87 results on '"Paterson, A.H."'
Search Results
2. Characterization of tissue tolerance to iron by molecular markers in different lines of rice
- Author
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Wu, P., Hu, B., Liao, C.Y., Zhu, J.M., Wu, Y.R., Senadhira, D., and Paterson, A.H.
- Published
- 1998
Catalog
3. A framework linkage map of bermudagrass (Cynodon dactylon × transvaalensis) based on single-dose restriction fragments
- Author
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Bethel, C.M., Sciara, E.B., Estill, J.C., Bowers, J.E., Hanna, W., and Paterson, A.H.
- Published
- 2006
- Full Text
- View/download PDF
4. A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops (1)([W])
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Feltus, F.A., Singh, H.P., Lohithaswa, H.C., Schulze, S.R., Silva, T.D., and Paterson, A.H.
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Medicinal plants -- Genetic aspects ,Medicinal plants -- Physiological aspects ,Genetic polymorphisms -- Research ,Nucleotide sequencing -- Research ,Biological sciences ,Science and technology - Published
- 2006
5. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
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Paterson, A.H., Bowers, J.E., and Chapman, B.A.
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Grain -- Research ,Genomes -- Research ,Science and technology - Abstract
Integration of structural genomic data from a largely assembled rice genome sequence, with phylogenetic analysis of sequence samples for many other taxa, suggests that a polyploidization event occurred [approximately equal to] 70 million years ago, before the divergence of the major cereals from one another but after the divergence of the Poales from the Liliales and Zingiberales. Ancient polyploidization and subsequent 'diploidization' (loss) of many duplicated gene copies has thus shaped the genomes of all Poaceae cereal, forage, and biomass crops. The Poaceae appear to have evolved as separate lineages for [approximately equal to] 50 million years, or two-thirds of the time since the duplication event. Chromosomes that are predicted to be homoeologs resulting from this ancient duplication event account for a disproportionate share of incongruent loci found by comparison of the rice sequence to a detailed sorghum sequence-tagged site-based genetic map. Differential gene loss during diploidization may have contributed many of these incongruities. Such predicted homoeologs also account for a disproportionate share of duplicated sorghum loci, further supporting the hypothesis that the polyploidization event was common to sorghum and rice. Comparative gene orders along paleo-homoeologous chromosomal segments provide a means to make phylogenetic inferences about chromosome structural rearrangements that differentiate among the grasses. Superimposition of the timing of major duplication events on taxonomic relationships leads to improved understanding of comparative gene orders, enhancing the value of data from botanical models for crop improvement and for further exploration of genomic biodiversity. Additional ancient duplication events probably remain to be discovered in other angiosperm lineages. colinearity | chromosome structural rearrangement | gene order | genome duplication | rice more...
- Published
- 2004
6. Convergent evolution of perenniality in rice and sorghum
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Hu, F.Y., Tao, D.Y., Sacks, E., Fu, B.Y., Xu, P., Li, J., Yang, Y., McNally, K., Khush, G.S., Paterson, A.H., and Li, Z.-K.
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Perennials -- Genetic aspects ,Rice ,Sorghum -- Genetic aspects ,Science and technology - Abstract
Annual and perennial habit are two major strategies by which grasses adapt to seasonal environmental change, and these distinguish cultivated cereals from their wild relatives. Rhizomatousness, a key trait contributing to perenniality, was investigated by using an [F.sub.2] population from a cross between cultivated rice (Oryza sativa) and its wild relative, Oryza longistaminata. Molecular mapping based on a complete simple sequence-repeat map revealed two dominant-complementary genes controlling rhizomatousness. Rhz3 was mapped to the interval between markers OSR16 [1.3 centimorgans (cM)] and OSR13 (8.1 cM) on rice chromosome 4 and Rhz2 located between RM119 (2.2 cM) and RM273 (7.4 cM) on chromosome 3. Comparative mapping indicated that each gene closely corresponds to major quantitative trait loci (QTLs) controlling rhizomatousness in Sorghum propinquum, a wild relative of cultivated sorghum. Correspondence of these genes in rice and sorghum, which diverged from a common ancestor [approximately equal to] 50 million years ago, suggests that the two genes may be key regulators of rhizome development in many Poaceae. Many additional QTLs affecting abundance of rhizomes in O. longistaminata were identified, most of which also corresponded to the locations of S. propinquum QTLs. Convergent evolution of independent mutations at, in some cases, corresponding genes may have been responsible for the evolution of annual cereals from perennial wild grasses. DNA markers closely linked to Rhz2 and Rhz3 will facilitate cloning of the genes, which may contribute significantly to our understanding of grass evolution, advance opportunities to develop perennial cereals, and offer insights into environmentally benign weed-control strategies. more...
- Published
- 2003
7. Development of genomic resources for cotton (Gossypium hirsutum L.): BAC library construction, preliminary STC analysis, and identification of clones associated with fiber development
- Author
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Tomkins, J.P., Peterson, D.G., Yang, T.J., Main, D., Wilkins, T.A., Paterson, A.H., and Wing, R.A.
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- 2001
- Full Text
- View/download PDF
8. Disomic inheritance, suppressed recombination, and allelic interactions govern apospory in buffelgrass as revealed by genome mapping. (Cell Biology & Molecular Genetics)
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Jessup, R.W., Burson, B.L., Burow, G.B., Wang, Y.-W., Chang, C., Li, Z., Paterson, A.H., and Hussey, M.A.
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Plant genetics -- Research -- Analysis -- Genetic aspects ,Reproduction, Asexual -- Genetic aspects -- Analysis -- Research ,Cytogenetics -- Research -- Analysis -- Genetic aspects ,Genomes -- Analysis -- Genetic aspects -- Research ,Plants -- Reproduction ,Cenchrus ciliaris -- Research -- Genetic aspects -- Analysis ,Genetic recombination -- Analysis -- Genetic aspects -- Research ,Agricultural industry ,Business - Abstract
Molecular tools have not identified the gene(s) governing apomixis nor have they been used to successfully transfer the trait to important, sexually reproducing food crops. Several molecular studies addressing apomixis in grasses have used interspecific and intergeneric hybrids. The failure to recover specific [F.sub.1] genotypes from these wide crosses can be caused by unfavorable interactions between the gametes, zygote, embryo, endosperm, and/or maternal tissue. These interactions can eliminate recombinant genotypes with valuable information towards linkage analyses of the trait. Buffelgrass [Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.], a polymorphic species with interfertile apomictic and sexual genotypes, offers an opportunity to genetically map apomixis by means of intraspecific hybrids with eupioid genomes. This study reports a linkage map of the apospory region in buffelgrass. Apospory, classified by progeny testing and cytologically observing megagametophytes, mapped to a single locus in the apomictic parent's genome. Two buffelgrass cDNAs (pPAP3A07 and pPAPSC08) and three previously reported apospory markers (UGT197, QH8, and OPC4) were tightly linked (1.4 centimorgans, cM) to the trait. As a tetraploid species (2n = 4x = 36), four copies of each chromosome are expected in buffelgrass. A single homolog and two homeologs were identified for the chromosome carrying apospory, indicating the formation of two bivalents during meiosis and the disomic inheritance of apospory in buffelgrass. Allelic bridges between the parents revealed suppressed recombination in the apospory linkage group. Segregation distortion between a marker on the sexual parent's homolog to the apospory linkage group and a marker on a separate maternal linkage group suggested specific allelic combinations in female gametes affect offspring survival in buffelgrass., APOMIXIS, asexual plant reproduction through seeds, results from the parthenogenetic development of an unreduced egg cell into a viable embryo (Bashaw and Hanna, 1990). Because apomixis permits the clonal propagation [...] more...
