Fruit Weight Is Controlled by \u3cem\u3eCell Size Regulator\u3c/em\u3e Encoding a Novel Protein That Is Expressed in Maturing Tomato Fruits

Increases in fruit weight of cultivated vegetables and fruits accompanied the domestication of these crops. Here we report on the positional cloning of a quantitative trait locus (QTL) controlling fruit weight in tomato. The derived allele of Cell Size Regulator (CSR-D) increases fruit weight predominantly through enlargement of the pericarp areas. The expanded pericarp tissues result from increased mesocarp cell size and not from increased number of cell layers. The effect of CSR on fruit weight and cell size is found across different genetic backgrounds implying a consistent impact of the locus on the trait. In fruits, CSR expression is undetectable early in development from floral meristems to the rapid cell proliferation stage after anthesis. Expression is low but detectable in growing fruit tissues and in or around vascular bundles coinciding with the cell enlargement stage of the fruit maturation process. CSR encodes an uncharacterized protein whose clade has expanded in the Solanaceae family. The mutant allele is predicted to encode a shorter protein due to a 1.4 kb deletion resulting in a 194 amino-acid truncation. Co-expression analyses and GO term enrichment analyses suggest association of CSR with cell differentiation in fruit tissues and vascular bundles. The derived allele arose in Solanum lycopersicum var cerasiforme and appears completely fixed in many cultivated tomato’s market classes. This finding suggests that the selection of this allele was critical to the full domestication of tomato from its intermediate ancestors

Mapatge de gens candidats implicats en la qualitat del fruit al presseguer

[cat] En els darrers anys, la important reconversió varietal ha permès una millor qualitat, més adaptada tan a les exigències de la producció com de la distribució i del consumidor. La primera generació de milloradors van posar tot el seu èmfasi en millorar les característiques comercials de la fruita com el color, la fermesa i el sabor. Tanmateix el mercat actual exigeix altres atributs de tipus organolèptic i nutricional, addicionals als anteriors. Entendre la base genètica que controla cadascun dels caràcters determinarà la nostra capacitat per obtenir uns fruits més atractius i sans per al consumidor. A la població 'Texas' × 'Earlygold' (T×E) s'han mapat 206 gens candidats (GCs) relacionats amb l'expressió dels caràcters de qualitat de la fruita (creixement i maduració del fruit, textura, color, contingut de sucres i àcids orgànics i aroma) i 18 gens al·lergògens de presseguer i/o ametller responsables de l'aparició de reaccions al·lèrgiques. La comparació entre la posició dels GCs mapats i la dels QTLs detectats ha permès trobar algunes co-localitzacions. Addicionalment, l'anàlisi comparativa entre la seqüència dels marcadors mapats a Prunus amb el mapa de la maduixa diploide i la seqüència completa de la pomera mostra elements comuns. La presència de blocs sintènics facilitarà la transferència del coneixement genètic entre les tres espècies i, a la vegada, permetrà proposar un hipotètic genoma ancestral per la família Rosaceae.||RESUMEN En los últimos años, la importante reconversión varietal ha permitido una mejor calidad, más adaptada tanto a las exigencias de la producción como de la distribución y del consumidor. La primera generación de mejoradores puso todo su énfasis en mejorar las características comerciales de la fruta como el color, la firmeza y el sabor. Sin embargo el mercado actual exige otros atributos de tipo organoléptico y nutricional, adicionales a los anteriores. Entender la base genética que controla cada uno de los caracteres determinará nuestra capacidad para obtener unos frutos más atractivos y sanos para el consumidor. En la población 'Texas' × 'Earlygold' (T×E) se han mapeado 206 genes candidatos (GCs) relacionados con la expresión de los caracteres de calidad de la fruta (crecimiento y maduración del fruto, textura, color, contenido de azúcares y ácidos orgánicos y aroma) y 18 genes alérgenos de melocotonero y/o almendro responsables de la aparición de reacciones alérgicas. La comparación entre la posición de los GCs mapeados y la de los QTLs detectados ha permitido encontrar algunas co-localizaciones. Adicionalmente, el análisis comparativo entre la secuencia de los marcadores mapeados a Prunus con el mapa de la fresa diploide y la secuencia completa del manzano muestra elementos comunes. La presencia de bloques sinténicos facilitará la transferencia del conocimiento genético entre las tres especies y, a la vez, permitirá proponer un hipotético genoma ancestral para la familia Rosaceae.[eng] Fruit quality is a very important trait in breeding programs of rosaceous crops. In addition to attributes such as appearance, flavour, scent and texture, breeders focus more and more on crucial aspects like nutritional quality and the absence or significant reductions of allergenic compounds for fruit health and safety. Understanding the genetic basis that controls each character determines our ability to obtain more attractive and healthy fruit to consumers. In the present study 206 candidate genes (CGs) associated with the expression of the characteristics of fruit quality (growth and fruit ripening, texture, colour, sugar content and organic acids and aroma) and 18 genes peach and / or almond allergens responsible for allergic reactions have been mapped in the Prunus reference map. The comparison between the position of the CGs and the QTLs previously detected allow us to find some co-localizations. Additionally, the comparative analysis between the sequences of molecular markers that are anchored into the Prunus and Fragaria reference maps and the Malus genome sequence shows common features. The presence of syntenic blocks facilitates the transference of genetic information between the three species and, in turn, would propose a hypothetical ancestral genome for Rosaceae family.[spa] En los últimos años, la importante reconversión varietal ha permitido una mejor calidad, más adaptada tanto a las exigencias de la producción como de la distribución y del consumidor. La primera generación de mejoradores puso todo su énfasis en mejorar las características comerciales de la fruta como el color, la firmeza y el sabor. Sin embargo el mercado actual exige otros atributos de tipo organoléptico y nutricional, adicionales a los anteriores. Entender la base genética que controla cada uno de los caracteres determinará nuestra capacidad para obtener unos frutos más atractivos y sanos para el consumidor. En la población 'Texas' × 'Earlygold' (T×E) se han mapeado 206 genes candidatos (GCs) relacionados con la expresión de los caracteres de calidad de la fruta (crecimiento y maduración del fruto, textura, color, contenido de azúcares y ácidos orgánicos y aroma) y 18 genes alérgenos de melocotonero y/o almendro responsables de la aparición de reacciones alérgicas. La comparación entre la posición de los GCs mapeados y la de los QTLs detectados ha permitido encontrar algunas co-localizaciones. Adicionalmente, el análisis comparativo entre la secuencia de los marcadores mapeados a Prunus con el mapa de la fresa diploide y la secuencia completa del manzano muestra elementos comunes. La presencia de bloques sinténicos facilitará la transferencia del conocimiento genético entre las tres especies y, a la vez, permitirá proponer un hipotético genoma ancestral para la familia Rosaceae

