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Liu H.,Huazhong Agricultural University | Wang X.,Huazhong Agricultural University | Warburton M.L.,Corn Host Plant Resistance Research Unit | Wen W.,Huazhong Agricultural University | And 7 more authors.
Molecular Plant | Year: 2015

The temperate-tropical division of early maize germplasms to different agricultural environments was arguably the greatest adaptation process associated with the success and near ubiquitous importance of global maize production. Deciphering this history is challenging, but new insight has been gained from examining 558 529 single nucleotide polymorphisms, expression data of 28 769 genes, and 662 traits collected from 368 diverse temperate and tropical maize inbred lines in this study. This is a new attempt to systematically exploit the mechanisms of the adaptation process in maize. Our results indicate that divergence between tropical and temperate lines apparently occurred 3400-6700 years ago. Seven hundred and one genomic selection signals and transcriptomic variants including 2700 differentially expressed individual genes and 389 rewired co-expression network genes were identified. These candidate signals were found to be functionally related to stress responses, and most were associated with directionally selected traits, which may have been an advantage under widely varying environmental conditions faced by maize as it was migrated away from its domestication center. Our study also clearly indicates that such stress adaptation could involve evolution of protein-coding sequences as well as transcriptome-level regulatory changes. The latter process may be a more flexible and dynamic way for maize to adapt to environmental changes along its short evolutionary history. © 2015 The Author.


Yan J.,International Maize and Wheat Improvement Center | Yan J.,Cornell University | Kandianis C.B.,Urbana University | Kandianis C.B.,Purdue University | And 27 more authors.
Nature Genetics | Year: 2010

Breeding to increase Β-carotene levels in cereal grains, termed provitamin A biofortification, is an economical approach to address dietary vitamin A deficiency in the developing world. Experimental evidence from association and linkage populations in maize (Zea mays L.) demonstrate that the gene encoding Β-carotene hydroxylase 1 (crtRB1) underlies a principal quantitative trait locus associated with Β-carotene concentration and conversion in maize kernels. crtRB1 alleles associated with reduced transcript expression correlate with higher Β-carotene concentrations. Genetic variation at crtRB1 also affects hydroxylation efficiency among encoded allozymes, as observed by resultant carotenoid profiles in recombinant expression assays. The most favorable crtRB1 alleles, rare in frequency and unique to temperate germplasm, are being introgressed via inexpensive PCR marker-assisted selection into tropical maize germplasm adapted to developing countries, where it is most needed for human health. © 2010 Nature America, Inc. All rights reserved.


Li L.,China Agricultural University | Li H.,China Agricultural University | Li Q.,China Agricultural University | Yang X.,China Agricultural University | And 8 more authors.
PLoS ONE | Year: 2011

The ratio of saturated to unsaturated fatty acids in maize kernels strongly impacts human and livestock health, but is a complex trait that is difficult to select based on phenotype. Map-based cloning of quantitative trait loci (QTL) is a powerful but time-consuming method for the dissection of complex traits. Here, we combine linkage and association analyses to fine map QTL-Pal9, a QTL influencing levels of palmitic acid, an important class of saturated fatty acid. QTL-Pal9 was mapped to a 90-kb region, in which we identified a candidate gene, Zea mays fatb (Zmfatb), which encodes acyl-ACP thioesterase. An 11-bp insertion in the last exon of Zmfatb decreases palmitic acid content and concentration, leading to an optimization of the ratio of saturated to unsaturated fatty acids while having no effect on total oil content. We used three-dimensional structure analysis to explain the functional mechanism of the ZmFATB protein and confirmed the proposed model in vitro and in vivo. We measured the genetic effect of the functional site in 15 different genetic backgrounds and found a maximum change of 4.57 mg/g palmitic acid content, which accounts for ~20-60% of the variation in the ratio of saturated to unsaturated fatty acids. A PCR-based marker for QTL-Pal9 was developed for marker-assisted selection of nutritionally healthier maize lines. The method presented here provides a new, efficient way to clone QTL, and the cloned palmitic acid QTL sheds lights on the genetic mechanism of oil biosynthesis and targeted maize molecular breeding.


