Journal articles 2013
Documents
Roles of root aerenchyma development and its associated QTL in dry matter production under transient moisture stress in rice
Niones JM, Suralta RR, Inukai Y and Yamauchi A (2013). Roles of root aerenchyma development and its associated QTL in dry matter production under transient moisture stress in rice. Plant Production Science 16(3):205–216. (G3008.06)
Abstract: Enhanced aerenchyma development in rice under transient drought-to-waterlogged (TDW) stress promotes root system development by promoting lateral root production. This study analyzed the quantitative trait loci (QTLs) associated with the plasticity in aerenchyma development under TD-W stress. A mapping population of 60 F2 genotypes of chromosome segment substituted lines (CSSL) derived from CSSL47 and Nipponbare crosses were grown in rootboxes and evaluated for shoot and root growth, and aerenchyma development (expressed as root porosity). The TD-W stress was imposed starting with water saturated soil condition at sowing and then to progressive drought from 0 to 21 days after sowing (DAS) prior to exposure to sudden waterlogging for another 17 days (21 to 38 DAS). We performed simple and composite interval mapping to identify QTLs for aerenchyma development. QTL associated with aerenchyma development was mapped on the short-arm of chromosome 12 and designated as qAER-12. The effect of qAER-12 on the plasticity in aerenchyma development under TD-W was significantly associated with the increase in lateral root elongation and branching. This resulted in greater root system development as expressed in total root length and consequently contributed to higher dry matter production. This qAER-12 is probably the first reported QTL associated with aerenchyma development in rice under TD-W and is a useful trait for the improvement of the adaptive capability under fluctuating soil moisture conditions.
Niones JM, Suralta RR, Inukai Y and Yamauchi A (2013). Roles of root aerenchyma development and its associated QTL in dry matter production under transient moisture stress in rice. Plant Production Science 16(3):205–216. (G3008.06)
Abstract: Enhanced aerenchyma development in rice under transient drought-to-waterlogged (TDW) stress promotes root system development by promoting lateral root production. This study analyzed the quantitative trait loci (QTLs) associated with the plasticity in aerenchyma development under TD-W stress. A mapping population of 60 F2 genotypes of chromosome segment substituted lines (CSSL) derived from CSSL47 and Nipponbare crosses were grown in rootboxes and evaluated for shoot and root growth, and aerenchyma development (expressed as root porosity). The TD-W stress was imposed starting with water saturated soil condition at sowing and then to progressive drought from 0 to 21 days after sowing (DAS) prior to exposure to sudden waterlogging for another 17 days (21 to 38 DAS). We performed simple and composite interval mapping to identify QTLs for aerenchyma development. QTL associated with aerenchyma development was mapped on the short-arm of chromosome 12 and designated as qAER-12. The effect of qAER-12 on the plasticity in aerenchyma development under TD-W was significantly associated with the increase in lateral root elongation and branching. This resulted in greater root system development as expressed in total root length and consequently contributed to higher dry matter production. This qAER-12 is probably the first reported QTL associated with aerenchyma development in rice under TD-W and is a useful trait for the improvement of the adaptive capability under fluctuating soil moisture conditions.
Full article
A survey of genes involved in Arachis stenosperma resistance to Meloidogyne arenaria race 1
Morgante CV, Brasileiro ACM, Roberts PA, Guimaraes LA, Araujo ACG, Fonseca LN, Leal-Bertioli SCM, Bertioli DJ and Guimaraes PM (2013). A survey of genes involved in Arachis stenosperma resistance to Meloidogyne arenaria race 1. Functional Plant Biology 40(12):1298–1309 (DOI: 10.1071/FP13096). (G6010.01)
Abstract: Root-knot nematodes constitute a constraint for important crops, including peanut (Arachis hypogaea L.). Resistance to Meloidogyne arenaria has been identified in the peanut wild relative Arachis stenosperma Krapov. & W. C. Greg., in which the induction of feeding sites by the nematode was inhibited by an early hypersensitive response (HR). Here, the transcription expression profiles of 19 genes selected from Arachis species were analysed using quantitative reverse transcription–polymerase chain reaction (qRT-PCR), during the early phases of an A. stenosperma–M. arenaria interaction. Sixteen genes were significantly differentially expressed in infected and non-infected roots, in at least one of the time points analysed: 3, 6, and 9 days after inoculation. These genes are involved in the HR and production of secondary metabolites related to pathogen defence. Seven genes encoding a resistance protein MG13, a helix-loop helix protein, an ubiquitin protein ligase, a patatin-like protein, a catalase, a DUF538 protein, and a resveratrol synthase, were differentially expressed in all time points analysed. Transcripts of two genes had their spatial and temporal distributions analysed by in situ hybridisation that validated qRT-PCR data. The identification of candidate resistance genes involved in wild peanut resistance to Meloidogyne can provide additional resources for peanut breeding and transgenic approaches.