Fruit weight is controlled by <i>Cell Size Regulator</i> encoding a novel protein that is expressed in maturing tomato fruits

<div><p>Increases in fruit weight of cultivated vegetables and fruits accompanied the domestication of these crops. Here we report on the positional cloning of a quantitative trait locus (QTL) controlling fruit weight in tomato. The derived allele of <i>Cell Size Regulator</i> (<i>CSR-</i>D) increases fruit weight predominantly through enlargement of the pericarp areas. The expanded pericarp tissues result from increased mesocarp cell size and not from increased number of cell layers. The effect of <i>CSR</i> on fruit weight and cell size is found across different genetic backgrounds implying a consistent impact of the locus on the trait. In fruits, <i>CSR</i> expression is undetectable early in development from floral meristems to the rapid cell proliferation stage after anthesis. Expression is low but detectable in growing fruit tissues and in or around vascular bundles coinciding with the cell enlargement stage of the fruit maturation process. <i>CSR</i> encodes an uncharacterized protein whose clade has expanded in the Solanaceae family. The mutant allele is predicted to encode a shorter protein due to a 1.4 kb deletion resulting in a 194 amino-acid truncation. Co-expression analyses and GO term enrichment analyses suggest association of CSR with cell differentiation in fruit tissues and vascular bundles. The derived allele arose in <i>Solanum lycopersicum</i> var <i>cerasiforme</i> and appears completely fixed in many cultivated tomato’s market classes. This finding suggests that the selection of this allele was critical to the full domestication of tomato from its intermediate ancestors.</p></div

