Journal articles 2015
Documents
Genotypic variation in grain yield and flowering pattern in terminal and intermittent drought screening methods in rainfed lowland rice
Monkham T, Jongdee B, Pantuwan G, Sanitchon J, Mitchell JH and Fukai S (2015). Genotypic variation in grain yield and flowering pattern in terminal and intermittent drought screening methods in rainfed lowland rice. Field Crops Research 175:26–36 (DOI: 10.1016/j.fcr.2015.02.003). Not open access; view abstract. (G3008.06)
Monkham T, Jongdee B, Pantuwan G, Sanitchon J, Mitchell JH and Fukai S (2015). Genotypic variation in grain yield and flowering pattern in terminal and intermittent drought screening methods in rainfed lowland rice. Field Crops Research 175:26–36 (DOI: 10.1016/j.fcr.2015.02.003). Not open access; view abstract. (G3008.06)
Interrelationship among yield and yield contributing traits in RILs and their parents in Chickpea (Cicer arietinum L.)
Joshi P and Yasin M (2015). Interrelationship among yield and yield contributing traits in RILs and their parents in Chickpea (Cicer arietinum L.). Indian Journal of Applied and Pure Biology 30(1):97–100. (G7009.02)
Abstract: Two hundred fifty two recombinant inbred lines generated from diverse Desi (ICC 283) and Kabuli (ICC 8261) parents were grown in RBD during rabi 2011-12 and interrelationship amongst yield traits was worked out. Seed yield showed positive association with biological yield, harvest index & plant height and negative with days to 50% flowering & days to maturity. Good plant vigour with high biological yield & plant height directly affect the yield. Long reproductive phase influence the high sink transfer and resulted high harvest index. Late flowering and late maturity observed in prostrate and spreading plant growth habit bearing RILs showed negative association with seed yield. The path analysis showed biological yield, plant height and harvest index is directly contributing to seed yield but delayed flowering and maturity increase vegetative period and reduce reproductive phase specially in prostrate and spreading plant growth habits bearing RILs showed negative indirect effect on seed yield.
Joshi P and Yasin M (2015). Interrelationship among yield and yield contributing traits in RILs and their parents in Chickpea (Cicer arietinum L.). Indian Journal of Applied and Pure Biology 30(1):97–100. (G7009.02)
Abstract: Two hundred fifty two recombinant inbred lines generated from diverse Desi (ICC 283) and Kabuli (ICC 8261) parents were grown in RBD during rabi 2011-12 and interrelationship amongst yield traits was worked out. Seed yield showed positive association with biological yield, harvest index & plant height and negative with days to 50% flowering & days to maturity. Good plant vigour with high biological yield & plant height directly affect the yield. Long reproductive phase influence the high sink transfer and resulted high harvest index. Late flowering and late maturity observed in prostrate and spreading plant growth habit bearing RILs showed negative association with seed yield. The path analysis showed biological yield, plant height and harvest index is directly contributing to seed yield but delayed flowering and maturity increase vegetative period and reduce reproductive phase specially in prostrate and spreading plant growth habits bearing RILs showed negative indirect effect on seed yield.
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Linkage analysis and map construction in genetic populations of clonal F1 and double cross
Zhang L, Li H and Wang J (2015). Linkage analysis and map construction in genetic populations of clonal F1 and double cross. G3 5(3):427–439 (DOI:10.1534/g3.114.016022). (G8009.10)
Abstract: In this study, we considered four categories of molecular markers based on the number of distinguishable alleles at the marker locus and the number of distinguishable genotypes in clonal F1 progenies. For two marker loci, there are nine scenarios that allow the estimation of female, male, and/or combined recombination frequencies. In a double cross population derived from four inbred lines, five categories of markers are classified and another five scenarios are present for recombination frequency estimation. Theoretical frequencies of identifiable genotypes were given for each scenario, from which the maximum likelihood estimates of one or more of the three recombination frequencies could be estimated. If there was no analytic solution, then Newton-Raphson method was used to acquire a numerical solution. We then proposed to use an algorithm in Traveling Salesman Problem to determine the marker order. Finally, we proposed a procedure to build the two haploids of the female parent and the two haploids of the male parent in clonal F1. Once the four haploids were built, clonal F1 hybrids could be exactly regarded as a double cross population. Efficiency of the proposed methods was demonstrated in simulated clonal F1 populations and one actual maize double cross. Extensive comparisons with software JoinMap4.1, OneMap, and R/qtl show that the methodology proposed in this article can build more accurate linkage maps in less time.