- Published
- 2002
9. Paleopolyploidy and its Impact on the Structure and Function of Modern Plant Genomes
- Author
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Paterson, A.H., primary
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- 2008
- Full Text
- View/download PDF
10. Paleo-polyploidization in Lycophytes
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Wang, J. Yu, J. Sun, P. Li, C. Song, X. Lei, T. Li, Y. Yuan, J. Sun, S. Ding, H. Duan, X. Shen, S. Shen, Y. Li, J. Meng, F. Xie, Y. Wang, J. Hou, Y. Zhang, J. Zhang, X. Li, X.-Q. Paterson, A.H. Wang, X. more...
- Subjects
fungi ,food and beverages - Abstract
Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring approximately 13–15 million years ago (MYA) and another about 125–142 MYA, during the evolution of the genome of Selaginella moellendorffii, a model lycophyte. In addition, comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleo-polyploidization events than seed plants. Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants. © 2020 more...
- Published
- 2020
11. Molecular mapping of genes affecting pubescence of cotton
- Author
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Wright, R.J., Thaxton, P.M., El-Zik, K.M., and Paterson, A.H.
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Cotton -- Research ,Chromosome mapping -- Research ,Genotype -- Research ,Trichomes -- Research ,Biological sciences - Abstract
A study was conducted to analyze the molecular mapping of genes influencing the pubescence of cotton. Trichome density was quantified using a qualitative grading system and a quantitative measure of leaf trichome density. Results indicated that the frequency distributions of lear trichome counts correlated with the genetic control of the trait. Findings also showed that direct trichome counts were more sensitive than qualitative indices. more...
- Published
- 1999
12. Molecular breeding of groundnut for enhanced productivity and food security in the semi- arid tropics: opportunities and challenges
- Author
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Dwivedi, S.L, primary, Crouch, J.H, additional, Nigam, S.N, additional, Ferguson, M.E, additional, and Paterson, A.H, additional
- Published
- 2003
- Full Text
- View/download PDF
13. Plant-pathogen microevolution: molecular basis for the origin of a fungal disease in maize
- Author
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Multani, D.S., Meeley, R.B., Paterson, A.H., Gray, J., Briggs, S.P., and Johal, G.S.
- Subjects
Plant-pathogen relationships -- Research ,Fungal diseases of plants -- Research ,Corn -- Diseases and pests ,Science and technology - Abstract
A new and severe disease of maize caused by a previously unknown fungal pathogen, Cochliobolus carbonum race 1, was first described in 1938. The molecular events that led to the sudden appearance of this disease are described in this paper. Resistance to C. carbonum race 1 was found to be widespread in maize and is conferred by a pair of unlinked duplicate genes, Hm1 and Hm2. Here, we demonstrate that resistance is the wild-type condition in maize. Two events, a transposon insertion in Hm1 and a deletion in Hm2, led to the loss of resistance, resulting in the origin of a new disease. None of the other plant species tested is susceptible to C. carbonum race 1, and they all possess candidate genes with high homology to Hm1 and Hm2. In sorghum and rice, these homologs map to two chromosomal regions that are syntenic with the maize Hm1 and Hm2 loci, indicating that they are related to the maize genes by vertical descent. These results suggest that the Hm-encoded resistance is of ancient origin and probably is conserved in all grasses. more...
- Published
- 1998
14. The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales
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Song, X., Sun, P., Yuan, J., Gong, K., Li, N., Meng, F., Zhang, Z., Li, X., Hu, J., Wang, J., Yang, Q., Jiao, B., Nie, F., Liu, T., Chen, W., Feng, S., Pei, Q., Yu, T., Kang, X., Zhao, W., Cui, C., Yu, Y., Wu, T., Shan, L., Liu, M., Qin, Z., Lin, H., Varshney, R.K., Li, X‐Q, Paterson, A.H., Wang, X., Song, X., Sun, P., Yuan, J., Gong, K., Li, N., Meng, F., Zhang, Z., Li, X., Hu, J., Wang, J., Yang, Q., Jiao, B., Nie, F., Liu, T., Chen, W., Feng, S., Pei, Q., Yu, T., Kang, X., Zhao, W., Cui, C., Yu, Y., Wu, T., Shan, L., Liu, M., Qin, Z., Lin, H., Varshney, R.K., Li, X‐Q, Paterson, A.H., and Wang, X. more...
- Abstract
Celery (Apium graveolens L. 2n = 2x = 22), a member of the Apiaceae family, is among the most important and globally grown vegetables. Here, we report a high‐quality genome sequence assembly, anchored to 11 chromosomes, with total length of 3.33 Gb and N50 scaffold length of 289.78 Mb. Most (92.91%) of the genome is composed of repetitive sequences, with 62.12% of 31 326 annotated genes confined to the terminal 20% of chromosomes. Simultaneous bursts of shared long‐terminal repeats (LTRs) in different Apiaceae plants suggest inter‐specific exchanges. Two ancestral polyploidizations were inferred, one shared by Apiales taxa and the other confined to Apiaceae. We reconstructed 8 Apiales proto‐chromosomes, inferring their evolutionary trajectories from the eudicot common ancestor to extant plants. Transcriptome sequencing in three tissues (roots, leaves and petioles), and varieties with different‐coloured petioles, revealed 4 and 2 key genes in pathways regulating anthocyanin and coumarin biosynthesis, respectively. A remarkable paucity of NBS disease‐resistant genes in celery (62) and other Apiales was explained by extensive loss and limited production of these genes during the last ~10 million years, raising questions about their biotic defence mechanisms and motivating research into effects of chemicals, for example coumarins, that give off distinctive odours. Celery genome sequencing and annotation facilitates further research into important gene functions and breeding, and comparative genomic analyses in Apiales. more...
- Published
- 2020
15. Reply to: Evaluating two different models of peanut’s origin
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Zhuang, W., Wang, X., Paterson, A.H., Chen, H., Yang, M., Zhang, C., Sun, P., Zheng, Y., Wang, L., Xie, W., Chu, W., Fu, H., Varshney, R.K., Zhuang, W., Wang, X., Paterson, A.H., Chen, H., Yang, M., Zhang, C., Sun, P., Zheng, Y., Wang, L., Xie, W., Chu, W., Fu, H., and Varshney, R.K. more...
- Published
- 2020
16. High density molecular linkage maps of the tomato and potato genomes
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Tanskley, S.D., Ganal, M.W., Prince, J.P., de Vicente, M.C., Bonierbale, M.W., Broun, P., Fulton, T.M., Giovannoni, J.J., Grandillo, S., Martin, G.B., Messeguer, R., Miller, J. C., Miller, L., Paterson, A.H., Pineda, O., Roder, M.S., Wing, R.A., Wu, W., and Young, N.D. more...
