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| Open AccessThe barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei
Leaf rust is an economically significant disease of barley. Here the authors describe cloning of the barley Rph3 leaf rust resistance gene and reveal it encodes a predicted transmembrane protein that is expressed upon infection by Rph3-avirulent Puccinia hordei isolates.
- Hoan X. Dinh
- , Davinder Singh
- & Mohammad Pourkheirandish
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Article
| Open AccessGenomic distances reveal relationships of wild and cultivated beets
While a large amount of genomic resources is available, the phylogeny of wild and cultivated beets remains unclear. Here, the authors use the k-mer-based Mash method to analyze resequenced genomes of 606 accessions of the genus Beta and reveal Greece as the domestication site of sugar beet.
- Felix L. Sandell
- , Nancy Stralis-Pavese
- & Juliane C. Dohm
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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
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| Open AccessBreeding future crops to feed the world through de novo domestication
By the end of this century, a 50% increase in agricultural productivity is required to feed the world. Recent studies have demonstrated de novo domestication of wild plants as a new crop breeding strategy to meet future food challenges.
- Hong Yu
- & Jiayang Li
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Article
| Open AccessNatural variation in Glume Coverage 1 causes naked grains in sorghum
Low glume coverage is the preferred for easy threshing in grain production, but the genetic basis remains unclear. Here, the authors report the gene GC1, which encodes an atypical G protein γ subunit, negatively regulates sorghum glume coverage and the naturally truncated alleles can be useful in the naked grain breeding.
- Peng Xie
- , Sanyuan Tang
- & Qi Xie
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Article
| Open AccessThe barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics
The genes underlying stripe rust host specificity between wheat and barley remain unknown. Here, the authors report that Rps6, Rps7 and Rps8 determine host species specificity in barley at different stages of the pathogen lifecycle and the barley powdery mildew immune receptor Mla8 and Rps7 are the same gene.
- Jan Bettgenhaeuser
- , Inmaculada Hernández-Pinzón
- & Matthew J. Moscou
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Article
| Open AccessInteraction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes
The all-flesh type of tomato fruits is caused by mutation of the MBP3 gene, however, knocking down MBP3 in certain genotypes also affect plant and fruit development. Here, the authors show that a natural mutation of AGL11, a close homolog of MBP3, is responsible for the phenotypic divergence.
- Baowen Huang
- , Guojian Hu
- & Mondher Bouzayen
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Article
| Open AccessA giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean
While multiple resistance-to-Phytophthora sojae loci/alleles have been mapped in soybean, many of them have become ineffective to newly evolved isolates. Here, the authors show that a 27.7-kb nucleotide-binding site-leucine-rich repeat gene confers broad-spectrum resistance to P. sojae in soybean.
- Weidong Wang
- , Liyang Chen
- & Jianxin Ma
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Article
| Open AccessAn ethylene biosynthesis enzyme controls quantitative variation in maize ear length and kernel yield
Considerable genetic variation exists in maize ear size and kernel number. Here the authors show that variation in a gene encoding an ethylene biosynthetic enzyme impacts ear length, flower fertility and kernel yield suggesting an important role for ethylene signaling during inflorescence development.
- Qiang Ning
- , Yinan Jian
- & Zuxin Zhang
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Article
| Open AccessA nonS-locus F-box gene breaks self-incompatibility in diploid potatoes
Diploid potatoes are typically self-incompatible, complicating efforts to breed diploid cultivars. Here the authors report map-based cloning of the S-locus inhibitor (Sli) gene in potato which encodes a non S-locus F-box protein that is expressed in pollen and can functions like a general S-RNase inhibitor to overcome self-incompatibility.
- Ling Ma
- , Chunzhi Zhang
- & Yi Shang
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Article
| Open AccessNeofunctionalisation of the Sli gene leads to self-compatibility and facilitates precision breeding in potato
The S-locus inhibitor (Sli) gene could allow potato breeding by facilitating production of diploid inbred lines. Here the authors show that Sli encodes an F-box protein with a promoter insertion enhancing expression in pollen can overcome pollen rejection in the styles of diploid potato.
