Journal articles 2015
Documents
Translational genomics in agriculture: Some examples in grain legumes
Varshney RK, Kudapa H, Pazhamala L, Chitikineni A, Thudi M, Bohra A, Gaur PM, Janila P, Fikre A, Kimurto P and Ellis N (2015). Translational genomics in agriculture: Some examples in grain legumes. Critical Reviews in Plant Sciences 34(1–3):169–194 (DOI: 10.1080/07352689.2014.897909). First published online in October 2014.
Recent advances in genomics and associated disciplines like bioinformatics have made it possible to develop genomic resources, such as large-scale sequence data for any crop species. While these datasets have been proven very useful for the understanding of genome architecture and dynamics as well as facilitating the discovery of genes, an obligation for, and challenge to the scientific community is to translate genome information to develop products, i.e. superior lines for trait(s) of interest. We call this approach, “translational genomics in agriculture” (TGA). TGA is currently in practice for cereal crops, such as maize (Zea mays) and rice (Oryza sativa), mainly in developed countries and by the private sector; progress has been slow for legume crops. Grown globally on 62.8 million ha with a production of 53.2 million tons and a value of nearly 24.2 billion dollars, the majority of these legumes have low crop productivity (<1 ton/ hectare) and are in the developing countries of sub Saharan Africa, Asia and South America. Interestingly, the last five years have seen enormous progress in genomics for these legume crops. Therefore, it is time to implement TGA in legume crops in order to enhance crop productivity and to ensure food security in developing countries. Prospects, as well as some success stories of TGA, in addition to advances in genomics, trait mapping and gene expression analysis are discussed for five leading legume crops, chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), groundnut (Arachis hypogaea), pigeonpea (Cajanus cajan) and soybean (Glycine max). Some efforts have also been outlined to initiate/ accelerate TGA in three additional legume crops namely faba bean (Vicia faba), lentil (Lens culinaris) and pea (Pisum sativum).
Varshney RK, Kudapa H, Pazhamala L, Chitikineni A, Thudi M, Bohra A, Gaur PM, Janila P, Fikre A, Kimurto P and Ellis N (2015). Translational genomics in agriculture: Some examples in grain legumes. Critical Reviews in Plant Sciences 34(1–3):169–194 (DOI: 10.1080/07352689.2014.897909). First published online in October 2014.
Recent advances in genomics and associated disciplines like bioinformatics have made it possible to develop genomic resources, such as large-scale sequence data for any crop species. While these datasets have been proven very useful for the understanding of genome architecture and dynamics as well as facilitating the discovery of genes, an obligation for, and challenge to the scientific community is to translate genome information to develop products, i.e. superior lines for trait(s) of interest. We call this approach, “translational genomics in agriculture” (TGA). TGA is currently in practice for cereal crops, such as maize (Zea mays) and rice (Oryza sativa), mainly in developed countries and by the private sector; progress has been slow for legume crops. Grown globally on 62.8 million ha with a production of 53.2 million tons and a value of nearly 24.2 billion dollars, the majority of these legumes have low crop productivity (<1 ton/ hectare) and are in the developing countries of sub Saharan Africa, Asia and South America. Interestingly, the last five years have seen enormous progress in genomics for these legume crops. Therefore, it is time to implement TGA in legume crops in order to enhance crop productivity and to ensure food security in developing countries. Prospects, as well as some success stories of TGA, in addition to advances in genomics, trait mapping and gene expression analysis are discussed for five leading legume crops, chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), groundnut (Arachis hypogaea), pigeonpea (Cajanus cajan) and soybean (Glycine max). Some efforts have also been outlined to initiate/ accelerate TGA in three additional legume crops namely faba bean (Vicia faba), lentil (Lens culinaris) and pea (Pisum sativum).
