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Article
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A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution
Modern sugarcane cultivars have complicated genome due to interspecific crosses and multiple backcrossing. Here, the authors report the haplotype-resolved, chromosome-level genome assembly of a modern hybrid sugarcane cultivar and reveal the expansion of genes related to sugar accumulation and smut resistance.
- Yixue Bao
- , Qing Zhang
- & Muqing Zhang
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Article
| Open Access
A distal enhancer guides the negative selection of toxic glycoalkaloids during tomato domestication
This study identified a distal enhancer GE1, which acts as the key regulator controlling steroidal glycoalkaloids metabolism by modulating the GAME gene cluster and guides negative selection of steroidal glycoalkaloids production during tomato domestication.
- Feng Bai
- , Peng Shu
- & Mingchun Liu
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Article
| Open Access
An ARF gene mutation creates flint kernel architecture in dent maize
The mutation of ARFTF17 results in the development of flint kernel architecture in dent maize by reducing excessive pericarp length. This discovery holds significant potential for enhancing grain quality in elite, high-yielding dent maize hybrids.
- Haihai Wang
- , Yongcai Huang
- & Yongrui Wu
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Article
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A double-stranded RNA binding protein enhances drought resistance via protein phase separation in rice
Drought is one of the major abiotic stresses affecting rice growth and development. Here, the authors identify a dsRNA-binding protein positively regulates rice drought resistance through promoting stability of OsNCED4 mRNAs, transcript of a key gene for the biosynthesis of abscisic acid, via protein phase separation.
- Huaijun Wang
- , Tiantian Ye
- & Lizhong Xiong
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Article
| Open Access
Genetic gains underpinning a little-known strawberry Green Revolution
Cultivated strawberry is a hybrid species with a 250-year domestication history. Here, the authors use genomic prediction and a historically important breeding population to show that the introduction of photoperiod-insensitive hybrids and genetic gains from breeding have been catalysts for a strawberry Green Revolution.
- Mitchell J. Feldmann
- , Dominique D. A. Pincot
- & Steven J. Knapp
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Article
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Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein
Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. Here, the authors report the cloning of powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima encoding a mixed lineage kinase domain-like (MLKL) protein.
- Huanhuan Li
- , Wenqiang Men
- & Wenxuan Liu
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Article
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A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination
Japonica rice generally has greater capacity for low temperatures germination (LTG) than indica rice. Here, the authors report an E2 ubiquitin-conjugating enzyme-encoding gene OsUBC12 can increase LTG in japonica rice by negatively regulate ABA signaling via promoting the proteasomal degradation of OsSnRK1.1.
- Chuanzhong Zhang
- , Hongru Wang
- & Jun Fang
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Article
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Natural variation in OsMYB8 confers diurnal floret opening time divergence between indica and japonica subspecies
Florets of indica rice open earlier than japonica rice, hindering utilization of the cross subspecies heterosis. Here, the authors show that an OsMYB8-OsJAR1 module regulates diurnal floret opening time divergences between the two subspecies.
- Yajun Gou
- , Yueqin Heng
- & Rongxin Shen
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Article
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Natural variation of STKc_GSK3 kinase TaSG-D1 contributes to heat stress tolerance in Indian dwarf wheat
Indian dwarf wheat (Triticum sphaerococcum) is thermotolerant, but the underlying mechanism is unclear. Here, the authors report the cloning of the heat tolerance gene encoding a STKc_GSK3 kinase and its variation affects phosphorylation level of downstream TaPIF4 in determining thermotolerance.
- Jie Cao
- , Zhen Qin
- & Mingming Xin
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Article
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Natural variation in BnaA9.NF-YA7 contributes to drought tolerance in Brassica napus L
Rapeseed production is often threatened by drought stress. Here, the authors report transcription factor BnaA9.NFYA7 negatively regulates rapeseed drought tolerance through ABA signal transduction pathway via feedback inhibition of the expression of BnaABF3/4s-related genes.
- Jia Wang
- , Lin Mao
- & Liezhao Liu
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Article
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A genomic toolkit for winged bean Psophocarpus tetragonolobus
Winged bean is a tropical legume that can produce similar level of seed protein to soybean. Here, the authors report the genome assembly, population genetics, QTL mapping of the plant architecture, protein content and phytonutrients for this species.
- Wai Kuan Ho
- , Alberto Stefano Tanzi
- & Sean Mayes
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Article
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Genetic control of thermomorphogenesis in tomato inflorescences
Mechanisms underlying changes in inflorescence development in response to high ambient temperature remain unclear. Here, the authors report the cloning of the MIB2, encoding a homology of SPATULA, and its activation of CONSTANS-Like1 for determining tomato inflorescence branching at high ambient temperature.
- Shuai Sun
- , Zhiqiang Liu
- & Xia Cui
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Article
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A mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice
Seed dormancy is the preferred trait in rice production as it can prevent preharvest sprouting. Here, the authors report that MODD (mediator of OsbZIP46 deactivation and degradation) negatively regulates seed dormancy by inhibiting the transcriptional activity of ABSCISIC ACID INSENSITIVES (ABIs).