Zhang L, Li H and Wang J (2015). Linkage analysis and map construction in genetic populations of clonal F1 and double cross. G3 5(3):427–439 (DOI:10.1534/g3.114.016022). (G8009.10)
Abstract: In this study, we considered four categories of molecular markers based on the number of distinguishable alleles at the marker locus and the number of distinguishable genotypes in clonal F1 progenies. For two marker loci, there are nine scenarios that allow the estimation of female, male, and/or combined recombination frequencies. In a double cross population derived from four inbred lines, five categories of markers are classified and another five scenarios are present for recombination frequency estimation. Theoretical frequencies of identifiable genotypes were given for each scenario, from which the maximum likelihood estimates of one or more of the three recombination frequencies could be estimated. If there was no analytic solution, then Newton-Raphson method was used to acquire a numerical solution. We then proposed to use an algorithm in Traveling Salesman Problem to determine the marker order. Finally, we proposed a procedure to build the two haploids of the female parent and the two haploids of the male parent in clonal F1. Once the four haploids were built, clonal F1 hybrids could be exactly regarded as a double cross population. Efficiency of the proposed methods was demonstrated in simulated clonal F1 populations and one actual maize double cross. Extensive comparisons with software JoinMap4.1, OneMap, and R/qtl show that the methodology proposed in this article can build more accurate linkage maps in less time.
Mapping QTL for chlorophyll fluorescence kinetics parameters at seedling stage as indicators of heat tolerance in wheat
Azam F, Chang X and Jing R (2015). Mapping QTL for chlorophyll fluorescence kinetics parameters at seedling stage as indicators of heat tolerance in wheat. Euphytica 202(2):245–258 (DOI: 10.1007/s10681-014-1283-1). First published online in October 2014. (G7010.02.01)
Abstract: High temperature or heat stress is one of the most important abiotic stresses that affect wheat production in almost every part of the world. Parameters of chlorophyll fluorescence kinetics (PCFKs) are the most powerful and reliable characters available to understand the impact of various abiotic stresses on plant physiological processes and heat tolerance. The present research was aimed to identify genomic regions controlling PCFKs at early growth stages of wheat through quantitative trait loci analysis by applying heat stress for different duration of time. A doubled haploid population derived from the cross of two Chinese wheat cultivars Hanxuan 10 and Lumai 14 was exposed to 38 °C for 2, 4, 6 and 8 h of heat stress and PCFKs (initial fluorescence, maximum fluorescence, variable fluorescence and maximum quantum efficiency of photosystem II) were measured. A total of 37 QTLs were identified for the target traits, among which 13 were detected under normal temperature of 25 °C and the remaining 24 under the stressful temperature of 38 °C. Stable or consistently expressed QTLs for initial, maximum and variable fluorescence were detected on chromosomes 1A, 1B, 2B, 4A and 7D. In addition, 24 QTLs were clustered in 9 clusters on chromosomes 1A, 1B, 2B, 3B, 3D, 4A, 5A and 7D. These QTL hot spot regions along with stable QTLs should be targeted for better understanding the genetic basis of chlorophyll fluorescence kinetics parameters in future mapping studies.
Azam F, Chang X and Jing R (2015). Mapping QTL for chlorophyll fluorescence kinetics parameters at seedling stage as indicators of heat tolerance in wheat. Euphytica 202(2):245–258 (DOI: 10.1007/s10681-014-1283-1). First published online in October 2014. (G7010.02.01)
Abstract: High temperature or heat stress is one of the most important abiotic stresses that affect wheat production in almost every part of the world. Parameters of chlorophyll fluorescence kinetics (PCFKs) are the most powerful and reliable characters available to understand the impact of various abiotic stresses on plant physiological processes and heat tolerance. The present research was aimed to identify genomic regions controlling PCFKs at early growth stages of wheat through quantitative trait loci analysis by applying heat stress for different duration of time. A doubled haploid population derived from the cross of two Chinese wheat cultivars Hanxuan 10 and Lumai 14 was exposed to 38 °C for 2, 4, 6 and 8 h of heat stress and PCFKs (initial fluorescence, maximum fluorescence, variable fluorescence and maximum quantum efficiency of photosystem II) were measured. A total of 37 QTLs were identified for the target traits, among which 13 were detected under normal temperature of 25 °C and the remaining 24 under the stressful temperature of 38 °C. Stable or consistently expressed QTLs for initial, maximum and variable fluorescence were detected on chromosomes 1A, 1B, 2B, 4A and 7D. In addition, 24 QTLs were clustered in 9 clusters on chromosomes 1A, 1B, 2B, 3B, 3D, 4A, 5A and 7D. These QTL hot spot regions along with stable QTLs should be targeted for better understanding the genetic basis of chlorophyll fluorescence kinetics parameters in future mapping studies.
