|
|
|
题名
|
作者
|
年代
|
出处
|
被引量
|
| 1 | Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement显示文摘Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut. | Xiaoping Chen Qing Lu Hao Liu Jianan Zhang Yanbin Hong Haofa Lan Haifen Li Jinpeng Wang Haiyan Liu Shaoxiong Li Manish K.Pandey Zhikang Zhang Guiyuan Zhou Jigao Yu Guoqiang Zhang Jiaqing Yuan Xingyu Li Shijie Wen Fanbo Meng Shanlin Yu Xiyin Wang Kadambot H.M.Siddique Zhong-Jian Liu Andrew H.Paterson Rajeev K.Varshney Xuanqiang Liang | 2019 | Molecular Plant2019，12，7： | 23 |
| 2 | Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction显示文摘The first paradigm of plant breeding involves direct selection-based phenotypic observation,followed by predictive breeding using statistical models for quantitative traits constructed based on genetic experimental design and,more recently,by incorporation of molecular marker genotypes.However,plant performance or phenotype(P)is determined by the combined effects of genotype(G),envirotype(E),and genotype by environment interaction(GEI).Phenotypes can be predicted more precisely by training a model using data collected from multiple sources,including spatiotemporal omics(genomics,phenomics,and enviromics across time and space).Integration of 3D information profiles(G-P-E),each with multidimensionality,provides predictive breeding with both tremendous opportunities and great challenges.Here,we first review innovative technologies for predictive breeding.We then evaluate multidimensional information profiles that can be integrated with a predictive breeding strategy,particularly envirotypic data,which have largely been neglected in data collection and are nearly untouched in model construction.We propose a smart breeding scheme,integrated genomic-enviromic prediction(iGEP),as an extension of genomic prediction,using integrated multiomics information,big data technology,and artificial intelligence(mainly focused on machine and deep learning).We discuss how to implement iGEP,including spatiotemporal models,environmental indices,factorial and spatiotemporal structure of plant breeding data,and cross-species prediction.A strategy is then proposed for prediction-based crop redesign at both the macro(individual,population,and species)and micro(gene,metabolism,and network)scales.Finally,we provide perspectives on translating smart breeding into genetic gain through integrative breeding platforms and open-source breeding initiatives.We call for coordinated efforts in smart breeding through iGEP,institutional partnerships,and innovative technological support. | Yunbi Xu Xingping Zhang Huihui Li Hongjian Zheng Jianan Zhang Michael S.Olsen Rajeev K.Varshney Boddupalli M.Prasanna Qian Qian | 2022 | Molecular Plant2022，15，11： | 7 |
| 3 | Fast integration and accumulation of beneficial breeding alleles through an AB–NAMIC strategy in wheat显示文摘Wheat(Triticum aestivum)is among the most important staple crops for safeguarding the food security of the growing world population.To bridge the gap between genebank diversity and breeding programs,we developed an advanced backcross-nested association mapping plus inter-crossed population(AB-NAMIC)by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core collection.Selective backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB-NAMIC population.We performed phenotyping of 590 AB-NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660K SNP array.Genome-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in AB-NAMIC.Notably,genome-wide association studies in AB-NAMIC detected the candidate gene TaSWEET6-7B(TraesCS7B03G1216700),which has high homology to the rice SWEET6b gene and exerts strong effects on adaptation and yield traits.The commercial release of two derived AB-NAMIC lines attests to its direct applicability in wheat improvement.Valuable information on genome-wide association studymapping,candidate genes,and their haplotypes for breeding traits are available through WheatGAB.Our research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks. | Chengzhi Jiao Chenyang Hao Tian Li Abhishek Bohra Lanfen Wang Jian Hou Hongxia Liu Hong Liu Jing Zhao Yamei Wang Yunchuan Liu Zhiwei Wang Xin Jing Xiue Wang Rajeev K.Varshney Junjie Fu Xueyong Zhang | 2023 | Plant Communications2023，4，3： | 3 |
| 4 | Diversification of primary gene pool through introgression of resistance to foliar diseases from synthetic amphidiploids to cultivated groundnut(Arachis hypogaea L.)显示文摘Groundnut(Arachis hypogaea L.)is widely grown and consumed around the world and is considered to have originated from a single hybridization event between two wild diploids.The utilization of wild germplasm in breeding programs has been restricted by reproductive barriers between wild and cultivated species and technical difficulties in making large numbers of crosses.Efforts to overcome these hurdles have resulted in the development of synthetic amphidiploids,namely ISATGR 278-18(Arachis duranesis×Arachis batizocoi)and ISATGR 5B(Arachis magna×A.batizocoi),which possess several desirable traits,including resistance to foliar diseases that generally cause huge yield losses annually in groundnut growing areas of Asia,America,and Africa.With an objective to improve foliar disease resistance,the primary gene pool was diversified