Full article
Transcriptome profiling of wild Arachis from water-limited environments uncovers drought tolerance candidate genes
Brasileiro ACM, Morgante CV, Araujo ACG, Leal-Bertioli SCM, Silva AK, Martins ACQ, Vinson CC, Santos CMR, Bonfim O, Togawa RC, Saraiva MAP, Bertioli DJ and Guimaraes PM (2015). Transcriptome profiling of wild Arachis from water-limited environments uncovers drought tolerance candidate genes. Plant Molecular Biology Reporter Published online: 11 April 2015 (DOI 10.1007/s11105-015-0882-x). (G6010.01)
Abstract: Peanut (Arachis hypogaea L.) is an important legume cultivated mostly in drought-prone areas where its productivity can be limited by water scarcity. The development of more drought-tolerant varieties is, therefore, a priority for peanut breeding programs worldwide. In contrast to cultivated peanut, wild relatives have a broader genetic diversity and constitute a rich source of resistance/tolerance alleles to biotic and abiotic stresses. The present study takes advantage of this diversity to identify drought-responsive genes by analyzing the expression profile of two wild species, Arachis duranensis and Arachis magna (AA and BB genomes, respectively), in response to progressive water deficit in soil. Data analysis from leaves and roots of A. duranensis (454 sequencing) and A. magna (suppression subtractive hybridization (SSH)) stressed and control complementary DNA (cDNA) libraries revealed several differentially expressed genes in silico, and 44 of them were selected for further validation by quantitative RT-PCR (qRT-PCR). This allowed the identification of drought-responsive candidate genes, such as Expansin, Nitrilase, NAC, and bZIP transcription factors, displaying significant levels of differential expression during stress imposition in both species. This is the first report on identification of differentially expressed genes under drought stress and recovery in wild Arachis species. The generated transcriptome data, besides being a valuable resource for gene discovery, will allow the characterization of new alleles and development of molecular markers associated with drought responses in peanut. These together constitute important tools for the peanut breeding program and also contribute to a better comprehension of gene modulation in response to water deficit and rehydration.
Brasileiro ACM, Morgante CV, Araujo ACG, Leal-Bertioli SCM, Silva AK, Martins ACQ, Vinson CC, Santos CMR, Bonfim O, Togawa RC, Saraiva MAP, Bertioli DJ and Guimaraes PM (2015). Transcriptome profiling of wild Arachis from water-limited environments uncovers drought tolerance candidate genes. Plant Molecular Biology Reporter Published online: 11 April 2015 (DOI 10.1007/s11105-015-0882-x). (G6010.01)
Abstract: Peanut (Arachis hypogaea L.) is an important legume cultivated mostly in drought-prone areas where its productivity can be limited by water scarcity. The development of more drought-tolerant varieties is, therefore, a priority for peanut breeding programs worldwide. In contrast to cultivated peanut, wild relatives have a broader genetic diversity and constitute a rich source of resistance/tolerance alleles to biotic and abiotic stresses. The present study takes advantage of this diversity to identify drought-responsive genes by analyzing the expression profile of two wild species, Arachis duranensis and Arachis magna (AA and BB genomes, respectively), in response to progressive water deficit in soil. Data analysis from leaves and roots of A. duranensis (454 sequencing) and A. magna (suppression subtractive hybridization (SSH)) stressed and control complementary DNA (cDNA) libraries revealed several differentially expressed genes in silico, and 44 of them were selected for further validation by quantitative RT-PCR (qRT-PCR). This allowed the identification of drought-responsive candidate genes, such as Expansin, Nitrilase, NAC, and bZIP transcription factors, displaying significant levels of differential expression during stress imposition in both species. This is the first report on identification of differentially expressed genes under drought stress and recovery in wild Arachis species. The generated transcriptome data, besides being a valuable resource for gene discovery, will allow the characterization of new alleles and development of molecular markers associated with drought responses in peanut. These together constitute important tools for the peanut breeding program and also contribute to a better comprehension of gene modulation in response to water deficit and rehydration.
Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis
Leal-Bertioli S, Shirasawa K, Abernathy B, Moretzsohn M, Chavarro C, Clevenger J, Ozias-Akins P, Jackson S and Bertioli D (2015). Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis. Genetics 199(4):1093–1105 (DOI: 10.1534/genetics.115.174607). (G6010.01)
Abstract: Arachis hypogaea L. (cultivated peanut) is an allotetraploid (2n = 4x = 40) with an AABB genome type. Based on cytogenetic studies it has been assumed that peanut and wild-derived induced AABB allotetraploids have classic allotetraploid genetic behavior with diploid-like disomic recombination only between homologous chromosomes, at the exclusion of recombination between homeologous chromosomes. Using this assumption, numerous linkage map and quantitative trait loci studies have been carried out. Here, with a systematic analysis of genotyping and gene expression data, we show that this assumption is not entirely valid. In fact, autotetraploid-like tetrasomic recombination is surprisingly frequent in recombinant inbred lines generated from a cross of cultivated peanut and an induced allotetraploid derived from peanut's most probable ancestral species. We suggest that a better, more predictive genetic model for peanut is that of a "segmental allotetraploid" with partly disomic, partly tetrasomic genetic behavior. This intermediate genetic behavior has probably had a previously overseen, but significant, impact on the genome and genetics of cultivated peanut.
Leal-Bertioli S, Shirasawa K, Abernathy B, Moretzsohn M, Chavarro C, Clevenger J, Ozias-Akins P, Jackson S and Bertioli D (2015). Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis. Genetics 199(4):1093–1105 (DOI: 10.1534/genetics.115.174607). (G6010.01)
Abstract: Arachis hypogaea L. (cultivated peanut) is an allotetraploid (2n = 4x = 40) with an AABB genome type. Based on cytogenetic studies it has been assumed that peanut and wild-derived induced AABB allotetraploids have classic allotetraploid genetic behavior with diploid-like disomic recombination only between homologous chromosomes, at the exclusion of recombination between homeologous chromosomes. Using this assumption, numerous linkage map and quantitative trait loci studies have been carried out. Here, with a systematic analysis of genotyping and gene expression data, we show that this assumption is not entirely valid. In fact, autotetraploid-like tetrasomic recombination is surprisingly frequent in recombinant inbred lines generated from a cross of cultivated peanut and an induced allotetraploid derived from peanut's most probable ancestral species. We suggest that a better, more predictive genetic model for peanut is that of a "segmental allotetraploid" with partly disomic, partly tetrasomic genetic behavior. This intermediate genetic behavior has probably had a previously overseen, but significant, impact on the genome and genetics of cultivated peanut.
Studies on breeding of Yunhan strong gluten wheat varieties for drought resistance and high yield
Li X, Chai Y, Zhao Z, Sun L, Yao J, Bi H and Xi J (2015). Studies on breeding of Yunhan strong gluten wheat varieties for drought resistance and high yield. Chinese Agricultural Science Bulletin 31(12):29–35. Article in Chinese with abstract in English. (G7010.02.01)
Abstract: In order to breeding the high-quality, high-yield, strong gluten and drought-resistant wheat varieties which are suitable for Huanghuai dry land of our country, the research focused on the high yield and high quality breeding goal of strong gluten and high quality foreign germplasm usage. The author used strategies and methods like rational parent combination, adjusting the flowering for inter-breed, assistant selections with high molecular weight glutenin subunit protein molecular marker detections and measuring the quantity and quality of gluten, ecological-adaptation-oriented feature selection identification and ecological selection in multi-points for year. Alternative identification and selections in rain fed and irrigated land, strengthened systematic observation and comprehensive evaluation for better lines, and selections from better lines were conducted. The application of the systematic methods had solved the technical problems of bad adaptability to drought, heat, frost resistance, and maturity of foreign germplasms and hybrids with spring and winter varieties. The research bred a series of strong gluten wheat varieties which were represented by ‘Yunhan20410’,‘Yunhan 618’, achieved the innovation improvement which changed the strong gluten to the strong and stable gluten. They raised 2%-10% production than‘Jinmai 47’and had more drought-resistance and more heat-tolerance. We obtained the combination of high yield and drought resistance with the strong gluten traits.