- Subjects
Linkage (Genetics) -- Research ,Chromosome mapping -- Research ,Tomatoes -- Genetic aspects ,Potatoes -- Genetic aspects ,Biological sciences - Abstract
High density molecular linkage maps describing tomato and potato genomes were constructed for analysis. The maps are composed of over 1000 markers possessing average spaces of 1.2cM (ca.900kb). Since the two maps were derived on a single probe set, breakpoints corresponding to 5 chromosomal inversions which would explain genome variation can be identified. The presence of such maps for tomato and potato provides bases for chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies involving the two crops. more...
- Published
- 1992
17. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication
- Author
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Zhuang, W., Chen, H., Yang, M., Wang, J., Pandey, M.K., Zhang, C., Chang, W-C, Zhang, L., Zhang, X., Tang, R., Garg, V., Wang, X., Tang, H., Chow, C-N, Deng, Y., Wang, D., Khan, A.W., Yang, Q., Cai, T., Bajaj, P., Wu, K., Guo, B., Li, J., Liang, F., Hu, J., Liao, B., Liu, S., Chitikineni, A., Yan, H., Zheng, Y., Shan, S., Liu, Q., Xie, D., Wang, Z., Khan, S.A., Ali, N., Zhao, C., Li, X., Luo, Z., Zhang, S., Zhuang, R., Peng, Z., Wang, S., Mamadou, G., Zhuang, Y., Zhao, Z., Yu, W., Xiong, F., Quan, W., Yuan, M., Li, Y., Zou, H., Xia, H., Zha, L., Fan, J., Yu, J., Xie, W., Yuan, J., Chen, K., Zhao, S., Chu, W., Chen, Y., Sun, P., Meng, F., Zhuo, T., Zhao, Y., Li, C., He, G., Wang, C., Kavikishor, P.B., Pan, R-L, Paterson, A.H., Ming, R., Varshney, R.K., Zhuang, W., Chen, H., Yang, M., Wang, J., Pandey, M.K., Zhang, C., Chang, W-C, Zhang, L., Zhang, X., Tang, R., Garg, V., Wang, X., Tang, H., Chow, C-N, Deng, Y., Wang, D., Khan, A.W., Yang, Q., Cai, T., Bajaj, P., Wu, K., Guo, B., Li, J., Liang, F., Hu, J., Liao, B., Liu, S., Chitikineni, A., Yan, H., Zheng, Y., Shan, S., Liu, Q., Xie, D., Wang, Z., Khan, S.A., Ali, N., Zhao, C., Li, X., Luo, Z., Zhang, S., Zhuang, R., Peng, Z., Wang, S., Mamadou, G., Zhuang, Y., Zhao, Z., Yu, W., Xiong, F., Quan, W., Yuan, M., Li, Y., Zou, H., Xia, H., Zha, L., Fan, J., Yu, J., Xie, W., Yuan, J., Chen, K., Zhao, S., Chu, W., Chen, Y., Sun, P., Meng, F., Zhuo, T., Zhao, Y., Li, C., He, G., Wang, C., Kavikishor, P.B., Pan, R-L, Paterson, A.H., Ming, R., and Varshney, R.K. more...
- Abstract
High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42–0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement. more...
- Published
- 2019
18. Sequencing of cultivated peanut, Arachis hypogaea, yields insights into genome evolution and oil improvement
- Author
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Chen, X., Lu, Q., Liu, H., Zhang, J., Hong, Y., Lan, H., Li, H., Wang, J., Li, S., Pandey, M.K., Zhang, Z., Zhou, G., Yu, J., Zhang, G., Yuan, J., Li, X., Wen, S., Meng, F., Yu, S., Wang, X., Siddique, K.H.M., Liu, Z-J, Paterson, A.H., Varshney, R.K., Liang, X., Chen, X., Lu, Q., Liu, H., Zhang, J., Hong, Y., Lan, H., Li, H., Wang, J., Li, S., Pandey, M.K., Zhang, Z., Zhou, G., Yu, J., Zhang, G., Yuan, J., Li, X., Wen, S., Meng, F., Yu, S., Wang, X., Siddique, K.H.M., Liu, Z-J, Paterson, A.H., Varshney, R.K., and Liang, X. more...
- Abstract
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. more...
- Published
- 2019
19. W527: The genome of Arachis hypogaea provide insight into the evolution and domestication
- Author
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Zhuang, W., Chen, H., Meng, Y., Wang, J., Pandey, M.K., Zhang, C., Yang, Q., Cai, T., Deng, Y., Paterson, A.H., Wang, X., Ming, R., Varshney, R.K., Zhuang, W., Chen, H., Meng, Y., Wang, J., Pandey, M.K., Zhang, C., Yang, Q., Cai, T., Deng, Y., Paterson, A.H., Wang, X., Ming, R., and Varshney, R.K. more...
- Published
- 2019
20. Erratum: Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
- Author
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Varshney, R.K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R.K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S.K., Wang, H., Jiang, Y., Couderc, M., Katta, M.A.V.S.K., Paudel, D.R., Mungra, K.D., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N.A., Conner, J.A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O.P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H.D., Cubry, P., Rhoné, B., Gueye, M.C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R.S., Singh, B., Yadav, R.S., Lyons, E., Datta, S.K., Hash, C.T., Devos, K.M., Buckler, E.S., Bennetzen, J.L., Paterson, A.H., Ozias-Akins, P., Grando, S., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., Xu, X., Varshney, R.K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R.K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S.K., Wang, H., Jiang, Y., Couderc, M., Katta, M.A.V.S.K., Paudel, D.R., Mungra, K.D., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N.A., Conner, J.A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O.P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H.D., Cubry, P., Rhoné, B., Gueye, M.C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R.S., Singh, B., Yadav, R.S., Lyons, E., Datta, S.K., Hash, C.T., Devos, K.M., Buckler, E.S., Bennetzen, J.L., Paterson, A.H., Ozias-Akins, P., Grando, S., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., and Xu, X. more...
- Abstract
In the version of this article initially published, in the HTML, the wrong Creative Commons Attribution license (cc-by-nc rather than cc-by) was inserted. The error has been corrected in the HTML version of the article more...
- Published
- 2018
21. Gene copy number evolution during tetraploid cotton radiation
- Author
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Rong, J., Feltus, F.A., Liu, L., Lin, L., and Paterson, A.H.
- Subjects
Polyploidy -- Research ,Evolution -- Research ,Nucleotide sequence -- Usage ,Biological sciences - Published
- 2010
22. Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids
- Author
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Buggs, R.J.A., Doust, A.N., Tate, J.A., Koh, J., Soltis, K., Feltus, F,A., Paterson, A.H., Soltis, P.S., and Soltis, D.E.
