Journal articles 2012
Documents
Plant nutrition: Rooting for more phosphorus
Kochian LV (2012). Plant nutrition: Rooting for more phosphorus. Nature 488(7412):466–467. (DOI: 10.1038/488466a). Not open access: view abstract online
Kochian LV (2012). Plant nutrition: Rooting for more phosphorus. Nature 488(7412):466–467. (DOI: 10.1038/488466a). Not open access: view abstract online
Phenotyping pearl millet for adaptation to drought
Vadez V, Hash T, Bidinger FR and Kholova J (2012). Phenotyping pearl millet for adaptation to drought. Frontiers in Plant Physiology 3:386. (DOI: 10.3389/fphys.2012.00386).
Pearl millet is highly resilient to some of the driest areas of the world, like the Sahel area or fringes of the Thar desert in India. Despite this, there is a wealth of variation in pearl millet genotypes for their adaptation to drought and the object of this paper was to review some related work in the past 25 years to harness these capacities toward the breeding of better adapted cultivars. Work on short duration cultivars has been a major effort. Pearl millet has also some development plasticity thanks to a high tillering ability, which allows compensating for possible drought-related failure of the main culm under intermittent drought. The development of molecular tools for breeding has made great progress in the last 10–15 years and markers, maps, EST libraries, BACs are now available and a number of quantitative trait loci (QTLs) for different traits, including drought, have been identified. Most of the work on drought has focused on the drought tolerance index (DTI), an index that reflect the genetic differences in drought adaptation that are independent of flowering time and yield potential.
Vadez V, Hash T, Bidinger FR and Kholova J (2012). Phenotyping pearl millet for adaptation to drought. Frontiers in Plant Physiology 3:386. (DOI: 10.3389/fphys.2012.00386).
Pearl millet is highly resilient to some of the driest areas of the world, like the Sahel area or fringes of the Thar desert in India. Despite this, there is a wealth of variation in pearl millet genotypes for their adaptation to drought and the object of this paper was to review some related work in the past 25 years to harness these capacities toward the breeding of better adapted cultivars. Work on short duration cultivars has been a major effort. Pearl millet has also some development plasticity thanks to a high tillering ability, which allows compensating for possible drought-related failure of the main culm under intermittent drought. The development of molecular tools for breeding has made great progress in the last 10–15 years and markers, maps, EST libraries, BACs are now available and a number of quantitative trait loci (QTLs) for different traits, including drought, have been identified. Most of the work on drought has focused on the drought tolerance index (DTI), an index that reflect the genetic differences in drought adaptation that are independent of flowering time and yield potential.
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.
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 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.
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.
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.
ParentChecker: a computer program for automated inference of missing parental genotype calls and linkage phase correction
Hu Z, Ehlers JD, Roberts PA, Close TJ, Lucas MR, Wanamaker S, Xu S (2012). ParentChecker: a computer program for automated inference of missing parental genotype calls and linkage phase correction. BMC Genetics 13:9. (DOI: 10.1186/1471-2156-13-9). (G6010.02/G7010.07.01).
ParentChecker is a user-friendly tool that uses the segregation patterns of progeny to infer missing genotype information of parental lines that have been used to construct a mapping population. It can also be used to automate correction of linkage phase errors in genotypic data that are in ABH format.
ParentChecker efficiently improves genetic mapping datasets for cases where parental information is incomplete by automating the process of inferring missing genotypes of inbred mapping populations and can also be used to correct linkage phase errors in ABH formatted datasets.
Hu Z, Ehlers JD, Roberts PA, Close TJ, Lucas MR, Wanamaker S, Xu S (2012). ParentChecker: a computer program for automated inference of missing parental genotype calls and linkage phase correction. BMC Genetics 13:9. (DOI: 10.1186/1471-2156-13-9). (G6010.02/G7010.07.01).
ParentChecker is a user-friendly tool that uses the segregation patterns of progeny to infer missing genotype information of parental lines that have been used to construct a mapping population. It can also be used to automate correction of linkage phase errors in genotypic data that are in ABH format.
ParentChecker efficiently improves genetic mapping datasets for cases where parental information is incomplete by automating the process of inferring missing genotypes of inbred mapping populations and can also be used to correct linkage phase errors in ABH formatted datasets.
Opportunities for exploiting variations in haulm fodder traits of intermittent drought tolerant lines in a reference collection of groundnut (Arachis hypogeae L.)
Blümmel M, Ratnakumar P, and Vadez V (2012). Opportunities for exploiting variations in haulm fodder traits of intermittent drought tolerant lines in a reference collection of groundnut (Arachis hypogeae L.). Field Crops Research 126:200–206, ISSN 0378-4290. (DOI:10.1016/j.fcr.2011.10.004). Not open access: view abstract
Blümmel M, Ratnakumar P, and Vadez V (2012). Opportunities for exploiting variations in haulm fodder traits of intermittent drought tolerant lines in a reference collection of groundnut (Arachis hypogeae L.). Field Crops Research 126:200–206, ISSN 0378-4290. (DOI:10.1016/j.fcr.2011.10.004). Not open access: view abstract
Next-generation sequencing technologies: opportunities and obligations in plant genomics
Varshney RK and May GD (2012). Next-generation sequencing technologies: opportunities and obligations in plant genomics. Briefings in Functional Genomics 11(1):1–2. (DOI: 10.1093/bfgp/els001). Not open access: view abstract
Varshney RK and May GD (2012). Next-generation sequencing technologies: opportunities and obligations in plant genomics. Briefings in Functional Genomics 11(1):1–2. (DOI: 10.1093/bfgp/els001). Not open access: view abstract
