[Show abstract][Hide abstract] ABSTRACT: Maize was first domesticated in a restricted valley in south-central Mexico. It was diffused throughout the Americas over thousands of years, and following the discovery of the New World by Columbus, was introduced into Europe. Trade and colonization introduced it further into all parts of the world to which it could adapt. Repeated introductions, local selection and adaptation, a highly diverse gene pool and outcrossing nature, and global trade in maize led to difficulty understanding exactly where the diversity of many of the local maize landraces originated. This is particularly true in Africa and Asia, where historical accounts are scarce or contradictory. Knowledge of post-domestication movements of maize around the world would assist in germplasm conservation and plant breeding efforts. To this end, we used SSR markers to genotype multiple individuals from hundreds of representative landraces from around the world. Applying a multidisciplinary approach combining genetic, linguistic, and historical data, we reconstructed possible patterns of maize diffusion throughout the world from American "contribution" centers, which we propose reflect the origins of maize worldwide. These results shed new light on introductions of maize into Africa and Asia. By providing a first globally comprehensive genetic characterization of landraces using markers appropriate to this evolutionary time frame, we explore the post-domestication evolutionary history of maize and highlight original diversity sources that may be tapped for plant improvement in different regions of the world.
Full-text · Article · Aug 2013 · Theoretical and Applied Genetics
[Show abstract][Hide abstract] ABSTRACT: The organization of maize (Zea mays L.) germplasm into genetically divergent heterotic groups is the foundation of a successful hybrid maize breeding program. In this study, 94 CIMMYT maize lines (CMLs) and 54 United States germplasm enhancement of maize (GEM) lines were assembled and characterized using 1,266 single nucleotide polymorphisms (SNPs) with high quality. Based on principal component analysis (PCA), the GEM lines and CMLs were clearly separated. In the GEM lines, there were two groups classified by PCA corresponding to the heterotic groups “stiff stalk” and “non-stiff stalk”. CMLs did not form obvious subgroups by PCA. The allelic frequency of each SNP differed in GEM lines and CMLs. In total, 3.6% alleles (46/1,266) of CMLs are absent in GEM lines and 4.4% alleles (56/1,266) of GEM lines are absent in CMLs. The performance of F1 plants (n = 654) produced by crossing between different groups based on pedigree information was evaluated at the breeding nurseries of two CIMMYT stations. Genomic estimated phenotypic values of plant height and days to anthesis for a testing set of 45 F1 crosses were predicted based on the training data of 600 F1 crosses using a best linear unbiased prediction method. The prediction accuracy benefitted from the adoption of the markers associated with quantitative trait loci for both traits; however, it does not necessarily increase with an increase in marker density. It is suggested that genomic selection combined with association analysis could improve prediction efficiency and reduce cost. For hybrid maize breeding in the tropics, incorporating GEM lines which have unique alleles and clear heterotic patterns into tropically adapted lines could be beneficial for enhancing heterosis in grain yields.
[Show abstract][Hide abstract] ABSTRACT: Dendrogram of different germplasm groups (Tuxpeno core, CML-A, CML-B, CML-A/B, GEM-SS, GEM-NSS, CIMMYT populations, U.S. landraces). Clades with greater than 50% bootstrap support are indicated.
[Show abstract][Hide abstract] ABSTRACT: Distribution of Tuxpeño core accessions (299 accessions with available information) by the collection information in maize mega-environments (MEs) defined by a GIS approach.
[Show abstract][Hide abstract] ABSTRACT: The tropical maize race Tuxpeño is a well-known race of Mexican dent germplasm which has greatly contributed to the development of tropical and subtropical maize gene pools. In order to investigate how it could be exploited in future maize improvement, a panel of maize germplasm accessions was assembled and characterized using genome-wide Single Nucleotide Polymorphism (SNP) markers. This panel included 321 core accessions of Tuxpeño race from the International Maize and Wheat Improvement Center (CIMMYT) germplasm bank collection, 94 CIMMYT maize lines (CMLs) and 54 U.S. Germplasm Enhancement of Maize (GEM) lines. The panel also included other diverse sources of reference germplasm: 14 U.S. maize landrace accessions, 4 temperate inbred lines from the U.S. and China, and 11 CIMMYT populations (a total of 498 entries with 795 plants). Clustering analyses (CA) based on Modified Rogers Distance (MRD) clearly partitioned all 498 entries into their corresponding groups. No sub clusters were observed within the Tuxpeño core set. Various breeding strategies for using the Tuxpeño core set, based on grouping of the studied germplasm and genetic distance among them, were discussed. In order to facilitate sampling diversity within the Tuxpeño core, a minicore subset of 64 Tuxpeño accessions (20% of its usual size) representing the diversity of the core set was developed, using an approach combining phenotypic and molecular data. Untapped diversity represents further use of the Tuxpeño landrace for maize improvement through the core and/or minicore subset available to the maize community.
