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| Open AccessJoint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids
Genetic dissection of hybrids is more difficult than inbreds as nonadditive effects are involved. Here, the authors report a pipeline for joint analysis of phenotypes, effects, and generations and demonstrate its usefulness in identification of loci associated with quality traits and improving predict accuracy in genomic selection of hybrid rice.
- Lanzhi Li
- , Xingfei Zheng
- & Zhongli Hu
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Article
| Open AccessGenome analyses reveal population structure and a purple stigma color gene candidate in finger millet
Finger millet is an orphan crop key to food security of people living in eastern Africa, India and Nepal. Here, the authors assemble its genome, conduct population genetics analyses to infer the diversification history, and reveal a candidate gene for purple coloration of anthers and stigma.
- Katrien M. Devos
- , Peng Qi
- & Damaris A. Odeny
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Article
| Open AccessGenome-wide association studies identify OsWRKY53 as a key regulator of salt tolerance in rice
Only a few genetic variants have been identified to mediate salt tolerance in major crops and their molecular mechanisms are largely unknown. Here, the authors identify WRKY53 as a negative regulator of salt tolerance in rice, and show that it directly trans-regulates expression of MKK10.2 and HKT1;5 to meditate salt tolerance.
- Jun Yu
- , Chengsong Zhu
- & Jianmin Wan
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Article
| Open AccessDynamic chromatin architecture of the porcine adipose tissues with weight gain and loss
Here the authors study diet-induced weight gain/loss to identify chromatin architectures in adipose tissue (AT) associated obesity in a pig model. They found parallels and species-specific regulatory elements in humans and pigs that underpin AT specialization.
- Long Jin
- , Danyang Wang
- & Mingzhou Li
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Article
| Open AccessOsMADS17 simultaneously increases grain number and grain weight in rice
The trade-off between grain number and grain weight is a major obstacle for increasing rice yield. Here, the authors show that variation in 5’ UTR of OsMADS17 can simultaneously increase grain number and grain weight through decreasing mRNA translation efficiency.
- Yuanjie Li
- , Sheng Wu
- & Chuanqing Sun
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Article
| Open AccessEngineering α-carboxysomes into plant chloroplasts to support autotrophic photosynthesis
Engineering carboxysomes into crop chloroplasts is a potential route to improve photosynthesis and crop yield. Here, the authors engineer functional CO2-fixing modules into tobacco chloroplasts to improve their photosynthesis and productivity.
- Taiyu Chen
- , Marta Hojka
- & Lu-Ning Liu
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Article
| Open AccessUDP-glucosyltransferase OsUGT75A promotes submergence tolerance during rice seed germination
Elongated coleoptile contributes submergence tolerance during germination of direct seeded rice. Here, the authors show that natural variation of rice coleoptile length is determined by the glycosyltransferase encoding gene OsUGT75A by reducing free ABA and JA levels through glycosylation of these two phytohormones.
- Yongqi He
- , Shan Sun
- & Zhoufei Wang
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Article
| Open AccessChromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding
Lablab is a legume native to Africa and cultivated throughout the tropics for food and forage; however, as an orphan crop, limited genomic resources hampers its genetic improvement. Here, an African-led South-North plant genome collaboration produces an improved genome assembly and population genomic resource to accelerate its breeding.
- Isaac Njaci
- , Bernice Waweru
- & Chris S. Jones
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Article
| Open AccessAnalyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum
Chrysanthemum is an important ornamental species with great economic value. Here, the authors assemble the haploid genome of C. morifolium, reveal its segmental allopolyploid genomic composition (AA’B), and identify candidate genes associated with flower development, petal shape, and flower colour.
- Aiping Song
- , Jiangshuo Su
- & Fadi Chen
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Article
| Open AccessThe methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine
DNA methylation level declines during aging of mammals. Here, the authors report single-base resolution landscape of cytosine DNA methylation at different ages of Chinese pine and show that the global cytosine DNA methylation gradually increases as age progresses.