Li X, Chai Y, Zhao Z, Sun L, Yao J, Bi H and Xi J (2015). Studies on breeding of Yunhan strong gluten wheat varieties for drought resistance and high yield. Chinese Agricultural Science Bulletin 31(12):29–35. Article in Chinese with abstract in English. (G7010.02.01)
Abstract: In order to breeding the high-quality, high-yield, strong gluten and drought-resistant wheat varieties which are suitable for Huanghuai dry land of our country, the research focused on the high yield and high quality breeding goal of strong gluten and high quality foreign germplasm usage. The author used strategies and methods like rational parent combination, adjusting the flowering for inter-breed, assistant selections with high molecular weight glutenin subunit protein molecular marker detections and measuring the quantity and quality of gluten, ecological-adaptation-oriented feature selection identification and ecological selection in multi-points for year. Alternative identification and selections in rain fed and irrigated land, strengthened systematic observation and comprehensive evaluation for better lines, and selections from better lines were conducted. The application of the systematic methods had solved the technical problems of bad adaptability to drought, heat, frost resistance, and maturity of foreign germplasms and hybrids with spring and winter varieties. The research bred a series of strong gluten wheat varieties which were represented by ‘Yunhan20410’,‘Yunhan 618’, achieved the innovation improvement which changed the strong gluten to the strong and stable gluten. They raised 2%-10% production than‘Jinmai 47’and had more drought-resistance and more heat-tolerance. We obtained the combination of high yield and drought resistance with the strong gluten traits.
Registration of the Ki14 × B73 recombinant inbred mapping population of maize
Pratt RC, Holland JB, Balint-Kurti PJ, Coles ND, Zwonitzer JC, Casey MA and McMullens MC (2015). Registration of the Ki14 × B73 recombinant inbred mapping population of maize. Journal of Plant Registrations 9(2):262–265 (DOI: 10.3198/jpr2014.06.0041crmp). Not open access; view abstract.
Pratt RC, Holland JB, Balint-Kurti PJ, Coles ND, Zwonitzer JC, Casey MA and McMullens MC (2015). Registration of the Ki14 × B73 recombinant inbred mapping population of maize. Journal of Plant Registrations 9(2):262–265 (DOI: 10.3198/jpr2014.06.0041crmp). Not open access; view abstract.
Quantitative trait loci mapping for traits related to the progression of wheat flag leaf senescence
Wang S, Liang Z, Sun D, Dong F, Chen W, Wang H and Jing R (2015). Quantitative trait loci mapping for traits related to the progression of wheat flag leaf senescence. Journal of Agricultural Science Published online as FirstView Article: 24 September 2014 (DOI: 10.1017/S002185961400094X). Not open access; view abstract. (G7010.02.01)
Wang S, Liang Z, Sun D, Dong F, Chen W, Wang H and Jing R (2015). Quantitative trait loci mapping for traits related to the progression of wheat flag leaf senescence. Journal of Agricultural Science Published online as FirstView Article: 24 September 2014 (DOI: 10.1017/S002185961400094X). Not open access; view abstract. (G7010.02.01)
QTL mapping for plant height and yield components in common wheat under water limited and full irrigation environments
Li X, Xia X, Xiao Y, He Z, Wang D, Trethowan R, Wang H, Chen X (2015). QTL mapping for plant height and yield components in common wheat under water limited and full irrigation environments. Crop & Pasture Science Accepted for publication. View abstract. (G7010.02.01)
Li X, Xia X, Xiao Y, He Z, Wang D, Trethowan R, Wang H, Chen X (2015). QTL mapping for plant height and yield components in common wheat under water limited and full irrigation environments. Crop & Pasture Science Accepted for publication. View abstract. (G7010.02.01)
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.
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.
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.