- Subjects
Compositae -- Genetic aspects ,Compositae -- Natural history ,Polyploidy -- Analysis ,Gene silencing -- Analysis ,Biological sciences - Published
- 2009
23. Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype
- Author
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Jang, C.S., Kamps, T.L., Tang, H., Bowers, J.E., Lemke, C., and Paterson, A.H.
- Subjects
Stems (Botany) -- Genetic aspects ,Plant genetics -- Research ,Sorghum -- Genetic aspects ,Evolutionary biology -- Research ,Biological sciences - Published
- 2009
24. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
- Author
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Varshney, R.K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R.K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S.K., Wang, H., Jiang, Y., Couderc, M., Katta, M.A.V.S.K., Paudel, D.R., Mungra, K.D., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N.A., Conner, J.A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O.P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H.D., Cubry, P., Rhoné, B., Gueye, M.C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R.S., Singh, B., Yadav, R.S., Lyons, E., Datta, S.K., Hash, C.T., Devos, K.M., Buckler, E., Bennetzen, J.L., Paterson, A.H., Ozias-Akins, P., Grando, S., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., Xu, X., Varshney, R.K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R.K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S.K., Wang, H., Jiang, Y., Couderc, M., Katta, M.A.V.S.K., Paudel, D.R., Mungra, K.D., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N.A., Conner, J.A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O.P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H.D., Cubry, P., Rhoné, B., Gueye, M.C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R.S., Singh, B., Yadav, R.S., Lyons, E., Datta, S.K., Hash, C.T., Devos, K.M., Buckler, E., Bennetzen, J.L., Paterson, A.H., Ozias-Akins, P., Grando, S., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., and Xu, X. more...
- Abstract
Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop. more...
- Published
- 2017
25. Genome alignment spanning major poaceae lineages reveals heterogeneous evolutionary rates and alters inferred dates for key evolutionary events
- Author
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Wang, X. Wang, J. Jin, D. Guo, H. Lee, T.-H. Liu, T. Paterson, A.H.
- Subjects
food and beverages - Abstract
Multiple comparisons among genomes can clarify their evolution, speciation, and functional innovations. To date, the genome sequences of eight grasses representing the most economically important Poaceae (grass) clades have been published, and their genomic-level comparison is an essential foundation for evolutionary, functional, and translational research. Using a formal and conservative approach, we aligned these genomes. Direct comparison of paralogous gene pairs all duplicated simultaneously reveal striking variation in evolutionary rates among whole genomes, with nucleotide substitution slowest in rice and up to 48% faster in other grasses, adding a new dimension to the value of rice as a grass model. We reconstructed ancestral genome contents for major evolutionary nodes, potentially contributing to understanding the divergence and speciation of grasses. Recent fossil evidence suggests revisions of the estimated dates of key evolutionary events, implying that the pan-grass polyploidization occurred ∼96 million years ago and could not be related to the Cretaceous-Tertiary mass extinction as previously inferred. Adjusted dating to reflect both updated fossil evidence and lineage-specific evolutionary rates suggested that maize subgenome divergence and maize-sorghum divergence were virtually simultaneous, a coincidence that would be explained if polyploidization directly contributed to speciation. This work lays a solid foundation for Poaceae translational genomics. © 2015 The Author. more...
- Published
- 2015
26. Global agricultural intensification during climate change: A role for genomics
- Author
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Abberton, M., Batley, J., Bentley, A., Bryant, J., Cai, H., Cockram, J., Costa de Oliveira, A., Cseke, L.J., Dempewolf, H., De Pace, C., Edwards, D., Gepts, P., Greenland, A., Hall, A.E., Henry, R., Hori, K., Howe, G.T., Hughes, S., Humphreys, M., Lightfoot, D., Marshall, A., Mayes, S., Nguyen, H.T., Ogbonnaya, F.C., Ortiz, R., Paterson, A.H., Tuberosa, R., Valliyodan, B., Varshney, R.K., Yano, M., Abberton, M., Batley, J., Bentley, A., Bryant, J., Cai, H., Cockram, J., Costa de Oliveira, A., Cseke, L.J., Dempewolf, H., De Pace, C., Edwards, D., Gepts, P., Greenland, A., Hall, A.E., Henry, R., Hori, K., Howe, G.T., Hughes, S., Humphreys, M., Lightfoot, D., Marshall, A., Mayes, S., Nguyen, H.T., Ogbonnaya, F.C., Ortiz, R., Paterson, A.H., Tuberosa, R., Valliyodan, B., Varshney, R.K., and Yano, M. more...
- Abstract
Agriculture is now facing the ‘perfect storm’ of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change. more...
- Published
- 2016
27. Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens
- Author
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Chen, X., Li, H., Pandey, M.K., Yang, Q., Wang, X., Garg, V., Chi, X., Doddamani, D., Hong, Y., Upadhyaya, H., Guo, H., Khan, A.W., Zhu, F., Zhang, X., Pan, L., Pierce, G.J., Zhou, G., Krishnamohan, K.A.V.S., Chen, M., Zhong, N., Agarwal, G., Li, S., Chitikineni, A., Zhang, G-Q, Sharma, S., Chen, N., Liu, H., Janila, P., Wang, M., Wang, T., Sun, J., Li, X., Li, C., Yu, L., Wen, S., Singh, S., Yang, Z., Zhao, J., Zhang, C., Yu, Y., Bi, J., Liu, Z-J, Paterson, A.H., Wang, S., Liang, X., Varshney, R.K., Yu, S., Chen, X., Li, H., Pandey, M.K., Yang, Q., Wang, X., Garg, V., Chi, X., Doddamani, D., Hong, Y., Upadhyaya, H., Guo, H., Khan, A.W., Zhu, F., Zhang, X., Pan, L., Pierce, G.J., Zhou, G., Krishnamohan, K.A.V.S., Chen, M., Zhong, N., Agarwal, G., Li, S., Chitikineni, A., Zhang, G-Q, Sharma, S., Chen, N., Liu, H., Janila, P., Wang, M., Wang, T., Sun, J., Li, X., Li, C., Yu, L., Wen, S., Singh, S., Yang, Z., Zhao, J., Zhang, C., Yu, Y., Bi, J., Liu, Z-J, Paterson, A.H., Wang, S., Liang, X., Varshney, R.K., and Yu, S. more...
- Abstract
Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45–56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis. For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity. more...
- Published
- 2016
28. Advanced backcross quantitative trait locus analysis of fiber elongation in a cross between Gossypium hirsutum and G. mustelinum
- Author
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UCL - SST/ELI/ELIA - Agronomy, Wang, B., Draye, Xavier, Zhang, Z., Zhuang, Z., Lloyd May, O., Paterson, A.H., Chee, P.W., UCL - SST/ELI/ELIA - Agronomy, Wang, B., Draye, Xavier, Zhang, Z., Zhuang, Z., Lloyd May, O., Paterson, A.H., and Chee, P.W. more...
