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| Open AccessWithin-individual phenotypic plasticity in flowers fosters pollination niche shift
Floral phenotypes impact interactions between plants and pollinators. Here, the authors show that Moricandia arvensis displays discrete seasonal plasticity in floral phenotype, with large, lilac flowers attracting long-tongued bees in spring and small, rounded, white flowers attracting generalist pollinators in summer.
- José M. Gómez
- , Francisco Perfectti
- & Rubén Torices
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Article
| Open AccessGradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
Existing plant pan-genomic studies usually report considerable intraspecific whole gene presence-absence variation. Here, the authors use pan-genomic approach to reveal gradual polyploid genome evolution by analyzing of Brachypodium hybridum and its diploid progenitors.
- Sean P. Gordon
- , Bruno Contreras-Moreira
- & John P. Vogel
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Article
| Open AccessGenome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties
Wild teas are considered as valuable resource for studying domestication and breeding. Here, Zhang et al. report genome of wild tea DASZ and transcriptome of 217 accessions, which clarify pedigree of Chinese tea cultivars and show tea may not have undergone long-term artificial directional selection on flavor-related metabolites.
- Weiyi Zhang
- , Youjun Zhang
- & Weiwei Wen
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Article
| Open AccessNatural variations at the Stay-Green gene promoter control lifespan and yield in rice cultivars
Breeding crops with delayed senescence could plausibly increase grain yield. Here the authors show that variation at the rice SGR locus contributes to differences in senescence between indica and japonica subspecies and show that introgression can increase yield in an elite indica rice variety.
- Dongjin Shin
- , Sichul Lee
- & Hong Gil Nam
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Article
| Open AccessA rare gain of function mutation in a wheat tandem kinase confers resistance to powdery mildew
Powdery mildew is a major threat to world wheat yields. Here the authors describe the map-based cloning of Pm24, a gain-of-function powdery mildew resistance allele that encodes a tandem kinase-pseudokinase protein with a deletion in a kinase domain that is endemic to certain wheat landraces.
- Ping Lu
- , Li Guo
- & Zhiyong Liu
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Article
| Open AccessA helitron-induced RabGDIα variant causes quantitative recessive resistance to maize rough dwarf disease
Maize rough dwarf disease threatens its production. Here, the authors show that a helitron transposon insertion in the Rab GDP dissociation inhibitor alpha leads to recessive viral resistance by affecting its interaction with viral P7-1 protein and that all naturally occurring alleles come from a single mutation event after domestication.
- Qingcai Liu
- , Suining Deng
- & Mingliang Xu
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Article
| Open AccessA common wild rice-derived BOC1 allele reduces callus browning in indica rice transformation
Callus browning heavily affects indica rice transformation regeneration. Here, the authors show transposon insertion in the promoter of BOC1 gene, encoding a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE protein, can upregulate its expression and decrease callus browning in cultivated rice by releasing oxidative stress.
- Kun Zhang
- , Jingjing Su
- & Yongcai Fu
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Article
| Open AccessHaplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus
Trait introgression requires universal markers, but cross-species transferability of current SNP markers can be as low as 2%. Here, the authors use an AmpSeq haplotype strategy targeting the collinear core genome for marker development and show transferability increases to 91.4% in the Vitis genus.
- Cheng Zou
- , Avinash Karn
- & Lance Cadle-Davidson
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Article
| Open AccessCryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed
Developmental plasticity of plant root systems has been intensively studied, but the mechanisms underpinning robustness remain unclear. Here, the authors show that DNA-methylation-mediated transcriptional repression serves as a backup system to control lateral root development when auxin signalling is perturbed.
- Zaigham Shahzad
- , Ross Eaglesfield
- & Anna Amtmann
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Article
| Open AccessNatural variation of an EF-hand Ca2+-binding-protein coding gene confers saline-alkaline tolerance in maize
Saline-alkaline stress affects worldwide crops production, but the tolerance mechanisms have not been fully elucidated. Here, the authors show that EF-hand Ca2 + -binding-protein coding gene ZmNSA1 can regulate root H + efflux, Na + homeostasis, and saline-alkaline tolerance in maize.