No need to breed for enhanced colonization by arbuscular mycorrhizal fungi to improve low-P adaptation of West African sorghums
Leiser WL, Olatoye MO, Rattunde HFW, Neumann G, Weltzien E and Haussmann BIG (2015). No need to breed for enhanced colonization by arbuscular mycorrhizal fungi to improve low-P adaptation of West African sorghums. Plant and Soil Published online: 14 March 2015 (DOI: 10.1007/s11104-015-2437-1). Not open access; view abstract. (G7010.03.03)
Leiser WL, Olatoye MO, Rattunde HFW, Neumann G, Weltzien E and Haussmann BIG (2015). No need to breed for enhanced colonization by arbuscular mycorrhizal fungi to improve low-P adaptation of West African sorghums. Plant and Soil Published online: 14 March 2015 (DOI: 10.1007/s11104-015-2437-1). Not open access; view abstract. (G7010.03.03)
Novel QTLs in an interspecific backcross Oryza sativa x Oryza glaberrima for resistance to iron toxicity in rice
Dufey I, Draye X, Lutts S, Lorieux M, Martinez C and Bertin P (2015). Novel QTLs in an interspecific backcross Oryza sativa x Oryza glaberrima for resistance to iron toxicity in rice. Euphytica Published online: 1 February 2015 (DOI 10.1007/s10681-014-1342-7). Not open access; view abstract. (G3005.10)
Dufey I, Draye X, Lutts S, Lorieux M, Martinez C and Bertin P (2015). Novel QTLs in an interspecific backcross Oryza sativa x Oryza glaberrima for resistance to iron toxicity in rice. Euphytica Published online: 1 February 2015 (DOI 10.1007/s10681-014-1342-7). Not open access; view abstract. (G3005.10)
Phosphorous efficiency and tolerance traits for selection of sorghum for performance in phosphorous-limited environments
Leiser WL, Rattunde HFW, Piepho H-P, Weltzien E, Diallo A, Toure A and Hausmann BIG (2015). Phosphorous efficiency and tolerance traits for selection of sorghum for performance in phosphorous-limited environments. Crop Science 55 Published online: 27 March 2015 (DOI: 10.2135/cropsci2014.05.0392). (G7010.03.03)
Abstract: Sorghum (Sorghum bicolor (L.) Moench) is widely cultivated in West Africa (WA) on soils with low phosphorus (P) availability. Large genetic variation for grain yield (GY) under low-P conditions was observed among WA sorghum genotypes, but information is lacking on the usefulness of P-tolerance ratios (relative performance in –P [no P fertilizer] vs. +P [with P fertilizer] conditions) and measures of P-acquisition and internal P-use efficiency as selection criteria for enhancing GY under low-P conditions. We evaluated 70 WA sorghum genotypes for GY performance under −P and +P conditions for 5 yr in two locations in Mali and assessed P acquisition (e.g., P content in biomass) and P-use efficiency (e.g., grain produced per unit P uptake) traits under −P and +P conditions in one site in 2010. Significant genetic variation existed for all P-tolerance ratios across multiple sites. Photoperiod-sensitive landrace genotypes showed significantly better P tolerance and less delay of heading under P-limited conditions compared with photoperiod-insensitive varieties. Genotypic correlations of P-tolerance ratios to GY under −P were moderate. Phosphorous acquisition and P-use efficiency traits independent of harvest index were of similar importance for GY under −P conditions in statistically independent trials. However grain-P and stover-P concentrations from one −P trial showed only weak correlations with GYs in statistically independent trials. Highest predicted gains for −P GY were obtained by theoretical index selection based on −P GY combined with P-use efficiency traits (e.g., low-grain P concentration). Such index selection is expected to achieve both increased sorghum productivity and P sustainability in the P-limited WA production systems.
