Journal articles 2013
Documents
Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought
Swamy BPM, Ahmed HU, Henry A, Mauleon R, Dixit S, Vikram P, Tilatto R, Verulkar SB, Perraju P, Mandal NP, Variar M, Robin S, Chandrababu R, Singh ON, Dwivedi JL, Das SP, Mishra KK, Yadaw RB, Aditya TL, Karmakar B, Satoh K, Moumeni A, Kikuchi S, Leung H, Kumar A (2013). Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought. PLoS ONE 8(5):e62795. (DOI: 10.1371/journal.pone.0062795). (G3008.06).
Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge.
Swamy BPM, Ahmed HU, Henry A, Mauleon R, Dixit S, Vikram P, Tilatto R, Verulkar SB, Perraju P, Mandal NP, Variar M, Robin S, Chandrababu R, Singh ON, Dwivedi JL, Das SP, Mishra KK, Yadaw RB, Aditya TL, Karmakar B, Satoh K, Moumeni A, Kikuchi S, Leung H, Kumar A (2013). Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought. PLoS ONE 8(5):e62795. (DOI: 10.1371/journal.pone.0062795). (G3008.06).
Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge.
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High-resolution single nucleotide polymorphism genotyping reveals a significant problem among breeder resources
Lucas MR, Huynh B-L, Ehlers JD, Roberts PA, Close TJ (2013). High-resolution single nucleotide polymorphism genotyping reveals a significant problem among breeder resources. The Plant Genome 6(1):1–5. (DOI: 10.3835/plantgenome2012.08.0020). (G6010.02/ G7010.07).
The logistics associated with a modern breeding program can be complex, relying on accuracy and communication between plant breeders, pathologists, quantitative geneticists, and support staff. International and academic facets may bring additional challenges to already error prone activities including the development, maintenance, and distribution of lines. Furthermore, practices such as bulking of seed and the maintenance of within accession variation among landraces must be considered when pursuing marker-assisted approaches to breeding.
Lucas MR, Huynh B-L, Ehlers JD, Roberts PA, Close TJ (2013). High-resolution single nucleotide polymorphism genotyping reveals a significant problem among breeder resources. The Plant Genome 6(1):1–5. (DOI: 10.3835/plantgenome2012.08.0020). (G6010.02/ G7010.07).
The logistics associated with a modern breeding program can be complex, relying on accuracy and communication between plant breeders, pathologists, quantitative geneticists, and support staff. International and academic facets may bring additional challenges to already error prone activities including the development, maintenance, and distribution of lines. Furthermore, practices such as bulking of seed and the maintenance of within accession variation among landraces must be considered when pursuing marker-assisted approaches to breeding.
High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development
Clark RT, Famoso AN, Zhao K, Shaff JE, Craft JE, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV. 2013. High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell Environment 36(2):454–466. (DOI: 10.1111/j.1365-3040.2012.02587.x). Also published online in 2012. (G7010.03.01). Not open access: view abstract
Clark RT, Famoso AN, Zhao K, Shaff JE, Craft JE, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV. 2013. High-throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell Environment 36(2):454–466. (DOI: 10.1111/j.1365-3040.2012.02587.x). Also published online in 2012. (G7010.03.01). Not open access: view abstract
Identification and hybridization usage of CIMMYT wheat germplasms
Chai Y, Li X, Zhao Z, Sun L, Li Y and Ma G (2013). Identification and hybridization usage of CIMMYT wheat germplasms. Chinese Agricultural Science Bulletin 29(33):56–61. Article in Chinese with abstract in English. (G7010.02.01)
Abstract: In order to improve wheat germplasm diversity, increase wheat yield and quality, agronomic and quality characters were evaluated for 145 foreign wheat germplasms in the field in southern Shanxi Province. The results showed that, these germplasms were weak vernal wheat, which might be sown on late Oct. as germplasm use in southern Shanxi Province. The coefficients of variance of spikes per plant, kernels per spike, 1000-grain weight and yield were 15.7%, 16.03%, 12.23% and 23.96% respectively. Most of the germplasms had better intergrated traits, especially in seed gluten. Agronomic traits had greater genetic diversity. Plant height and 1000-grain weight had significantly correlation with yield. Thirty-two germplasms yielded more than 3750 kg/hm2. We selected 8 trong gluten wheat germplasms and 35 better intergrated traits germplasms which had large spike, spikelets with many kernels as key germplasms for breeding. We adjusted the sowing date to meet flowering of these materials for hybridization with good local strains and produced abundant F3, BCF2 and BC1F1 generation. New drought-tolerance materials and strains with large spike and high yielding may be selected from the CIMMYT generations.