- Abstract
In an effort to explore the secondary gene pool for the enhancement of upland cotton (Gossypium hirsutum L.) germplasm, we developed advanced-generation backcross populations by crossing G. hirsutum (PD94042) and Gossypium mustelinum Miers ex Watt (AD4-8), then backcrossing to the G. hirsutum parent for three cycles. Genome-wide mapping revealed introgressed alleles at an average of 13.8% of loci in each BC3F1 plant, collectively representing G. mustelinum introgression in 80.9% of the genome. Twenty-one BC3F1 plants were selfed to generate BC3F2 families of 127 to 160 plants per family (totaling 3203 plants), which were field-tested for fiber elongation and genetically mapped. One-way ANOVA detected 15 nonoverlapping quantitative trail loci (QTLs) distributed over 12 chromosomes. Individual loci explained from 10.0 to 25.24% of phenotypic variance. Nine stringent QTLs were detected in one-way ANOVAs and composite interval mapping; two of the nine QTLs explained more than 20% of variance and one was detected in four different families simultaneously with similar additive effects. Although the G. mustelinum parent does not produce spinnable fiber, G. mustelinum alleles contributed to increased fiber elongation for three of the nine stringent QTLs and five of the 15 total QTLs. Two-way ANOVA detected significant (P < 0.001) among-family genotype effects and genotype × family interactions, suggesting that the phenotypic effects of some introgressed chromosomal segments are dependent on the existence of other chromosomal segments. Gossypium mustelinum alleles that contribute to increased fiber elongation are of great interest to be further exploited in cotton breeding. © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA All rights reserved. more...
- Published
- 2016
29. Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea)
- Author
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Yu, Q.Y., Guyot, Romain, Kochko, Alexandre de, Byers, A., Navajas-Perez, R., Langston, B.J., Dubreuil Tranchant, Christine, Paterson, A.H., Poncet, Valérie, Nagai, C., and Ming, R.
- Subjects
allotetraploid ,evolution ,Coffea ,comparative genomics ,transposable elements ,genetic divergence - Abstract
Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n = 4x = 44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n = 2x = 22). C. arabica ((CCEEa)-C-a-E-a-E-a) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C. eugenioides (EE). To investigate the patterns and degree of DNA sequence divergence between the Arabica and Robusta coffee genomes, we identified orthologous bacterial artificial chromosomes (BACs) from C. arabica and C. canephora, and compared their sequences to trace their evolutionary history. Although a high level of sequence similarity was found between BACs from C. arabica and C. canephora, numerous chromosomal rearrangements were detected, including inversions, deletions and insertions. DNA sequence identity between C. arabica and C. canephora orthologous BACs ranged from 93.4% (between E-a and C-a) to 94.6% (between C-a and C). Analysis of eight orthologous gene pairs resulted in estimated ages of divergence between 0.046 and 0.665 million years, indicating a recent origin of the allotetraploid species C. arabica. Analysis of transposable elements revealed differential insertion events that contributed to the size increase in the C-a sub-genome compared to its diploid relative. In particular, we showed that insertion of a Ty1-copia LTR retrotransposon occurred specifically in C. arabica, probably shortly after allopolyploid formation. The two sub-genomes of C. arabica, C-a and E-a, showed sufficient sequence differences, and a whole-genome shotgun approach could be suitable for sequencing the allotetraploid genome of C. arabica. more...
- Published
- 2011
30. Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects
- Author
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Kole, C., Muthamilarasan, M., Henry, R., Edwards, D., Sharma, R., Abberton, M., Batley, J., Bentley, A., Blakeney, M., Bryant, J., Cai, H., Cakir, M., Cseke, L.J., Cockram, J., de Oliveira, A.C., De Pace, C., Dempewolf, H., Ellison, S., Gepts, P., Greenland, A., Hall, A., Hori, K., Hughes, S., Humphreys, M.W., Iorizzo, M., Ismail, A.M., Marshall, A., Mayes, S., Nguyen, H.T., Ogbonnaya, F.C., Ortiz, R., Paterson, A.H., Simon, P.W., Tohme, J., Tuberosa, R., Valliyodan, B., Varshney, R.K., Wullschleger, S.D., Yano, M., Prasad, M., Kole, C., Muthamilarasan, M., Henry, R., Edwards, D., Sharma, R., Abberton, M., Batley, J., Bentley, A., Blakeney, M., Bryant, J., Cai, H., Cakir, M., Cseke, L.J., Cockram, J., de Oliveira, A.C., De Pace, C., Dempewolf, H., Ellison, S., Gepts, P., Greenland, A., Hall, A., Hori, K., Hughes, S., Humphreys, M.W., Iorizzo, M., Ismail, A.M., Marshall, A., Mayes, S., Nguyen, H.T., Ogbonnaya, F.C., Ortiz, R., Paterson, A.H., Simon, P.W., Tohme, J., Tuberosa, R., Valliyodan, B., Varshney, R.K., Wullschleger, S.D., Yano, M., and Prasad, M. more...
- Abstract
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security. more...
- Published
- 2015
31. A Comparative Genomics Strategy for Targeted Discovery of Single-Nucleotide Polymorphisms and Conserved-Noncoding Sequences in Orphan Crops1[W]
- Author
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Feltus, F.A., Singh, H.P., Lohithaswa, H.C., Schulze, S.R., Silva, T.D., and Paterson, A.H.
- Subjects
Crops, Agricultural ,Expressed Sequence Tags ,Base Sequence ,Genotype ,Molecular Sequence Data ,food and beverages ,Genomics ,Genome Analysis ,Poaceae ,Polymorphism, Single Nucleotide ,Chromosomes, Plant ,Introns ,Untranslated Regions ,Sequence Alignment ,Conserved Sequence - Abstract
Completed genome sequences provide templates for the design of genome analysis tools in orphan species lacking sequence information. To demonstrate this principle, we designed 384 PCR primer pairs to conserved exonic regions flanking introns, using Sorghum/Pennisetum expressed sequence tag alignments to the Oryza genome. Conserved-intron scanning primers (CISPs) amplified single-copy loci at 37% to 80% success rates in taxa that sample much of the approximately 50-million years of Poaceae divergence. While the conserved nature of exons fostered cross-taxon amplification, the lesser evolutionary constraints on introns enhanced single-nucleotide polymorphism detection. For example, in eight rice (Oryza sativa) genotypes, polymorphism averaged 12.1 per kb in introns but only 3.6 per kb in exons. Curiously, among 124 CISPs evaluated across Oryza, Sorghum, Pennisetum, Cynodon, Eragrostis, Zea, Triticum, and Hordeum, 23 (18.5%) seemed to be subject to rigid intron size constraints that were independent of per-nucleotide DNA sequence variation. Furthermore, we identified 487 conserved-noncoding sequence motifs in 129 CISP loci. A large CISP set (6,062 primer pairs, amplifying introns from 1,676 genes) designed using an automated pipeline showed generally higher abundance in recombinogenic than in nonrecombinogenic regions of the rice genome, thus providing relatively even distribution along genetic maps. CISPs are an effective means to explore poorly characterized genomes for both DNA polymorphism and noncoding sequence conservation on a genome-wide or candidate gene basis, and also provide anchor points for comparative genomics across a diverse range of species. more...
