Journal articles 2012
Documents
A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing platforms
Kudapa H, Bharti AH, Cannon SB, Farmer AD, Mulaosmanovic B, Kramer R, Bohra A, Weeks NT, Crow JA, Tuteja R, Shah T, Dutta S, Gupta DK, Singh A, Gaikwad K, Sharma TR, May GD, Singh NK, and Varshney RK (2012). A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing platforms. Molecular Plant 5(5):1020–1028. (DOI:10.1093/mp/ssr111).
A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript assembly contigs (TACs) with an N50 of 1510 bp, the largest one being ;8 kb. Of the 21 434 TACs, 16 622 (77.5%) could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions (ISRs).
Kudapa H, Bharti AH, Cannon SB, Farmer AD, Mulaosmanovic B, Kramer R, Bohra A, Weeks NT, Crow JA, Tuteja R, Shah T, Dutta S, Gupta DK, Singh A, Gaikwad K, Sharma TR, May GD, Singh NK, and Varshney RK (2012). A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing platforms. Molecular Plant 5(5):1020–1028. (DOI:10.1093/mp/ssr111).
A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript assembly contigs (TACs) with an N50 of 1510 bp, the largest one being ;8 kb. Of the 21 434 TACs, 16 622 (77.5%) could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions (ISRs).
Full article (
A mixed model QTL analysis for sugarcane multiple-harvest-location trial data
Pastina MM, Malosetti M, Gazaffi R, Mollinari M, Margarido GRA, Oliveira KM, Pinto LR, Souza AP, van Eeuwijk FA and Garcia AAF (2012). A mixed model QTL analysis for sugarcane multiple-harvest-location trial data. Theoretical and Applied Genetics 124 (5) 835–849. (DOI 10.1007/s00122-011-1748-8).
Pastina MM, Malosetti M, Gazaffi R, Mollinari M, Margarido GRA, Oliveira KM, Pinto LR, Souza AP, van Eeuwijk FA and Garcia AAF (2012). A mixed model QTL analysis for sugarcane multiple-harvest-location trial data. Theoretical and Applied Genetics 124 (5) 835–849. (DOI 10.1007/s00122-011-1748-8).
A promoter-swap strategy between the AtALMT and AtMATE genes increased Arabidopsis aluminium resistance and improved carbon-use efficiency for aluminium resistance
Liu J, Luo X, Shaff J, Liang C, Jia X, Li Z, Magalhães J and Kochian LV (2012). A promoter-swap strategy between the AtALMT and AtMATE genes increased Arabidopsis aluminium resistance and improved carbon-use efficiency for aluminium resistance. The Plant Journal 71(2):327–337. (DOI: 10.1111/j.1365-313X.2012.04994.x).
The primary mechanism of Arabidopsis aluminum (Al) resistance is based on root Al exclusion, resulting from Al-activated root exudation of the Al3+-chelating organic acids, malate and citrate. Root malate exudation is the major contributor to Arabidopsis Al resistance, and is conferred by expression of AtALMT1, which encodes the root malate transporter. Root citrate exudation plays a smaller but still significant role in Arabidopsis Al resistance, and is conferred by expression of AtMATE, which encodes the root citrate transporter. In this study, we demonstrate that levels of Al-activated root organic acid exudation are closely correlated with expression of the organic acid transporter genes AtALMT1 and AtMATE.
Liu J, Luo X, Shaff J, Liang C, Jia X, Li Z, Magalhães J and Kochian LV (2012). A promoter-swap strategy between the AtALMT and AtMATE genes increased Arabidopsis aluminium resistance and improved carbon-use efficiency for aluminium resistance. The Plant Journal 71(2):327–337. (DOI: 10.1111/j.1365-313X.2012.04994.x).
The primary mechanism of Arabidopsis aluminum (Al) resistance is based on root Al exclusion, resulting from Al-activated root exudation of the Al3+-chelating organic acids, malate and citrate. Root malate exudation is the major contributor to Arabidopsis Al resistance, and is conferred by expression of AtALMT1, which encodes the root malate transporter. Root citrate exudation plays a smaller but still significant role in Arabidopsis Al resistance, and is conferred by expression of AtMATE, which encodes the root citrate transporter. In this study, we demonstrate that levels of Al-activated root organic acid exudation are closely correlated with expression of the organic acid transporter genes AtALMT1 and AtMATE.
A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae)
Billot C, Rivallan R, Sall MN, Fonceka D, Deu M, Glaszmann J-C, Noyer J-L, Rami J-F, Risterucci A-M, Wincker P, Ramu P and Hash CT (2012). A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae). American Journal of Botany 99(6):e245–e250. (DOI: 10.3732/ajb.1100548).
Discrepancies in terms of genotyping data are frequently observed when comparing simple sequence repeat (SSR) data sets across genotyping technologies and laboratories. This technical concern introduces biases that hamper any synthetic studies or comparison of genetic diversity between collections. To prevent this for Sorghum bicolor, we developed a control kit of 48 SSR markers.
Billot C, Rivallan R, Sall MN, Fonceka D, Deu M, Glaszmann J-C, Noyer J-L, Rami J-F, Risterucci A-M, Wincker P, Ramu P and Hash CT (2012). A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae). American Journal of Botany 99(6):e245–e250. (DOI: 10.3732/ajb.1100548).
Discrepancies in terms of genotyping data are frequently observed when comparing simple sequence repeat (SSR) data sets across genotyping technologies and laboratories. This technical concern introduces biases that hamper any synthetic studies or comparison of genetic diversity between collections. To prevent this for Sorghum bicolor, we developed a control kit of 48 SSR markers.
