100 amino acids. Renamed proteins: Solyc06g073940 (SlCSR-like1), Solyc01g009260 (SlCSR-like2), Solyc01g009270 (SlCSR-like3), Solyc06g084280 (SlFAF1/2a), Solyc06g008990 (SlFAF1/2b), Solyc09g065140 (SlFAF1/2c), Solyc01g079740 (SlFAF3/4a), Solyc06g054310 (SlFAF3/4b), PGSC0003DMP400005394 (StCSR), CA11g16000 (CaCSR), Sme2.5_00683.1_g00009 (SmCSR), PGSC0003DMP400023251 (StCSR-like2), PGSC0003DMP400023246 (StCSR-like3), Sme2.5_01340.1_g00001 (SmCSR-like2/3), CA01g13730 (CaCSR-like2/3b), CA01g13720 (CaCSR-like2/3a), PGSC0003DMP400010456 (StCSR-like1), Sme2.5_00076.1_g00022 (SmCSR-like1), CA06g22610 (CaCSR-like1), Cc01g07830 (CcCSR-like1/2/3), Sin1010620 (SiCSR-like1/2/3), mgv1a004589m (MgCSR-like1/2/3), mrna23163.1-v1.0-hybrid (FvFAF-like), ppa002898m (PpFAF-like), Potri.009G016600 (PtFAF-like_a), Potri.001G216000.2 (PtFAF-like_b), Cla008617 (ClFAF-like1), Csa6M426380 (CsFAF-like1), Cla007326 (ClFAF-like2), Csa1M635920 (CsFAF-like2), VIT206s0009g003101 (VvFAF-like).
Fig 4.
Expression of CSR in tomato plant organs and fruit tissues.
(A) Expression of CSR-WT in tomato LA1589 plant tissues. Root: root; Hypo: hypocotyl; Cotyl: cotyledon; Apex: shoot apex including the SAM and youngest leaves; YL: young leaf; ML: mature leaf; YFB: young floral buds from 10 days after initiation and younger; ANT: whole flower at anthesis; 10 and 20 dpa: 10 and 20 days post anthesis developing fruit, respectively; Break: breaker stage fruit which is before turning color; IM/FM: inflorescence and floral meristem; 2, 4, and 6 dpi: 2, 4, and 6 days post initiation flower buds, respectively. Error bar indicates standard deviation. (B) CSR transcript accumulation in fw11.3 NILs fruit tissues during fruit development. Error bar: standard deviation. *The 33Col, 33Per, 33SPl and TCol samples represent one replicate. Col: columella; Per: pericarp; S: seeds; SPl: seeds and placenta; T: turning stage fruit. Numbers associated with the sample names represent the fruit developmental stage as days post anthesis. Hence, 7Col represents columella tissue collected 7 days post anthesis. (C) ClueGO enrichement in the CSR-D coexpression cluster. (D) ClueGO enrichment in the CSR-WT coexpression cluster. The dimension of the pie chart wedges is proportional to the number of terms included in each category. The most significant term of the group was used for annotation.
Fig 5.
Distribution of CSR wild type and derived allele in the tomato germplasm.
Ancestral allele in green, derived allele in burgundy. Black lines show binomial confidence intervals at 95%. Background colors highlight different species: S. pimpinellifolium (light green), S. lycopersicum var. cerasiforme (light brown) and S. lycopersicum var. lycopersicum (pink). Number of accessions in each category is given in parenthesis above the different genetically distinct classes [4].