Chai Y, Li X, Zhao Z, Sun L, Li Y and Ma G (2013). Identification and hybridization usage of CIMMYT wheat germplasms. Chinese Agricultural Science Bulletin 29(33):56–61. Article in Chinese with abstract in English. (G7010.02.01)
Abstract: In order to improve wheat germplasm diversity, increase wheat yield and quality, agronomic and quality characters were evaluated for 145 foreign wheat germplasms in the field in southern Shanxi Province. The results showed that, these germplasms were weak vernal wheat, which might be sown on late Oct. as germplasm use in southern Shanxi Province. The coefficients of variance of spikes per plant, kernels per spike, 1000-grain weight and yield were 15.7%, 16.03%, 12.23% and 23.96% respectively. Most of the germplasms had better intergrated traits, especially in seed gluten. Agronomic traits had greater genetic diversity. Plant height and 1000-grain weight had significantly correlation with yield. Thirty-two germplasms yielded more than 3750 kg/hm2. We selected 8 trong gluten wheat germplasms and 35 better intergrated traits germplasms which had large spike, spikelets with many kernels as key germplasms for breeding. We adjusted the sowing date to meet flowering of these materials for hybridization with good local strains and produced abundant F3, BCF2 and BC1F1 generation. New drought-tolerance materials and strains with large spike and high yielding may be selected from the CIMMYT generations.
Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum
Melo JO, Lana UGP, Piñeros MA, Alves VMC, Guimarães CT, Liu J, Zheng Y, Zhong S, Fei Z, Maron LG, Schaffert RE, Kochian LV and Magalhães JV (2013). Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum. The Plant Journal 73(2):276–288. (DOI: 10.1111/tpj.12029). (G3007.04).
Impaired root development caused by aluminum (Al) toxicity is a major cause of grain yield reduction in crops cultivated on acid soils, which are widespread worldwide. In sorghum, the major Al-tolerance locus, AltSB, is due to the function of SbMATE, which is an Al-activated root citrate transporter. Here we performed a molecular and physiological characterization of various AltSB donors and near-isogenic lines harboring various AltSB alleles. We observed a partial transfer of Al tolerance from the parents to the near-isogenic lines that was consistent across donor alleles, emphasizing the occurrence of strong genetic background effects related to AltSB.
Melo JO, Lana UGP, Piñeros MA, Alves VMC, Guimarães CT, Liu J, Zheng Y, Zhong S, Fei Z, Maron LG, Schaffert RE, Kochian LV and Magalhães JV (2013). Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum. The Plant Journal 73(2):276–288. (DOI: 10.1111/tpj.12029). (G3007.04).
Impaired root development caused by aluminum (Al) toxicity is a major cause of grain yield reduction in crops cultivated on acid soils, which are widespread worldwide. In sorghum, the major Al-tolerance locus, AltSB, is due to the function of SbMATE, which is an Al-activated root citrate transporter. Here we performed a molecular and physiological characterization of various AltSB donors and near-isogenic lines harboring various AltSB alleles. We observed a partial transfer of Al tolerance from the parents to the near-isogenic lines that was consistent across donor alleles, emphasizing the occurrence of strong genetic background effects related to AltSB.
Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum
Melo JO, Lana UGP, Piñeros MA, Alves VMC, Guimarães CT, Liu J, Zheng Y, Zhong S, Fei Z, Maron LG, Schaffert RE, Kochian LV and Magalhaes JV (2013). Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum. The Plant Journal 73(2):276–288 (DOI: 10.1111/tpj.12029). First published online in November 2012. Not open access; view abstract.
