Journal articles 2012
Documents
Development of a Mesoamerican intra-genepool genetic map for quantitative trait loci detection in a drought tolerant × susceptible common bean (Phaseolus vulgaris L.) cross.
Blair MW, Galeano CH, Tovar E, Muñoz Torres MC, Velasco Castrillón A, Beebe SE, Rao IM (2012). Development of a Mesoamerican intra-genepool genetic map for quantitative trait loci detection in a drought tolerant × susceptible common bean (Phaseolus vulgaris L.) cross. Molecular Breeding 29(1):71–88 (DOI 10.1007/s11032-010-9527-9). Also published online in 2010.
Blair MW, Galeano CH, Tovar E, Muñoz Torres MC, Velasco Castrillón A, Beebe SE, Rao IM (2012). Development of a Mesoamerican intra-genepool genetic map for quantitative trait loci detection in a drought tolerant × susceptible common bean (Phaseolus vulgaris L.) cross. Molecular Breeding 29(1):71–88 (DOI 10.1007/s11032-010-9527-9). Also published online in 2010.
Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut
Macedo SE, Moretzsohn MC, Leal-Bertioli SC, Alves DM, Gouvea EG, Azevedo VC, Bertioli DJ (2012). Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut. BMC Research Notes 5:86 10pp. (DOI:10.1186/1756-0500-5-86). (G6010.01)
Macedo SE, Moretzsohn MC, Leal-Bertioli SC, Alves DM, Gouvea EG, Azevedo VC, Bertioli DJ (2012). Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut. BMC Research Notes 5:86 10pp. (DOI:10.1186/1756-0500-5-86). (G6010.01)
Detection and integration of gene mapping of downy mildew resistance in maize inbred lines though linkage and association
Phumichai C, Chunwongse J, Jampatong S, Grudloyma P, Pulam T, Doungchan W, Wongkaew A and Kongsiri N (2012). Detection and integration of gene mapping of downy mildew resistance in maize inbred lines though linkage and association. Euphytica 187(3):369–379 (DOI: 10.1007/s10681-012-0699-8). Not open access; view abstract. (G4007.04)
Phumichai C, Chunwongse J, Jampatong S, Grudloyma P, Pulam T, Doungchan W, Wongkaew A and Kongsiri N (2012). Detection and integration of gene mapping of downy mildew resistance in maize inbred lines though linkage and association. Euphytica 187(3):369–379 (DOI: 10.1007/s10681-012-0699-8). Not open access; view abstract. (G4007.04)
Current state-of-art of sequencing technologies for plant genomics research
Thudi M, Li Y, Jackson SA, May GD, Varshney RK (2012). Current state-of-art of sequencing technologies for plant genomics research. Briefings in Functional Genomics (2012) 11 (1): 3-11. (DOI: 10.1093/bfgp/elr045). Not open access: view abstract
Thudi M, Li Y, Jackson SA, May GD, Varshney RK (2012). Current state-of-art of sequencing technologies for plant genomics research. Briefings in Functional Genomics (2012) 11 (1): 3-11. (DOI: 10.1093/bfgp/elr045). Not open access: view abstract
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
Construction of chromosome segment substitution lines in peanut (Arachis hypogaea L.) using a wild synthetic and QTL mapping for plant morphology
Foncéka D, Tossim H-A, Rivallan R, Vignes H, Lacut E, De Bellis F, Faye I, Ndoye O, Leal-Bertioli SCM, Valls JFM, de Bellis F, Faye I, Ndoye O, Leal-Bertioli SCM, Valls JFM, Bertioli DJ, Glaszmann J-C, Courtois B, Rami J-F* (2012). Construction of chromosome segment substitution lines in peanut (Arachis hypogaea L.) using a wild synthetic and QTL mapping for plant morphology. PLoS ONE 7(11):e48642 (DOI:10.1371/journal.pone.0048642). (G3005.05, G4008.49, G4007.13.03).
Chromosome segment substitution lines (CSSLs) are powerful QTL mapping populations that have been used to elucidate the molecular basis of interesting traits of wild species. Cultivated peanut is an allotetraploid with limited genetic diversity. Capturing the genetic diversity from peanut wild relatives is an important objective in many peanut breeding programs. In this study, we used a marker-assisted backcrossing strategy to produce a population of 122 CSSLs from the cross between the wild synthetic allotetraploid (A. ipae¨nsis6A. duranensis)4x and the cultivated Fleur11 variety.