Leiser WL, Rattunde HFW, Piepho H-P, Weltzien E, Diallo A, Toure A and Hausmann BIG (2015). Phosphorous efficiency and tolerance traits for selection of sorghum for performance in phosphorous-limited environments. Crop Science 55 Published online: 27 March 2015 (DOI: 10.2135/cropsci2014.05.0392). (G7010.03.03)
Abstract: Sorghum (Sorghum bicolor (L.) Moench) is widely cultivated in West Africa (WA) on soils with low phosphorus (P) availability. Large genetic variation for grain yield (GY) under low-P conditions was observed among WA sorghum genotypes, but information is lacking on the usefulness of P-tolerance ratios (relative performance in –P [no P fertilizer] vs. +P [with P fertilizer] conditions) and measures of P-acquisition and internal P-use efficiency as selection criteria for enhancing GY under low-P conditions. We evaluated 70 WA sorghum genotypes for GY performance under −P and +P conditions for 5 yr in two locations in Mali and assessed P acquisition (e.g., P content in biomass) and P-use efficiency (e.g., grain produced per unit P uptake) traits under −P and +P conditions in one site in 2010. Significant genetic variation existed for all P-tolerance ratios across multiple sites. Photoperiod-sensitive landrace genotypes showed significantly better P tolerance and less delay of heading under P-limited conditions compared with photoperiod-insensitive varieties. Genotypic correlations of P-tolerance ratios to GY under −P were moderate. Phosphorous acquisition and P-use efficiency traits independent of harvest index were of similar importance for GY under −P conditions in statistically independent trials. However grain-P and stover-P concentrations from one −P trial showed only weak correlations with GYs in statistically independent trials. Highest predicted gains for −P GY were obtained by theoretical index selection based on −P GY combined with P-use efficiency traits (e.g., low-grain P concentration). Such index selection is expected to achieve both increased sorghum productivity and P sustainability in the P-limited WA production systems.
Physiological mechanisms contributing to the QTL-combination effects on improved performance of IR64 rice NILs under drought
Henry A, Swamy BPM, Dixit S, Torres RD, Batoto TC, Manalili M, Anantha MS, Mandal NP and Kumar A (2015). Physiological mechanisms contributing to the QTL-combination effects on improved performance of IR64 rice NILs under drought. Journal of Experimental Botany 66(7):1787–1799 (DOI: 10.1093/jxb/eru506). (G3008.06)
Abstract: Characterizing the physiological mechanisms behind major-effect drought-yield quantitative trait loci (QTLs) can provide an understanding of the function of the QTLs—as well as plant responses to drought in general. In this study, we characterized rice (Oryza sativa L.) genotypes with QTLs derived from drought-tolerant traditional variety AdaySel that were introgressed into drought-susceptible high-yielding variety IR64, one of the most popular megavarieties in South Asian rainfed lowland systems. Of the different combinations of the four QTLs evaluated, genotypes with two QTLs (qDTY2.2 + qDTY4.1) showed the greatest degree of improvement under drought compared with IR64 in terms of yield, canopy temperature, and normalized difference vegetation index (NDVI). Furthermore, qDTY2.2 and qDTY4.1 showed a potential for complementarity in that they were each most effective under different severities of drought stress. Multiple drought-response mechanisms were observed to be conferred in the genotypes with the two-QTL combination: higher root hydraulic conductivity and in some cases greater root growth at depth. As evidenced by multiple leaf water status and plant growth indicators, these traits affected transpiration but not transpiration efficiency or harvest index. The results from this study highlight the complex interactions among major-effect drought-yield QTLs and the drought-response traits they confer, and the need to evaluate the optimal combinations of QTLs that complement each other when present in a common genetic background.
Henry A, Swamy BPM, Dixit S, Torres RD, Batoto TC, Manalili M, Anantha MS, Mandal NP and Kumar A (2015). Physiological mechanisms contributing to the QTL-combination effects on improved performance of IR64 rice NILs under drought. Journal of Experimental Botany 66(7):1787–1799 (DOI: 10.1093/jxb/eru506). (G3008.06)
Abstract: Characterizing the physiological mechanisms behind major-effect drought-yield quantitative trait loci (QTLs) can provide an understanding of the function of the QTLs—as well as plant responses to drought in general. In this study, we characterized rice (Oryza sativa L.) genotypes with QTLs derived from drought-tolerant traditional variety AdaySel that were introgressed into drought-susceptible high-yielding variety IR64, one of the most popular megavarieties in South Asian rainfed lowland systems. Of the different combinations of the four QTLs evaluated, genotypes with two QTLs (qDTY2.2 + qDTY4.1) showed the greatest degree of improvement under drought compared with IR64 in terms of yield, canopy temperature, and normalized difference vegetation index (NDVI). Furthermore, qDTY2.2 and qDTY4.1 showed a potential for complementarity in that they were each most effective under different severities of drought stress. Multiple drought-response mechanisms were observed to be conferred in the genotypes with the two-QTL combination: higher root hydraulic conductivity and in some cases greater root growth at depth. As evidenced by multiple leaf water status and plant growth indicators, these traits affected transpiration but not transpiration efficiency or harvest index. The results from this study highlight the complex interactions among major-effect drought-yield QTLs and the drought-response traits they confer, and the need to evaluate the optimal combinations of QTLs that complement each other when present in a common genetic background.