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

fs8.1 is a major quantitative trait locus (QTL) that controls the elongated shape of tomato (Solanum lycopersicum) fruit. In this study, we fine-mapped the locus from a 47Mb to a 3.03Mb interval on the long arm of chromosome 8. 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. To identify possible nucleotide polymorphisms that may underlie the fruit shape phenotype, genome sequence analyses between tomato cultivars carrying the mutant and WT allele were conducted. 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. Morphological and histological analyses showed that the effects of fs8.1 were mainly on reproductive organ elongation by increasing cell number in the proximal–distal direction. Fruit weight was also increased in fs8.1 compared with WT, which was predominantly attributed to the increased fruit length. By combining the findings from the different analyses, we consider 12 likely candidate genes to underlie fs8.1, including Solyc08g062580 encoding a pentatricopeptide repeat protein, Solyc08g061560 encoding a putative orthologue of ERECTA, which is known to control fruit morphology and inflorescence architecture in Arabidopsis, Solyc08g061910 encoding a GTL2-like trihelix transcription factor, Solyc08g061930 encoding a protein that regulates cytokinin degradation, and two genes, Solyc08g062340 and Solyc08g062450, encoding 17.6kDa class II small heat-shock proteins.Fil: Sun, Liang. Ohio State University; Estados UnidosFil: Rodríguez, Gustavo Rubén. Ohio State University; Estados Unidos. Universidad Nacional de Rosario. Facultad de Cs.agrarias. Departamento de Biologia. Cat.de Genetica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Cientifico Tecnológico Rosario; ArgentinaFil: Clevenger, Josh P.. Ohio State University; Estados UnidosFil: Illa Berenguer, Eudald. Ohio State University; Estados UnidosFil: Lin, Jinshan. Ohio State University; Estados UnidosFil: Blakeslee, Joshua J.. Ohio State University; Estados UnidosFil: Liu, Wenli. Cornell University; Estados UnidosFil: Fei, Zhangjun. Cornell University; Estados UnidosFil: Wijeratne, Asela. Ohio State University; Estados UnidosFil: Meulia, Tea. Ohio State University; Estados UnidosFil: Knaap, Esther van der. Ohio State University; Estados Unido

Cloning of the <i>fw11</i>.<i>3</i> QTL.

<p>(A) The <i>fw11</i>.<i>3</i> locus was mapped to the EP2028-EP2032 interval on tomato chromosome 11. The <i>fw11</i>.<i>3</i> 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 <i>fw11</i>.<i>3</i> 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 <i>t</i>-tests and transgenic (transgenically carrying the <i>CSR</i>-D allele) plants were compared to their non-transgenic (<i>CSR</i>-WT) sibs. *, p ≤ 0.05; **, p ≤ 0.01; ***, p ≤ 0.001.</p

Phylogenic and motif analysis of FAF domain-containing proteins.

<p>(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: <i>Solanum lycopersicum</i> (Sl), <i>Solanum tuberosum</i> (St), <i>Solanum melongena</i> (Sm), <i>Capsicum annuum</i> (Ca), <i>Coffea canephora</i> (Cc), <i>Sesamum indicum</i> (Si), <i>Mimulus guttatus</i> (Mg), <i>Arabidopsis thaliana</i> (At), <i>Fragaria vesca</i> (Fv), <i>Prunus persica</i> (Pp), <i>Populus trichocarpa</i> (Pt), <i>Citrullus lanatus</i> (Cl), <i>Cucumis sativus</i> (Cs), <i>Vitis vinifera</i> (Vv), and <i>Selaginella moellendorffii</i> (Smo). <i>Selaginella moellendorfii</i> (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).</p

Fruit and cellular structure of <i>fw11</i>.<i>3</i> NILs in the Howard German background.

<p>(A) Medio-lateral section of <i>fw11</i>.<i>3</i>-WT fruit. Size bar = 1 cm. The pericarp, columella and placenta tissues are shown. (B) Medio-lateral section of <i>fw11</i>.<i>3</i>-D fruit. Size bar = 1 cm. (C) Hand cut section of a <i>fw11</i>.<i>3</i>-WT pericarp from a representative mature green fruit stained with toluidine blue. Size bar = 1 mm. (D) Hand cut section of a <i>fw11</i>.<i>3</i>-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.</p

Expression of <i>CSR</i> in tomato plant organs and fruit tissues.

<p>(A) Expression of <i>CSR-</i>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 <i>fw11</i>.<i>3</i> 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 <i>CSR-D</i> coexpression cluster. (D) ClueGO enrichment in the <i>CSR-WT</i> 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.</p

Distribution of <i>CSR</i> wild type and derived allele in the tomato germplasm.

<p>Ancestral allele in green, derived allele in burgundy. Black lines show binomial confidence intervals at 95%. Background colors highlight different species: <i>S</i>. <i>pimpinellifolium</i> (light green), <i>S</i>. <i>lycopersicum</i> var. <i>cerasiforme</i> (light brown) and <i>S</i>. <i>lycopersicum</i> var. <i>lycopersicum</i> (pink). Number of accessions in each category is given in parenthesis above the different genetically distinct classes [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006930#pgen.1006930.ref004" target="_blank">4</a>].</p

Fruit structure analyses in medio-lateral sections of the <i>fw11</i>.<i>3</i> NILs.

<p>Fruit structure analyses in medio-lateral sections of the <i>fw11</i>.<i>3</i> NILs.</p