Journal articles 2013
Documents
Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding
Bandillo N, Raghavan C, Muyco PA, Sevilla MAL, Lobina IT, Dilla-Ermita CJ, Tung C-w, McCouch S, Thomson M, Mauleon R, Singh RK, Gregorio G, Redoña E and Leung H (2013). Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 2013, 6:11.
This article describes the development of Multi-parent Advanced Generation Inter-Cross populations (MAGIC) in rice and discusses potential applications for mapping quantitative trait loci (QTLs) and for rice varietal development. We have developed 4 multi-parent populations: indica MAGIC (8 indica parents); MAGIC plus (8 indica parents with two additional rounds of 8-way F1 inter-crossing); japonica MAGIC (8 japonica parents); and Global MAGIC (16 parents – 8 indica and 8 japonica). The parents used in creating these populations are improved varieties with desirable traits for biotic and abiotic stress tolerance, yield, and grain quality. The purpose is to fine map QTLs for multiple traits and to directly and indirectly use the highly recombined lines in breeding programs. These MAGIC populations provide a useful germplasm resource with diverse allelic combinations to be exploited by the rice community.
Bandillo N, Raghavan C, Muyco PA, Sevilla MAL, Lobina IT, Dilla-Ermita CJ, Tung C-w, McCouch S, Thomson M, Mauleon R, Singh RK, Gregorio G, Redoña E and Leung H (2013). Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 2013, 6:11.
This article describes the development of Multi-parent Advanced Generation Inter-Cross populations (MAGIC) in rice and discusses potential applications for mapping quantitative trait loci (QTLs) and for rice varietal development. We have developed 4 multi-parent populations: indica MAGIC (8 indica parents); MAGIC plus (8 indica parents with two additional rounds of 8-way F1 inter-crossing); japonica MAGIC (8 japonica parents); and Global MAGIC (16 parents – 8 indica and 8 japonica). The parents used in creating these populations are improved varieties with desirable traits for biotic and abiotic stress tolerance, yield, and grain quality. The purpose is to fine map QTLs for multiple traits and to directly and indirectly use the highly recombined lines in breeding programs. These MAGIC populations provide a useful germplasm resource with diverse allelic combinations to be exploited by the rice community.
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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)
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
Diversity analysis of agronomic and quality characters of foreign wheat germplasm resources
Chai Y, Li X, Zhao Z, Sun L, Li Y and Jing L (2013). Diversity analysis of agronomic and quality characters of foreign wheat germplasm resources. Journal of Agriculture 3(9):1–8. Article in Chinese with abstract in English. (G7010.02.01)
Abstract: In order to gain knowledge of genetic diversity of wheat and improve their usage efficiency as germplasm resource. Diversities of agronomic and quality characters were analyzed for 146 foreign wheat germplasm in the field in southern Shanxi Province, basing on the data statistic analysis, principal component and cluster analysis methods. The average coefficient of variance was 10.9%, and the average diversity index was 1.4 with 18 wheat characters. It was-to seed yield, spike length, kernels per spike, spikes per plant, 1000-grain weight, stability time, tensile area, maximum resistance, sedimentation value and development time. Principal component and cluster analysis were used to 31 high-yield germplasm resources. The additive contributing rate of first eight principal components was 92.73%, eight major discriminating characteristics were selected to reflect the comprehensive economic characters and quality characters. According to the genetic distance, 31 germplasm resources were divided into 7 groups. Each group had different characteristics and showed abundant genetic diversity in agronomic and quality characters.
Chai Y, Li X, Zhao Z, Sun L, Li Y and Jing L (2013). Diversity analysis of agronomic and quality characters of foreign wheat germplasm resources. Journal of Agriculture 3(9):1–8. Article in Chinese with abstract in English. (G7010.02.01)
Abstract: In order to gain knowledge of genetic diversity of wheat and improve their usage efficiency as germplasm resource. Diversities of agronomic and quality characters were analyzed for 146 foreign wheat germplasm in the field in southern Shanxi Province, basing on the data statistic analysis, principal component and cluster analysis methods. The average coefficient of variance was 10.9%, and the average diversity index was 1.4 with 18 wheat characters. It was-to seed yield, spike length, kernels per spike, spikes per plant, 1000-grain weight, stability time, tensile area, maximum resistance, sedimentation value and development time. Principal component and cluster analysis were used to 31 high-yield germplasm resources. The additive contributing rate of first eight principal components was 92.73%, eight major discriminating characteristics were selected to reflect the comprehensive economic characters and quality characters. According to the genetic distance, 31 germplasm resources were divided into 7 groups. Each group had different characteristics and showed abundant genetic diversity in agronomic and quality characters.
Facing the challenges of global agriculture today: what can we do about drought?
Okono A, Monneveux P and Ribaut J-M (2013). Facing the challenges of global agriculture today: what can we do about drought? Frontiers in Plant Physiology 4:289. (DOI: 10.3389/fphys.2013.00289).
It is estimated that the planet's demand for food and feed crops will almost double by 2050 (Foley et al., 2011). Globally, rainfed agriculture is practised in 80% of the total agricultural area and generates 62% of the world's staple food (FAOSTAT, 2011). Taking into consideration global water scarcity and increases in demand for non-agricultural uses of water, expansion of the area under irrigation in developing countries does not appear to be a realistic scenario to address the challenge of food security.
Okono A, Monneveux P and Ribaut J-M (2013). Facing the challenges of global agriculture today: what can we do about drought? Frontiers in Plant Physiology 4:289. (DOI: 10.3389/fphys.2013.00289).
