Journal articles 2012
Documents
Analysis of constituents for phenotyping drought tolerance in crop improvement
Setter TL (2012). Analysis of constituents for phenotyping drought tolerance in crop improvement. Frontiers in Physiology 3:180. (DOI: 10.3389/fphys.2012.00180).
Investigators now have a wide range of analytical tools to use in measuring metabolites, proteins and transcripts in plant tissues. These tools have the potential to assist genetic studies that seek to phenotype genetic lines for heritable traits that contribute to drought tolerance. To be useful for crop breeding, hundreds or thousands of genetic lines must be assessed. This review considers the utility of assaying certain constituents with roles in drought tolerance for phenotyping genotypes. Abscisic acid (ABA), organic and inorganic osmolytes, compatible solutes, and late embryogenesis abundant proteins, are considered. Confounding effects that require appropriate tissue and timing specificity, and the need for high-throughput and analytical cost efficiency are discussed. With future advances in analytical methods and the value of analyzing constituents that provide information on the underlying mechanisms of drought tolerance, these approaches are expected to contribute to development crops with improved drought tolerance.
Setter TL (2012). Analysis of constituents for phenotyping drought tolerance in crop improvement. Frontiers in Physiology 3:180. (DOI: 10.3389/fphys.2012.00180).
Investigators now have a wide range of analytical tools to use in measuring metabolites, proteins and transcripts in plant tissues. These tools have the potential to assist genetic studies that seek to phenotype genetic lines for heritable traits that contribute to drought tolerance. To be useful for crop breeding, hundreds or thousands of genetic lines must be assessed. This review considers the utility of assaying certain constituents with roles in drought tolerance for phenotyping genotypes. Abscisic acid (ABA), organic and inorganic osmolytes, compatible solutes, and late embryogenesis abundant proteins, are considered. Confounding effects that require appropriate tissue and timing specificity, and the need for high-throughput and analytical cost efficiency are discussed. With future advances in analytical methods and the value of analyzing constituents that provide information on the underlying mechanisms of drought tolerance, these approaches are expected to contribute to development crops with improved drought tolerance.
Phenotyping cowpeas for adaptation to drought
Hall A (2012). Phenotyping cowpeas for adaptation to drought. Frontiers in Plant Physiology 3:155. (DOI: 10.3389/fphys.2012.00155).
Methods for phenotyping cowpeas for adaptation to drought are reviewed. Key factors involve achieving optimal time of flowering and cycle length, and appropriate morphology for different types of cultivars as they relate to their utilization for dry grain, hay, and fresh pea production. Strong resistance to vegetative-stage drought is available and should be incorporated.The extreme ability of extra-early erect cowpea cultivars to escape terminal drought should be exploited in zones with very short rainfall seasons. In zones with the possibility of limited rainfall in the middle of the growing season,resistance to mid-season drought, and the delayed-leaf-senescence trait can be valuable. Breeding for water-us e efficiency, deeper rooting, and heat tolerance are discussed. Diseases and pests that influence adaptation to drought are considered. Resistance to the organism causing ashy stem blight disease should be incorporated because this disease can destroy cowpea seedlings under hot, dry soil conditions. The value of varietal intercrops with contrasting types of cowpea cultivars in enhancing adaptation to drought is described. Implications of cowpea/cereal rotations for cowpea breeding are discussed. Breeding strategies for enhancing cowpea adaptation to drought are described.
Hall A (2012). Phenotyping cowpeas for adaptation to drought. Frontiers in Plant Physiology 3:155. (DOI: 10.3389/fphys.2012.00155).
