Journal articles 2012
Documents
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.
Full article
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.
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).
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
The future of grain legumes in cropping systems
Sinclair TR, Vadez V (2012). The future of grain legumes in cropping systems. Crop and Pasture Science 63, 501–512. (http://dx.doi.org/10.1071/CP12128). Not open access: view abstract
Sinclair TR, Vadez V (2012). The future of grain legumes in cropping systems. Crop and Pasture Science 63, 501–512. (http://dx.doi.org/10.1071/CP12128). Not open access: view abstract
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
Whole-genome scanning for mapping determinacy in Pigeonpea (Cajanus spp.)
Mir RR, Saxena RK, Saxena KB, Upadhyaya HD, Kilian A, Cook DR, Varshney RK (2012). Whole-genome scanning for mapping determinacy in Pigeonpea (Cajanus spp.). Plant Breeding Published online. (DOI: 10.1111/j.1439-0523.2012.02009.x). View abstract
Mir RR, Saxena RK, Saxena KB, Upadhyaya HD, Kilian A, Cook DR, Varshney RK (2012). Whole-genome scanning for mapping determinacy in Pigeonpea (Cajanus spp.). Plant Breeding Published online. (DOI: 10.1111/j.1439-0523.2012.02009.x). View abstract
Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice
Shrestha R, Matteis L, Skofic M, Portugal A, McLaren G, Hyman G and Arnaud E (2012). Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice. Frontiers in Physiology 3:326 pp. 1–10. (DOI: 10.3389/fphys.2012.00326). (G4009.03/G4010.06/G4011.01/G4011.10).
The Crop Ontology (CO) of the Generation Challenge Programme (GCP) (http://cropontology.org/) is developed for the Integrated Breeding Platform (https://www.integratedbreeding.net/) by several centers of The Consultative Group on International Agricultural Research (CGIAR): Bioversity, CIMMYT, CIP, ICRISAT, IITA, and IRRI. Integrated breeding necessitates that breeders access genotypic and phenotypic data related to a given trait. The Crop Ontology provides validated trait names used by the crop communities of practice for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries.
Shrestha R, Matteis L, Skofic M, Portugal A, McLaren G, Hyman G and Arnaud E (2012). Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice. Frontiers in Physiology 3:326 pp. 1–10. (DOI: 10.3389/fphys.2012.00326). (G4009.03/G4010.06/G4011.01/G4011.10).
The Crop Ontology (CO) of the Generation Challenge Programme (GCP) (http://cropontology.org/) is developed for the Integrated Breeding Platform (https://www.integratedbreeding.net/) by several centers of The Consultative Group on International Agricultural Research (CGIAR): Bioversity, CIMMYT, CIP, ICRISAT, IITA, and IRRI. Integrated breeding necessitates that breeders access genotypic and phenotypic data related to a given trait. The Crop Ontology provides validated trait names used by the crop communities of practice for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries.
Plant nutrition: Rooting for more phosphorus
Kochian LV (2012). Plant nutrition: Rooting for more phosphorus. Nature 488(7412):466–467. (DOI: 10.1038/488466a). Not open access: view abstract online
Kochian LV (2012). Plant nutrition: Rooting for more phosphorus. Nature 488(7412):466–467. (DOI: 10.1038/488466a). Not open access: view abstract online
The protein kinase PSTOL1 from traditional rice confers tolerance of phosphorus deficiency
Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M & Heuer S (2012). The protein kinase PSTOL1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488(7412):535–539. (DOI: 10.1038/nature11346). Not open access: view abstract online
Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M & Heuer S (2012). The protein kinase PSTOL1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488(7412):535–539. (DOI: 10.1038/nature11346). Not open access: view abstract online