- Jiang Li
- , Fangxu Han
- & Shihui Niu
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Article
| Open AccessSelection and adaptive introgression guided the complex evolutionary history of the European common bean
Common bean has two distinct domestication centers in Mesoamerica and in the Andes. The authors show that the Andean is the first gene pool successfully introduced in Europe and identify signature of pervasive introgression among gene pools and of selection for flowering underlying adaptation.
- Elisa Bellucci
- , Andrea Benazzo
- & Roberto Papa
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Article
| Open AccessPan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
Pan-genomes provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Here, the authors report a new rice pan-genome including 73 Asian rice and two wild relatives (Oryza rufipogon and O. punctata), and reveal the prevalence and scale of large inversions across the pan-genome.
- Yong Zhou
- , Zhichao Yu
- & Rod A. Wing
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Article
| Open AccessAllelic variation of TaWD40-4B.1 contributes to drought tolerance by modulating catalase activity in wheat
Drought stress limits wheat production around the world. Here, the authors report allelic variation of a WD40 encoding gene TaWD40-4B.1 contributes to wheat drought tolerance by interacting with canonical catalases as a chaperone to promote their activities to avoid ROS over accumulation.
- Geng Tian
- , Shubin Wang
- & Mengcheng Wang
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Article
| Open AccessGenomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus
Grass pea is a multi-stress tolerant orphan crop and developing cultivars with decreased accumulation of the neurotoxin β-L-oxalyl-2,3-diaminopropionic acid (β-L-ODAP) is one of its breeding objectives. Here, the authors assemble its genome and reveal genes involved in the biosynthesis of β-L-ODAP.
- Anne Edwards
- , Isaac Njaci
- & Peter M. F. Emmrich
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Article
| Open AccessTiller Number1 encodes an ankyrin repeat protein that controls tillering in bread wheat
Tiller number is an important agronomic trait of wheat. Here, the authors clone a positive regulator of wheat tiller number and show that the encoded ankyrin repeat protein can promote tiller bud outgrowth through inhibiting ABA biosynthesis and signaling.
- Chunhao Dong
- , Lichao Zhang
- & Xu Liu
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| Open AccessDosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat root growth
Introgression of the short arm of rye chromosome one into common wheat increases root biomass and drought tolerance, but the underlying genetic basis is unknown. Here, the authors report that dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate the differences of wheat root architecture.
- Gilad Gabay
- , Hanchao Wang
- & Jorge Dubcovsky
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Article
| Open AccessComplementary peptides represent a credible alternative to agrochemicals by activating translation of targeted proteins
Feeding an increasing world population in the context of climate change is one of the grand challenges faced by our generation. Here, the authors show that external application of synthetic complementary peptides can increase the abundance of target proteins to modulate plant growth or stress resistance.
- Mélanie Ormancey
- , Bruno Guillotin
- & Jean-Philippe Combier
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Article
| Open AccessImproving cassava bacterial blight resistance by editing the epigenome
Activating the expression of host susceptibility (S) genes is one of the strategies plant pathogens employed to promote infection of their host. Here, the authors show that targeted methylation at the TAL20 effector binding element of the cassava SWEET10a gene lead to resistance to Xanthomonas phaseoli.
- Kira M. Veley
- , Kiona Elliott
- & Rebecca S. Bart
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Article
| Open AccessHigh-frequency synthetic apomixis in hybrid rice
Previously, a proof-of-concept for low frequency synthetic apomixis was established in a laboratory strain of rice by combining MiMe mutations with the egg cell expression of the embryogenic trigger - BBM1. Here, the authors achieve clonal seed formation in hybrid rice with almost full penetrance and higher fertility.
- Aurore Vernet
- , Donaldo Meynard
- & Emmanuel Guiderdoni
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Article
| Open AccessGraph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon
The power of pangenomic graphs to improve genetic mapping is still unclear. Here, the authors demonstrate its value in identification of genetic variants associated with disease resistance traits in melon using PanPipes, a pangenome construction and low-coverage genotype-by-sequencing pipeline.
