Journal articles 2012
Documents
Markers for quantitative inheritance of resistance to foliar thrips in cowpea
Lucas MR, Ehlers JD, Roberts PA, Close TJ (2012). Markers for quantitative inheritance of resistance to foliar thrips in cowpea. Crop Science 52(5):2075–2081. (DOI:10.2135/cropsci2011.12.0684). (G6010.02/G7010.07.01). Not open access: view abstract
Lucas MR, Ehlers JD, Roberts PA, Close TJ (2012). Markers for quantitative inheritance of resistance to foliar thrips in cowpea. Crop Science 52(5):2075–2081. (DOI:10.2135/cropsci2011.12.0684). (G6010.02/G7010.07.01). Not open access: view abstract
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
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).
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Approaches towards nitrogen- and phosphorus-efficient rice
Vinod KK, Heuer S (2012). Approaches towards nitrogen- and phosphorus-efficient rice. AoB PLANTS 2012: pls028; (DOI:10.1093/aobpla/pls028).
For thedevelopment of nutrient-efficient rice,a holistic approach should be followed combining optimized fertilizer management with enhanced nutrient uptake via a vigorous root system, leading to increased grain filling and yield. Despite an increasing number of N- and P-related genes and QTLs being reported, very feware actively used inmolecular breeding programmes. The complex regulation of N- and P-related pathways challenges breeders and the research community to identify large-effect genes/QTLs. For this it will be important to focus more on the analysis of tolerant genotypes rather than model plants, since tolerance pathways may employ a different set of genes.
Vinod KK, Heuer S (2012). Approaches towards nitrogen- and phosphorus-efficient rice. AoB PLANTS 2012: pls028; (DOI:10.1093/aobpla/pls028).
For thedevelopment of nutrient-efficient rice,a holistic approach should be followed combining optimized fertilizer management with enhanced nutrient uptake via a vigorous root system, leading to increased grain filling and yield. Despite an increasing number of N- and P-related genes and QTLs being reported, very feware actively used inmolecular breeding programmes. The complex regulation of N- and P-related pathways challenges breeders and the research community to identify large-effect genes/QTLs. For this it will be important to focus more on the analysis of tolerant genotypes rather than model plants, since tolerance pathways may employ a different set of genes.
TaWIR1 contributes to post-penetration resistance to Magnaporthe oryzae, but not Blumeria graminis f. sp. tritici in wheat
Tufan HA, McGrann GRD, MacCormack R and Boyd LA (2012). TaWIR1 contributes to post-penetration resistance to Magnaporthe oryzae, but not Blumeria graminis f. sp. tritici in wheat. Molecular Plant Pathology 13(7):653–665 (DOI: 10.1111/j.1364-3703.2011.00775.x). Not open access; view abstract. (G3005.11)
Tufan HA, McGrann GRD, MacCormack R and Boyd LA (2012). TaWIR1 contributes to post-penetration resistance to Magnaporthe oryzae, but not Blumeria graminis f. sp. tritici in wheat. Molecular Plant Pathology 13(7):653–665 (DOI: 10.1111/j.1364-3703.2011.00775.x). Not open access; view abstract. (G3005.11)
Genetic diversity in Iranian chickpea (Cicer arietinum L.) landraces as revealed by microsatellite markers
Naghavi MR, Monfared SR and Gomez H (2012). Genetic diversity in Iranian chickpea (Cicer arietinum L.) landraces as revealed by microsatellite markers. Czech Journal of Genetics and Plant Breeding 48(3):131–138.
Abstract: To estimate the genetic diversity of chickpea germplasm from Iran, a total of 307 landraces from 4 regions including: northern areas (29 from Ardebil, 3 from Qazvin and 5 from Mazanderan provinces), temperate (16 from Kermanshah, 2 from Semnan, 54 from Khorasan and 20 from Kerman provinces), semi-arid (28 from Ghom and 56 from Isfahan provinces) and cold areas (15 from West Azarbayjan, 52 from Tehran and 27 from East Azarbayjan provinces) were analysed using 16 microsatellite loci. The number of alleles per microsatellite locus ranged from 8 to 29, with an average of 19.31 per locus. A high level of genetic diversity in the northern area (He = 0.76), even with a limited number of available landraces (37) compared with the other three regions (84–94), might confirm the northern Persia as part of the chickpea centre of origin. The neighbour-joining tree showed a low relationship between molecular divergence and the geographical grouping of chickpea. Moreover, cluster analyses based on molecular data showed that the northern area was separated clearly from the other three regions, indicating a physical barrier or geographical and environmental differences among these regions. A wide genetic diversity of Iranian chickpea landraces is a critical component for future selection and use of this germplasm for future breeding of chickpea.
