A common genetic mechanism underlies morphological diversity in fruits and other plant organs

Wu, Shan; Zhang, Biyao; Keyhaninejad, Neda; Rodríguez, Gustavo; Kim, Hyun Jung; Chakrabarti, Manohar; Illa-Berenguer, Eudald; Taitano, Nathan K; Gonzalo, María José; Díaz, Aurora; Pan, Yupeng; Leisner, Courtney P.; Halterman, Dennis; Buell, C. Robin; Weng, Yiqun; Jansky, Shelley; Eck, Herman J. van; Willemsen, Johan H.; Monforte, Antonio J.; Meulia, Tea; Knaap, Esther van der

doi:10.1038/s41467-018-07216-8

Cited by 182 publications

(241 citation statements)

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“…Consistent with this conclusion is the finding that, in rice, a mutation in an α‐tubulin gene ( Srs5 mutant) affected grain dimension traits (Segami et al ., ). Similarly, the interaction between the OVATE family proteins and TRM were shown to regulate cell division and alter fruit shape in tomato (Wu et al ., ).…”

Section: Discussionmentioning

confidence: 97%

“…Developmental pathways that affect morphological diversity of plant organs through the interaction with TRM appear to be common in plants. For example, it was shown that the interaction of the OVATE family proteins with TRM regulates cell division and alters fruit shape in tomato, and possibly in melon and cucumber (Wu et al ., ). The high level of cross‐species conservation of pathways controlling grain morphology and weight (Li et al ., ) suggests that the homologs of TRM in wheat might also be involved in biological pathways defining similar traits.…”

Section: Introductionmentioning

confidence: 97%

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Gene editing of the wheat homologs of TONNEAU1‐recruiting motif encoding gene affects grain shape and weight in wheat

et al. 2019

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Grain size and weight are important components of a suite of yield-related traits in crops. Here, we showed that the CRISPR-Cas9 gene editing of TaGW7, a homolog of rice OsGW7 encoding a TONNEAU1-recruiting motif (TRM) protein, affects grain shape and weight in allohexaploid wheat. By editing the TaGW7 homoeologs in the B and D genomes, we showed that mutations in either of the two or both genomes increased the grain width and weight but reduced the grain length. The effect sizes of mutations in the TaGW7 gene homoeologs coincided with the relative levels of their expression in the B and D genomes. The effects of gene editing on grain morphology and weight traits were dosage dependent with the double-copy mutant showing larger effect than the respective single copy mutants. The TaGW7-centered gene co-expression network indicated that this gene is involved in the pathways regulating cell division and organ growth, also confirmed by the cellular co-localization of TaGW7 with aand b-tubulin proteins, the building blocks of microtubule arrays. The analyses of exome capture data in tetraploid domesticated and wild emmer, and hexaploid wheat revealed the loss of diversity around TaGW7-associated with domestication selection, suggesting that TaGW7 is likely to play an important role in the evolution of yield component traits in wheat. Our study showed how integrating CRISPR-Cas9 system with cross-species comparison can help to uncover the function of a gene fixed in wheat for allelic variants targeted by domestication selection and select targets for engineering new gene variants for crop improvement.

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Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 97%

Gene editing of the wheat homologs of TONNEAU1‐recruiting motif encoding gene affects grain shape and weight in wheat

et al. 2019

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“…One remarkable example is a 31-kb deletion upstream of tomato OVATE Family Protein 20 (SlOFP20). The deletion is associated with reduced expression of SlOFP20 and contributes to natural fruit shape variation in the tomato germplasm 41 . A 3-bp deletion in the promoter of tomato Al-ACTIVATED MALATE TRANSPORTER9 (Sl-ALMT9) was selected during tomato domestication.…”

Section: Deletions and Inversionsmentioning

confidence: 99%

Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement

Sapkota

Knaap

2020

Hortic Res

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Directed breeding of horticultural crops is essential for increasing yield, nutritional content, and consumer-valued characteristics such as shape and color of the produce. However, limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches. Natural genetic changes in cisregulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression. Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner. The advent of CRISPR/Cas-mediated cis-regulatory region engineering (cis-engineering) provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement. Here, we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops. We describe strategies and limitations for its use in crop improvement, including de novo cis-regulatory element (CRE) discovery, precise genome editing, and transgene-free genome editing. In addition, we discuss the challenges and prospects regarding current technologies and achievements. CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.