- Yibo Cao
- , Ming Zhang
- & Caifu Jiang
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Article
| Open AccessTwo dominant boreal conifers use contrasting mechanisms to reactivate photosynthesis in the spring
Boreal conifers regulate photosynthesis to maximize seasonal growth while limiting damage due to light and cold stress. Here Yang et al. show that two major conifer species achieve this via different means as Scots pine, but not Norway spruce, activates alternative electron sinks during spring.
- Qi Yang
- , Nicolás E. Blanco
- & Åsa Strand
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Article
| Open AccessLong-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
The South African quality protein maize (QPM) cultivars have the desired high lysine content and kernel hardness due to o2 mutation and the introgression of modifiers of o2 (Mo2) QTLs, respectively. Here, the authors assemble the genome of a QPM line and identify candidate genes underlying Mo2 QTLs.
- Changsheng Li
- , Xiaoli Xiang
- & Wenqin Wang
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Article
| Open AccessThe tin1 gene retains the function of promoting tillering in maize
Unlike the other domesticated maize, sweet maize and popcorn retain tillering growth habit, but the underlying mechanism is unknown. Here, the authors identify a transcription factor tin1 that maintains outgrowth of tiller independent of tb1 and show its conservation in foxtail millet and rice.
- Xuan Zhang
- , Zhelong Lin
- & Zhongwei Lin
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Article
| Open AccessComponents of the ribosome biogenesis pathway underlie establishment of telomere length set point in Arabidopsis
Major effect loci controlling natural, heritable variation in telomere length are not known. Here, the authors use QTL mapping and transgenic manipulations in Arabidopsis to implicate the rRNA-processing genes NOP2A and RPL5 in telomere length set point regulation in this model species.
- Liliia R. Abdulkina
- , Callie Kobayashi
- & Eugene V. Shakirov
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Article
| Open AccessThe indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency
Indica rice has higher nitrate assimilation and nitrogen use efficiency (NUE) than japonica rice, but the mechanism is unclear. Here, the authors reveal that the difference is partly due to allelic variation of a nitrate reductase encoding gene and this indica allele can increase yield potential and NUE.
- Zhenyu Gao
- , Yufeng Wang
- & Qian Qian
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Article
| Open AccessThe wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype
Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes which contribute to large fruit size by comparative and population genomics analyses.
- Dasen Xie
- , Yuanchao Xu
- & Zhonghua Zhang
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Article
| Open AccessGenome-wide association mapping of date palm fruit traits
Date palm is an important fruit crop in the Middle East and North Africa. Here, the authors report an improved genome assembly of this species and perform GWAS mapping of sex determining region and 21 fruit traits using high density SNP data generated from re-sequencing of the mapping population.
- Khaled M. Hazzouri
- , Muriel Gros-Balthazard
- & Michael D. Purugganan
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Article
| Open AccessGSNOR provides plant tolerance to iron toxicity via preventing iron-dependent nitrosative and oxidative cytotoxicity
How plants deal with iron toxicity is still unclear. Here, the authors reveal that S-nitrosoglutathione-reductase (GSNOR) provides tolerance to iron toxicity by preventing iron-dependent nitrosative and oxidative cytotoxicity in Arabidopsis, legumes, and rice.
- Baohai Li
- , Li Sun
- & Wolfgang Busch
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Article
| Open AccessSequencing of Chinese castor lines reveals genetic signatures of selection and yield-associated loci
Castor is an important industrial oil crop, but knowledge on its genetic diversity is limited. Here, Fan et al. show geographic pattern of Chinese castors that have developed during domestication by population genetic analyses, and reveal candidate genes associated with agronomically important traits.