- Justin N. Vaughn
- , Sandra E. Branham
- & William P. Wechter
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Article
| Open AccessGenome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass
Paspalum vaginatum is a stress tolerant wild relative of maize and sorghum. Here, the authors assemble its genome at pseudomolecule level and reveal the role of trehalose mediated autophagy in increasing maize biomass productivity under nutrient-deficit conditions.
- Guangchao Sun
- , Nishikant Wase
- & James C. Schnable
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Article
| Open AccessGenomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii
Tree peony (Paeonia ostii) has the largest chromosome of any sequenced plants to date. Here, the authors assemble its genome and reveal the association of a list of candidate genes with fatty acid biosynthesis and the possible contribution of transposon and histone expansion to maintain the giga-chromosomes.
- Junhui Yuan
- , Sanjie Jiang
- & Yonghong Hu
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Article
| Open AccessChromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops
Genome evolution of Allium genus and genomic basis underlying the pungency flavor formation remain poorly understood. Here, the authors assemble the genome of bunching onion and conduct population genetics analyses to reveal Allium genome evolution, flavor formation and domestication history.
- Nanqiao Liao
- , Zhongyuan Hu
- & Jing-Quan Yu
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Article
| Open AccessN6-methyladenosine RNA modification promotes viral genomic RNA stability and infection
Wheat production is threatened by wheat yellow mosaic virus (WYMV). Here, via genome-wide association study, the authors report that a putative methyltransferase B positively regulates WYMV infection through enhancing viral genomic RNA stability by N6-methyladenosine RNA modification.
- Tianye Zhang
- , Chaonan Shi
- & Jian Yang
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Article
| Open AccessNatural variation of Dt2 determines branching in soybean
Shoot branching is critical in determining soybean yield. Here, the authors report natural variation of Dt2 in controlling soybean branching number and the interaction of Dt2 with GmAgl22 and GmSoc1a to activate transcription of GmAp1a and GmAp1d.
- Qianjin Liang
- , Liyu Chen
- & Zhixi Tian
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Article
| Open AccessPopulation genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races
Factors defining wheat stem rust pathogen (Pgt) virulence remain poorly characterized. Comparative population genomics based on Pgt haplotypes suggest that structural variation and admixture through somatic hybridization and sexual recombination play an important role in broadening Pgt virulence.
- Yuanwen Guo
- , Bliss Betzen
- & Eduard Akhunov
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Article
| Open AccessVariation in the fruit development gene POINTED TIP regulates protuberance of tomato fruit tip
While auxin has been implicated in the development of tomato fruit with pointed tips, the mechanism are largely unknown. Here, the authors report variation of a C2H2-type zinc finger transcription factor affects transcription of FUL2, which consequently regulates auxin transport and distribution to determine tomato fruit shape.
- Jianwen Song
- , Lele Shang
- & Junhong Zhang
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Article
| Open AccessGenomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding
Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits.
- Jiantao Guan
- , Jintao Zhang
- & Lixia Wang
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| Open AccessA NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination
Current studies of maize kernel development mostly focus on endosperm and embryo development, and little is known about the control of the nucellus tissue. Here, the authors report a NAC-EXPB15 pathway that regulate maize kernel size by modulating nucellus elimination and early endosperm development.
- Qin Sun
- , Yunfu Li
- & Fazhan Qiu
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Article
| Open AccessGenome-wide association study identifies a gene responsible for temperature-dependent rice germination
Physiology of seed germination has been optimized for various climatic conditions. Here, the authors report a 14-3-3 protein encoding gene GF14h is responsible for temperature-dependent rice germination by regulating ABA-responsive genes and contributes to the geographical adaptation of rice.
- Hideki Yoshida
- , Ko Hirano
- & Makoto Matsuoka
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Article
| Open AccessRegain flood adaptation in rice through a 14-3-3 protein OsGF14h
Waterlogging tolerance is important in direct seeding rice cultivation practice. Here, the authors identify a 14-3-3 protein-coding gene OsGF14h in weedy rice that confers anaerobic germination and anaerobic seedling development tolerance by balancing ABA signaling and GA biosynthesis.