by introgressing foliar disease resistance in five cultivated genotypes(ICGV 91114,ICGS 76,ICGV 91278,JL 24,and DH 86)from synthetic amphidiploids using a backcross breeding approach.Several introgression lines with resistance to two foliar diseases(rust and late leaf spot)were identified with levels of resistance equal to the donors.These backcross derived lines have shown a wide range of variation for several morphological and agronomic traits.These lines,after further evaluation and selection,can serve as donors in future breeding programs aimed atdeveloping improved cultivars with desirable agronomic traits,high resilience to biotic/abiotic stresses and a broadened genetic base. | Varsha Kumari M.V.C.Gowda Vinod Tasiwal Manish K.Pandey Ramesh S.Bhat Nalini Mallikarjuna Hari D.Upadhyaya Rajeev K.Varshney | 2014 | The Crop Journal2014，2，Z1： | 3 |
| 5 | Resistance to Aspergillus flavus in maize and peanut:Molecular biology, breeding, environmental stress,and future perspectives显示文摘The colonization of maize(Zea mays L.) and peanut(Arachis hypogaea L.) by the fungal pathogen Aspergillus flavus results in the contamination of kernels with carcinogenic mycotoxins known as aflatoxins leading to economic losses and potential health threats to humans. The regulation of aflatoxin biosynthesis in various Aspergillus spp. has been extensively studied, and has been shown to be related to oxidative stress responses. Given that environmental stresses such as drought and heat stress result in the accumulation of reactive oxygen species(ROS) within host plant tissues, host-derived ROS may play an important role in cross-kingdom communication between host plants and A. flavus. Recent technological advances in plant breeding have provided the tools necessary to study and apply knowledge derived from metabolomic, proteomic, and transcriptomic studies in the context of productive breeding populations. Here, we review the current understanding of the potential roles of environmental stress, ROS, and aflatoxin in the interaction between A.flavus and its host plants, and the current status in molecular breeding and marker discovery for resistance to A. flavus colonization and aflatoxin contamination in maize and peanut. We will also propose future directions and a working model for continuing research efforts linking environmental stress tolerance and aflatoxin contamination resistance in maize and peanut. | Jake C.Fountain Pawan Khera Liming Yang Spurthi N.Nayak Brian T.Scully Robert D.Lee Zhi-Yuan Chen Robert C.Kemerait Rajeev K.Varshney Baozhu Guo | 2015 | The Crop Journal2015，3，3： | 3 |
| 6 | Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China,India and the US using simple sequence repeat markers显示文摘Cultivated peanut is grown worldwide as richsource of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat(SSR)markers and to assess the genetic diversity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content(PIC) were 0.480 and 0.429, respectively.Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US,China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations(P_1, P_2), which was consistent with the dendrogram based on genetic distance(G_1, G_2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies. | Hui Wang Pawan Khera Bingyan.Huang Mei Yuan Ramesh Katam Weijian Zhuang Karen Harris-Shultz Kim M.Moore Albert K.Culbreath Xinyou Zhang Rajeev K.Varshney Lianhui Xie Baozhu Guo | 2016 | Journal of Integrative Plant Biology2016，58，5： | 2 |
| 7 | Molecular markers and their applications in wheat breeding显示文摘 | P. K.Gupta R. K.Varshney P. C.Sharma B.Ramesh | 2008 | Plant Breeding2008，，5： | 1 |
| 8 | Back to wild relatives for future breeding through super-pangenome显示文摘Crop wild relatives(CWRs)deliver untapped genetic diversity,as they contain valuable breeding traits absent in the cultivated pool,e.g.,traits imparting climate resilience.Facilitating genetic material from CWRs to breeding programs can advance effective traits and broaden the genetic base of cultivated crops(Bohra et al.,2022).The availability of genetic diversity in crop breeding programs is important for accelerating crop production while safeguarding food safety and agricultural sustainability.Crop domestication and artificial selection have paved the way for crop cultivars tailored to evolving human requirements and modern cultivation practices.However,domestication and breeding have significantly reduced genetic diversity in modern crops(Khan et al.,2020;Bohra et al.,2022).Owing to the extensive genetic and phenotypic variability,CWRs serve as valuable genetic reservoirs for crop improvement(Bohra et al.,2022;Li et al.,2023).The use of CWRs in breeding programs is not that straightforward,as linkage drags often remain difficult to overcome. | Ali Raza Abhishek Bohra Vanika Garg Rajeev K.Varshney | 2023 | Molecular Plant2023，16，9： | 0 |