- Naihui Guo
- , Shengjia Tang
- & Peisong Hu
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Article
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Wheat Pm55 alleles exhibit distinct interactions with an inhibitor to cause different powdery mildew resistance
Powdery mildew threatens worldwide wheat production. Here, the authors report the cloning of two powdery mildew resistant Pm55 alleles and show that they exhibit distinct interactions with the inhibitor SuPm55 to cause different resistance.
- Chuntian Lu
- , Jie Du
- & Ruiqi Zhang
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Comment
| Open Access
Integrative and inclusive genomics to promote the use of underutilised crops
Underutilised crops or orphan crops are important for diversifying our food systems towards food and nutrition security. Here, the authors discuss how the development of underutilised crop genomic resource should align with their breeding and capacity building strategies, and leverage advances made in major crops.
- Oluwaseyi Shorinola
- , Rose Marks
- & Mark A. Chapman
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Article
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MADS1-regulated lemma and awn development benefits barley yield
HvMADS1 in barley positively regulates awn length and lemma width by promoting cell proliferation through direct action on the expression of HvSHI and HvDL. In wheat, MADS1 conservatively regulates awn length.
- Yueya Zhang
- , Chaoqun Shen
- & Dabing Zhang
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Article
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Decoding the gene regulatory network of endosperm differentiation in maize
The cereal endosperm constitutes most of the grain by volume. Here the authors use single-cell analysis of maize developing endosperm to decode gene regulatory networks that likely control endosperm growth and offer a framework for crop improvement.
- Yue Yuan
- , Qiang Huo
- & Zeyang Ma
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Article
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Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat
The analysis of wheat cultivars reveals that variations in histone modification, rather than DNA sequence, are closely linked to the expression of nitrogen metabolism genes and distinct agronomic traits. The findings suggest that epigenetic regulation plays a crucial role in cultivar-specific adaptation to low nitrogen conditions in wheat.
- Hao Zhang
- , Zhiyuan Jin
- & Jun Xiao
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Article
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A toxin-antidote system contributes to interspecific reproductive isolation in rice
Orzya meridionalis is a wild rice species that has reproductive isolation with Asian cultivated rice. Here, the authors report the cloning of the second locus controlling hybrid male sterility between the two species and show the encoded toxin-antidote system provides stacked reproductive isolation for maintaining species identity.
- Shimin You
- , Zhigang Zhao
- & Jianmin Wan
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| Open Access
Single amino acid change alters specificity of the multi-allelic wheat stem rust resistance locus SR9
Among all wheat rust resistance genes, SR9 has the largest number of alleles. Here, the authors use gene cloning, complementation and comparative genetics to resolve the relationship among Sr9 alleles, confirm their allelic identities, and show that a single amino acid change leads to resistance to Ug99.
- Jianping Zhang
- , Jayaveeramuthu Nirmala
- & Evans Lagudah
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Article
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Copy number variation of the restorer Rf4 underlies human selection of three-line hybrid rice breeding
Ctyoplasmic male sterility gene WA352 and its fertility restorer Rf4 are widely used for commercial three-line hybrid rice production. Here, the authors investigate the origin, evolution, and variation of Rf4, and show that copy number variation of Rf4 contributes of fertility restoration in a dosage-dependent manner.
- Zhe Zhao
- , Zhi Ding
- & Letian Chen
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Article
| Open Access
Leveraging data from the Genomes-to-Fields Initiative to investigate genotype-by-environment interactions in maize in North America
The Genomes-to-Fields (G2F) initiative has collected large amount of maize phenotype and genotype data. Here, the authors develop an automated workflow for curating the data, matching it with public weather and soil data, and generating environmental covariates for phenotypic data, which pave the way for several GxE investigations.
- Marco Lopez-Cruz
- , Fernando M. Aguate
- & Gustavo de los Campos
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Article
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PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes
How plant height is adaptive to high latitudes and high density planting is unclear. Here, the authors report a retrotransposon insertion in a WD40 protein encoding gene PH13 affects its interaction with GmCOP1s and increases the abundance of STF1/2, leading to reduced soybean height and increased shade resistance.
- Chao Qin
- , Ying-hui Li
- & Bin Liu
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Article
| Open Access
Robotized indoor phenotyping allows genomic prediction of adaptive traits in the field
Robotized indoor phenotyping allows measuring of plant physiological traits at high throughput, but is often considered as non-relevant for field conditions. Here, the authors show that maize traits measured indoor translate to the field and can be inferred via genomic prediction.
- Jugurta Bouidghaghen
- , Laurence Moreau
- & François Tardieu
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Article
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UV-B irradiation-activated E3 ligase GmILPA1 modulates gibberellin catabolism to increase plant height in soybean
Gibberellins (GA) negatively regulate UVB-mediated suppression of plant height in plants. Here, the authors show that GmILPA1-mediated degradation of GmGA2ox-like protein counteract the UV-B-mediated reduction of bioactive GAs contributing to the linkage between the affection of UV-B and GA on plant height of soybean.
