Journal articles 2007
Documents
Use of crop models to understand genotype by environment interactions for drought in real-world and simulated plant breeding trials
Chapman SC (2008). Use of crop models to understand genotype by environment interactions for drought in real-world and simulated plant breeding trials. Euphytica published online 4 December 2007. Also printed in 2008. (DOI: 10.1007/s10681-007-9623-z). Not open access: view abstract
Chapman SC (2008). Use of crop models to understand genotype by environment interactions for drought in real-world and simulated plant breeding trials. Euphytica published online 4 December 2007. Also printed in 2008. (DOI: 10.1007/s10681-007-9623-z). Not open access: view abstract
Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.)
Blair MW, Díaz JM, Hidalgo R, Díaz LM, Duque MC (2007). Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.). Theoretical Applied Genetics 116(1): 29–43. (DOI: 10.1007/s00122-007-0644-8). Not open access: view abstract
Blair MW, Díaz JM, Hidalgo R, Díaz LM, Duque MC (2007). Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.). Theoretical Applied Genetics 116(1): 29–43. (DOI: 10.1007/s00122-007-0644-8). Not open access: view abstract
Bacteriophage lambda genomic library construction of Oryza sativa L. var. Pokkali
Rahman S, Masa-aki Ohto, Seraj S and Blumwald E (2007). Bacteriophage lambda genomic library construction of Oryza sativa L. var. Pokkali. Plant Tissue Culture and Biotechnology 17(2):149–159. (DOI: 10.3329/ptcb.v17i2.3235).
A major QTL called ‘Saltol’ on rice chromosome 1 has been identified as linked to salinity tolerance traits of the landrace, Pokkali. A genomic library of Pokkali rice variety was constructed in bacteriophage Lamda Fix II with 20 kb inserts. Plaques containing genes implicated to salt tolerance have been identified using probes homologous to S-Ad methionine synthetase (SAM) and cation chloride co-transporter after two rounds of hybridization. Clearly demarcated plaques of the two clones of interest have been lifted out for DNA isolation and subsequent characterization to be followed by subcloning into TAC vectors for Agrobacterium-mediated transformation of large genomic fragments into sensitive rice.
Rahman S, Masa-aki Ohto, Seraj S and Blumwald E (2007). Bacteriophage lambda genomic library construction of Oryza sativa L. var. Pokkali. Plant Tissue Culture and Biotechnology 17(2):149–159. (DOI: 10.3329/ptcb.v17i2.3235).
A major QTL called ‘Saltol’ on rice chromosome 1 has been identified as linked to salinity tolerance traits of the landrace, Pokkali. A genomic library of Pokkali rice variety was constructed in bacteriophage Lamda Fix II with 20 kb inserts. Plaques containing genes implicated to salt tolerance have been identified using probes homologous to S-Ad methionine synthetase (SAM) and cation chloride co-transporter after two rounds of hybridization. Clearly demarcated plaques of the two clones of interest have been lifted out for DNA isolation and subsequent characterization to be followed by subcloning into TAC vectors for Agrobacterium-mediated transformation of large genomic fragments into sensitive rice.
Exploiting the functionality of root systems for dry, saline, and nutrient deficient environments in a changing climate
Vadez V, Krishnamurthy L, Kashiwagi JW, Kholova J, Devi JM, Sharma KK, Bhatnagar-Mathur P, Hoisington DA, Hash CT, Bidinger FR, and Keatinge JDH (2007). Exploiting the functionality of root systems for dry, saline, and nutrient deficient environments in a changing climate. Journal of SAT Agricultural Research 4(1): 64pp. (Special Symposium edition).
Increasing episodes of drought, lack of sufficient nutrients, exposure to toxic minerals, and soil compaction are just a few examples of the environmental constraints that the roots are exposed to during plant growth. Understanding how roots respond to these stresses is crucial for improving crop production under such conditions. Yet, investigating roots is a very difficult task and, therefore, very little is known about the precise role that the roots play in contributing to plant adaptation to hostile environments.
Vadez V, Krishnamurthy L, Kashiwagi JW, Kholova J, Devi JM, Sharma KK, Bhatnagar-Mathur P, Hoisington DA, Hash CT, Bidinger FR, and Keatinge JDH (2007). Exploiting the functionality of root systems for dry, saline, and nutrient deficient environments in a changing climate. Journal of SAT Agricultural Research 4(1): 64pp. (Special Symposium edition).