- Ernst-Jan Eggers
- , Ate van der Burgt
- & Pim Lindhout
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Article
| Open AccessGenome assembly and population genomic analysis provide insights into the evolution of modern sweet corn
Sweet corn is one of the most important vegetables in North America and has undergone different selection pressures than non-sweet cultivars. Here, the authors report its genome assembly and reveal the evolutionary history of modern sweet corn through population genomic analyses.
- Ying Hu
- , Vincent Colantonio
- & Marcio F. R. Resende Jr.
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Article
| Open AccessAnnual aboveground carbon uptake enhancements from assisted gene flow in boreal black spruce forests are not long-lasting
The long-term effectiveness of assisted gene flow of trees could be jeopardised by rapid climate change. Here the authors analyse a large dataset of relocated black spruce populations in Canada, finding that local adaptation to climate of origin improved NPP responses, but only for up to ~15 years after planting.
- Martin P. Girardin
- , Nathalie Isabel
- & Patrick Lenz
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Article
| Open AccessGenome-wide association studies provide insights into the genetic determination of fruit traits of pear
Studies of fruit quality traits in pears are lagging behind the other major fruit trees. Here, the authors conduct GWAS of fruit quality and phenological traits in a panel of 312 sand pear accessions using SNPs called from resequencing data, and reveal the involvement of a lignin formation-related protein in regulating stone cell development.
- Ming-Yue Zhang
- , Cheng Xue
- & Jun Wu
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Article
| Open AccessThe genetic basis of cytoplasmic male sterility and fertility restoration in wheat
The development of hybrid wheat cultivars is hampered by the lack of an effective way to control male fertility in breeding lines. Here, the authors report the identification of two restorer-of-fertility genes Rf1 and Rf3 that can restore fertility of wheat plants carrying Triticum timopheevii-type cytoplasmic male sterility.
- Joanna Melonek
- , Jorge Duarte
- & Ian Small
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Article
| Open AccessPh2 encodes the mismatch repair protein MSH7-3D that inhibits wheat homoeologous recombination
In the allohexaploid genome of wheat, meiotic recombination between homoeologues is suppressed through the action of several loci. Here, the authors report the cloning of the long sought-after gene Ph2 and show its function in reduction of homoeologous recombination.
- Heïdi Serra
- , Radim Svačina
- & Pierre Sourdille
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Article
| Open AccessA wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch
Septoria tritici blotch (STB) is a devastating foliar disease affecting worldwide wheat production. Here, the authors report a cysteine-rich receptor-like kinase that can confer resistance to Zymoseptoria tritici, the pathogen that causes STB, and slow penetration and intercellular growth of the pathogen.
- Cyrille Saintenac
- , Florence Cambon
- & Thierry Langin
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Article
| Open AccessFIS1 encodes a GA2-oxidase that regulates fruit firmness in tomato
Fruit firmness is an important target for breeders and a key determinant of shelf life for many fruits. Here the authors show that mutating tomato FIS1, a GA2-oxidase, increases the concentration of bioactive gibberellins, enhances cutin and wax biosynthesis and increases fruit firmness.
- Ren Li
- , Shuai Sun
- & Xia Cui
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Article
| Open AccessCarotenoids modulate kernel texture in maize by influencing amyloplast envelope integrity
Very little is known about how vitreous endosperm in the mature maize kernel is created. Here, via map-based cloning, the authors find that mutation of a β-carotene hydroxylase 3 encoding gene Ven1 affects carotenoids and lipids composition, which consequently influences amyloplast envelope integrity.
- Haihai Wang
- , Yongcai Huang
- & Yongrui Wu
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Article
| Open AccessChromosome-level genome assembly of a parent species of widely cultivated azaleas
Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.