Setimela P.S.,International Maize and Wheat Improvement Center | Warburton M.L.,Corn Host Plant Resistance Research Unit | Erasmus T.,INCOTEC South Africa Pty Ltd
South African Journal of Plant and Soil | Year: 2016

Maize (Zea mays L.) plays a dominant role in farming systems in sub-Saharan Africa (SSA). There has been a four-to-five-fold increase in the number of seed companies in SSA in the last decade, and yet more than half of small-holder farmers still grow traditional and unimproved varieties. The adoption of open-pollinated varieties (OPVs) and hybrids is around 44% of all farmers in SSA. Open-pollinated varieties are heterogeneous, and some local seed suppliers may attempt to take advantage of this to adulterate seed bags with cheaper food grain. This study sought to use a bulked DNA fingerprinting method to determine the identity and level of genetic purity among 35 seed lots of ZM521, a popular African OPV, maintained by various sources and the foundation seed source of ZM521 maintained by CIMMYT. From each seed lot, 20 individuals were bulked and analysed with 15 fluorescently labelled simple sequence repeat markers on an automatic DNA sequencer, allowing allele frequency to be determined from the bulk using peak intensity. The 35 seed lots grouped according to the source of foundation seed from which each seed lot was derived, and large genetic divergences were observed among different OPVs and hybrids. © 2016 Southern African Plant & Soil Sciences Committee


Semagn K.,International Maize and Wheat Improvement Center | Magorokosho C.,CIMMYT | Vivek B.S.,Indian International Crops Research Institute for the Semi Arid Tropics | Makumbi D.,International Maize and Wheat Improvement Center | And 4 more authors.
BMC Genomics | Year: 2012

Background: Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays.Results: Genetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays.Conclusions: There were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding. © 2012 Semagn et al; licensee BioMed Central Ltd.


Mideros S.X.,Cornell University | Warburton M.L.,Corn Host Plant Resistance Research Unit | Jamann T.M.,Cornell University | Windham G.L.,Corn Host Plant Resistance Research Unit | And 2 more authors.
Crop Science | Year: 2014

Mycotoxin contamination of maize (Zea mays L.) exposes people to grave health consequences in subsistence agricultural settings and to economical losses in quality-regulated markets. Genetic variation for resistance to aflatoxin accumulation in maize has been reported in many studies. Resistance can act at multiple steps at which there is fungal-plant interaction. In this study, we report the identification and mapping of quantitative trait loci (QTL) for multiple traits or components of resistance to Aspergillus flavus using different genetic tools and resources. For QTL mapping, we used a B73 × CML322 population of recombinant inbred lines. Ten QTL were found using two QTL mapping methods, six of which were located on the same chromosome segments using both approaches. These QTL were located in maize bins 4.08, 4.09, 8.02, 8.03, 10.06 and 10.07. Various sources of near-isogenic lines (NILs) for selected loci were tested. The resistance QTL located in bin 4.08 was confirmed using a NIL pair. Finally, we conducted a meta-analysis of QTL using data from 12 populations in which resistance to Aspergillus, Fusarium, or Giberella ear rots has been mapped. This meta-analysis indicated that the QTL in bin 4.08 has been reported in four mapping populations. Overall, we found evidence for significant QTL × year interactions and that QTL were distributed in a manner consistent with an infinitesimal model. The largest-effect QTL, located in bin 4.08, is a good candidate for further characterization and use. © Crop Science Society of America.


Semagn K.,International Maize and Wheat Improvement Center | Beyene Y.,International Maize and Wheat Improvement Center | Warburton M.L.,Corn Host Plant Resistance Research Unit | Tarekegne A.,CIMMYT | And 4 more authors.
BMC Genomics | Year: 2013

Background: Identification of QTL with large phenotypic effects conserved across genetic backgrounds and environments is one of the prerequisites for crop improvement using marker assisted selection (MAS). The objectives of this study were to identify meta-QTL (mQTL) for grain yield (GY) and anthesis silking interval (ASI) across 18 bi-parental maize populations evaluated in the same conditions across 2-4 managed water stressed and 3-4 well watered environments.Results: The meta-analyses identified 68 mQTL (9 QTL specific to ASI, 15 specific to GY, and 44 for both GY and ASI). Mean phenotypic variance explained by each mQTL varied from 1.2 to 13.1% and the overall average was 6.5%. Few QTL were detected under both environmental treatments and/or multiple (>4 populations) genetic backgrounds. The number and 95% genetic and physical confidence intervals of the mQTL were highly reduced compared to the QTL identified in the original studies. Each physical interval of the mQTL consisted of 5 to 926 candidate genes.Conclusions: Meta-analyses reduced the number of QTL by 68% and narrowed the confidence intervals up to 12-fold. At least the 4 mQTL (mQTL2.2, mQTL6.1, mQTL7.5 and mQTL9.2) associated with GY under both water-stressed and well-watered environments and detected up to 6 populations may be considered for fine mapping and validation to confirm effects in different genetic backgrounds and pyramid them into new drought resistant breeding lines. This is the first extensive report on meta-analysis of data from over 3100 individuals genotyped using the same SNP platform and evaluated in the same conditions across a wide range of managed water-stressed and well-watered environments. © 2013 Semagn et al.; licensee BioMed Central Ltd.