- Wei Fan
- , Jianjun Lu
- & Peng Cui
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Article
| Open AccessNatural variation of OsGluA2 is involved in grain protein content regulation in rice
Grain protein content determines rice nutrition quality. Here, the authors show that a single nucleotide polymorphism in the promoter region of OsGluA2, encoding a glutelin type-A2 precursor, is responsible for glutelin content difference between the indica and japonica rice subspecies.
- Yihao Yang
- , Min Guo
- & Changjie Yan
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Article
| Open AccessA high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour
Existing apple genome assemblies all derive from Golden Delicious. Here, the authors combine different sequencing technologies to assemble a high quality genome of an anther-derived homozygous genotype HFTH1 and find the association of a retrotransposon and red fruit colour.
- Liyi Zhang
- , Jiang Hu
- & Peihua Cong
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Article
| Open AccessA reference-grade wild soybean genome
Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al. report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci.
- Min Xie
- , Claire Yik-Lok Chung
- & Hon-Ming Lam
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Article
| Open AccessRetrotranspositional landscape of Asian rice revealed by 3000 genomes
Transposable elements (TE) are the dominant constituent of plant genomes. Here the authors develop a tool to analyze TE insertion sites in 3000 rice genomes and provide evidence for recent TE activity during cultivation and that external, rather than genetic, stimuli trigger most activations.
- Marie-Christine Carpentier
- , Ernandes Manfroi
- & Olivier Panaud
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Article
| Open AccessPatterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica
Despite the prevalence of genome duplication in plants, little is known about the evolutionary patterns of entire subgenomes. Here the authors resequence allopolyploid Arabidopsis kamchatica genome to estimate diversity, linkage disequilibrium and strengths of both positive and purifying selection.
- Timothy Paape
- , Roman V. Briskine
- & Kentaro K. Shimizu
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Article
| Open AccessNatural variation at XND1 impacts root hydraulics and trade-off for stress responses in Arabidopsis
Soil water uptake is a major determinant of plant performance and stress tolerance. Here the authors show that, by affecting xylem formation in the root, natural variation at the Arabidopsis XND1 locus has contrasting effects on root hydraulics and drought tolerance versus pathogen resistance.
- Ning Tang
- , Zaigham Shahzad
- & Christophe Maurel
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Article
| Open AccessNatural selection of a GSK3 determines rice mesocotyl domestication by coordinating strigolactone and brassinosteroid signaling
Long mesocotyl is a critical trait for the application of rice deep direct seeding or mechanized dry seeding cultivation method. Here, Sun et al. find OsGSK2 is selected for mesocotyl length variation during domestication and it coordinates strigolactone and brassinosteroid signaling to determine mesocotyl elongation.
- Shiyong Sun
- , Tao Wang
- & Xuelu Wang
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Article
| Open AccessGS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality
Rice grain shape or size is an important trait associated with both yield and appearance quality. Here, the authors identify GS9 as a negative transcription regulator of slender grain and show it can improve grain shape and appearance independently from other previously identified grain size genes.
- Dong-Sheng Zhao
- , Qian-Feng Li
- & Qiao-Quan Liu
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Article
| Open AccessA G-protein pathway determines grain size in rice
Grain size is a major determinant of cereal yield. Here the authors characterize five subunits of the rice heterotrimeric G proteins and find that manipulating the three Gγ proteins can achieve designed grain size, which provides a predictable approach to improving grain yield and quality.
- Shengyuan Sun
- , Lei Wang
- & Qifa Zhang
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| Open AccessG-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice
Cereal crops' grain yield and quality are traits that are usually considered to be negatively correlated. Here, the authors show that interaction of G-protein βγ subunits with an alternatively spliced MADS1lgy3 protein can increase rice grain yield and quality simultaneously in field conditions.
- Qian Liu
- , Ruixi Han
- & Xiangdong Fu
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Article
| Open AccessGenetic variations in ARE1 mediate grain yield by modulating nitrogen utilization in rice
Understanding the regulatory mechanisms of nitrogen assimilation is crucial for developing crop cultivars with improved nitrogen utilization efficiency (NUE). Here the authors identify a new negative regulator of NUE and mutation of this gene increases 10–20% rice grain yield under nitrogen-limiting field conditions.
