Journal articles 2012
Documents
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
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.
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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 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 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).