- Fu-Sheng Yang
- , Shuai Nie
- & Jian-Feng Mao
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Article
| Open AccessDiscovery of beneficial haplotypes for complex traits in maize landraces
Genetic variations present in landraces are critical for crop genetic improvement. Here, the authors map haplotype-trait associations in ~1000 doubled haploid lines derived from three European maize landraces and identify beneficial haplotypes for quantitative traits that are not present in breeding lines.
- Manfred Mayer
- , Armin C. Hölker
- & Chris-Carolin Schön
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Article
| Open AccessDiversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints
Genebanks hold comprehensive collections of wild species, wild relatives, and landraces that are useful for genetic improvement. Here, the authors report the genotype of nearly 80,000 wheat accessions using DArTseq technology to show the less explored genetic diversity.
- Carolina Sansaloni
- , Jorge Franco
- & Kevin Pixley
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Article
| Open AccessFonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate
Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.
- Michael Abrouk
- , Hanin Ibrahim Ahmed
- & Simon G. Krattinger
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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 AccessUDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice
Increasing grain yield needs to be put in the context of environmental stress. Here, the authors reveal that a UDP-glucosyltransferase is associated with regulation of rice grain size, abiotic stress tolerance, flavonoid-mediated auxin signaling, and redirection of carbon flux to flavonoid glycosides synthesis.
- Nai-Qian Dong
- , Yuwei Sun
- & Hong-Xuan Lin
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Article
| Open AccessMarker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9
Existing examples of targeted gene insertion in plants either rely on a selectable marker gene or result in short DNA inserts. Here, the authors use an optimized CRISPR-Cas9 method to insert a 5.2 kb carotenoid biosynthesis cassette into genomic safe harbors in rice, and obtain marker-free lines with high carotenoid content.
- Oliver Xiaoou Dong
- , Shu Yu
- & Pamela C. Ronald
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Article
| Open AccessA serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 regulates maize grain yield
Selection of kernel number per ear has improved maize yield, but the genetic base is unclear. Here, the authors reveal that a serine/threonine protein kinase KNR6 is a positive regulator of the trait and show in vitro evidences that KNR6 may function through phosphorylating an Arf GTPase-activating protein.
- Haitao Jia
- , Manfei Li
- & Zuxin Zhang
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Article
| Open AccessNeo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice
A transposon insertion in the regulatory region of maize Tb1 gene leads to increased apical dominance and a reduction of tillering. Here, the authors showed that a duplicated rice Tb1 orthologue, OsTb2, has gained a regulatory effect on tillering opposite that of OsTb1 during artificial selection only in upland japonica rice.
- Jun Lyu
- , Liyu Huang
- & Fengyi Hu
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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 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 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 AccessGenome-wide associated study identifies NAC42-activated nitrate transporter conferring high nitrogen use efficiency in rice
Improving crop nitrogen use efficiency can facilitate sustainable production, however, the genetic mechanisms have not been fully revealed. Here, the authors discover the NAC42-NPF6.1 signaling cascade mainly derives from indica and wild rice and demonstrate the potential of using the allele for cultivar improvement.
- Weijie Tang
- , Jian Ye
- & Jianmin Wan
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Article
| Open AccessDissecting a heterotic gene through GradedPool-Seq mapping informs a rice-improvement strategy
Developing hybrid rice cultivars requires time consuming random crossing. Here, the authors develop a new next generation sequencing-based quantitative trait locus mapping method to dissect heterotic gene OsMADS1 and demonstrate the feasibility of pyramiding two genes to achieve large heterotic effect.
- Changsheng Wang
- , Shican Tang
- & Bin Han
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Article
| Open AccessVariation of a major facilitator superfamily gene contributes to differential cadmium accumulation between rice subspecies
Grain of indica rice accumulates more toxic cadmium (Cd) than japonica, but the underlying genetic basis is unclear. Here, the authors show that natural variation of OsCd1 contributes to divergence in grain Cd accumulation and transferring japonica allele to indica rice leads to reduced Cd accumulation.
- Huili Yan
- , Wenxiu Xu
- & Zhenyan He
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Article
| Open AccessMeta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor
Flavor is one of the most important traits for improving tomato sensory quality and consumer acceptability. Here, the authors report meta-analysis of genome-wide association studies of flavor related traits and show genetic insights into the influence of human selection during domestication and improvement.
