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Article
| Open AccessTwo telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis
Chili pepper (Capsicum) is an important vegetables known for fruit pungency given by capsaicinoids. Here, the authors assemble the telomere-to-telomere genomes of a pungent pepper C. annuum and its non-pungent wild relative C. rhomboideum and reveal insights into Capsicum evolution and capsaicinoid biosynthesis.
- Weikai Chen
- , Xiangfeng Wang
- & Li Guo
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Matters Arising
| Open AccessThe wheat stripe rust resistance gene YrNAM is Yr10
- Katherine Dibley
- , Matthias Jost
- & Peng Zhang
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Article
| Open AccessA pair of atypical NLR-encoding genes confers Asian soybean rust resistance in soybean
Asian soybean rust (ASR) is a devastating disease of soybean. Here, the author report the identification of an atypical pair of nucleotide-binding leucine-rich repeat (NLR) encoding genes and how they function together to confer broad-spectrum resistance to ASR.
- Qingnan Hao
- , Hongli Yang
- & Xinan Zhou
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Article
| Open AccessA membrane associated tandem kinase from wild emmer wheat confers broad-spectrum resistance to powdery mildew
Powdery mildew is a fungal leaf disease that reduces yield and grain quality in susceptible wheat varieties. Here, the authors report the cloning of the wild emmer wheat originated powdery mildew resistance gene Pm36 as a membrane associated tandem kinase and its possible resistance mechanism.
- Miaomiao Li
- , Huaizhi Zhang
- & Zhiyong Liu
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Article
| Open AccessA 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 AccessA 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 AccessWheat 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
| Open AccessGenetic 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
| Open AccessDynamics of extrachromosomal circular DNA in rice
Comparing to other biological systems, our understanding of plant extrachromosomal circular DNA (eccDNA) is limited. Here, the authors profile eccDNA from six rice tissues and investigate eccDNA characteristics, formation mechanisms, distribution, and functional implications.
- Jundong Zhuang
- , Yaoxin Zhang
- & Tingting Lu
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Article
| Open AccessA 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
| Open AccessNatural 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
| Open AccessGWAS reveals determinants of mobilization rate and dynamics of an active endogenous retrovirus of cattle
Endogenous retroviruses constitute 5–10% of mammalian genome space. This study characterize the bovine ERVK[2-1- LTR] clade showing that its activity varies between individuals as a function of the number of inherited autonomous elements, yet that most de novo insertions are non-autonomous elements lacking functional genes.
- Lijing Tang
- , Benjamin Swedlund
- & Carole Charlier
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Article
| Open AccessNatural 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
| Open AccessNatural 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
| Open AccessA 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
| Open AccessPorous borders at the wild-crop interface promote weed adaptation in Southeast Asia
Genome-wide evidence to support that wild rice can contribute to weedy rice evolution by hybridization and adaptive introgression is very limited. Here, the authors sequence the weedy rice genomes and show reproductively compatible wild rice can contribute to weedy rice evolution.
- Lin-Feng Li
- , Tonapha Pusadee
- & Kenneth M. Olsen
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Article
| Open AccessGenetic 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
| Open AccessA 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
| Open AccessA chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm
Coffea arabica is an allotetraploid hybrid of C. eugenioides and C. canephora and contributes to approximately 60% of world coffee production. Here, the authors report its chromosome-level genome assembly and identify that chromosomal abnormalities and introgression from C. canephora may contribute to diversity and pathogen resistance.
- Simone Scalabrin
- , Gabriele Magris
- & Michele Morgante
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Article
| Open AccessMolecular quantitative trait loci in reproductive tissues impact male fertility in cattle
Investigating the genetics of male fertility requires comprehensive genotype and phenotype data. Here, the authors characterize the transcriptional complexity of bovine male reproductive tissues to identify loci associated with male fertility.
- Xena Marie Mapel
- , Naveen Kumar Kadri
- & Hubert Pausch
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Article
| Open AccessWheat 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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Editorial
| Open AccessEfficient genetic improvement of orphan crops cannot follow the old path
Orphan crops hold the potential to diversify our food systems. Considering their unique characteristics, our deep understanding of major crops, and the availability of modern genomic tools, taking a different research path from what major crops have gone through could accelerate the genetic improvement of orphan crops.
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Comment
| Open AccessIntegrative 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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Editorial
| Open AccessFeeding the future global population
Climate change is exacerbating challenges both for global food production and from its environmental impacts. Sustainable and socially responsible solutions for future world-wide food security are urgently needed.
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Article
| Open AccessMicrobiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis
The underlying mechanisms of host-driven assembly of phyllosphere microbiota remain largely unknown. Here, 4-hydroxycinnamic acid synthesized by the rice plant’s PAL02 in the phenylpropanoid biosynthesis pathway is shown to be the main driver for enrichment of Pseudomonadales bacteria.
- Pin Su
- , Houxiang Kang
- & Yong Liu
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Article
| Open AccessSoybean reduced internode 1 determines internode length and improves grain yield at dense planting
Many cereal crops have been bred to be more compact to allow high-density planting, but soybean has remained relatively overlooked. Here, the authors describe a compact soybean mutant, reduced internode 1, that significantly enhances grain yield under high-density planting conditions compared to an elite cultivar.
- Shichen Li
- , Zhihui Sun
- & Sijia Lu
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Article
| Open AccessGlobal genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing
Indicine cattle make up half of all cattle populations worldwide. Using a large genomic dataset, this study finds historic migrations and extensive introgression with domestic and wild bovine species has facilitated this species physiological adaptation to extreme environments.