- Published
- 2006
32. Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes
- Author
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Ming, R., Liu, S.-C., Lin, Y.-R., Da Silva, J., Wilson, W., Braga, D., Deynze, A. van, Wenslaff, T.F., Wu, K.K., Moore, P.H., Burnquist, W., Sorrells, M.E., Irvine, J.E., and Paterson, A.H.
- Subjects
Sugarcane -- Genetic aspects ,Sorghum -- Genetic aspects ,Chromosome mapping -- Research ,Diploidy -- Research ,Polyploidy -- Research ,Genomes -- Research ,Biological sciences - Abstract
The complex polyploid genomes of three Saccharum species have been aligned with the compact diploid genome of Sorghum (2n = 2x = 20). A set of 428 DNA probes from different Poaceae (grasses) detected 2460 loci in [F.sub.1] progeny of the crosses Saccharum officinarum Green German x S. spontaneum IND 81-146, and S. spontaneum PIN 84-1 x S. officinarum Muntok Java. Thirty-one DNA probes detected 226 loci in S. officinarum LA Purple X S. robustum Molokai 5829. Genetic maps of the six Saccharum genotypes, including up to 72 linkage groups, were assembled into 'homologous groups' based on parallel arrangements of duplicated loci. About 84% of the loci mapped by 242 common probes were homologous between Saccharum and Sorghum. Only one interchromosomal and two intrachromosomal rearrangements differentiated both S. officinarum and S. spontaneum from Sorghum, but 11 additional cases of chromosome structural polymorphism were found within Saccharum. Diploidization was advanced in S. robustum, incipient in S. officinarum, and absent in S. spontaneum, consistent with biogeographic data suggesting that S. robustum is the ancestor of S. officinarum, but raising new questions about the antiquity of S. spontaneum. The densely mapped Sorghum genome will be a valuable tool in ongoing molecular analysis of the complex Saccharum genome. more...
- Published
- 1998
33. A comparative assessment of the utility of PCR-based marker systems in pearl millet
- Author
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Thudi, M., Senthilvel, S., Bottley, A., Tom Hash, C., Reddy, A.R., Feltus, A.F., Paterson, A.H., Hoisington, D.A., Varshney, R.K., Thudi, M., Senthilvel, S., Bottley, A., Tom Hash, C., Reddy, A.R., Feltus, A.F., Paterson, A.H., Hoisington, D.A., and Varshney, R.K. more...
- Abstract
A set of 22 pearl millet inbred lines including the parents of eleven mapping populations, was screened with 627 markers including 100 pearl millet genomic SSRs (gSSRs), 60 pearl millet EST-SSRs (eSSRs), 410 intron sequence haplotypes (ISHs), and 57 exon sequence haplotypes (ESHs). In all, 267 (59%) of the markers were informative for at least one of the 11 mapping populations, which segregate for traits like drought and salinity tolerance; host plant resistance to downy mildew, rust and blast; fertility restoration and sterility and maintenance of cytoplasmic male sterility etc. An average of 116 polymorphic markers was identified per mapping population. The average PIC values and number of profiles (P) per polymorphic marker were: gSSRs (PIC = 0.62, P = 6.1), ISHs (PIC = 0.39, P = 2.6), eSSRs (PIC = 0.36, P = 3.1) and ESHs (PIC = 0.35, P = 3.1). A high correlation (r > 0.97, P < 0.05) was observed between the patterns of diversity exposed by the different marker systems. The polymorphic markers identified are suitable for the de novo construction, or the supplementation of pearl millet linkage maps. The genetic relationships identified among the panel of inbred lines may be useful in designing strategies to improve the use of available genetic variation in the context of pearl millet breeding. more...
- Published
- 2010
34. Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development
- Author
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UCL - AGRO/RAGR - Rattachement AGRO, UCL - SST/ELI/ELIA - Agronomy, Rong, Yunkang, Feltus, F. Alex, Waghmare, Vijay N., Pierce, Gary J., Chee, P.W., Draye, Xavier, Saranga, Yehoshua, Wright, R.J., Wilkins, Thea A., May, O. Lloyd, Smith, C.W., Gannaway, John R., Wendel, Jonathan F., Paterson, A.H., UCL - AGRO/RAGR - Rattachement AGRO, UCL - SST/ELI/ELIA - Agronomy, Rong, Yunkang, Feltus, F. Alex, Waghmare, Vijay N., Pierce, Gary J., Chee, P.W., Draye, Xavier, Saranga, Yehoshua, Wright, R.J., Wilkins, Thea A., May, O. Lloyd, Smith, C.W., Gannaway, John R., Wendel, Jonathan F., and Paterson, A.H. more...
- Published
- 2007
35. Toward Sequencing the Sorghum Genome. A U.S. National Science Foundation-Sponsored Workshop Report
- Author
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Kresovich, S., Barbazuk, B., Bedell, J.A., Borrell, A., Buell, C.R., Burke, J., Clifton, S., Codonnier-Pratt, M.M., Cox, S., Dahlberg, J., Erpelding, J., Fulton, T.M., Fulton, B., Fulton, L., Gingle, A.R., Hash, C.T., Huang, Y., Jordan, D., Klein, P.E., Klein, R.R., Magalhaes, J., McCombie, R., Moore, P., Mullet, J.E., Ozias-Akins, P., Paterson, A.H., Porter, K., Pratt, L., Roe, B., Rooney, W., Schnable, P.S., Stelly, D.M., Tuinstra, M., Ware, D., Warek, U., Kresovich, S., Barbazuk, B., Bedell, J.A., Borrell, A., Buell, C.R., Burke, J., Clifton, S., Codonnier-Pratt, M.M., Cox, S., Dahlberg, J., Erpelding, J., Fulton, T.M., Fulton, B., Fulton, L., Gingle, A.R., Hash, C.T., Huang, Y., Jordan, D., Klein, P.E., Klein, R.R., Magalhaes, J., McCombie, R., Moore, P., Mullet, J.E., Ozias-Akins, P., Paterson, A.H., Porter, K., Pratt, L., Roe, B., Rooney, W., Schnable, P.S., Stelly, D.M., Tuinstra, M., Ware, D., and Warek, U. more...
- Abstract
Members of the worldwide sorghum (Sorghum spp.) community, including private sector and international scientists as well as community representatives from closely related crops such as sugarcane (Saccharum spp.) and maize (Zea mays), met in St. Louis, Missouri, on November 9, 2004, to lay the groundwork for future advances in sorghum genomics and, in particular, to coordinate plans for sequencing of the sorghum genome. Key developments that made this workshop timely included advances in knowledge of the sorghum genome that provide for the development of a genetically anchored physical map to guide sequence assembly and annotation, the growing role of the sorghum genome as a nucleation point for comparative genomics of diverse tropical grasses including many leading crops, and the need for dramatically increased sorghum production to sustain human populations in many regions where its inherent abiotic stress tolerance makes it an essential staple. This report reviews current knowledge of the sorghum genome, a community-endorsed schema for integrating this knowledge into a finished sequence, and early plans for translating the sequence into sustained advances to benefit a worldwide group of stakeholders. more...