Methods for phenotyping cowpeas for adaptation to drought are reviewed. Key factors involve achieving optimal time of flowering and cycle length, and appropriate morphology for different types of cultivars as they relate to their utilization for dry grain, hay, and fresh pea production. Strong resistance to vegetative-stage drought is available and should be incorporated.The extreme ability of extra-early erect cowpea cultivars to escape terminal drought should be exploited in zones with very short rainfall seasons. In zones with the possibility of limited rainfall in the middle of the growing season,resistance to mid-season drought, and the delayed-leaf-senescence trait can be valuable. Breeding for water-us e efficiency, deeper rooting, and heat tolerance are discussed. Diseases and pests that influence adaptation to drought are considered. Resistance to the organism causing ashy stem blight disease should be incorporated because this disease can destroy cowpea seedlings under hot, dry soil conditions. The value of varietal intercrops with contrasting types of cowpea cultivars in enhancing adaptation to drought is described. Implications of cowpea/cereal rotations for cowpea breeding are discussed. Breeding strategies for enhancing cowpea adaptation to drought are described.
The cassava genome: current progress, future directions
Prochnik S, Reddy Marri P, Desany B, Rabinowicz PD, Kodira C, Mohiuddin M, Rodriguez F, Fauquet C, Tohme J, Harkins T, Rokhsar DS, Rounsley S (2012). The cassava genome: current progress, future directions. Tropical Plant Biology published online: 7pp. (DOI 10.1007/s12042-011-9088-z).
Prochnik S, Reddy Marri P, Desany B, Rabinowicz PD, Kodira C, Mohiuddin M, Rodriguez F, Fauquet C, Tohme J, Harkins T, Rokhsar DS, Rounsley S (2012). The cassava genome: current progress, future directions. Tropical Plant Biology published online: 7pp. (DOI 10.1007/s12042-011-9088-z).
Functional marker mapping and association analysis of gene W16 in common wheat
Lei M, Li A, Chang X, Xu Z, Ma Y, Liu H, Jing R (2012). Functional marker mapping and association analysis of gene W16 in common wheat. Scientia Agricultura Sinica 45(9):1667–1675. (DOI: 10.3864/j.issn.0578-1752.2012.09.001). (G7010.02.01). Article in Chinese with abstract in English. Not open access: view abstract
Lei M, Li A, Chang X, Xu Z, Ma Y, Liu H, Jing R (2012). Functional marker mapping and association analysis of gene W16 in common wheat. Scientia Agricultura Sinica 45(9):1667–1675. (DOI: 10.3864/j.issn.0578-1752.2012.09.001). (G7010.02.01). Article in Chinese with abstract in English. Not open access: view abstract
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants
D’Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci A-M, Weissenbach J, Ruiz M, Glaszmann J-C, Quétier F, Yahiaoui N & Wincker P (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410): 213–217. (DOI:10.1038/nature11241).
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish)1. Pests and diseases have gradually become adapted, representing an imminent danger for global banana production3,4.
D’Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci A-M, Weissenbach J, Ruiz M, Glaszmann J-C, Quétier F, Yahiaoui N & Wincker P (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410): 213–217. (DOI:10.1038/nature11241).
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish)1. Pests and diseases have gradually become adapted, representing an imminent danger for global banana production3,4.
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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.
Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops.
Mir R, Zaman-Allah M, Sreenivasulu N, Trethowan R, Varshney R (2012). Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. Theoretical and Applied Genetics published online 21pp. Issn: 0040-5752. (DOI: 10.1007/s00122-012-1904-9).
Mir R, Zaman-Allah M, Sreenivasulu N, Trethowan R, Varshney R (2012). Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. Theoretical and Applied Genetics published online 21pp. Issn: 0040-5752. (DOI: 10.1007/s00122-012-1904-9).
Genetic dissection of developmental behaviour of grain weight in wheat under diverse temperature and water regimes
Li S, Wang C, Chang X, Jing R (2012). Genetic dissection of developmental behaviour of grain weight in wheat under diverse temperature and water regimes. Genetica 140(7-9):393–405. (DOI: 10.1007/s10709-012-9688-z). (G7010.02.01). Not open access: view abstract
Li S, Wang C, Chang X, Jing R (2012). Genetic dissection of developmental behaviour of grain weight in wheat under diverse temperature and water regimes. Genetica 140(7-9):393–405. (DOI: 10.1007/s10709-012-9688-z). (G7010.02.01). Not open access: view abstract
Genetic structure, linkage disequilibrium and signature of selection in sorghum; lessons from physically anchored DArT markers
Bouchet S, Pot D, Deu M, Rami JF, Billot C, Perrier CX, Rivallan R, Gardes L, Xia L, Wenzl P, Kilian K, Glaszmann JC (2012). Genetic structure, linkage disequilibrium and signature of selection in sorghum; lessons from physically anchored DArT markers. PLoS ONE 7(3):e33470 (DOI:10.1371/journal.pone.0033470).