Increasing episodes of drought, lack of sufficient nutrients, exposure to toxic minerals, and soil compaction are just a few examples of the environmental constraints that the roots are exposed to during plant growth. Understanding how roots respond to these stresses is crucial for improving crop production under such conditions. Yet, investigating roots is a very difficult task and, therefore, very little is known about the precise role that the roots play in contributing to plant adaptation to hostile environments.
Extending the repertoire of microsatellite markers for genetic linkage mapping and germplasm screening in chickpea
Varshney RK, Horres R, Molina C, Nayak S, Jungmann R, Swamy P, Winter P, Jayashree B, Kahl G and Hoisington DA (2007). Extending the repertoire of microsatellite markers for genetic linkage mapping and germplasm screening in chickpea. Journal of SAT Agricultural Research 5(1):3pp.
Molecular markers and genetic linkage maps are the prerequisites for undertaking molecular breeding activities. However, the progress towards development of a reasonable number of molecular markers has been very slow in cultivated species of chickpea (Cicer arietinum). One of the main reasons for this may be attributed to the low level of genetic diversity present in the cultivated gene pools of these species, at least with the detection tools that are currently available. Among various molecular markers currently available, microsatellite or SSR (simple sequence repeat) markers are often chosen as the preferred markers for a variety of applications in breeding because of their multi-allelic nature, co-dominant inheritance, relative abundance and extensive genome coverage (Gupta and Varshney 2000).
Varshney RK, Horres R, Molina C, Nayak S, Jungmann R, Swamy P, Winter P, Jayashree B, Kahl G and Hoisington DA (2007). Extending the repertoire of microsatellite markers for genetic linkage mapping and germplasm screening in chickpea. Journal of SAT Agricultural Research 5(1):3pp.
Molecular markers and genetic linkage maps are the prerequisites for undertaking molecular breeding activities. However, the progress towards development of a reasonable number of molecular markers has been very slow in cultivated species of chickpea (Cicer arietinum). One of the main reasons for this may be attributed to the low level of genetic diversity present in the cultivated gene pools of these species, at least with the detection tools that are currently available. Among various molecular markers currently available, microsatellite or SSR (simple sequence repeat) markers are often chosen as the preferred markers for a variety of applications in breeding because of their multi-allelic nature, co-dominant inheritance, relative abundance and extensive genome coverage (Gupta and Varshney 2000).
Development of cost-effective SNP assays for chickpea genome analysis and breeding
Varshney RK, Nayak S, Jayashree B, Eshwar K, Upadhyaya HD and Hoisington DA (2007). Development of cost-effective SNP assays for chickpea genome analysis and breeding. Journal of SAT Agricultural Research 3(1):29–31.
Although microsatellite or simple sequence repeat (SSR) markers have been the preferred markers for plant genetics and breeding, single nucleotide polymorphisms (SNPs) are the most common class that detect the smallest unit of genetic variation present in genomes (Rafalski 2002). Marker technologies exploiting the potential of SNPs provide the possibility of constructing genetic maps at 100-fold higher marker densities than with other types of DNA polymorphisms (Cho et al. 1999, Sachidanandam et al. 2001). Identification and mapping of SNPs has been initiated recently for crop species like rice (Oryza sativa) (Feltus et al. 2004), maize (Zea mays) (Tenaillon et al. 2001), wheat (Triticum aestivum) (Somers et al. 2003), barley (Hordeum vulgare) (Kota et al. 2001, Rostoks et al. 2005), ryegrass (Lolium multiflorum) (Miura et al. 2005) and rye (Secale cereale) (Varshney et al. 2007).
Varshney RK, Nayak S, Jayashree B, Eshwar K, Upadhyaya HD and Hoisington DA (2007). Development of cost-effective SNP assays for chickpea genome analysis and breeding. Journal of SAT Agricultural Research 3(1):29–31.
Although microsatellite or simple sequence repeat (SSR) markers have been the preferred markers for plant genetics and breeding, single nucleotide polymorphisms (SNPs) are the most common class that detect the smallest unit of genetic variation present in genomes (Rafalski 2002). Marker technologies exploiting the potential of SNPs provide the possibility of constructing genetic maps at 100-fold higher marker densities than with other types of DNA polymorphisms (Cho et al. 1999, Sachidanandam et al. 2001). Identification and mapping of SNPs has been initiated recently for crop species like rice (Oryza sativa) (Feltus et al. 2004), maize (Zea mays) (Tenaillon et al. 2001), wheat (Triticum aestivum) (Somers et al. 2003), barley (Hordeum vulgare) (Kota et al. 2001, Rostoks et al. 2005), ryegrass (Lolium multiflorum) (Miura et al. 2005) and rye (Secale cereale) (Varshney et al. 2007).