- Qing Wang
- , Jinqiang Nian
- & Jianru Zuo
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Article
| Open AccessA defensin-like protein drives cadmium efflux and allocation in rice
Crops that allocate heavy metals to leaves rather than grains could allow phytoremediation of polluted soil while producing food that is safe to eat. Here, the authors show that a defensin-like protein promotes cadmium secretion from rice cells and allocation to leaves without causing accumulation in grain.
- Jin-Song Luo
- , Jing Huang
- & Ji-Ming Gong
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Article
| Open AccessHigh contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consumer computing hardware, and demonstrate its usefulness in resolving complex structural variation.
- Todd P. Michael
- , Florian Jupe
- & Joseph R. Ecker
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Article
| Open AccessA naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions
Epigenetic variation underlies various aspects of phenotypic diversity of plants. Here, He et al show a naturally occurring epiallele controls Arabidopsis leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE (PPH), and is associated with local climate adaptation.
- Li He
- , Wenwu Wu
- & Jian-Kang Zhu
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Article
| Open AccessDifferentially evolved glucosyltransferases determine natural variation of rice flavone accumulation and UV-tolerance
In contrast to flavonols, the functions of plant flavones are largely unknown. Here, the authors report the two differentially evolved glucosyltranferases (flavone 7-O-glucosyltransferase and flavone 5-O-glucosyltransferase) determine natural variation of rice flavone accumulation and UV-tolerance.
- Meng Peng
- , Raheel Shahzad
- & Jie Luo
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Article
| Open AccessNOG1 increases grain production in rice
Rice grain yield is a quantitative trait determined by multiple genes. Here, the authors find NOG1, which encodes an enoyl-CoA hydratase/isomerase in fatty acid β-oxidation pathway, can increase grain yield by enhancing grain number per panicle without affecting the other yield component traits.
- Xing Huo
- , Shuang Wu
- & Chuanqing Sun
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Article
| Open AccessNatural variation of YELLOW SEEDLING1 affects photosynthetic acclimation of Arabidopsis thaliana
Natural genetic variation of photosynthesis is an underexplored resource for plant genetic improvement. Here, the authors find allelic variations of YS1 affect Arabidopsis photosynthesis acclimation using genome-wide association study, reverse genetics, and quantitative complementation approaches.
- Roxanne van Rooijen
- , Willem Kruijer
- & Mark G. M. Aarts
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Article
| Open AccessNatural allelic variation of FRO2 modulates Arabidopsis root growth under iron deficiency
Iron is an essential micronutrient for plants and a lack of iron availability limits crop yield in many parts of the world. Here the authors show that natural variation in root growth ofArabidopsis plants under iron deficiency can be caused by allelic variation at the FRO2locus.
- Santosh B. Satbhai
- , Claudia Setzer
- & Wolfgang Busch
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Article
| Open AccessA natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice
Breeding of rice with ideal plant architecture has increased rice yield worldwide. Here Zhanget al. show that, in the super rice variety YY12, this ideal plant architecture trait arose from three distal tandem repeats that are associated with an open chromatin state and increased expression of the IPA1gene.
- Lin Zhang
- , Hong Yu
- & Jiayang Li
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Article
| Open AccessOn the post-glacial spread of human commensal Arabidopsis thaliana
Population structure of the model plantArabidopsis thaliana is shaped by glacial refugia and recent admixture. Here the authors show that genetically distinct groups of A. thalianahave spread east-west across Europe since the most recent ice age, likely as a result of human activity.
- Cheng-Ruei Lee
- , Hannes Svardal
- & Magnus Nordborg
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Article
| Open AccessComparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals
The plant metabolome is often considered as a bridge between genomic and phenotypic variation. Here, the authors perform metabolic and phenotypic genome-wide association studies in rice grain, and compare to prior studies on rice leaf and maize kernel, to demonstrate a new strategy to investigate complex traits.