Semagn K.,International Maize and Wheat Improvement Center | Magorokosho C.,CIMMYT | Ogugo V.,International Maize and Wheat Improvement Center | Makumbi D.,International Maize and Wheat Improvement Center | Warburton M.L.,Corn Host Plant Resistance Research Unit
Molecular Breeding | Year: 2014

Molecular characterization of open-pollinated maize varieties (OPVs) is fundamentally important in maize germplasm improvement. We investigated the extent of genetic differences, patterns of relationships, and population structure among 218 diverse OPVs widely used in southern and eastern Africa using the model-based population structure, analysis of molecular variance, cluster analysis, principal component analysis, and discriminant analysis. The OPVs were genotyped with 51 microsatellite markers and the fluorescent detection system of the Applied Biosystems 3730 Capillary Sequencer. The number of alleles detected in each OPV varied from 72 to 155, with an overall mean of 127.6. Genetic distance among the OPVs varied from 0.051 to 0.434, with a mean of 0.227. The different multivariate methods suggest the presence of 2–4 possible groups, primarily by maturity groups but also with overlapping variation between breeding programs, mega-environments, and specific agronomic traits. Nearly all OPVs in group 1 and group 2 belong to the intermediate-late and early maturity groups, respectively. Group 3 consisted of mainly intermediate maturing OPVs, while group 4 contained OPVs of different maturity groups. The OPVs widely used in eastern Africa either originated from the southern African maize breeding programs, or the majority of inbred lines used as parents by the two breeding programs in developing the OPVs might be genetically related. Some of the OPVs are much older than others, but they still did not show a clear pattern of genetic differentiation as compared with the recently developed ones, which is most likely due to recycling of the best parental lines in forming new OPVs. © 2014, Springer Science+Business Media Dordrecht.


Kelley R.Y.,Mississippi State University | Williams W.P.,Corn Host Plant Resistance Research Unit | Mylroie J.E.,Mississippi State University | Boykin D.L.,U.S. Department of Agriculture | And 4 more authors.
PLoS ONE | Year: 2012

Background: Aspergillus flavus infection and aflatoxin contamination of maize pose negative impacts in agriculture and health. Commercial maize hybrids are generally susceptible to this fungus. Significant levels of host plant resistance have been observed in certain maize inbred lines. This study was conducted to identify maize genes associated with host plant resistance or susceptibility to A. flavus infection and aflatoxin accumulation. Results: Genome wide gene expression levels with or without A. flavus inoculation were compared in two resistant maize inbred lines (Mp313E and Mp04:86) in contrast to two susceptible maize inbred lines (Va35 and B73) by microarray analysis. Principal component analysis (PCA) was used to find genes contributing to the larger variances associated with the resistant or susceptible maize inbred lines. The significance levels of gene expression were determined by using SAS and LIMMA programs. Fifty candidate genes were selected and further investigated by quantitative RT-PCR (qRT-PCR) in a time-course study on Mp313E and Va35. Sixteen of the candidate genes were found to be highly expressed in Mp313E and fifteen in Va35. Out of the 31 highly expressed genes, eight were mapped to seven previously identified quantitative trait locus (QTL) regions. A gene encoding glycine-rich RNA binding protein 2 was found to be associated with the host hypersensitivity and susceptibility in Va35. A nuclear pore complex protein YUP85-like gene was found to be involved in the host resistance in Mp313E. Conclusion: Maize genes associated with host plant resistance or susceptibility were identified by a combination of microarray analysis, qRT-PCR analysis, and QTL mapping methods. Our findings suggest that multiple mechanisms are involved in maize host plant defense systems in response to Aspergillus flavus infection and aflatoxin accumulation. These findings will be important in identification of DNA markers for breeding maize lines resistant to aflatoxin accumulation.


De La Fuente G.N.,Texas A&M University | Murray S.C.,Texas A&M University | Isakeit T.,Texas A&M University | Park Y.-S.,Texas A&M University | And 4 more authors.
PLoS ONE | Year: 2013

Maize (Zea mays L.) lipoxygenases (ZmLOXs) are well recognized as important players in plant defense against pathogens, especially in cross kingdom lipid communication with pathogenic fungi. This study is among the first to investigate genetic diversity at important gene paralogs ZmLOX4 and ZmLOX5. Sequencing of these genes in 400 diverse maize lines showed little genetic diversity and low linkage disequilibrium in the two genes. Importantly, we identified one inbred line in which ZmLOX5 has a disrupted open reading frame, a line missing ZmLOX5, and five lines with a duplication of ZmLOX5. Tajima's D test suggests that both ZmLOX4 and ZmLOX5 have been under neutral selection. Further investigation of haplotype data revealed that within the ZmLOX family members only ZmLOX12, a monocot specific ZmLOX, showed strong linkage disequilibrium that extends further than expected in maize. Linkage disequilibrium patterns at these loci of interest are crucial for future candidate gene association mapping studies. ZmLOX4 and ZmLOX5 mutations and copy number variants are under further investigation for crop improvement.

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