- Published
- 2005
36. Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach : I. Fiber elongation
- Author
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UCL - UCL/UCL - Secteur UCL, UCL - SST/ELI/ELIA - Agronomy, Chee, P.W., Draye, Xavier, Jiang, C-X., Decanini, Laura, DELMONTE, Terrie A., BREDHAUER, Robert, Smith, C.W., Paterson, A.H., UCL - UCL/UCL - Secteur UCL, UCL - SST/ELI/ELIA - Agronomy, Chee, P.W., Draye, Xavier, Jiang, C-X., Decanini, Laura, DELMONTE, Terrie A., BREDHAUER, Robert, Smith, C.W., and Paterson, A.H. more...
- Published
- 2005
37. Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach : III. Fiber length
- Author
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UCL - UCL/UCL - Secteur UCL, UCL - SST/ELI/ELIA - Agronomy, Chee, P.W., Draye, Xavier, Jiang, C-X., Decanini, Laura, DELMONTE, Terrie A., BREDHAUER, Robert, Smith, C.W., Paterson, A.H., UCL - UCL/UCL - Secteur UCL, UCL - SST/ELI/ELIA - Agronomy, Chee, P.W., Draye, Xavier, Jiang, C-X., Decanini, Laura, DELMONTE, Terrie A., BREDHAUER, Robert, Smith, C.W., and Paterson, A.H. more...
- Published
- 2005
38. Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation
- Author
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UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, UCL - SST/ELI/ELIA - Agronomy, Draye, Xavier, Lin, Y.R., Qian, X., Bowers, J.E., Burow, G.B., Morrel, P.L., Peterson, D.G., Presting, G.G., Ren, S.X., Wing, R.A., Paterson, A.H., UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, UCL - SST/ELI/ELIA - Agronomy, Draye, Xavier, Lin, Y.R., Qian, X., Bowers, J.E., Burow, G.B., Morrel, P.L., Peterson, D.G., Presting, G.G., Ren, S.X., Wing, R.A., and Paterson, A.H. more...
- Published
- 2001
39. Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton)
- Author
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UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, UCL - SST/ELI/ELIA - Agronomy, Jiang, C-X., Chee, P.W., Draye, Xavier, Morrel, P.L., Smith, C.W., Paterson, A.H., UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, UCL - SST/ELI/ELIA - Agronomy, Jiang, C-X., Chee, P.W., Draye, Xavier, Morrel, P.L., Smith, C.W., and Paterson, A.H. more...
- Published
- 2000
40. Comparative genomics of plant chromosomes
- Author
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UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, UCL - SST/ELI/ELIA - Agronomy, Paterson, A.H., Bowers, J.E., Burow, M.D., Draye, Xavier, Elsik, C.G., Jiang, C-X., Lan, T.H., Lin, Y.R., Ming, R.G., Wright, R.J., UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, UCL - SST/ELI/ELIA - Agronomy, Paterson, A.H., Bowers, J.E., Burow, M.D., Draye, Xavier, Elsik, C.G., Jiang, C-X., Lan, T.H., Lin, Y.R., Ming, R.G., and Wright, R.J. more...
- Published
- 2000
41. Locus-specific contig assembly in highly-duplicated genomes, using the BAC-RF method
- Author
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UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, UCL - SST/ELI/ELIA - Agronomy, Lin, Y.R., Draye, Xavier, Qian, X., Ren, S., Zhu, L.H., Tomkins, J., Wing, R., Li, Z., Paterson, A.H., UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, UCL - SST/ELI/ELIA - Agronomy, Lin, Y.R., Draye, Xavier, Qian, X., Ren, S., Zhu, L.H., Tomkins, J., Wing, R., Li, Z., and Paterson, A.H. more...
- Published
- 2000
42. EVOLUTIONARY HISTORY OF THE ANGIOSPERMS AND ITS RELEVANCE TO BRASSICA
- Author
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Paterson, A.H., primary, Bowers, J.E., additional, Estill, J.C., additional, Osborn, T.C., additional, Pires, J.C., additional, Amasino, R., additional, Quiros, C.F., additional, and Farnham, M., additional more...
- Published
- 2006
- Full Text
- View/download PDF
43. Registration of 'NemaTAM' peanut. (Registrations Of Cultivars)
- Author
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Simpson, C.E., Starr, J.L., Church, G.T., Burow, M.D., and Paterson, A.H.
- Subjects
Texas Agricultural Experiment Station -- Licensing agreements -- Product development ,Peanuts -- Product development -- Licensing agreements -- Identification and classification ,Agricultural industry ,Business ,Company licensing agreement ,Identification and classification ,Licensing agreements ,Licensing, certification and accreditation ,Product development - Abstract
'NemaTAM' (Reg. no. CV-74, PI 631175) is a runner market-type peanut (Arachis hypogaea L. subsp. hypogaea var. hypogaea) cultivar with a high level of resistance to root-knot nematode [Meloidogyne arenaria [...] more...
- Published
- 2003
44. Identification of Molecular Markers Linked to Leaf Curl Virus Disease Resistance in Cotton
- Author
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Aslam, M., primary, Jiang, C., additional, Wright, R., additional, and Paterson, A.H., additional
- Published
- 1998
- Full Text
- View/download PDF
45. Genetic dissection of cotton physiological responses to arid conditions and their inter-relationships with productivity.
- Author
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Saranga, Y., Jiang, C.-X., Wright, R.J., Yakir, D., and Paterson, A.H.
- Subjects
COTTON ,SEA Island cotton ,PLANT genetics ,DROUGHT tolerance ,PLANT physiology ,PLANT-water relationships - Abstract
Testing of the extent to which different complex traits share common genetic control provides a means to distinguish associations that are truly diagnostic of genetic potential for improved adaptation to abiotic stress, from incidental phenotypic correlations. In two generations of progeny from a cross between Gossypium hirsutum and Gossypium barbadense, quantitative trait loci (QTL) mapping was used to evaluate correspondence in genetic control of selected physiological measures and productivity under water-limited and well-watered environments, respectively. A total of 33 QTLs were detected for five physiological variables [osmotic potential (OP), carbon isotope ratio ( δ
13 C; indicator of water use efficiency), canopy temperature, chlorophyll a and b], and 46 QTLs for five measures of crop productivity [dry matter, seed cotton yield (SC), harvest index, boll weight, and boll number]. QTL likelihood intervals for high SC and low OP corresponded in three genomic regions, two of which mapped to homoeologous locations on the two subgenomes of tetraploid cotton. QTLs for δ13 C showed only incidental association with productivity, indicating that high water use efficiency can be associated with either high or low productivity. Different cotton species have evolved different alleles related to physiological responses and productivity under water deficit, which may permit the development of genotypes that are better-adapted to arid conditions. [ABSTRACT FROM AUTHOR] more...- Published
- 2004
- Full Text
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46. Segmental allotetraploidy and allelic interactions in buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.) as revealed by genome mapping.
- Author
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Jessup, R. W., Burson, B.L., Burow, G., Wang, Y.-W., Chang, C., Li, Z., Paterson, A.H., and Hussey, M.A.