Bouchet S, Pot D, Deu M, Rami JF, Billot C, Perrier CX, Rivallan R, Gardes L, Xia L, Wenzl P, Kilian K, Glaszmann JC (2012). Genetic structure, linkage disequilibrium and signature of selection in sorghum; lessons from physically anchored DArT markers. PLoS ONE 7(3):e33470 (DOI:10.1371/journal.pone.0033470).
The effect of tetraploidization of wild Arachis on leaf morphology and other drought-related traits
Leal-Bertioli SCM, Bertioli DJ, Guimarães PM, Pereira TD, Galhardo I, Silva JP, Brasileiro ACM, Oliveira RS, Silva PIT, Vadez V, Araujo ACG (2012). The effect of tetraploidization of wild Arachis on leaf morphology and other drought-related traits. Environmental and Experimental Botany, Volume 84: 17–24. (DOI: 10.1016/j.envexpbot.2012.04.005.) (G6010.01)
Cultivated peanut is an allotetraploid (genome type AABB) with a very narrow genetic base, therefore wild species are an attractive source of new variability and traits. Because most wild species are diploid, the first step of introgression usually involves hybridization of wild species and polyploidization to produce a synthetic allotetraploid (AABB) that is sexually compatible with peanut. This study investigates drought- related traits such as leaf morphology, transpiration profile, chlorophyll meter readings (SCMR), specific leaf area (SLA) and transpiration rate per leaf area for two wild diploids (Arachis duranensis and Arachis ipaënsis) that could be of interest for improvement of the peanut crop. Furthermore, the inheritance of the traits from the diploid to the tetraploid state was investigated. Results showed that whilst some diploid traits such as SCMR, are maintained through hybridization and polyploidization, most characters, such as the leaf area, stomata size, trichome density and transpiration profile, are substantially modified. The study concludes that direct evaluations of drought-related traits in wild diploids may be useful for evaluation of wild species to be used in introgression. However, evaluations on wild-derived synthetic tetraploids are likely to be more informative.
Leal-Bertioli SCM, Bertioli DJ, Guimarães PM, Pereira TD, Galhardo I, Silva JP, Brasileiro ACM, Oliveira RS, Silva PIT, Vadez V, Araujo ACG (2012). The effect of tetraploidization of wild Arachis on leaf morphology and other drought-related traits. Environmental and Experimental Botany, Volume 84: 17–24. (DOI: 10.1016/j.envexpbot.2012.04.005.) (G6010.01)
Cultivated peanut is an allotetraploid (genome type AABB) with a very narrow genetic base, therefore wild species are an attractive source of new variability and traits. Because most wild species are diploid, the first step of introgression usually involves hybridization of wild species and polyploidization to produce a synthetic allotetraploid (AABB) that is sexually compatible with peanut. This study investigates drought- related traits such as leaf morphology, transpiration profile, chlorophyll meter readings (SCMR), specific leaf area (SLA) and transpiration rate per leaf area for two wild diploids (Arachis duranensis and Arachis ipaënsis) that could be of interest for improvement of the peanut crop. Furthermore, the inheritance of the traits from the diploid to the tetraploid state was investigated. Results showed that whilst some diploid traits such as SCMR, are maintained through hybridization and polyploidization, most characters, such as the leaf area, stomata size, trichome density and transpiration profile, are substantially modified. The study concludes that direct evaluations of drought-related traits in wild diploids may be useful for evaluation of wild species to be used in introgression. However, evaluations on wild-derived synthetic tetraploids are likely to be more informative.