- Jian Sun
- , Guangchen Zhang
- & Wenfu Chen
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Article
| Open AccessGenetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome
Diet affects the human gut microbiome, but studies linking crop genetics to seed traits that influence the human gut microbiome are lacking. Here, the authors develop an in vitro microbiome screening method and reveal the association between sorghum genes regulating condensed tannin biosynthesis and human gut microbiome.
- Qinnan Yang
- , Mallory Van Haute
- & Andrew K. Benson
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Article
| Open AccessThree types of genes underlying the Gametophyte factor1 locus cause unilateral cross incompatibility in maize
Unilateral cross incompatibility (UCI) is a type of prezygotic reproductive isolation, which is associated with multiple loci in maize. Here, the authors use genetic analysis to separate the Ga1 locus into two functional components and identify seven linked genes encoding three types of proteins.
- Yuebin Wang
- , Wenqiang Li
- & Jianbing Yan
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Article
| Open AccessCloning southern corn rust resistant gene RppK and its cognate gene AvrRppK from Puccinia polysora
Southern corn rust (SCR) caused by Puccinia polysora is a major maize disease that can result in major yield loss. Here, the authors report the expression of a CC-NB-LRR type of R gene RppK results in SCR resistance in susceptible maize lines and it can recognize the effector AvrRppK produced by P. polysora.
- Gengshen Chen
- , Bao Zhang
- & Zhibing Lai
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Article
| Open AccessNatural variation of DROT1 confers drought adaptation in upland rice
Genetic basis of the drought tolerance of upland rice is unclear. Here, the authors report the cloning of a COBRA-like protein encoding gene DROT1 and reveal that it is repressed by ERF3 and activated by ERF71 to help control the balance between growth and drought tolerance in upland rice.
- Xingming Sun
- , Haiyan Xiong
- & Zichao Li
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Article
| Open AccessDispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference
The contribution of ancient haplotypes to domestication is largely unknown. Here, the authors develop an ancestral genomic haploblock dissection method to generate a mosaic pan-ancestry genomic map and reveal that the domesticated polyploidy wheat emerged from the admixture of six founder wild emmer linages.
- Zihao Wang
- , Wenxi Wang
- & Weilong Guo
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Article
| Open AccessA natural uORF variant confers phosphorus acquisition diversity in soybean
Improving phosphorus (P) acquisition efficiency is important for sustainable agriculture. Here, the authors report a natural variation in an upstream open reading frame of a SEC12-like gene GmPHF1 is crucial for protein abundance and spatial distribution of GmPHF1, which contribute to P acquisition diversity in soybean.
- Zilong Guo
- , Hongrui Cao
- & Hong Liao
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Article
| Open AccessDisentangling the genetic basis of rhizosphere microbiome assembly in tomato
Genetics factors involved in rhizosphere microbiomes assembly remain largely elusive. Here, the authors integrate microbiomics and quantitative plant genetics to reveal genetic loci associated with specific microbes and rhizobacterial traits underlying microbiome assembly in tomato.
- Ben O. Oyserman
- , Stalin Sarango Flores
- & Jos M. Raaijmakers
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Article
| Open AccessIdentifying plant genes shaping microbiota composition in the barley rhizosphere
A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere. Here, the authors report QTLs and the associated candidate genes underlying rhizosphere microbiome composition in barley.
- Carmen Escudero-Martinez
- , Max Coulter
- & Davide Bulgarelli
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Article
| Open AccessThe 3D architecture of the pepper genome and its relationship to function and evolution
The organization of chromatin into self-interacting domains is universal among eukaryotic genomes. Here, the authors report a reference-grade pepper genome assembly and use this reference to help describe the relationship among 3D chromatin conformation, chromatin function, and gene expression.