[Show abstract][Hide abstract] ABSTRACT: Maize (Zea mays L. ssp. mays) was domesticated from one wild species ancestor, the Balsas teosinte (Zea mays ssp. parviglumis) about 9000years ago. Higher levels of gene diversity are found in teosinte taxa compared to maize, following domestication
and selection bottlenecks. Diversity in maize can be increased via gene flow from teosinte, which has certainly occurred from
various taxa, but the rate of flow from different teosinte taxa and the final impact on maize evolution has been difficult
to measure. One hundred populations from six Zea taxa, both domesticated (maize) and wild (teosinte), including domesticated landraces from Asia, Africa, and the Americas,
were genotyped with 17 SSR markers using 15 individuals per population. Overall levels of diversity were high, and populations
could be distinguished based on markers. Relationships between populations followed most published reports, or can now help
resolve previously conflicting reports. Gene flow into maize from different teosinte groups, and gene flow between different
teosintes, was estimated. Evidence for contributions from the Balsas teosintes and from Chalco teosintes (Z. mays ssp. mexicana) to the maize gene pool was found, as well as from Chalco into ssp. mexicana race “Durango” and Z. mays ssp. huehuetenengensis. These contributions are almost certainly the result of post-domestication (and ongoing) exchanges. This information must
give more impetus to in situ conservation of teosinte species, and use of these teosintes to continue to direct the evolution of maize, especially in
response to new diseases, insect pests, and other biotic and abiotic stresses.
KeywordsCrop evolution–Gene flow–Maize (Zea mays ssp. mays)–Molecular markers–Teosinte
Full-text · Article · Dec 2011 · Genetic Resources and Crop Evolution
[Show abstract][Hide abstract] ABSTRACT: A total of 550 maize inbred lines collected from global breeding programs were evaluated for drought resistance under both well-watered and water-stressed environments. The evaluation was based on multiple measurements of biomass taken before and after the drought stress was applied using the normalized difference vegetation index (NDVI), along with other selection criteria including anthesis-silking interval, leaf senescence, chlorophyll content, root capacitance, final grain yield, and grain yield components. Kernel weight was the most stable trait under drought stress. Correlations between the primary trait (grain yield) and the secondary traits, except the root capacitance and ASI under water-stressed condition, were all significant. Root capacitance had relatively low heritability and low genetic correlation with other drought resistance criteria, and is not recommended as a drought resistance criterion. Significant reduction of NDVI values measured in the afternoon when the leaves became rolling, compared to those measured in the morning when the leaves were open, provides a reliable index for leaf rolling, which however was not significantly correlated with grain yield. NDVIs measured across different developmental stages were highly correlated with each other and with most of the secondary traits as well as, grain yield, indicating that NDVI can be used as a secondary trait for large-scale drought resistance screening. Regression models built based on non-yield drought criteria and yield components explained about 40% and 95% of the variation for the grain yield, respectively. Some maize lines developed in China for temperate regions showed strong drought resistance comparable to tropical maize lines when tested under tropical condition, indicating that temperate lines with a wide adaptability can be used in drought resistance breeding for both temperate and tropical environments.
Full-text · Article · Oct 2011 · Fuel and Energy Abstracts
[Show abstract][Hide abstract] ABSTRACT: Understanding of genetic diversity and linkage disequilibrium (LD) decay in diverse maize germplasm is fundamentally important for maize improvement. A total of 287 tropical and 160 temperate inbred lines were genotyped with 1943 single nucleotide polymorphism (SNP) markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from genic and intergenic regions. Intronic SNPs revealed a substantial higher variation than exonic SNPs. The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the 10 kb-window and gene-window haplotypes. The polymorphic information content values revealed by the haplotypes (0.436-0.566) were generally much higher than individual SNPs (0.247-0.259). Cluster analysis classified the 447 maize lines into two major groups, corresponding to temperate and tropical types. The level of genetic diversity and subpopulation structure were associated with the germplasm origin and post-domestication selection. Compared to temperate lines, the tropical lines had a much higher level of genetic diversity with no significant subpopulation structure identified. Significant variation in LD decay distance (2-100 kb) was found across the genome, chromosomal regions and germplasm groups. The average of LD decay distance (10-100 kb) in the temperate germplasm was two to ten times larger than that in the tropical germplasm (5-10 kb). In conclusion, tropical maize not only host high genetic diversity that can be exploited for future plant breeding, but also show rapid LD decay that provides more opportunity for selection.
[Show abstract][Hide abstract] ABSTRACT: Cluster dendrogram constructed for 447 maize inbred lines genotyped with 1943 SNP markers. Two major groups were identified as “Chinese maize lines” and “CIMMYT maize lines”. Six groups were identified within “Chinese maize lines” by different colors as Lancaster, Landrace from Southwest China, SPT, BSSS, PA, and PB
[Show abstract][Hide abstract] ABSTRACT: Detailed information of SNPs used in the study. The SNP name, chromosome, physical position, SNP type, gene name and ID harboring SNPs, minor allele frequency, polymorphic information content (PIC), and heterozygosity were provided.
