Journal articles 2012
Documents
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
Phenotyping chickpeas and pigeonpeas for adaptation to drought
Upadhyaya HD, Kashiwagi J, Varshney RK, Gaur PM, Saxena KB, Krishnamurthy L, Gowda CLL, Pundir RPS, Chaturvedi SK, Basu PS and Singh IP (2012). Phenotyping chickpeas and pigeonpeas for adaptation to drought. Frontiers in Plant Physiology 3:179. (DOI: 10.3389/fphys.2012.00179).
The chickpea and pigeonpea are protein-rich grain legumes used for human consumption in many countries. Grain yield of these crops is low to moderate in the semi-arid tropics with large variation due to high GxE interaction. In the Indian subcontinent chickpea is grown in the post-rainy winter season on receding soil moisture, and in other countries during the cool and dry post winter or spring seasons. The pigeonpea is sown during rainy season which flowers and matures in post-rainy season. The rainy months are hot and humid with diurnal temperature varying between 25 and 35˚C (maximum) and 20 and 25˚C (minimum) with an erratic rainfall. The available soil water during post-rainy season is about 200–250 mm which is bare minimum to meet the normal evapotranspiration. Thus occur- rence of drought is frequent and at varying degrees. To enhance productivity of these crops cultivars tolerant to drought need to be developed.
Upadhyaya HD, Kashiwagi J, Varshney RK, Gaur PM, Saxena KB, Krishnamurthy L, Gowda CLL, Pundir RPS, Chaturvedi SK, Basu PS and Singh IP (2012). Phenotyping chickpeas and pigeonpeas for adaptation to drought. Frontiers in Plant Physiology 3:179. (DOI: 10.3389/fphys.2012.00179).
The chickpea and pigeonpea are protein-rich grain legumes used for human consumption in many countries. Grain yield of these crops is low to moderate in the semi-arid tropics with large variation due to high GxE interaction. In the Indian subcontinent chickpea is grown in the post-rainy winter season on receding soil moisture, and in other countries during the cool and dry post winter or spring seasons. The pigeonpea is sown during rainy season which flowers and matures in post-rainy season. The rainy months are hot and humid with diurnal temperature varying between 25 and 35˚C (maximum) and 20 and 25˚C (minimum) with an erratic rainfall. The available soil water during post-rainy season is about 200–250 mm which is bare minimum to meet the normal evapotranspiration. Thus occur- rence of drought is frequent and at varying degrees. To enhance productivity of these crops cultivars tolerant to drought need to be developed.
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.
Phenotyping maize for adaptation to drought
Araus JL, Serret MD, Edmeades GO (2012). Phenotyping maize for adaptation to drought. Frontiers in Plant Physiology 3:305. (DOI: 10.3389/fphys.2012.00305).
The need of a better adaptation of crops to drought is an issue of increasing urgency. However, enhancing the tolerance of maize has, therefore, proved to be somewhat elusive in terms of plant breeding. In that context, proper phenotyping remains as one of the main factors limiting breeding advance. Topics covered by this review include the conceptual framework for identifying secondary traits associated with yield response to drought and how to measure these secondary traits in practice.
Araus JL, Serret MD, Edmeades GO (2012). Phenotyping maize for adaptation to drought. Frontiers in Plant Physiology 3:305. (DOI: 10.3389/fphys.2012.00305).
The need of a better adaptation of crops to drought is an issue of increasing urgency. However, enhancing the tolerance of maize has, therefore, proved to be somewhat elusive in terms of plant breeding. In that context, proper phenotyping remains as one of the main factors limiting breeding advance. Topics covered by this review include the conceptual framework for identifying secondary traits associated with yield response to drought and how to measure these secondary traits in practice.
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
Markers for breeding heat-tolerant cowpea
Lucas MR, Ehlers JD, Huynh BL, Diop NN, Roberts PA, and Close TJ (2012). Markers for breeding heat-tolerant cowpea. Molecular Breeding published online 13 November 2012. Also printed in 2013. (DOI: 10.1007/s11032-012-9810-z.) (G6010.02/G7010.07.01). Not open access: view online
Lucas MR, Ehlers JD, Huynh BL, Diop NN, Roberts PA, and Close TJ (2012). Markers for breeding heat-tolerant cowpea. Molecular Breeding published online 13 November 2012. Also printed in 2013. (DOI: 10.1007/s11032-012-9810-z.) (G6010.02/G7010.07.01). Not open access: view online
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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Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome
Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JD, Varshney RK (2012). Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. American Journal of Botany 99(2):186–192. (DOI: 10.3732/ajb.1100419). Not open access: view abstract
Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JD, Varshney RK (2012). Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. American Journal of Botany 99(2):186–192. (DOI: 10.3732/ajb.1100419). Not open access: view abstract
Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies
Xu P, X Wu, Wang B, Luo J, Liu Y, Ehlers JD, Close TJ, Roberts PA, Lu Z, Wang S and Li G (2012). Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies. Heredity 109:34–40. (DOI:10.1038/hdy.2012.8). (G6010.02/G7010.07.01). Not open access: view abstract online
Xu P, X Wu, Wang B, Luo J, Liu Y, Ehlers JD, Close TJ, Roberts PA, Lu Z, Wang S and Li G (2012). Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies. Heredity 109:34–40. (DOI:10.1038/hdy.2012.8). (G6010.02/G7010.07.01). Not open access: view abstract online
Advances in Arachis genomics for peanut improvement
Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK (2012). Advances in Arachis genomics for peanut improvement. Biotechnology Advances 30(3):639–651. ISSN 0734-9750. (DOI: 10.1016/j.biotechadv.2011.11.001). Not open access: view abstract
Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK (2012). Advances in Arachis genomics for peanut improvement. Biotechnology Advances 30(3):639–651. ISSN 0734-9750. (DOI: 10.1016/j.biotechadv.2011.11.001). Not open access: view abstract
