Journal articles 2012
Documents
Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.)
Sujay V, Gowda MVC, Pandey MK, Bhat RS, Khedikar YP, Nadaf HL, Gautami B, Sarvamangala BC, Lingaraju S, Radhakrishan T, Knapp SJ, Varshney RK (2012). Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). Molecular Breeding 30(2):773–788. (DOI: 10.1007/s11032-011-9661-z)
Late leaf spot (LLS) and rust have the greatest impact on yield losses worldwide in groundnut (Arachis hypogaea L.). With the objective of identifying tightly linked markers to these diseases, a total of 3,097 simple sequence repeats (SSRs) were screened on the parents of two recombinant inbred line (RIL) populations, namely TAG 24 9 GPBD 4 (RIL-4) and TG 26 9 GPBD 4 (RIL-5), and segregation data were obtained for 209 marker loci for each of the mapping populations. Linkage map analysis of the 209 loci resulted in the mapping of 188 and 181 loci in RIL-4 and RIL-5 respectively. Using 143 markers.
Sujay V, Gowda MVC, Pandey MK, Bhat RS, Khedikar YP, Nadaf HL, Gautami B, Sarvamangala BC, Lingaraju S, Radhakrishan T, Knapp SJ, Varshney RK (2012). Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). Molecular Breeding 30(2):773–788. (DOI: 10.1007/s11032-011-9661-z)
Late leaf spot (LLS) and rust have the greatest impact on yield losses worldwide in groundnut (Arachis hypogaea L.). With the objective of identifying tightly linked markers to these diseases, a total of 3,097 simple sequence repeats (SSRs) were screened on the parents of two recombinant inbred line (RIL) populations, namely TAG 24 9 GPBD 4 (RIL-4) and TG 26 9 GPBD 4 (RIL-5), and segregation data were obtained for 209 marker loci for each of the mapping populations. Linkage map analysis of the 209 loci resulted in the mapping of 188 and 181 loci in RIL-4 and RIL-5 respectively. Using 143 markers.
Full article (700.79 kB)
Mapping QTLs for seedling traits and heat tolerance indices in common wheat
Li S-P, Chang X-P, Wang C-S and Jing R-L (2012). Mapping QTLs for seedling traits and heat tolerance indices in common wheat. Acta Botanica Boreali-Occidentalia Sinica 32(8):1525–1533. Article in Chinese with abstract in English. Not open access; view journal website. (G7010.02.01)
Li S-P, Chang X-P, Wang C-S and Jing R-L (2012). Mapping QTLs for seedling traits and heat tolerance indices in common wheat. Acta Botanica Boreali-Occidentalia Sinica 32(8):1525–1533. Article in Chinese with abstract in English. Not open access; view journal website. (G7010.02.01)
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.
Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection
Guimarães PM, Brasileiro ACM, Morgante CV, Martins ACQ, Pappas G, Silva OB, Togawa R, Leal-Bertioli SCM, Araujo ACG, Moretzsohn MC and Bertioli DJ (2012). Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection. BMC Genomics 13:387 (DOI: 10.1186/1471-2164-13-387). (G6010.01)
Abstract: Background Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development.
Results Transcriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton, and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR.
Conclusions This study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to biological processes such as fungal diseases and water limited stress. Moreover, it will also facilitate basic and applied research on the genetics of peanut through the development of new molecular markers and the study of adaptive variation across the genus.
Guimarães PM, Brasileiro ACM, Morgante CV, Martins ACQ, Pappas G, Silva OB, Togawa R, Leal-Bertioli SCM, Araujo ACG, Moretzsohn MC and Bertioli DJ (2012). Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection. BMC Genomics 13:387 (DOI: 10.1186/1471-2164-13-387). (G6010.01)
Abstract: Background Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development.
Results Transcriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton, and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR.
Conclusions This study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to biological processes such as fungal diseases and water limited stress. Moreover, it will also facilitate basic and applied research on the genetics of peanut through the development of new molecular markers and the study of adaptive variation across the genus.
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.
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.
![Genetic and physical mapping of candidate genes for resistance to Fusarium oxysporum f.sp. tracheiphilum Race 3 in cowpea [Vigna unguiculata (L.) Walp]](http://generationcp.org/images/~thumbs.Pottorff_Genetic-physical-mapping-cowpea_journal.pone.0041600.pdf.1365227757.png)
Genetic and physical mapping of candidate genes for resistance to Fusarium oxysporum f.sp. tracheiphilum Race 3 in cowpea [Vigna unguiculata (L.) Walp]
Pottorff M, Wanamaker S, Ma YQ, Ehlers JD, Roberts PA, Close TJ (2012). Genetic and physical mapping of candidate genes for resistance to Fusarium oxysporum f.sp. tracheiphilum Race 3 in cowpea [Vigna unguiculata (L.) Walp]. PLoS ONE 7(7):e41600. (DOI: 10.1371/journal.pone.0041600). (G6010.02/G7010.07.01).