Morgante CV, Brasileiro ACM, Roberts PA, Guimaraes LA, Araujo ACG, Fonseca LN, Leal-Bertioli SCM, Bertioli DJ and Guimaraes PM (2013). A survey of genes involved in Arachis stenosperma resistance to Meloidogyne arenaria race 1. Functional Plant Biology 40(12):1298–1309 (DOI: 10.1071/FP13096). (G6010.01)
Abstract: Root-knot nematodes constitute a constraint for important crops, including peanut (Arachis hypogaea L.). Resistance to Meloidogyne arenaria has been identified in the peanut wild relative Arachis stenosperma Krapov. & W. C. Greg., in which the induction of feeding sites by the nematode was inhibited by an early hypersensitive response (HR). Here, the transcription expression profiles of 19 genes selected from Arachis species were analysed using quantitative reverse transcription–polymerase chain reaction (qRT-PCR), during the early phases of an A. stenosperma–M. arenaria interaction. Sixteen genes were significantly differentially expressed in infected and non-infected roots, in at least one of the time points analysed: 3, 6, and 9 days after inoculation. These genes are involved in the HR and production of secondary metabolites related to pathogen defence. Seven genes encoding a resistance protein MG13, a helix-loop helix protein, an ubiquitin protein ligase, a patatin-like protein, a catalase, a DUF538 protein, and a resveratrol synthase, were differentially expressed in all time points analysed. Transcripts of two genes had their spatial and temporal distributions analysed by in situ hybridisation that validated qRT-PCR data. The identification of candidate resistance genes involved in wild peanut resistance to Meloidogyne can provide additional resources for peanut breeding and transgenic approaches.
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement
Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M-C, Thudi M, Gowda CLL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J & Cook DR (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology (2013). (DOI:10.1038/nbt.2491).
Chickpea (Cicer arietinum) is the second most widely grown legume crop after soya bean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ~738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.
Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M-C, Thudi M, Gowda CLL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J & Cook DR (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology (2013). (DOI:10.1038/nbt.2491).
Chickpea (Cicer arietinum) is the second most widely grown legume crop after soya bean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ~738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.
Phenotypic approaches to drought in cassava: review
Okogbenin E, Setter TL, Ferguson M, Mutegi R, Ceballos H, Olasanmi B and Fregene M (2013). Phenotypic approaches to drought in cassava: review. Frontiers in Plant Physiology 4:93. (DOI: 10.3389/fphys.2013.00093). (G7009.09/G7010.01.03).
Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process.
Okogbenin E, Setter TL, Ferguson M, Mutegi R, Ceballos H, Olasanmi B and Fregene M (2013). Phenotypic approaches to drought in cassava: review. Frontiers in Plant Physiology 4:93. (DOI: 10.3389/fphys.2013.00093). (G7009.09/G7010.01.03).
Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process.
Variation in carbon isotope discrimination and its relationship with harvest index in the reference collection of chickpea germplasm
Krishnamurthy L, Kashiwagi J, Tobita S, Ito O, Upadhyaya HD, Gowda CLL, Gaur PM, Sheshshayee MS, Singh S, Vadez V, Varshney RK (2013). Variation in carbon isotope discrimination and its relationship with harvest index in the reference collection of chickpea germplasm. Functional Plant Biology, pp1–12. Published online 2 July 2013. (DOI: http://dx.doi.org/10.1071/FP13088). (G4008.12). Not open access: view online
Krishnamurthy L, Kashiwagi J, Tobita S, Ito O, Upadhyaya HD, Gowda CLL, Gaur PM, Sheshshayee MS, Singh S, Vadez V, Varshney RK (2013). Variation in carbon isotope discrimination and its relationship with harvest index in the reference collection of chickpea germplasm. Functional Plant Biology, pp1–12. Published online 2 July 2013. (DOI: http://dx.doi.org/10.1071/FP13088). (G4008.12). Not open access: view online
Evaluation of a collection of rice landraces from Burkina Faso for resistance or tolerance to rice yellow mottle virus
Kam H, Laing MD, Séré Y, Thiémélé D, Ghesquière A, Ahmadi N, Ndjiondjop M-N (2013). Evaluation of a collection of rice landraces from Burkina Faso for resistance or tolerance to rice yellow mottle virus. Journal of Plant Pathology 95(3):485–492 (DOI: 10.4454/JPP.V95I3.014). Not open access; view abstract. (G4009.02.01)