It is estimated that the planet's demand for food and feed crops will almost double by 2050 (Foley et al., 2011). Globally, rainfed agriculture is practised in 80% of the total agricultural area and generates 62% of the world's staple food (FAOSTAT, 2011). Taking into consideration global water scarcity and increases in demand for non-agricultural uses of water, expansion of the area under irrigation in developing countries does not appear to be a realistic scenario to address the challenge of food security.
Plant breeding: Discovery in a dry spell
Eisenstein M.(2013). Plant breeding: Discovery in a dry spell. Nature 501: S7–S9. Published online 25 September 2013. (DOI:10.1038/501S7a). Not open access: view online
Eisenstein M.(2013). Plant breeding: Discovery in a dry spell. Nature 501: S7–S9. Published online 25 September 2013. (DOI:10.1038/501S7a). Not open access: view online
Identification and hybridization usage of CIMMYT wheat germplasms
Chai Y, Li X, Zhao Z, Sun L, Li Y and Ma G (2013). Identification and hybridization usage of CIMMYT wheat germplasms. Chinese Agricultural Science Bulletin 29(33):56–61. Article in Chinese with abstract in English. (G7010.02.01)
Abstract: In order to improve wheat germplasm diversity, increase wheat yield and quality, agronomic and quality characters were evaluated for 145 foreign wheat germplasms in the field in southern Shanxi Province. The results showed that, these germplasms were weak vernal wheat, which might be sown on late Oct. as germplasm use in southern Shanxi Province. The coefficients of variance of spikes per plant, kernels per spike, 1000-grain weight and yield were 15.7%, 16.03%, 12.23% and 23.96% respectively. Most of the germplasms had better intergrated traits, especially in seed gluten. Agronomic traits had greater genetic diversity. Plant height and 1000-grain weight had significantly correlation with yield. Thirty-two germplasms yielded more than 3750 kg/hm2. We selected 8 trong gluten wheat germplasms and 35 better intergrated traits germplasms which had large spike, spikelets with many kernels as key germplasms for breeding. We adjusted the sowing date to meet flowering of these materials for hybridization with good local strains and produced abundant F3, BCF2 and BC1F1 generation. New drought-tolerance materials and strains with large spike and high yielding may be selected from the CIMMYT generations.
Chai Y, Li X, Zhao Z, Sun L, Li Y and Ma G (2013). Identification and hybridization usage of CIMMYT wheat germplasms. Chinese Agricultural Science Bulletin 29(33):56–61. Article in Chinese with abstract in English. (G7010.02.01)
Abstract: In order to improve wheat germplasm diversity, increase wheat yield and quality, agronomic and quality characters were evaluated for 145 foreign wheat germplasms in the field in southern Shanxi Province. The results showed that, these germplasms were weak vernal wheat, which might be sown on late Oct. as germplasm use in southern Shanxi Province. The coefficients of variance of spikes per plant, kernels per spike, 1000-grain weight and yield were 15.7%, 16.03%, 12.23% and 23.96% respectively. Most of the germplasms had better intergrated traits, especially in seed gluten. Agronomic traits had greater genetic diversity. Plant height and 1000-grain weight had significantly correlation with yield. Thirty-two germplasms yielded more than 3750 kg/hm2. We selected 8 trong gluten wheat germplasms and 35 better intergrated traits germplasms which had large spike, spikelets with many kernels as key germplasms for breeding. We adjusted the sowing date to meet flowering of these materials for hybridization with good local strains and produced abundant F3, BCF2 and BC1F1 generation. New drought-tolerance materials and strains with large spike and high yielding may be selected from the CIMMYT generations.
Fast-track introgression of “QTL-hotspot” for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea
Varshney RK, Gaur PM, Chamarthi SK, Krishnamurthy L, Tripathi S, Kashiwagi J, Samineni S, Singh VK, Thudi M, Jaganathan D (2013). Fast-track introgression of “QTL-hotspot” for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea. The Plant Genome 6(3). (DOI: 10.3835/plantgenome2013.07.0022).
A “QTL-hotspot” containing quantitative trait loci (QTL) for several root and drought tolerance traits was transferred through marker-assisted backcrossing into JG 11, a leading variety of chickpea (Cicer arietinum L.) in India from the donor parent ICC 4958. Foreground selection with up to three simple sequence repeat markers, namely TAA170, ICCM0249, and STMS11, and background selection with up to 10 amplified fragment length polymorphism primer combinations was undertaken. After undertaking three backcrosses with foreground and background selection and selfing, 29 BC3F2 plants homozygous for two markers (ICCM0249 and TAA170) were selected and referred as introgression lines (ILs).
Varshney RK, Gaur PM, Chamarthi SK, Krishnamurthy L, Tripathi S, Kashiwagi J, Samineni S, Singh VK, Thudi M, Jaganathan D (2013). Fast-track introgression of “QTL-hotspot” for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea. The Plant Genome 6(3). (DOI: 10.3835/plantgenome2013.07.0022).
A “QTL-hotspot” containing quantitative trait loci (QTL) for several root and drought tolerance traits was transferred through marker-assisted backcrossing into JG 11, a leading variety of chickpea (Cicer arietinum L.) in India from the donor parent ICC 4958. Foreground selection with up to three simple sequence repeat markers, namely TAA170, ICCM0249, and STMS11, and background selection with up to 10 amplified fragment length polymorphism primer combinations was undertaken. After undertaking three backcrosses with foreground and background selection and selfing, 29 BC3F2 plants homozygous for two markers (ICCM0249 and TAA170) were selected and referred as introgression lines (ILs).
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.