- Wei Chen
- , Wensheng Wang
- & Jie Luo
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Article
| Open AccessThe plastid metalloprotease FtsH6 and small heat shock protein HSP21 jointly regulate thermomemory in Arabidopsis
Exposure of plants to heat can promote increased tolerance to subsequent heat stress. Here, the authors show that prolonged expression of Arabidopsissmall heat shock protein HSP21 promotes this thermomemory effect and that HSP21 levels are regulated by the plastid metalloprotease FtsH6 during the memory period.
- Mastoureh Sedaghatmehr
- , Bernd Mueller-Roeber
- & Salma Balazadeh
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Article
| Open AccessA heavy metal P-type ATPase OsHMA4 prevents copper accumulation in rice grain
Copper (Cu) is an essential mineral nutrient but high concentrations in rice grain can cause toxicity. Here the authors provide evidence that natural variation in rice grain Cu concentration is caused by altered sequestration of Cu into root vacuoles due to a single amino acid substitution in the OsHMA4 transporter.
- Xin-Yuan Huang
- , Fenglin Deng
- & Jian Feng Ma
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Article
| Open AccessA transposable element in a NAC gene is associated with drought tolerance in maize seedlings
Drought is a major cause of yield loss in maize and understanding the genetic determinants of natural variation in drought tolerance may aid breeding programs produce more tolerant varieties. Here, Mao et al.identify a MITE transposon insertion in a NAC transcription factor, which is associated with natural variation in drought tolerance.
- Hude Mao
- , Hongwei Wang
- & Feng Qin
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Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis
The genetic distance between parents influences hybrid performance in plants. Here Miller et al. show that Arabidopsishybrids produced from diverse parental ecotypes have reduced expression of stress responsive genes at certain times of the day and this correlates with greater biomass production.
- Marisa Miller
- , Qingxin Song
- & Z. Jeffrey Chen
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Article
| Open AccessCombining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice
Next-generation sequencing technology has made the generation of huge amounts of genetic data possible, but phenotype characterization remains slow and difficult. Here the authors develop a high-throughput phenotyping facility for rice that is able to accurately identify and characterize traits related to morphology, biomass and yield.
- Wanneng Yang
- , Zilong Guo
- & Lizhong Xiong
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Natural variation in arsenate tolerance identifies an arsenate reductase in Arabidopsis thaliana
Arsenic tolerance in plants is critical for their adaptation to some soils and has therefore played an important role in plant distribution. Here, the authors identify a quantitative trait locus encoding an arsenate reductase enzyme that confers arsenic tolerance in plants.
- Eduardo Sánchez-Bermejo
- , Gabriel Castrillo
- & Antonio Leyva
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Article
| Open AccessInduced and natural variation of promoter length modulates the photoperiodic response of FLOWERING LOCUS T
Gene expression at FLOWERING LOCUS T controls floral transition in many plants and is regulated by both environmental signals and internal cues. Liu et al. show that the distance between two regulatory sequences in the FT promoter varies with geographical location and determines responsiveness to photoperiod.
- Liangyu Liu
- , Jessika Adrian
- & Franziska Turck
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Regulatory change at Physalis Organ Size 1 correlates to natural variation in tomatillo reproductive organ size
The genetic basis of plant reproductive organ size is poorly understood. Here, the authors suggest that variation in the gene, Physalis Organ Size 1, regulates reproductive organ size in tomatillo and provides insight into the evolution of the genetic regulation of plant morphology.
- Li Wang
- , Lingli He
- & Chaoying He
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Natural variation in PTB1 regulates rice seed setting rate by controlling pollen tube growth
Understanding the genetic factors that regulate panicle architecture is important for improving rice yields. In this study, Li et al. demonstrate that the gene PTB1is critical for regulating panicle seed setting rate and pollen tube growth.
- Shuangcheng Li
- , Wenbo Li
- & Ping Li