Foncéka D, Tossim H-A, Rivallan R, Vignes H, Lacut E, De Bellis F, Faye I, Ndoye O, Leal-Bertioli SCM, Valls JFM, de Bellis F, Faye I, Ndoye O, Leal-Bertioli SCM, Valls JFM, Bertioli DJ, Glaszmann J-C, Courtois B, Rami J-F* (2012). Construction of chromosome segment substitution lines in peanut (Arachis hypogaea L.) using a wild synthetic and QTL mapping for plant morphology. PLoS ONE 7(11):e48642 (DOI:10.1371/journal.pone.0048642). (G3005.05, G4008.49, G4007.13.03).
Chromosome segment substitution lines (CSSLs) are powerful QTL mapping populations that have been used to elucidate the molecular basis of interesting traits of wild species. Cultivated peanut is an allotetraploid with limited genetic diversity. Capturing the genetic diversity from peanut wild relatives is an important objective in many peanut breeding programs. In this study, we used a marker-assisted backcrossing strategy to produce a population of 122 CSSLs from the cross between the wild synthetic allotetraploid (A. ipae¨nsis6A. duranensis)4x and the cultivated Fleur11 variety.
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Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64
Sharoni AM, Nuruzzaman M, Satoh K, Moumeni A, Attia K, Venuprasad R, Serraj R, Kumar A, Leung H, RaWul Islam AKM, Kikuchi S (2012). Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. Molecular Genetics and Genomics 287(1):1–19. (DOI: 10.1007/s00438-011-0659-3).
Sharoni AM, Nuruzzaman M, Satoh K, Moumeni A, Attia K, Venuprasad R, Serraj R, Kumar A, Leung H, RaWul Islam AKM, Kikuchi S (2012). Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. Molecular Genetics and Genomics 287(1):1–19. (DOI: 10.1007/s00438-011-0659-3).
Can genomics boost productivity of orphan crops?
Varshney RK, Ribaut J-M , Buckler ES, Tuberosa R, Rafalski JA and Langridge P (2012). Can genomics boost productivity of orphan crops? Nature Biotechnology 30:1172–1176. (DOI: 10.1038/nbt.2440).
Advances in genomics over the past 20 years have enhanced the precision and efficiency of breeding programsin many temperate cereal crops. One of the first applications of genomics-assisted breeding has been the introgression of loci for resistance to biotic stresses or major quantitative trait loci (QTLs) for tolerance to abiotic stresses into elite genotypes through marker-assisted backcrossing (MABC)4. For instance, introgression of a major QTL for submergence tolerance (Sub1) into widely grown rice varieties has substantially improved yield in >15 million hectares of rain-fed low-land rice in South and Southeast Asia5. Despite this success story, the overall adoption of genomics-assisted breeding in developing countries is still limited especially for complex traits like yield under environmental stress in several other crops.
Varshney RK, Ribaut J-M , Buckler ES, Tuberosa R, Rafalski JA and Langridge P (2012). Can genomics boost productivity of orphan crops? Nature Biotechnology 30:1172–1176. (DOI: 10.1038/nbt.2440).
Advances in genomics over the past 20 years have enhanced the precision and efficiency of breeding programsin many temperate cereal crops. One of the first applications of genomics-assisted breeding has been the introgression of loci for resistance to biotic stresses or major quantitative trait loci (QTLs) for tolerance to abiotic stresses into elite genotypes through marker-assisted backcrossing (MABC)4. For instance, introgression of a major QTL for submergence tolerance (Sub1) into widely grown rice varieties has substantially improved yield in >15 million hectares of rain-fed low-land rice in South and Southeast Asia5. Despite this success story, the overall adoption of genomics-assisted breeding in developing countries is still limited especially for complex traits like yield under environmental stress in several other crops.
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.
Breeding the Thai jasmine rice variety KDML105 for non-age related broad-spectrum resistance to bacterial blight disease based on combined marker-assisted and phenotypic selection
Win KM, Korinsak S, Jantaboon J, Siangliw M, Lanceras-Siangliw J, Sirithunya P, Vanavichit A, Pantuwan G, Jongdee B, Sidhiwong N and Toojinda T (2012). Breeding the Thai jasmine rice variety KDML105 for non-age related broad-spectrum resistance to bacterial blight disease based on combined marker-assisted and phenotypic selection. Field Crops Research 137:186–194. (DOI: 10.1016/j.fcr.2012.09.007). (G4009.09). Not open access: view abstract
Win KM, Korinsak S, Jantaboon J, Siangliw M, Lanceras-Siangliw J, Sirithunya P, Vanavichit A, Pantuwan G, Jongdee B, Sidhiwong N and Toojinda T (2012). Breeding the Thai jasmine rice variety KDML105 for non-age related broad-spectrum resistance to bacterial blight disease based on combined marker-assisted and phenotypic selection. Field Crops Research 137:186–194. (DOI: 10.1016/j.fcr.2012.09.007). (G4009.09). Not open access: view abstract