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“…6f). Previous study showed the mutation of STYLISH1(STY1) and NGATHA(NGA), both participate in the development of gynoecium by activating the expression of YUC, resulted in fruit with long and narrow styles in Arabidopsis [22][23]. To better understand of the CsOFP11 gene function, we detected the expression level of AtSTY1, AtNGA, and AtYUC4.…”

Section: Overexpression Csofp11 In Arabidopsismentioning

confidence: 99%

Genome-wide analysis of OVATE family proteins in cucumber (Cucumis sativus L.)

Han¹,

Song²,

Wang³

et al. 2019

Preprint

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29Background: OVATE family proteins (OFPs) are plant-specific proteins with the 30 conserved OVATE domain that regulating plant growth and development. Although 31 these OFPs have been studied in several species, the biological functions of this OFP 32 gene family remain largely unknown in cucumber (Cucumis sativus L.). 33Results: In this study, we identified 19 CsOFPs in cucumber. This CsOFPs are 34 distributed on seven chromosomes and can be divided into four subgroups. Most 35CsOFP genes are expressed in reproductive organs although have different expression 36 patterns. Cis-elements analysis showed that there are six kinds of hormone response 37 elements in CsOFPs and exogenous gibberellin treatment leads to a 'first increase then 38 decrease' expression pattern of CsOFP7, CsOFP11 and CsOFP12. Ectopic expression 39 of CsOFP11 in Arabidopsis resulted in shorter and blunt siliques.40 Conclusions: Together, these results indicated that CsOFPs may play important roles 41 in cucumber fruit development.42 43 44 45 Background 46 OVATE gene was originally identified in tomato， in which a natural mutation in OVATE 47 resulted in fruit from round to pear-shaped [1]. One century ago, pear-shaped fruit form 48 in tomato was proposed to be controlled by a single recessive quantitative trait locus 49 (QTL), which was named pyriform (pr) [2-3]. Later, additional studies showed that pr 50 was co-segregate with the locus determining oblate-to oval-shaped fruit, pr was 51 renamed ovate. Until 2002, the ovate gene was cloned in tomato. A single base 52 substitution (G-T) in OVATE caused a premature stop codon and the pear-shaped fruit 53 in tomato [1]. OVATE gene encodes a protein with a conserved 70 amino acid C-54 terminal domain, which was designated as OVATE domain, and proteins containing 55 this domain were named OVATE family proteins (OFPs) [4-6]. OFPs are widely 56 distributed in the plants. There are 19 AtOFPs in Arabidopsis, 26 SlOFPs in tomato, 45 57 ZmOFPs in maize and 33 OsOFPs in rice [4-5, 7-8]. While only 31 OsOFPs encode 58 full-length OFP proteins in rice [8]. 59 So far, the biological functions of OFPs in plants remain largely unknown, although 60 OFPs widely exist in plants. Limited studies in several different plant species including 61 Arabidopsis, tomato, pepper, banana and rice demonstrated that OFPs play important 62 roles in plant growth and development. Consistent with OVATE's negative role in 63 tomato fruit elongation, CaOVATE, an OVATE-like gene of Capsicum annuum, also 64 plays a negative role in determining fruit shape. Knockdown of CaOVATE through 65 virus-induced gene silencing in cv. "Mytilini Round" caused its fruit to a more oblong 66 shape [9]. Some studies suggested that GS9 could interact with OsOFP14 and OsOFP8 67 to regulate rice grain shape and knockout of GS9 resulted in slender grains [10]. 68 Moreover, the interaction pair MuMADS1 and MaOFP1 are antagonistically regulated 69 by ethylene and might participated in the process of fruit ripening in banana [11]. In 70 Arabidopsis, mos...

show abstract

A common genetic mechanism underlies morphological diversity in fruits and other plant organs

Cited by 182 publications

References 39 publications

Gene editing of the wheat homologs of TONNEAU1‐recruiting motif encoding gene affects grain shape and weight in wheat

Gene editing of the wheat homologs of TONNEAU1‐recruiting motif encoding gene affects grain shape and weight in wheat

Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement

Genome-wide analysis of OVATE family proteins in cucumber (Cucumis sativus L.)

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