Relationship between carbon isotope discrimination and grain yield in spring wheat under different water regimes and under saline conditions in the Ningxia Province (North-west China)
Xu X, Yuan H, Li SH and Monneveux P (2007). Relationship between carbon isotope discrimination and grain yield in spring wheat under different water regimes and under saline conditions in the Ningxia Province (North-west China). Journal of Agronomy and Crop Science 193(6):422–434. (DOI: 10.1111/j.1439-037X.2007.00281.x). Not open access: view abstract
Xu X, Yuan H, Li SH and Monneveux P (2007). Relationship between carbon isotope discrimination and grain yield in spring wheat under different water regimes and under saline conditions in the Ningxia Province (North-west China). Journal of Agronomy and Crop Science 193(6):422–434. (DOI: 10.1111/j.1439-037X.2007.00281.x). Not open access: view abstract
Stress-inducible expression of At DREB1A in transgenic peanut (Arachis hypogaea L.) increases transpiration efficiency under water-limiting condition
Bhatnagar-Mathur P, Devi MJ, Reddy DS, Lavanya M, Vadez V, Serraj R, Yamaguchi-Shinozaki K and Sharma KK (2007). Stress-inducible expression of At DREB1A in transgenic peanut (Arachis hypogaea L.) increases transpiration efficiency under water-limiting conditions. Plant Cell Reports 26(12):2071–2082. (DOI: 10.1007/s00299-007-0406-8). Not open access: view abstract
Bhatnagar-Mathur P, Devi MJ, Reddy DS, Lavanya M, Vadez V, Serraj R, Yamaguchi-Shinozaki K and Sharma KK (2007). Stress-inducible expression of At DREB1A in transgenic peanut (Arachis hypogaea L.) increases transpiration efficiency under water-limiting conditions. Plant Cell Reports 26(12):2071–2082. (DOI: 10.1007/s00299-007-0406-8). Not open access: view abstract
A Ds-insertion mutant of OSH6 (Oryza sativa Homeobox 6) exhibits outgrowth of vestigial leaf-like structures, bracts, in rice
Park SH, Kim CM, Je BI, Park SH, Park SJ, Piao HL, Xuan YH, Choe MS, Satoh K, Kikuchi S, Lee KH, Cha YS, Ahn BO, Ji HS, Yun DW, Lee MC, Suh SC, Eun MY and Han CD (2007). A Ds-insertion mutant of OSH6 (Oryza sativa Homeobox 6) exhibits outgrowth of vestigial leaf-like structures, bracts, in rice. Planta 227(1):1–12. (DOI: 10.1007/s00425-007-0576-1). Not open access: view abstract
Park SH, Kim CM, Je BI, Park SH, Park SJ, Piao HL, Xuan YH, Choe MS, Satoh K, Kikuchi S, Lee KH, Cha YS, Ahn BO, Ji HS, Yun DW, Lee MC, Suh SC, Eun MY and Han CD (2007). A Ds-insertion mutant of OSH6 (Oryza sativa Homeobox 6) exhibits outgrowth of vestigial leaf-like structures, bracts, in rice. Planta 227(1):1–12. (DOI: 10.1007/s00425-007-0576-1). Not open access: view abstract
An integrated pipeline of open source software adapted for multi-CPU architectures: use in the large-scale identification of single nucleotide polymorphisms
Jayashree B, Hanspal MS, Srinivasan R, Vigneshwaran R, Varshney RK, Naya S, Eshwar K, Ramesh N, Chandra S and Hoisington DA (2007). An integrated pipeline of open source software adapted for multi-CPU architectures: use in the large-scale identification of single nucleotide polymorphisms. Comparative and Functional Genomics 2007, Article ID 35604 7 pp7. (DOI: 10.1155/2007/35604).
The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets.
Jayashree B, Hanspal MS, Srinivasan R, Vigneshwaran R, Varshney RK, Naya S, Eshwar K, Ramesh N, Chandra S and Hoisington DA (2007). An integrated pipeline of open source software adapted for multi-CPU architectures: use in the large-scale identification of single nucleotide polymorphisms. Comparative and Functional Genomics 2007, Article ID 35604 7 pp7. (DOI: 10.1155/2007/35604).
The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets.