- Ningbo Chen
- , Xiaoting Xia
- & Chuzhao Lei
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Article
| Open AccessA papain-like cysteine protease-released small signal peptide confers wheat resistance to wheat yellow mosaic virus
Soil-borne wheat yellow mosaic virus (WYMV) poses a serious threat to global wheat production. Here, the authors report that the nuclear inclusion protease-a produced by WYMV interacts with a small peptide catalyzed by TaRD21A protease activity to mediate WYMV resistance through activating MAPK signaling pathway.
- Peng Liu
- , Chaonan Shi
- & Jian Yang
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Article
| Open AccessLoss-of-function of an α-SNAP gene confers resistance to soybean cyst nematode
Here, the authors show that the soybean GmSNAP02 gene confers a unique mode of resistance to the soybean cyst nematode Heterodera glycines through loss-of-function mutations that implicate GmSNAP02 as a nematode virulence target.
- Mariola Usovsky
- , Vinavi A. Gamage
- & Andrew M. Scaboo
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Article
| Open AccessA 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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Article
| Open AccessTransposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat
The direct impacts of transposable element dynamics on polyploid regulation and developmental specificity remain unclear. Here, the authors show that a large proportion of enhancer-like elements (ELEs) are mainly originated from RLG_famc7.3 specifically expanded in subgenome A, producing active nascent transcripts and influencing wheat spike development.
- Yilin Xie
- , Songbei Ying
- & Yijing Zhang
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Article
| Open AccessPan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits
A pan-genome can reduce bias in genetic diversity analysis inherent in using a single reference genome. Here, the authors assemble genomes of 10 diverse apple accessions, conduct pan-genome analysis together with three existing genomes, and reveal the role of mitogen-activated protein kinase homolog MMK2 in fruit coloration.
- Ting Wang
- , Shiyao Duan
- & Ting Wu
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Article
| Open AccessPolyethyleneimine-coated MXene quantum dots improve cotton tolerance to Verticillium dahliae by maintaining ROS homeostasis
Verticillum wilt is an important cotton disease caused by fungal pathogen Verticillium dahiae. Here, the authors assemble the genomes of defoliating and non-defoliating isolates of the pathogen, identify virulence gene SP3, and develop a disease control strategy using polyethyleneimine-coated MXene quantum dots.
- Ping Qiu
- , Jiayue Li
- & Longfu Zhu
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Article
| Open AccessSingle 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
| Open AccessUnzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization
The occurrence and consequences of polyploidization in clonally reproducing animals is unclear. Here, the authors generate 4 polyploid Meloidogyne genomes, identifying a telomeric element, resolving genome structures and extensive chromosome fusion events, and revealing origin patterns.
- Dadong Dai
- , Chuanshuai Xie
- & Ming Sun
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Article
| Open AccessLeveraging 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
| Open AccessPH13 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 AccessRobotized 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
| Open AccessA 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 AccessCloning 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
| Open AccessA de novo evolved gene contributes to rice grain shape difference between indica and japonica
Genetic bases of grain shape differentiation between the two subspecies of Asian cultivated rice have not been fully elucidated. Here, the authors report GSE9, a de novo gene evolved from a non-coding region of wild rice through acquisition of start codon, contributes to the grain shape difference between the two subspecies.
- Rujia Chen
- , Ning Xiao
- & Zefeng Yang
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Article
| Open AccessGenomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation
Existing genetics and genomics studies of peppers mainly focus on single species. Here, the authors report a pepper graph pan-genome and a genome variation map of 500 accessions from five domesticated species and close wild relatives to reveal their domestication, introgression and population differentiation.
- Feng Liu
- , Jiantao Zhao
- & Xuexiao Zou
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Article
| Open AccessA pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley
Rph7 is a previously mapped barley leaf rust resistance locus, but the causal resistance gene remains unclear. Here, combining a fine mapping approach with RNA-Seq based analysis, the authors clone Rph7 and show it encodes putative NAC transcription factor containing a C-terminal BED domain.
- Chunhong Chen
- , Matthias Jost
- & Peter M. Dracatos
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Article
| Open AccessQTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize
The lack of large-scale QTL cloning method hampers systematic dissection of genetic base of quantitative traits. Here, the authors develop a multi-omics data-based technique for large-scale and rapid cloning of quantitative genes of tassel branch number and discovery of selection signatures in maize breeding.
- Xi Wang
- , Juan Li
- & Lin Li
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Article
| Open AccessComparative 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 AccessAccurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences
Accurate haplotypes with abundant genomic variations benefit genetic research. Here, the authors accurately construct 1,874 pig haplotypes and demonstrate their applications in genome-wide association studies, prediction of breeding values and analyses of evolutionary selection.
- Xinkai Tong
- , Dong Chen
- & Lusheng Huang
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Article
| Open AccessA nuclear receptor HR96-related gene underlies large trans-driven differences in detoxification gene expression in a generalist herbivore
Adaptation to toxins in agricultural pests is often caused by increased expression of detoxification genes. Here, the authors reveal that variation in a family of transcriptional regulators facilitates rapid evolution to diverse pesticides and host plants.
- Meiyuan Ji
- , Marilou Vandenhole
- & Thomas Van Leeuwen
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Article
| Open AccessGenomic insight into domestication of rubber tree
Understanding the genetic basis of rubber tree domestication is critical for improving natural rubber production. Here, the authors assemble the genome of the rubber tree clone CATAS8-79 and conduct population and genetic association analyses to reveal the function of phytosulfokine in regulating number of laticifer rings.
- Jinquan Chao
- , Shaohua Wu
- & Wei-Min Tian
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Article
| Open AccessTwo complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice
The mechanisms of the partial reproductive isolation between the two subspecies of rice remains obscure. Here, the authors show that the two adjacent genes form a killer-protector system to induce hybrid male sterility and reproductive isolation between indica and japonica.
- Daiqi Wang
- , Hongru Wang
- & Ziqiang Liu