A role for root morphology and related candidate genes in P acquisition efficiency in maize
de Sousa SM, Clark RT, Mendes FF, de Oliveira AC, de Vasconcelos MJV, Parentoni SN, Kochian LV, Guimarães CT, Magalhães JV (2012). A role for root morphology and related candidate genes in P acquisition efficiency in maize. Functional Plant Biology 39(11):925–935. http://dx.doi.org/10.1071/FP12022. (G7010.03.01). Not open access: view abstract
de Sousa SM, Clark RT, Mendes FF, de Oliveira AC, de Vasconcelos MJV, Parentoni SN, Kochian LV, Guimarães CT, Magalhães JV (2012). A role for root morphology and related candidate genes in P acquisition efficiency in maize. Functional Plant Biology 39(11):925–935. http://dx.doi.org/10.1071/FP12022. (G7010.03.01). Not open access: view abstract
Advances in Arachis genomics for peanut improvement
Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK (2012). Advances in Arachis genomics for peanut improvement. Biotechnology Advances 30(3):639–651. ISSN 0734-9750. (DOI: 10.1016/j.biotechadv.2011.11.001). Not open access: view abstract
Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK (2012). Advances in Arachis genomics for peanut improvement. Biotechnology Advances 30(3):639–651. ISSN 0734-9750. (DOI: 10.1016/j.biotechadv.2011.11.001). Not open access: view abstract
Agro-morphological characterization of a population of introgression lines derived from crosses between IR 64 (Oryza sativa indica) and TOG 5681 (Oryza glaberrima) for drought tolerance
Bocco R, Lorieux M, Seck PA, Futakuchi K, Manneh B, Baimey H, Ndjiondjop MN (2012). Agro-morphological characterization of a population of introgression lines derived from crosses between IR 64 (Oryza sativa indica) and TOG 5681 (Oryza glaberrima) for drought tolerance. Plant Science 183:65–76, ISSN 0168-9452, (DOI: 10.1016/j.plantsci.2011.09.010). Not open access: view abstract
Bocco R, Lorieux M, Seck PA, Futakuchi K, Manneh B, Baimey H, Ndjiondjop MN (2012). Agro-morphological characterization of a population of introgression lines derived from crosses between IR 64 (Oryza sativa indica) and TOG 5681 (Oryza glaberrima) for drought tolerance. Plant Science 183:65–76, ISSN 0168-9452, (DOI: 10.1016/j.plantsci.2011.09.010). Not open access: view abstract
An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.)
(2012). An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS ONE 7(7):e41213. (DOI:10.1371/journal.pone.0041213).
(2012). An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS ONE 7(7):e41213. (DOI:10.1371/journal.pone.0041213).
![An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L) Millspaugh] derived from six mapping population](http://generationcp.org/images/~thumbs.Bohra_Intra-specific-consensus-genetic-pigeonpea_TAG-10.1007_s00122-012-1916-5.pdf.1365026250.png)
An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L) Millspaugh] derived from six mapping population
Bohra A, Saxena RK, Gnanesh BN, Saxena KB, Byregowda M, Rathore A, KaviKishor PB, Cook DR, Varshney RK (2012). An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L) Millspaugh] derived from six mapping populations. Theoretical and Applied Genetics 125(6):1325–1338. (DOI: 10.1007/s00122-012-1916-5).
Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750 kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59–140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6 cM have been constructed.
Bohra A, Saxena RK, Gnanesh BN, Saxena KB, Byregowda M, Rathore A, KaviKishor PB, Cook DR, Varshney RK (2012). An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L) Millspaugh] derived from six mapping populations. Theoretical and Applied Genetics 125(6):1325–1338. (DOI: 10.1007/s00122-012-1916-5).
Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750 kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59–140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6 cM have been constructed.
Analysis of constituents for phenotyping drought tolerance in crop improvement
Setter TL (2012). Analysis of constituents for phenotyping drought tolerance in crop improvement. Frontiers in Physiology 3:180. (DOI: 10.3389/fphys.2012.00180).
Investigators now have a wide range of analytical tools to use in measuring metabolites, proteins and transcripts in plant tissues. These tools have the potential to assist genetic studies that seek to phenotype genetic lines for heritable traits that contribute to drought tolerance. To be useful for crop breeding, hundreds or thousands of genetic lines must be assessed. This review considers the utility of assaying certain constituents with roles in drought tolerance for phenotyping genotypes. Abscisic acid (ABA), organic and inorganic osmolytes, compatible solutes, and late embryogenesis abundant proteins, are considered. Confounding effects that require appropriate tissue and timing specificity, and the need for high-throughput and analytical cost efficiency are discussed. With future advances in analytical methods and the value of analyzing constituents that provide information on the underlying mechanisms of drought tolerance, these approaches are expected to contribute to development crops with improved drought tolerance.
Setter TL (2012). Analysis of constituents for phenotyping drought tolerance in crop improvement. Frontiers in Physiology 3:180. (DOI: 10.3389/fphys.2012.00180).
Investigators now have a wide range of analytical tools to use in measuring metabolites, proteins and transcripts in plant tissues. These tools have the potential to assist genetic studies that seek to phenotype genetic lines for heritable traits that contribute to drought tolerance. To be useful for crop breeding, hundreds or thousands of genetic lines must be assessed. This review considers the utility of assaying certain constituents with roles in drought tolerance for phenotyping genotypes. Abscisic acid (ABA), organic and inorganic osmolytes, compatible solutes, and late embryogenesis abundant proteins, are considered. Confounding effects that require appropriate tissue and timing specificity, and the need for high-throughput and analytical cost efficiency are discussed. With future advances in analytical methods and the value of analyzing constituents that provide information on the underlying mechanisms of drought tolerance, these approaches are expected to contribute to development crops with improved drought tolerance.