| 9 | Trehalose:A sugar molecule involved in temperature stress management in plants显示文摘Trehalose(Tre)is a non-reducing disaccharide found in many species,including bacteria,fungi,invertebrates,yeast,and even plants,where it acts as an osmoprotectant,energy source,or protein/membrane protector.Despite relatively small amounts in plants,Tre concentrations increase following exposure to abiotic stressors.Trehalose-6-phosphate,a precursor of Tre,has regulatory functions in sugar metabolism,crop production,and stress tolerance.Among the various abiotic stresses,temperature extremes(heat or cold stress)are anticipated to impact crop production worldwide due to ongoing climate changes.Applying small amounts of Tre can mitigate negative physiological,metabolic,and molecular responses triggered by temperature stress.Trehalose also interacts with other sugars,osmoprotectants,amino acids,and phytohormones to regulate metabolic reprogramming that underpins temperature stress adaptation.Transformed plants expressing Tre-synthesis genes accumulate Tre and show improved stress tolerance.Genome-wide studies of Tre-encoding genes suggest roles in plant growth,development,and stress tolerance.This review discusses the functions of Tre in mitigating temperature stress—highlighting genetic engineering approaches to modify Tre metabolism,crosstalk,and interactions with other molecules—and in-silico approaches for identifying novel Tre-encoding genes in diverse plant species.We consider how this knowledge can be used to develop temperature-resilient crops essential for sustainable agriculture. | Ali Raza Savita Bhardwaj Md Atikur Rahman Pedro García-Caparrós Madiha Habib Faisal Saeed Sidra Charagh Christine H.Foyer Kadambot H.M.Siddique Rajeev K.Varshney | 2024 | The Crop Journal2024，12，1： | 0 |
| 10 | Improvement of three popular Indian groundnut varieties for foliar disease resistance and high oleic acid using SSR markers and SNP array in marker-assisted backcrossing显示文摘Foliar fungal diseases(rust and late leaf spot)incur large yield losses,in addition to the deterioration of fodder quality in groundnut worldwide.High oleic acid has emerged as a key market trait in groundnut,as it increases the shelf life of the produce/products in addition to providing health benefits to consumers.Marker-assisted backcrossing(MABC)is the most successful approach to introgressing or pyramiding one or more traits using traitlinked markers.We used MABC to improve three popular Indian cultivars(GJG 9,GG 20,and GJGHPS 1)for foliar disease resistance(FDR)and high oleic acid content.A total of 22 BC3F4 and 30 BC2F4 introgression lines(ILs)for FDR and 46 BC3F4 and 41 BC2F4 ILs for high oleic acid were developed.Recurrent parent genome analysis using the 58 K Axiom_Arachis array identified several lines showing upto 94%of genome recovery among second and third backcross progenies.Phenotyping of these ILs revealed FDR scores comparable to the resistant parent,GPBD 4,and ILs with high(~80%)oleic acid in addition to high genome recovery.These ILs provide further opportunities for pyramiding FDR and high oleic acid in all three genetic backgrounds as well as for conducting multi-location yield trials for further evaluation and release for cultivation in target regions of India. | Yaduru Shasidhar Murali T.Variath Manish K.Vishwakarma Surendra S.Manohar Sunil S.Gangurde Manda Sriswathi Hari Kishan Sudini Keshavji L.Dobariya Sandip K.Bera Thankappan Radhakrishnan Manish K.Pandey Pasupuleti Janila Rajeev K.Varshney | 2020 | The Crop Journal2020，8，1： | 0 |
| 11 | Transcriptome analysis of chickpea during heat stress unveils the signatures of long intergenic non-coding RNAs (lincRNAs) and mRNAs in the heat-QTL region显示文摘In plants, besides the role of messenger RNAs (mRNAs) in gene expression, long intergenic non-coding RNAs(lincRNAs) play a key role in regulating various biological processes. Chickpea (Cicer arietinum L.), an importantlegume crop, is sensitive to extreme temperature regimes. Here, we identified the lincRNAs and mRNAs in threechickpea genotypes contrasting for heat stress response (two tolerant- ICC 1356, ICC 15614;one sensitive- ICC4567) and investigated their role in heat stress. A total of 894 putative lincRNAs and 61,110 mRNAs wereidentified from leaf and root tissues at the vegetative and reproductive stages of the plant under control and heatstress conditions. Co-expression studies revealed the significant association of lincRNAs with mRNAs which areattributed to heat stress leaf samples at the reproductive stage. Further, mRNAs encoding heat shock transcriptionfactors (HSFs), heat shock proteins (HSPs), starch, and sucrose metabolism pathway genes played an essential rolein mitigating heat stress. Furthermore, three key lincRNAs underlying chickpea's heat-quantitative trait locus(QTL) region were identified. This study provided new insights into the regulation of heat stress tolerance inchickpea by identifying candidate lincRNAs and mRNAs. | Sailaja Bhogireddy Himabindu Kudapa Prasad Bajaj Vanika Garg Annapurna Chitikineni Sourav Nayak Rajeev K.Varshney | 2023 | Crop Design2023，2，1： | 0 |
| 12 | Abiotic stress tolerance:Genetics,genomics,and breeding显示文摘1.Tenth anniversary of The Crop Journal The Crop Journal will be 10 years old in October 2023.The journal is sponsored by the Crop Science Society of China,the Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,and China Science Publishing&Media Group Ltd.(Science Press).It is published by Science Press and Ke Ai (founded by China Science Publishing&Media Ltd.and Elsevier). | Yunbi Xu Feng Qin Chengcai Chu Rajeev K.Varshney | 2023 | The Crop Journal2023，11，4： | 0 |
您所在的机构暂未开通此部分的功能，请联系管理员