Fusarium oxysporum f.sp. tracheiphilum (Fot) is a soil-borne fungal pathogen that causes vascular wilt disease in cowpea. Fot race 3 is one of the major pathogens affecting cowpea production in California. Identification of Fot race 3 resistance determinants will expedite delivery of improved cultivars by replacing time-consuming phenotypic screening with selection based on perfect markers, thereby generating successful cultivars in a shorter time period. Resistance to Fot race 3 was studied in the RIL population California Blackeye 27 (resistant) x 24-125B-1 (susceptible). Biparental mapping identified a Fot race 3 resistance locus, Fot3-1, which spanned 3.56 cM on linkage group one of the CB27 x 24-125B-1 genetic map.
Pottorff M, Wanamaker S, Ma YQ, Ehlers JD, Roberts PA, Close TJ (2012). Genetic and physical mapping of candidate genes for resistance to Fusarium oxysporum f.sp. tracheiphilum Race 3 in cowpea [Vigna unguiculata (L.) Walp]. PLoS ONE 7(7):e41600. (DOI: 10.1371/journal.pone.0041600). (G6010.02/G7010.07.01).
Fusarium oxysporum f.sp. tracheiphilum (Fot) is a soil-borne fungal pathogen that causes vascular wilt disease in cowpea. Fot race 3 is one of the major pathogens affecting cowpea production in California. Identification of Fot race 3 resistance determinants will expedite delivery of improved cultivars by replacing time-consuming phenotypic screening with selection based on perfect markers, thereby generating successful cultivars in a shorter time period. Resistance to Fot race 3 was studied in the RIL population California Blackeye 27 (resistant) x 24-125B-1 (susceptible). Biparental mapping identified a Fot race 3 resistance locus, Fot3-1, which spanned 3.56 cM on linkage group one of the CB27 x 24-125B-1 genetic map.
Field phenotyping strategies and breeding for adaptation of rice to drought
Fischer KS, Fukai S, Kumar A, Leung H and Jongdee B (2012). Field phenotyping strategies and breeding for adaptation of rice to drought. Frontiers in Plant Physiology 3:282. (DOI: 10.3389/fphys.2012.00282).
This paper is a section of the book “Drought phenotyping in crops: from theory to practice” (Monneveux Philippe and Ribaut Jean-Marcel eds, published by CGIAR Generation Chal-lenge Programme. Texcoco, Mexico). The section describes recent experience in drought phenotyping in rice which is one of the most drought-susceptible crops. The section contains genetic and genomic resources for drought adaptation and methods for selection of drought-resistant varieties in rice. In appendix, there is experience from Thailand on integration of direct selection for grain yield and physiological traits to confer drought resistance.
Fischer KS, Fukai S, Kumar A, Leung H and Jongdee B (2012). Field phenotyping strategies and breeding for adaptation of rice to drought. Frontiers in Plant Physiology 3:282. (DOI: 10.3389/fphys.2012.00282).
This paper is a section of the book “Drought phenotyping in crops: from theory to practice” (Monneveux Philippe and Ribaut Jean-Marcel eds, published by CGIAR Generation Chal-lenge Programme. Texcoco, Mexico). The section describes recent experience in drought phenotyping in rice which is one of the most drought-susceptible crops. The section contains genetic and genomic resources for drought adaptation and methods for selection of drought-resistant varieties in rice. In appendix, there is experience from Thailand on integration of direct selection for grain yield and physiological traits to confer drought resistance.
Genetic and molecular mechanisms of aluminum tolerance in plants
Simões CC; Melo JO; Magalhaes JV; Guimarães CT (2012). Genetic and molecular mechanisms of aluminum tolerance in plants. Genetics and Molecular Research 11 (3):1949–1957. (DOI: 10.4238/2012.July.19.14). http://geneticsmr.com/articles/1770. (G7010.03.02).
Genes encoding membrane transporters and accessory transcription factors, as well as cis-elements that enhance gene expression are involved in Al tolerance in plants, thus studies of these genes and accessory factors should be the focus of molecular breeding efforts aimed at improving Al tolerance in crops. In this review, we describe the main genetic and molecular studies that led to the identification and cloning of genes associated with Al tolerance in plants. We include recent findings on the regulation of genes associated with Al tolerance. Understanding the genetic, molecular, and physiological aspects of Al tolerance in plants is important for generating cultivars adapted to acid soils, thereby contributing to food security worldwide.
Simões CC; Melo JO; Magalhaes JV; Guimarães CT (2012). Genetic and molecular mechanisms of aluminum tolerance in plants. Genetics and Molecular Research 11 (3):1949–1957. (DOI: 10.4238/2012.July.19.14). http://geneticsmr.com/articles/1770. (G7010.03.02).
Genes encoding membrane transporters and accessory transcription factors, as well as cis-elements that enhance gene expression are involved in Al tolerance in plants, thus studies of these genes and accessory factors should be the focus of molecular breeding efforts aimed at improving Al tolerance in crops. In this review, we describe the main genetic and molecular studies that led to the identification and cloning of genes associated with Al tolerance in plants. We include recent findings on the regulation of genes associated with Al tolerance. Understanding the genetic, molecular, and physiological aspects of Al tolerance in plants is important for generating cultivars adapted to acid soils, thereby contributing to food security worldwide.
An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.)
(2012). An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS ONE 7(7):e41213. (DOI:10.1371/journal.pone.0041213).
(2012). An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS ONE 7(7):e41213. (DOI:10.1371/journal.pone.0041213).