Melo JO, Lana UGP, Piñeros MA, Alves VMC, Guimarães CT, Liu J, Zheng Y, Zhong S, Fei Z, Maron LG, Schaffert RE, Kochian LV and Magalhaes JV (2013). Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum. The Plant Journal 73(2):276–288 (DOI: 10.1111/tpj.12029). First published online in November 2012. Not open access; view abstract.
Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes
Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SCM, Thudi M, Pandey MK, Rami J-F, Foncéka D, Gowda MVC, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S and Isobe S (2013). Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Research 20(2):173–184 (DOI: 10.1093/dnares/dss042). (G6010.01)
Abtract: The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)4×, were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.
Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SCM, Thudi M, Pandey MK, Rami J-F, Foncéka D, Gowda MVC, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S and Isobe S (2013). Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Research 20(2):173–184 (DOI: 10.1093/dnares/dss042). (G6010.01)
Abtract: The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)4×, were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.
Mapping QTL for heat tolerance at grain filling stage in common wheat
Li S-P, Chang X-P, Wang C-S and Jing R-L (2013). Mapping QTL for heat tolerance at grain filling stage in common wheat. Scientia Agricultura Sinica 46(10):2119–2129 (DOI: 10.3864/j.issn.0578-1752.2013.10.018). Article in Chinese with abstract in English. (G7010.02.01)
Abstract: Objective In this study, a doubled haploid (DH) population with 150 lines, which was derived from the cross of two Chinese common wheat cultivars Hanxuan 10 and Lumai 14, was used as the plant material to identify the heat tolerance index (HTI) for related physiological traits and thousand-grain weight (TGW) at grain filling stage in common wheat and carry out quantitative trait loci (QTL) analysis. The purpose was to identify the essential QTL with stable and remarkable effects and find a theoretical basis on marker-assisted selection for improving the heat tolerance in wheat breeding program.
Method The mixed-model-based composite interval mapping method was employed to identify QTL for HTI of related traits in two soil moisture environments.
Result A total of 12 additive QTL and 17 epistatic QTL for HTI of TGW and physiological traits related to heat tolerance were located on all chromosomes except 1D, 6D and 7B under two soil moisture conditions. One single additive QTL can explain 2.64%-11.41% phenotypic variance for HTI, and a pair of epistatic QTL can explain 2.45%-8.84% phenotypic variance for HTI. Nine of 12 additive QTL have interaction effects with the environments, and the interaction effect of single additive QTL with the environment can explain 1.41%-4.66% phenotypic variance for HTI. Only 5 of the 17 epistatic QTL exist interaction effects with the environments, and the interaction effect of single pair of QTL with the environment can explain 0.62%-2.32% phenotypic variance for HTI. The allelic contribution to the HTI QTL came from both parents. Some DH lines were more tolerant to the heat stress than their parents.
Conclusion To evaluate the heat tolerance at grain filling stage, the HTI for TGW is a direct criteria, the following two physiological index are indirect criteria, i.e. the HTI for flag leaves relative water content (IRWC) is an available index under rainfed condition, and the HTI for canopy temperature depression (ICTD) is suitable under well-watered condition. The QTL for HTIs mainly distribute on the chromosomes 1B, 2D, 5A, 5B, 6A, 6B and 7A, showing that these chromosomes have close relationship with heat-tolerance at grain filling stage. The genetic effects of QTL for TGW HTI and chlorophyll content (CC) mainly are additive effect, and that of CTD and chlorophyll fluorescence parameters (CFP) are mainly epistatic effect. The additive effect and the epistatic effect are almost equal in the genetic effect of the QTL for the RWC HTI.
