Journal articles 2012
Documents
Genetic diversity of provitamin A cassava in Uganda
Esuma W, Rubaihayo P, Pariyo A, Kawuki R, Wanjala B, Nzuki I, Harvey JJW, Baguma Y (2012). Genetic diversity of provitamin A cassava in Uganda. Journal of Plant Studies 1(1):60–71 (DOI: 10.5539/jps.v1n1p60).
Esuma W, Rubaihayo P, Pariyo A, Kawuki R, Wanjala B, Nzuki I, Harvey JJW, Baguma Y (2012). Genetic diversity of provitamin A cassava in Uganda. Journal of Plant Studies 1(1):60–71 (DOI: 10.5539/jps.v1n1p60).
Genetic insight into yield-associated traits of wheat grown in multiple rain-fed environments
Wu X, Chang X, Jing R (2012). Genetic insight into yield-associated traits of wheat grown in multiple rain-fed environments. PLoS ONE 7(2):e31249 (published online). (DOI:10.1371/journal.pone.0031249).
Wu X, Chang X, Jing R (2012). Genetic insight into yield-associated traits of wheat grown in multiple rain-fed environments. PLoS ONE 7(2):e31249 (published online). (DOI:10.1371/journal.pone.0031249).
Genetic structure, linkage disequilibrium and signature of selection in sorghum; lessons from physically anchored DArT markers
Bouchet S, Pot D, Deu M, Rami JF, Billot C, Perrier CX, Rivallan R, Gardes L, Xia L, Wenzl P, Kilian K, Glaszmann JC (2012). Genetic structure, linkage disequilibrium and signature of selection in sorghum; lessons from physically anchored DArT markers. PLoS ONE 7(3):e33470 (DOI:10.1371/journal.pone.0033470).
Bouchet S, Pot D, Deu M, Rami JF, Billot C, Perrier CX, Rivallan R, Gardes L, Xia L, Wenzl P, Kilian K, Glaszmann JC (2012). Genetic structure, linkage disequilibrium and signature of selection in sorghum; lessons from physically anchored DArT markers. PLoS ONE 7(3):e33470 (DOI:10.1371/journal.pone.0033470).
Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies
Xu P, X Wu, Wang B, Luo J, Liu Y, Ehlers JD, Close TJ, Roberts PA, Lu Z, Wang S and Li G (2012). Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies. Heredity 109:34–40. (DOI:10.1038/hdy.2012.8). (G6010.02/G7010.07.01). Not open access: view abstract online
Xu P, X Wu, Wang B, Luo J, Liu Y, Ehlers JD, Close TJ, Roberts PA, Lu Z, Wang S and Li G (2012). Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies. Heredity 109:34–40. (DOI:10.1038/hdy.2012.8). (G6010.02/G7010.07.01). Not open access: view abstract online
Genome-wide association studies for agronomical traits in a world wide spring barley collection
Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A (2012). Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biology 2012 12:16, online first (DOI:10.1186/1471-2229-12-16).
Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A (2012). Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biology 2012 12:16, online first (DOI:10.1186/1471-2229-12-16).
Getting the most out of sorghum low-input field trials in West Africa using spatial adjustment
Leiser WL, Rattunde HF, Piepho HP and Parzies HK (2012). Getting the most out of sorghum low-input field trials in West Africa using spatial adjustment. Journal of Agronomy and Crop Science, 198(5):349–359. (DOI: 10.1111/j.1439-037X.2012.00529.x). (G7010.03.03). Not open access: view abstract
Leiser WL, Rattunde HF, Piepho HP and Parzies HK (2012). Getting the most out of sorghum low-input field trials in West Africa using spatial adjustment. Journal of Agronomy and Crop Science, 198(5):349–359. (DOI: 10.1111/j.1439-037X.2012.00529.x). (G7010.03.03). Not open access: view abstract
Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection
Guimarães PM, Brasileiro ACM, Morgante CV, Martins ACQ, Pappas G, Silva OB, Togawa R, Leal-Bertioli SCM, Araujo ACG, Moretzsohn MC and Bertioli DJ (2012). Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection. BMC Genomics 13:387 (DOI: 10.1186/1471-2164-13-387). (G6010.01)
Abstract: Background Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development.
