Journal articles 2012
Documents
Phenotyping for drought adaptation in wheat using physiological traits
Monneveux P, Jing R, Misra SC (2012). Phenotyping for drought adaptation in wheat using physiological traits. Frontiers in Plant Physiology 3:429. (DOI: 10.3389/fphys.2012.00429).
Wheat (Triticum spp) is one of the first domesticated food crops. It represents the first source of calories (after rice) and an important source of proteins in developing countries. As a result of the Green Revolution, wheat yield sharply increased due to the use of improved varieties, irrigation, pesticides, and fertilizers. The rate of increase in world wheat production, however, slowed after 1980, except in China, India, and Pakistan. Being adapted to a wide range of moisture conditions, wheat is grown on more land area worldwide than any other crop, including in drought prone areas. In these marginal rain-fed environments where at least 60 m ha of wheat is grown, amount and distribution of rainfall are the predominant factors influencing yield variability. Intensive work has been carried out in the area of drought adaptation over the last decades. Breeding strategies for drought tolerance improvement include: definition of the target environment, choice and characterization of the testing environment, water stress management and characterization, and use of phenotyping traits with high heritability. The use of integrative traits, facilitated by the development and application of new technologies (thermal imaging, spectral reflectance, stable isotopes) is facilitating high throughput phenotyping and indirect selection, consequently favoring yield improvement in drought prone environments.
Monneveux P, Jing R, Misra SC (2012). Phenotyping for drought adaptation in wheat using physiological traits. Frontiers in Plant Physiology 3:429. (DOI: 10.3389/fphys.2012.00429).
Wheat (Triticum spp) is one of the first domesticated food crops. It represents the first source of calories (after rice) and an important source of proteins in developing countries. As a result of the Green Revolution, wheat yield sharply increased due to the use of improved varieties, irrigation, pesticides, and fertilizers. The rate of increase in world wheat production, however, slowed after 1980, except in China, India, and Pakistan. Being adapted to a wide range of moisture conditions, wheat is grown on more land area worldwide than any other crop, including in drought prone areas. In these marginal rain-fed environments where at least 60 m ha of wheat is grown, amount and distribution of rainfall are the predominant factors influencing yield variability. Intensive work has been carried out in the area of drought adaptation over the last decades. Breeding strategies for drought tolerance improvement include: definition of the target environment, choice and characterization of the testing environment, water stress management and characterization, and use of phenotyping traits with high heritability. The use of integrative traits, facilitated by the development and application of new technologies (thermal imaging, spectral reflectance, stable isotopes) is facilitating high throughput phenotyping and indirect selection, consequently favoring yield improvement in drought prone environments.
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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Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes
Hiremath PJ, Kumar A, Penmetsa RV, Farmer A, Schlueter JA, Chamarthi SK, Whaley AM, Carrasquilla-Garcia N, Gaur PM, Upadhyaya HD, Kavi Kishor PB, Shah TM, Cook DR and Varshney RK (2012). Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnology Journal published online: 17pp. (DOI: 10.1111/j.1467-7652.2012.00710.x)
Hiremath PJ, Kumar A, Penmetsa RV, Farmer A, Schlueter JA, Chamarthi SK, Whaley AM, Carrasquilla-Garcia N, Gaur PM, Upadhyaya HD, Kavi Kishor PB, Shah TM, Cook DR and Varshney RK (2012). Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnology Journal published online: 17pp. (DOI: 10.1111/j.1467-7652.2012.00710.x)
Water extraction and root traits in Oryza sativa × Oryza glaberrima introgression lines under different soil moisture regimes
Kijoji AA, Nchimbi-Msolla S, Kanyeka ZL, Klassen SP, Serraj R, Henry A (2012). Water extraction and root traits in Oryza sativa × Oryza glaberrima introgression lines under different soil moisture regimes. Functional Plant Biology 40:54–66. (DOI: 10.1071/FP12163). (G3008.06). Not open access: view abstract
Kijoji AA, Nchimbi-Msolla S, Kanyeka ZL, Klassen SP, Serraj R, Henry A (2012). Water extraction and root traits in Oryza sativa × Oryza glaberrima introgression lines under different soil moisture regimes. Functional Plant Biology 40:54–66. (DOI: 10.1071/FP12163). (G3008.06). Not open access: view abstract
Root attributes affecting water uptake of rice (Oryza sativa) under drought
Henry A, Cal AJ, Batoto TC, Torres RO, Serraj R (2012). Root attributes affecting water uptake of rice (Oryza sativa) under drought. Journal of Experimental Botany 63(13):4751–4763. (DOI: 10.1093/jxb/ers150). (G3008.06).
Lowland rice roots have a unique physiological response to drought because of their adaptation to flooded soil. Rice root attributes that facilitate growth under flooded conditions may affect rice response to drought, but the relative roles of root structural and functional characteristics for water uptake under drought in rice are not known. Morphological, anatomical, biochemical, and molecular attributes of soil-grown rice roots were measured to investigate the genotypic variability and genotype×environment interactions of water uptake under variable soil water regimes. Drought-resistant genotypes had the lowest night-time bleeding rates of sap from the root system in the field. Diurnal fluctuation predominated as the strongest source of variation for bleeding rates in the field and root hydraulic conductivity (Lpr) in the greenhouse, and was related to expression trends of various PIP and TIP aquapor- ins. Root anatomy was generally more responsive to drought treatments in drought-resistant genotypes. Suberization and compaction of sclerenchyma layer cells decreased under drought, whereas suberization of the endodermis increased, suggesting differential roles of these two cell layers for the retention of oxygen under flooded conditions (sclerenchyma layer) and retention of water under drought (endodermis). The results of this study point to the genetic variability in responsiveness to drought of rice roots in terms of morphology, anatomy, and function.
Henry A, Cal AJ, Batoto TC, Torres RO, Serraj R (2012). Root attributes affecting water uptake of rice (Oryza sativa) under drought. Journal of Experimental Botany 63(13):4751–4763. (DOI: 10.1093/jxb/ers150). (G3008.06).
Lowland rice roots have a unique physiological response to drought because of their adaptation to flooded soil. Rice root attributes that facilitate growth under flooded conditions may affect rice response to drought, but the relative roles of root structural and functional characteristics for water uptake under drought in rice are not known. Morphological, anatomical, biochemical, and molecular attributes of soil-grown rice roots were measured to investigate the genotypic variability and genotype×environment interactions of water uptake under variable soil water regimes. Drought-resistant genotypes had the lowest night-time bleeding rates of sap from the root system in the field. Diurnal fluctuation predominated as the strongest source of variation for bleeding rates in the field and root hydraulic conductivity (Lpr) in the greenhouse, and was related to expression trends of various PIP and TIP aquapor- ins. Root anatomy was generally more responsive to drought treatments in drought-resistant genotypes. Suberization and compaction of sclerenchyma layer cells decreased under drought, whereas suberization of the endodermis increased, suggesting differential roles of these two cell layers for the retention of oxygen under flooded conditions (sclerenchyma layer) and retention of water under drought (endodermis). The results of this study point to the genetic variability in responsiveness to drought of rice roots in terms of morphology, anatomy, and function.
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
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
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
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).
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