Li S-P, Chang X-P, Wang C-S and Jing R-L (2013). Mapping QTL for heat tolerance at grain filling stage in common wheat. Scientia Agricultura Sinica 46(10):2119–2129 (DOI: 10.3864/j.issn.0578-1752.2013.10.018). Article in Chinese with abstract in English. (G7010.02.01)
Abstract: Objective In this study, a doubled haploid (DH) population with 150 lines, which was derived from the cross of two Chinese common wheat cultivars Hanxuan 10 and Lumai 14, was used as the plant material to identify the heat tolerance index (HTI) for related physiological traits and thousand-grain weight (TGW) at grain filling stage in common wheat and carry out quantitative trait loci (QTL) analysis. The purpose was to identify the essential QTL with stable and remarkable effects and find a theoretical basis on marker-assisted selection for improving the heat tolerance in wheat breeding program.
Method The mixed-model-based composite interval mapping method was employed to identify QTL for HTI of related traits in two soil moisture environments.
Result A total of 12 additive QTL and 17 epistatic QTL for HTI of TGW and physiological traits related to heat tolerance were located on all chromosomes except 1D, 6D and 7B under two soil moisture conditions. One single additive QTL can explain 2.64%-11.41% phenotypic variance for HTI, and a pair of epistatic QTL can explain 2.45%-8.84% phenotypic variance for HTI. Nine of 12 additive QTL have interaction effects with the environments, and the interaction effect of single additive QTL with the environment can explain 1.41%-4.66% phenotypic variance for HTI. Only 5 of the 17 epistatic QTL exist interaction effects with the environments, and the interaction effect of single pair of QTL with the environment can explain 0.62%-2.32% phenotypic variance for HTI. The allelic contribution to the HTI QTL came from both parents. Some DH lines were more tolerant to the heat stress than their parents.
Conclusion To evaluate the heat tolerance at grain filling stage, the HTI for TGW is a direct criteria, the following two physiological index are indirect criteria, i.e. the HTI for flag leaves relative water content (IRWC) is an available index under rainfed condition, and the HTI for canopy temperature depression (ICTD) is suitable under well-watered condition. The QTL for HTIs mainly distribute on the chromosomes 1B, 2D, 5A, 5B, 6A, 6B and 7A, showing that these chromosomes have close relationship with heat-tolerance at grain filling stage. The genetic effects of QTL for TGW HTI and chlorophyll content (CC) mainly are additive effect, and that of CTD and chlorophyll fluorescence parameters (CFP) are mainly epistatic effect. The additive effect and the epistatic effect are almost equal in the genetic effect of the QTL for the RWC HTI.
Mapping QTLs for seedling root traits in a doubled haploid wheat population under different water regimes
Liu X, Li R, Chang X and Jing R (2013). Mapping QTLs for seedling root traits in a doubled haploid wheat population under different water regimes. Euphytica 189(1):51−66 (DOI: 10.1007/s10681-012-0690-4). First published online in May 2012. Not open access; view abstract. (G7010.02.01)
Liu X, Li R, Chang X and Jing R (2013). Mapping QTLs for seedling root traits in a doubled haploid wheat population under different water regimes. Euphytica 189(1):51−66 (DOI: 10.1007/s10681-012-0690-4). First published online in May 2012. Not open access; view abstract. (G7010.02.01)
Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources
Billot C, Ramu P, Bouchet S, Chantereau J, Deu M, Gardes L, Noyer J-L, Rami J-F, Rivallan R, Li Y, Lu P, Wang T, Folkertsma RT, Arnaud E, Upadhyaya HD, Glaszmann J-C, Hash CT (2013). Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources. PLoS One 8(4): e59714. (DOI: 10.1371/journal.pone.0059714). (G4005.01.03/ G4007.01).
Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated.
Billot C, Ramu P, Bouchet S, Chantereau J, Deu M, Gardes L, Noyer J-L, Rami J-F, Rivallan R, Li Y, Lu P, Wang T, Folkertsma RT, Arnaud E, Upadhyaya HD, Glaszmann J-C, Hash CT (2013). Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources. PLoS One 8(4): e59714. (DOI: 10.1371/journal.pone.0059714). (G4005.01.03/ G4007.01).
Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated.