Naghavi MR, Monfared SR and Gomez H (2012). Genetic diversity in Iranian chickpea (Cicer arietinum L.) landraces as revealed by microsatellite markers. Czech Journal of Genetics and Plant Breeding 48(3):131–138.
Abstract: To estimate the genetic diversity of chickpea germplasm from Iran, a total of 307 landraces from 4 regions including: northern areas (29 from Ardebil, 3 from Qazvin and 5 from Mazanderan provinces), temperate (16 from Kermanshah, 2 from Semnan, 54 from Khorasan and 20 from Kerman provinces), semi-arid (28 from Ghom and 56 from Isfahan provinces) and cold areas (15 from West Azarbayjan, 52 from Tehran and 27 from East Azarbayjan provinces) were analysed using 16 microsatellite loci. The number of alleles per microsatellite locus ranged from 8 to 29, with an average of 19.31 per locus. A high level of genetic diversity in the northern area (He = 0.76), even with a limited number of available landraces (37) compared with the other three regions (84–94), might confirm the northern Persia as part of the chickpea centre of origin. The neighbour-joining tree showed a low relationship between molecular divergence and the geographical grouping of chickpea. Moreover, cluster analyses based on molecular data showed that the northern area was separated clearly from the other three regions, indicating a physical barrier or geographical and environmental differences among these regions. A wide genetic diversity of Iranian chickpea landraces is a critical component for future selection and use of this germplasm for future breeding of chickpea.
Phenotyping for drought tolerance of crops in the genomics era
Tuberosa R (2012). Phenotyping for drought tolerance of crops in the genomics era. Frontiers in Plant Physiology 3:347. (DOI: 10.3389/fphys.2012.00347).
Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars
Tuberosa R (2012). Phenotyping for drought tolerance of crops in the genomics era. Frontiers in Plant Physiology 3:347. (DOI: 10.3389/fphys.2012.00347).
Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars
Field evaluation on functional roles of root plastic responses on dry matter production and grain yield of rice under cycles of transient soil moisture stresses using chromosome segment substitution lines
Niones JM, Suralta RR, Inukai Y and Yamauchi A (2012). Field evaluation on functional roles of root plastic responses on dry matter production and grain yield of rice under cycles of transient soil moisture stresses using chromosome segment substitution lines. Plant and Soil 359(1-2):107–120. (DOI: 10.1007/s11104-012-1178-7). (G3008.06). Not open access: view abstract
Niones JM, Suralta RR, Inukai Y and Yamauchi A (2012). Field evaluation on functional roles of root plastic responses on dry matter production and grain yield of rice under cycles of transient soil moisture stresses using chromosome segment substitution lines. Plant and Soil 359(1-2):107–120. (DOI: 10.1007/s11104-012-1178-7). (G3008.06). Not open access: view abstract
![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.
Breeding strategies for adaptation of pearl millet and sorghum to climate variability and change in West Africa
Haussmann BIG, Rattunde FH, Weltzien-Rattunde E, Traoré PSC, vom Brocke K, Parzies HK (2012). Breeding strategies for adaptation of pearl millet and sorghum to climate variability and change in West Africa. Journal of Agronomy and Crop Science, 198(5):327–339. (DOI: 10.1111/j.1439-037X.2012.00526.x). (G7010.03.03). Not open access: view abstract
Haussmann BIG, Rattunde FH, Weltzien-Rattunde E, Traoré PSC, vom Brocke K, Parzies HK (2012). Breeding strategies for adaptation of pearl millet and sorghum to climate variability and change in West Africa. Journal of Agronomy and Crop Science, 198(5):327–339. (DOI: 10.1111/j.1439-037X.2012.00526.x). (G7010.03.03). Not open access: view abstract