Kam H, Laing MD, Séré Y, Thiémélé D, Ghesquière A, Ahmadi N, Ndjiondjop M-N (2013). Evaluation of a collection of rice landraces from Burkina Faso for resistance or tolerance to rice yellow mottle virus. Journal of Plant Pathology 95(3):485–492 (DOI: 10.4454/JPP.V95I3.014). Not open access; view abstract. (G4009.02.01)
The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome
Bertioli DJ, Vidigal B, Nielen S, Ratnaparkhe MB, Lee T-H, Leal-Bertioli SCM, Kim C, Guimarães PM, Seijo G, Schwarzacher T, Paterson AH, Heslop-Harrison P and Araujo ACG (2013). The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome. Annals of Botany 112(3):545–559 (DOI: 10.1093/aob/mct128). Not open access; view abstract. (G6010.01)
Bertioli DJ, Vidigal B, Nielen S, Ratnaparkhe MB, Lee T-H, Leal-Bertioli SCM, Kim C, Guimarães PM, Seijo G, Schwarzacher T, Paterson AH, Heslop-Harrison P and Araujo ACG (2013). The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome. Annals of Botany 112(3):545–559 (DOI: 10.1093/aob/mct128). Not open access; view abstract. (G6010.01)
Association studies and legume synteny reveal haplotypes determining seed size in Vigna unguiculata
Lucas MR, Huynh B-L, da Silva Vinholes P, Cisse N, Drabo I, Ehlers JD, Roberts PA and Close TJ (2013). Association studies and legume synteny reveal haplotypes determining seed size in Vigna unguiculata. Frontiers in Plant Science 4:95. (DOI: 10.3389/fpls.2013.00095). (G6010.02/ G7010.07).
Highly specific seed market classes for cowpea and other grain legumes exist because grain is most commonly cooked and consumed whole. Size, shape, color, and texture are critical features of these market classes and breeders target development of cultivars for market acceptance. Resistance to biotic and abiotic stresses that are absent from elite breeding material are often introgressed through crosses to landraces or wild relatives. When crosses are made between parents with different grain quality characteristics, recovery of progeny with acceptable or enhanced grain quality is problematic. Thus genetic markers for grain quality traits can help in pyramiding genes needed for specific market classes.
Lucas MR, Huynh B-L, da Silva Vinholes P, Cisse N, Drabo I, Ehlers JD, Roberts PA and Close TJ (2013). Association studies and legume synteny reveal haplotypes determining seed size in Vigna unguiculata. Frontiers in Plant Science 4:95. (DOI: 10.3389/fpls.2013.00095). (G6010.02/ G7010.07).
Highly specific seed market classes for cowpea and other grain legumes exist because grain is most commonly cooked and consumed whole. Size, shape, color, and texture are critical features of these market classes and breeders target development of cultivars for market acceptance. Resistance to biotic and abiotic stresses that are absent from elite breeding material are often introgressed through crosses to landraces or wild relatives. When crosses are made between parents with different grain quality characteristics, recovery of progeny with acceptable or enhanced grain quality is problematic. Thus genetic markers for grain quality traits can help in pyramiding genes needed for specific market classes.
Assessment of genetic diversity in the sorghum reference set using EST-SSR markers
Ramu P, Billot C, Rami JF, Senthilvel S, Upadhyaya HD, Ananda Reddy L, Hash CT (2013). Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theoretical and Applied Genetics, published online 25 May 2013. (DOI: 10.1007/s00122-013-2117-6). (G4005.01.03/ G4007.01). Not open access: view abstract
Ramu P, Billot C, Rami JF, Senthilvel S, Upadhyaya HD, Ananda Reddy L, Hash CT (2013). Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theoretical and Applied Genetics, published online 25 May 2013. (DOI: 10.1007/s00122-013-2117-6). (G4005.01.03/ G4007.01). Not open access: view abstract
Using membrane transporters to improve crops for sustainable food production
Schroeder JI, Delhaize E, Frommer WB, Guerinot ML, Harrison MJ, Herrera-Estrella L, Horie T, Kochian LV, Munns R, Nishizawa NK, Tsay Y-F, Sanders D. 2013. Using membrane transporters to improve crops for sustainable food production. Nature 497(7447): 60–66. (DOI: 10.1038/nature11909). (G7010.03.01). Not open access: view abstract
Schroeder JI, Delhaize E, Frommer WB, Guerinot ML, Harrison MJ, Herrera-Estrella L, Horie T, Kochian LV, Munns R, Nishizawa NK, Tsay Y-F, Sanders D. 2013. Using membrane transporters to improve crops for sustainable food production. Nature 497(7447): 60–66. (DOI: 10.1038/nature11909). (G7010.03.01). Not open access: view abstract