QTL associated with lateral root plasticity in response to soil moisture fluctuation stress in rice
Niones JM, Inukai Y, Suralta RR and Yamauchi A (2015). QTL associated with lateral root plasticity in response to soil moisture fluctuation stress in rice. Plant and Soil Published online: 19 February 2015 (DOI: 10.1007/s11104-015-2404-x). (G3008.06)
Abstract: Background Lateral root (LR) plasticity is a key trait that plays a significant role in plant adaptation to fluctuating soil moisture stressed environments. We previously had demonstrated that promoted LR production (LR plasticity) contributed to the maintenance in shoot dry matter production and grain yield under soil moisture fluctuation (SMF) stress.
Aim To identify quantitative trait loci (QTLs) associated with LR plasticity under SMF condition and their contributions to shoot dry matter production.
Methods F2 lines derived from Nipponbare x chromosome segment substituted line number 47 (Nipponbare/Kasalath) backcrosses were used to analyze ten substituted chromosome regions with ‘Kasalath’ allele that are associated with root plasticity under SMF stress.
Results We mapped two closely linked QTLs on chromosome 12 region namely qTLRN-12 at seedling stage and qLLRN-12 at vegetative stage. Under SMF conditions, qTLRN-12 found at the flanking markers between TG154 and RM247 is responsible for the plasticity in total LR number while qLLRN-12 detected at the flanking markers between RM6296 and TG156 is associated with plasticity in L-type LR production. Kasalath genome contributed the corresponding alleles for increasing the mentioned root traits that resulted in a significant increase in shoot dry matter production under SMF stress.
Conclusion We identified two QTLs associated with LR plasticity on chromosome 12 which significantly contributed to the greater root system development and maintenance of total dry matter production under SMF stress.
Niones JM, Inukai Y, Suralta RR and Yamauchi A (2015). QTL associated with lateral root plasticity in response to soil moisture fluctuation stress in rice. Plant and Soil Published online: 19 February 2015 (DOI: 10.1007/s11104-015-2404-x). (G3008.06)
Abstract: Background Lateral root (LR) plasticity is a key trait that plays a significant role in plant adaptation to fluctuating soil moisture stressed environments. We previously had demonstrated that promoted LR production (LR plasticity) contributed to the maintenance in shoot dry matter production and grain yield under soil moisture fluctuation (SMF) stress.
Aim To identify quantitative trait loci (QTLs) associated with LR plasticity under SMF condition and their contributions to shoot dry matter production.
Methods F2 lines derived from Nipponbare x chromosome segment substituted line number 47 (Nipponbare/Kasalath) backcrosses were used to analyze ten substituted chromosome regions with ‘Kasalath’ allele that are associated with root plasticity under SMF stress.
Results We mapped two closely linked QTLs on chromosome 12 region namely qTLRN-12 at seedling stage and qLLRN-12 at vegetative stage. Under SMF conditions, qTLRN-12 found at the flanking markers between TG154 and RM247 is responsible for the plasticity in total LR number while qLLRN-12 detected at the flanking markers between RM6296 and TG156 is associated with plasticity in L-type LR production. Kasalath genome contributed the corresponding alleles for increasing the mentioned root traits that resulted in a significant increase in shoot dry matter production under SMF stress.
Conclusion We identified two QTLs associated with LR plasticity on chromosome 12 which significantly contributed to the greater root system development and maintenance of total dry matter production under SMF stress.
QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations
Meng L, Li H, Zhang L and Wang J (2015). QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. The Crop Journal (DOI: 10.1016/j.cj.2015.01.001). In press; published online on 23 February 2015. (G8009.10)
Abstract: QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are integrated in this software package: (1) BIN: binning of redundant markers; (2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci; (5) BIP: mapping of additive, dominant, and digenic epistasis genes; (6) MET: QTL-by-environment interaction analysis; (7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.
Meng L, Li H, Zhang L and Wang J (2015). QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. The Crop Journal (DOI: 10.1016/j.cj.2015.01.001). In press; published online on 23 February 2015. (G8009.10)
Abstract: QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are integrated in this software package: (1) BIN: binning of redundant markers; (2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci; (5) BIP: mapping of additive, dominant, and digenic epistasis genes; (6) MET: QTL-by-environment interaction analysis; (7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.