Results Transcriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton, and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR.
Conclusions This study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to biological processes such as fungal diseases and water limited stress. Moreover, it will also facilitate basic and applied research on the genetics of peanut through the development of new molecular markers and the study of adaptive variation across the genus.
Guimarães PM, Brasileiro ACM, Morgante CV, Martins ACQ, Pappas G, Silva OB, Togawa R, Leal-Bertioli SCM, Araujo ACG, Moretzsohn MC and Bertioli DJ (2012). Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection. BMC Genomics 13:387 (DOI: 10.1186/1471-2164-13-387). (G6010.01)
Abstract: Background Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development.
Results Transcriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton, and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR.
Conclusions This study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to biological processes such as fungal diseases and water limited stress. Moreover, it will also facilitate basic and applied research on the genetics of peanut through the development of new molecular markers and the study of adaptive variation across the genus.
Full article
Gray association grade analysis of physiological traits with yield of wheat under different water regimes
Shi W, Chang X, Jing R (2012). Gray association grade analysis of physiological traits with yield of wheat under different water regimes. Journal of Triticeae Crops 32(4):653–659. (G7010.02.01). Article in Chinese with abstract in English. Not open access: view online
The purpose of the present research is to reveal the variation of canopy temperature and photosynthetic characteristics and their impact on wheat (Triticum aestivum L.) yield under drought stress. A set of introgression BC3F5 lines (ILs) generated from repeated backcross [(Lumai 14 X Jinmai 47) X Lumai 14] were used as the plant materials. The donor parent Jinmai 47 was a drought tolerant cultivar, the recurrent parent Lumai 14 as a high yield potential cultivar under well-watered condition.
Shi W, Chang X, Jing R (2012). Gray association grade analysis of physiological traits with yield of wheat under different water regimes. Journal of Triticeae Crops 32(4):653–659. (G7010.02.01). Article in Chinese with abstract in English. Not open access: view online
The purpose of the present research is to reveal the variation of canopy temperature and photosynthetic characteristics and their impact on wheat (Triticum aestivum L.) yield under drought stress. A set of introgression BC3F5 lines (ILs) generated from repeated backcross [(Lumai 14 X Jinmai 47) X Lumai 14] were used as the plant materials. The donor parent Jinmai 47 was a drought tolerant cultivar, the recurrent parent Lumai 14 as a high yield potential cultivar under well-watered condition.
High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development
Clark RT, Famoso AN, Zhao K, Shaff JE, Craft JE, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV. 2013. High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell Environment Published online 3 September 2012. (DOI: 10.1111/j.1365-3040.2012.02587.x). Also printed in 2013. (G7010.03.01). Not open access: view abstract
Clark RT, Famoso AN, Zhao K, Shaff JE, Craft JE, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV. 2013. High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell Environment Published online 3 September 2012. (DOI: 10.1111/j.1365-3040.2012.02587.x). Also printed in 2013. (G7010.03.01). Not open access: view abstract
Highly informative genic and genomic SSR markers to facilitate molecular breeding in cultivated groundnut (Arachis hypogaea)
Pandey MK, Gautami B, Jayakumar T, Sriswathi M, Upadhyaya HD, Gowda MVC, Radhakrishnan T, Bertioli DJ, Knapp SJ, Cook DR, Varshney RK (2012). Highly informative genic and genomic SSR markers to facilitate molecular breeding in cultivated groundnut (Arachis hypogaea). Plant Breeding 131(1):139–147. Also published online in 2011. (DOI: 10.1111/j.1439-0523.2011.01911.x). View abstract online
Pandey MK, Gautami B, Jayakumar T, Sriswathi M, Upadhyaya HD, Gowda MVC, Radhakrishnan T, Bertioli DJ, Knapp SJ, Cook DR, Varshney RK (2012). Highly informative genic and genomic SSR markers to facilitate molecular breeding in cultivated groundnut (Arachis hypogaea). Plant Breeding 131(1):139–147. Also published online in 2011. (DOI: 10.1111/j.1439-0523.2011.01911.x). View abstract online