- Yi Liao
- , Juntao Wang
- & Changming Chen
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Article
| Open AccessPhysiological adaptive traits are a potential allele reservoir for maize genetic progress under challenging conditions
Phenomic and genomic approaches are required to evaluate the progress of breeding strategies. Here, the authors analyse 65 years of genetic progress in maize, showing that breeders have selected traits with stable effects on yield whereas not for adaptive traits key for climate change adaptation.
- Claude Welcker
- , Nadir Abusamra Spencer
- & François Tardieu
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Article
| Open AccessPOWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean
In soybean production, level of seed protein frequently shows a negative correlation with seed oil content and yield. Here, the authors report a CCT gene pleiotropically regulates these traits and the selection of larger seeds determining allele leads to higher oil content but lower protein content in soybean cultivars.
- Wolfgang Goettel
- , Hengyou Zhang
- & Yong-qiang Charles An
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Article
| Open AccessCloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii
The Aegilops tauschii-derived leaf rust resistance gene Lr42 has been widely used for breeding resistance wheat cultivars, but the molecular basis is unknown. Here, the authors show that Lr42 encodes an NLR-type of disease resistance gene by bulked segregant mapping in Ae. tauschii and confirm its function in common wheat.
- Guifang Lin
- , Hui Chen
- & Sanzhen Liu
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Article
| Open AccessStructural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies
Pangenomes have a number of advantages over linear reference assemblies. Here the authors use bovine haplotype-resolved assemblies to show that structural variant-based pangenomes are consistent regardless of sequence platform, assembler, or coverage, suggesting that rigid protocols may not be required.
- Alexander S. Leonard
- , Danang Crysnanto
- & Hubert Pausch
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Article
| Open AccessDosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize
The role of miRNAs in genome imbalance is unclear. Here, the authors show that cis miRNAs in aneuploids present a predominant gene-dosage effect, whereas trans miRNAs trend toward the inverse level by examining global miRNA modulation in haploid and diploid aneuploids with the varied dosage of multiple chromosomal segments in maize.
- Xiaowen Shi
- , Hua Yang
- & James A. Birchler
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Article
| Open AccessAgrobacterium expressing a type III secretion system delivers Pseudomonas effectors into plant cells to enhance transformation
Agrobacterium infection can cause defense responses in many plants, which leads to transformation recalcitrance. Here, the authors express type III secretion system in Agrobacterium to deliver effector proteins into plant cells to suppress host defense responses and thus enhance transformation in some plant species.
- Vidhyavathi Raman
- , Clemencia M. Rojas
- & Kirankumar S. Mysore
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Article
| Open AccessA dirigent family protein confers variation of Casparian strip thickness and salt tolerance in maize
Most crops are farmed under high transpiring environments, but our understanding of transpiration-dependent salt tolerance (TDST) remains limited. Here, the authors report a dirigent family protein is responsible for TDST by affecting lignin deposition at Casparian strip barrier and transportation of Na+ across the endodermis.
- Yanyan Wang
- , Yibo Cao
- & Caifu Jiang
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Article
| Open AccessA natural allele of OsMS1 responds to temperature changes and confers thermosensitive genic male sterility
Thermosensitive genic male-sterile (TGMS) lines are widely used for two-line hybrid rice breeding, but the mechanism of TGMS has not been fully elucidated. Here, the authors show that natural allele of the OsMS1 gene, encoding a histone binding PHD finger protein, responds to temperature change and confers TGMS in rice.
- Lunying Wu
- , Xiaohui Jing
- & Yunhai Li
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Article
| Open AccessA pair of non-Mendelian genes at the Ga2 locus confer unilateral cross-incompatibility in maize
Unilaterial cross-incompatibility (UCI) systems are regulated by a male-female gene pair that are genetically linked, but no pair of the male and female determinants has been isolated so far. Here, the authors report the cloning of a pair of pectin methylesterases encoding genes at the Ga2 locus confer UCI in maize.
- Zhibin Chen
- , Zhaogui Zhang
- & Huabang Chen