- Jiantao Zhao
- , Christopher Sauvage
- & Mathilde Causse
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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 AccessHyperacidification of Citrus fruits by a vacuolar proton-pumping P-ATPase complex
The sour taste of citrus fruit results from the extremely low pH of juice vesicle cell vacuoles. Here the authors provide genetic evidence that a vacuolar P-type ATPase, that is known to determine flower color in petunia via vacuolar acidification, is also responsible for extreme acidification in citrus.
- Pamela Strazzer
- , Cornelis E. Spelt
- & Francesca M. Quattrocchio
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Article
| Open AccessSingle gametophyte sequencing reveals that crossover events differ between sexes in maize
Meiotic crossover (CO) landscape differs inter- and intra-species, as well as between sexes. Here, the authors show that male meiosis produces more COs than female in maize and detect CO maturation inefficiency in some genetic backgrounds, which may help to improve breeding efficiency.
- Cheng Luo
- , Xiang Li
- & Jianbing Yan
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Article
| Open AccessGenome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement
Sweetpotato is an important food security crop providing rich source of macro- and micronutrients including carbohydrates and vitamins. Here, the authors assemble of the two diploid relatives of cultivated sweetpotato and identify genes and alleles associated with carotenoid biosynthesis from breeding lines.
- Shan Wu
- , Kin H. Lau
- & Zhangjun Fei
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Article
| Open AccessDeletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice
Plant architecture transition is one of the great consequences during rice domestication. Here, the authors find that chromosomal deletions linked to the previously known PROG1 gene also participate in plant architecture domestication in both Asian and African cultivated rice.
- Yongzhen Wu
- , Shuangshuang Zhao
- & Lubin Tan
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Article
| Open AccessCloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family
Yellow rust fungus severely limits global wheat production and breeding of durable resistance is challenging. Here Klymiuk et al. isolate the broad-spectrum Yr15 resistance gene from wild emmer wheat and show that it is a member of a distinct tandem kinase-pseudokinase family of plant proteins.
- Valentina Klymiuk
- , Elitsur Yaniv
- & Tzion Fahima
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Article
| Open AccessA PECTIN METHYLESTERASE gene at the maize Ga1 locus confers male function in unilateral cross-incompatibility
Unilateral cross-incompatibility between certain varieties of maize prevents cross-fertilization and can facilitate hybrid breeding. Here the authors show that a PECTIN METHYLESTERASE gene is able to overcome this reproductive barrier and confer fertility when expressed in pollen of the male parent.
- Zhaogui Zhang
- , Baocai Zhang
- & Huabang Chen
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Article
| Open AccessOverexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice
The effect of long noncoding RNAs (lncRNAs) on crop yield is unknown. Here, the authors show overexpression of a lncRNA, transcribed from the antisense strand of the previously discovered gene cluster LRK, can upregulate LRK genes’ expression, change histone modification status of LRK1, and increase rice grain yield.
- Ying Wang
- , Xiaojin Luo
- & Jinshui Yang
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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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Article
| 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 AccessEcology and genomics of an important crop wild relative as a prelude to agricultural innovation
Domestication reduces genetic diversity and constrains crop improvement. Here the authors identify factors that shaped species diversity in the wild progenitors of chickpea, and produce wild introgression populations that increase diversity for breeding by ~100-fold, including traits of agronomic relevance.
- Eric J.B. von Wettberg
- , Peter L. Chang
- & Douglas R. Cook
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Article
| Open AccessDeficiency of a triterpene pathway results in humidity-sensitive genic male sterility in rice
In flowering plants, the pollen coat surrounds the male germ cells and protects against dehydration, damage and pathogen attack. Here, the authors show that a deficiency in terpenoid synthesis results in rice pollen over-dehydration and leads to a humidity-sensitive conditional male sterile phenotype.
- Zheyong Xue
- , Xia Xu
- & Xiaoquan Qi