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GRASSES ,PLANT genetics - Abstract
Presents information on a study that aimed to better understand transmission genetics in buffelgrass and provide useful DNA markers for grass breeding programs through the construction of a framework buffelgrass linkage map. Materials and methods; Results of the assessment of DNA polymorphism; Chromosome associations. more...
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- 2003
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- View/download PDF
47. QTL analysis of genotype × environment interactions affecting cotton fiber quality.
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Paterson, A.H., Saranga, Y., Menz, M., Jiang, C.-X., and Wright, R.J.
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COTTON ,PLANT fibers ,GENETIC markers ,PLANT-water relationships ,WATER requirements for crops ,IRRIGATION farming ,WATER quality - Abstract
Cotton is unusual among major crops in that large acreages are grown under both irrigated and rainfed conditions, making genotype × environment interactions of even greater importance than usual in designing crop-improvement strategies. We describe the impact of well-watered versus water-limited growth conditions on the genetic control of fiber quality, a complex suite of traits that collectively determine the utility of cotton. Fiber length, length uniformity, elongation, strength, fineness, and color (yellowness) were influenced by 6, 7, 9, 21, 25 and 11 QTLs (respectively) that could be detected in one or more treatments. The genetic control of cotton fiber quality was markedly affected both by general differences between growing seasons ('years') and by specific differences in water management regimes. Seventeen QTLs were detected only in the water-limited treatment while only two were specific to the well-watered treatment, suggesting that improvement of fiber quality under water stress may be even more complicated than improvement of this already complex trait under well-watered conditions. In crops such as cotton with widespread use of both irrigated and rainfed production systems, the need to manipulate larger numbers of genes to confer adequate quality under both sets of conditions will reduce the expected rate of genetic gain. These difficulties may be partly ameliorated by efficiencies gained through identification and use of diagnostic DNA markers, including those identified herein. [ABSTRACT FROM AUTHOR] more...
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- 2003
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48. Molecular dissection of complex traits in autopolyploids: mapping QTLs affecting sugar yield and related traits in sugarcane.
- Author
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Ming, R., Wang, Y.-W., Draye, X., Moore, P.H., Irvine, J.E., and Paterson, A.H.
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SUGARCANE ,GENE mapping ,PLANT gene mapping ,GENETIC markers ,BIOMARKERS ,SACCHARUM - Abstract
Mapping quantitative trait loci (QTLs) for sugar yield and related traits will provide essential information for sugarcane improvement through marker-assisted selection. Two sugarcane segregating populations derived from interspecific crosses between Saccharum offinarum and Saccharum spontaneum with 264 and 239 individuals, respectively, were evaluated in three replications each for field performance from 1994 to 1996 at Weslaco, Texas. These two populations were analyzed for a total of 735 DNA marker loci to seek QTLs for sugar yield, pol, stalk weight, stalk number, fiber content and ash content. Among the 102 significant associations found between these six traits and DNA markers, 61 could be located on sugarcane linkage maps, while the other 41 were associated with unlinked DNA markers. Fifty of the 61 mapped QTLs were clustered in 12 genomic regions of seven sugarcane homologous groups. Many cases in which QTLs from different genotypes mapped to corresponding locations suggested that at least some of the QTLs on the same cluster might be different allelic forms of the same genes. With a few exceptions that explained part of the transgressive segregation observed for particular traits, the allele effects of most QTLs were consistent with the parental phenotype from which the allele was derived. Plants with a high sugar yield possessed a large number of positive QTLs for sugar yield components and a minimal number of negative QTLs. This indicates the potential effectiveness of marker-assisted selection for sugar yield in sugarcane. [ABSTRACT FROM AUTHOR] more...
- Published
- 2002
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49. Mapping QTLs for field resistance to the rice blast pathogen and evaluating their individual and combined utility in improved varieties.
- Author
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Tabien, R.E., Li, Z., Paterson, A.H., Marchetti, M.A., Stansel, J.W., and Pinson, S.R.M.
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RICE disease & pest resistance ,DISEASE resistance of plants ,GENE mapping ,CHROMOSOMES ,PLANT genetics ,PLANT diseases - Abstract
Lines from a Lemont × Teqing recombinant inbred population were evaluated for dilatory resistance to rice blast disease using: (1) the Standard Evaluation System (SES) for rating leaf blast, (2) the percentage diseased leaf area (%DLA), and (3) the area under a disease progress curve (AUDPC). RFLP mapping using 175 well-distributed loci revealed nine QTLs, one each on chromosomes 1, 2, 3, 4, 6, 7 and 9, with two loci on chromosome 12. All nine putative QTLs were associated with AUDPC, six with both a %DLA and a SES rating. Teqing contributed the resistance allele for all these loci except for the one located on chromosome 4. Individual QTLs accounted for 5–32% of the observed phenotypic variation, and combined QTL models accounted for 43–53%. Three QTLs were located near three of the four major resistance genes previously identified in this population. The resistances of both Lemont and Teqing were attributable to a combination of both major genes capable of inducing hypersensitive reactions and minor genes causing less-distinctive phenotypic differences. Interactions were noted between QTLs and major genes. Our findings are in support of the strategy of pyramiding major genes and QTLs in carefully selected combinations to develop improved varieties with resistance to the blast fungus that is both broad in spectrum and durable. [ABSTRACT FROM AUTHOR] more...
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- 2002
- Full Text
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50. Breeding Perennial Grain Crops.
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Cox, T.S., Bender, M., Picone, C., Van Tassel, D.L., Holland, J.B., Brummer, E.C., Zoeller, B.E., Paterson, A.H., and Jackson, W.
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SOIL conservation ,FOOD crops - Abstract
One-third of the planet's arable land has been lost to soil erosion in recent decades, and the pace of this degradation will increase as the limits of our food production capacity are stretched. The persistent problem of worldwide soil erosion has rekindled interest in perennial grain crops. All of our current grain crops are annuals; therefore, developing an array of new perennial grains — grasses, legumes, and others — will require a long-term commitment. Fortunately, many perennial species can be hybridized with related annual crops, allowing us to incorporate genes of domestication much more quickly than did our ancestors who first selected the genes. Some grain crops — including rye, rice, and sorghum — can be hybridized with close perennial relatives to establish new gene pools. Others, such as wheat, oat, maize, soybean, and sunflower, must be hybridized with more distantly related perennial species and genera. Finally, some perennial species with relatively high grain yields — intermediate wheatgrass, wildrye, lymegrass, eastern gamagrass, Indian ricegrass, Illinois bundleflower, Maximilian sunflower, and probably others — are candidates for direct domestication without interspecific hybridization. To ensure diversity in the field and foster further genetic improvement, breeders will need to develop deep gene pools for each crop. Discussions of breeding strategies for perennial grains have concentrated on allocation of photosynthetic resources between seeds and vegetative structures. However, perennials will likely be grown in more diverse agro-ecosystems and require arrays of traits very different from those usually addressed by breeders of annuals. The only way to address concerns about the feasibility of perennial grains is to carry out breeding programs with adequate resources on a sufficient time scale. A massive program for breeding perennial grains could be funded by diversion of a relatively small fraction of... [ABSTRACT FROM AUTHOR] more...
- Published
- 2002
- Full Text
- View/download PDF
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