- Jiaqi Sun
- , Shiyu Huang
- & Fengning Xiang
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Article
| Open Access
A natural mutation in the promoter of Ms-cd1 causes dominant male sterility in Brassica oleracea
A dominant genic male sterility (DGMS) mutant of Brassica oleracea was identified in 1970s and has been widely used for hybrid cabbage breeding, but its genetic basis is unclear. Here, the authors reveal that a 1-bp deletion in the promoter of the gene encoding a PHD-finger motif transcription factor is responsible for DGMS.
- Fengqing Han
- , Kaiwen Yuan
- & Honghao Lv
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Article
| Open Access
Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides
Leaf rust is one of the most severe foliar diseases of wheat. Here, the authors report the cloning of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides, and show it encodes a coiled-coil nucleotide-binding leucine-rich repeat protein.
- Hongna Li
- , Lei Hua
- & Shisheng Chen
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Article
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Comparative genomic analyses reveal the genetic basis of the yellow-seed trait in Brassica napus
Yellow-seed trait is preferred in rapeseed breeding as it can greatly improve seed oil yield and quality. Here, the authors assemble the genome of two rapeseed lines with yellow-seed and black-seed phenotypes, and clone an R2R3-MYB-type transcription factor encoding gene as a key regulator of seed color.
- Cunmin Qu
- , Meichen Zhu
- & Jiana Li
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Article
| Open Access
Sequencing trait-associated mutations to clone wheat rust-resistance gene YrNAM
Wheat stripe (yellow) rust is a devastating disease posing a threat to global production. Here, the authors report the cloning of a wheat stripe rust resistance gene encoding a protein with a NAM domain and a ZnF-BED domain using a strategy called sequencing trait-associated mutations (STAM).
- Fei Ni
- , Yanyan Zheng
- & Jiajie Wu
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Article
| Open Access
Generation of the transgene-free canker-resistant Citrus sinensis using Cas12a/crRNA ribonucleoprotein in the T0 generation
Development of canker-resistant citrus cultivars via traditional approaches is a lengthy and laborious process. Here, the authors report the generation of regulatory approval, transgene-free, canker-resistant sweet orange lines using Cas12a/crRNA ribonucleoprotein-based susceptibility gene editing strategy.
- Hang Su
- , Yuanchun Wang
- & Nian Wang
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Article
| Open Access
Genome-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 Access
OsMADS17 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 Access
An E2-E3 pair contributes to seed size control in grain crops
Researchers identify an E3 ligase SGD1 and its E2 partner responsible for grain yield control using foxtail millet, and reveal its conserved role in wheat, maize, and rice. Furthermore, SGD1 ubiquitinates the brassinosteroid receptor BRI1 thus stabilizing it and promoting grain yield in crops.
- Sha Tang
- , Zhiying Zhao
- & Xianmin Diao
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Article
| Open Access
UDP-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 Access
Chromosome-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 Access
Analyses 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 Access
Tiller 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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Article
| Open Access
Dosage 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 Access
Global crop yields can be lifted by timely adaptation of growing periods to climate change
'Crop growing periods and cultivars are key to crop adaptation. Here, the authors use a modelling approach that integrates farmers decision and biophysical crop models, showing the importance of cultivar, sowing date and growing period adaptation.'
- Sara Minoli
- , Jonas Jägermeyr
- & Christoph Müller
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Article
| Open Access
Natural 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 Access
GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet
Plant genotype alone appears to be insufficient to explain trait variations. This study integrates GWAS, MWAS and mGWAS in 827 foxtail millet cultivars, revealing that root-associated microbiota affect plant phenotypes in a host genotype-dependent manner.
- Yayu Wang
- , Xiaolin Wang
- & Huan Liu
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Article
| Open Access
Climate change may outpace current wheat breeding yield improvements in North America
Wheat breeding programmes improve yield by enhancing biotic and abiotic stress resistance. This study reveals that high temperature extremes adversely affect the productivity of new elite wheat breeding lines, and that future yield gains may be outpaced by the rapid advance of climate change.
- Tianyi Zhang
- , Yong He
- & Xiaoguang Yang
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Article
| Open Access
A 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 Access
Genome-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 Access
Regain 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 Access
Cloning 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 Access
Mutations in DNA polymerase δ subunit 1 co-segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses
Cassava mosaic disease is caused by geminiviruses and suppresses cassava yields throughout the tropics. Here, the authors show that mutations in MePOLD1, encoding DNA polymerase δ subunit 1, co-segregate with CMD2, the major source of genetic resistance for this disease.
- Yi-Wen Lim
- , Ben N. Mansfeld
- & Rebecca S. Bart
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Article
| Open Access
Physiological 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 Access
Cloning 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
A membrane associated tandem kinase from wild emmer wheat confers broad-spectrum resistance to powdery mildew