[Show abstract][Hide abstract] ABSTRACT: •
Teosinte species are the closest relatives of maize and represent an important but increasingly rare genetic resource for maize improvement and the study of evolution by domestication. Three morphologically and ecologically distinct teosinte populations were recently discovered in México. The taxonomic status of these rare and endangered populations was investigated by detailed comparisons to previously characterized wild Zea species. •
Three new teosinte populations were compared to known teosinte taxa on the basis of morphological, ecogeographic, cytological, and molecular characteristics. Phenetic and phylogenetic analyses were performed using morphological and molecular data, respectively. •
The newly discovered populations are distinct from each other and from other Zea species to represent three new entities based on their unique combinations of morphological, ecological, ploidy, and DNA markers. A perennial diploid population from Nayarit is distinguished by early maturing plants, and having male inflorescences with few tassel branches and long spikelets. A perennial tetraploid population from Michoacán is characterized by tall and late maturing plants, and having male inflorescences with many branches. An annual diploid population from Oaxaca is characterized by having male inflorescences with fewer branches and longer spikelets than those found in the sister taxa Z. luxurians and Z. nicaraguensis, plants with high thermal requirements, and very long seed dormancy. •
Evidence from multiple independent sources suggests placement of the three new populations of teosinte as distinct entities within section Luxuriantes of the genus Zea. However, more extensive DNA marker or sequence data are required to resolve the taxonomy of this genus.
Full-text · Article · Sep 2011 · American Journal of Botany
[Show abstract][Hide abstract] ABSTRACT: Twenty maize landrace accessions regenerated and conserved in five maize genebanks were investigated for genetic integrity
using 1,150 Single Nucleotide Polymorphisms (SNPs) and 235 SNP haplotypes. The genetic diversity of three accessions changed
significantly in terms of the average number of alleles per locus. Ten out of twenty accessions had significantly different
SNP allelic frequencies, either after regeneration or in the same accession held in different genebanks. The proportion of
loci with significant changes in SNP allelic frequency was very low (37/1,150). Changes in the major allelic frequency (MAF)
for the majority of SNP loci (60.2–75.2%) were less than 0.05. For SNP haplotypes, the genetic diversity of four accessions
changed significantly in terms of average number of haplotype alleles and polymorphic information content (PIC) per locus.
The proportion of SNP haplotype alleles lost in the later generations ranged between 0 and 22.6%, and at the same time 0–19.9%
of the SNP haplotype alleles appeared in later generations, however, these were absent in the earlier generations. Dynamic
changes in genetic integrity, in terms of presence and absence of genes (alleles), by both SNP and SNP haplotype analysis
were detected during regeneration. A suboptimum number of ears harvested in one generation can be combined with those from
another, repeated regeneration to capture the diversity of the previous generation. Use of molecular markers during regeneration
of accessions can help in understanding the extent of genetic integrity of the maize accessions in ex situ genebanks and in recommending the best practice for maintaining the original genetic diversity of the genebank accessions.
Full-text · Article · Feb 2011 · Genetic Resources and Crop Evolution
[Show abstract][Hide abstract] ABSTRACT: The growing demands for food, feed, and bio-energy worldwide will require a 2% per annum increase in global maize (Zea mays L.) production. Maize is one of the most important staple food crops across the developing world as well as being an important feed crop for global livestock production and the emerging biofuel industry. Maize genotypes can range from 0.5 to 5 m standing height at flowering, mature in 60 to 330 d from planting, produce 1 to 4 ears per plant, 10 to 1800 kernels per ear and yield from 0.5 to 23.5 Mg of grain per hectare. Even greater genetic diversity is present in related species yet surprisingly little of the maize-related biodiversity is present in the current elite breeding pools. Improved methods and tools for germplasm conservation, characterization, and data sharing, as well as for population improvement, gene pool enhancement, and genomics-aided breeding are urgently needed if increases in maize productivity, particularly in the developing world, are to keep pace with predicted increases in demand. Progress in the private sector, particularly with the development of temperate maize cultivars, is far beyond that of the public sector, particularly regarding tropical maize cultivar development. This article provides an overview of progress at the International Maize and Wheat Improvement Center (CIMMYT) with national partner across the developing world. Particular emphasis is given to issues related to the continued development of elite maize breeding material as global public goods, especially regarding the introgression of new variations from genetic resources and the legal and phytosanitary issues related to international exchange of maize germplasm.
[Show abstract][Hide abstract] ABSTRACT: Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm clearly clustered into two separate groups. The temperate germplasm could be further divided into six groups consistent with known heterotic patterns. The greatest genetic divergence was observed between temperate and tropical/subtropical lines, followed by the divergence between yellow and white kernel lines, whereas the least divergence was observed between dent and flint lines. Long-term selection for hybrid performance has contributed to significant allele differentiation between heterotic groups at 20% of the SNP loci. There appeared to be substantial levels of genetic variation between different breeding pools as revealed by missing and unique alleles. Two SNPs developed from the same candidate gene were associated with the divergence between two opposite Chinese heterotic groups. Associated allele frequency change at two SNPs and their allele missing in Brazilian germplasm indicated a linkage disequilibrium block of 142 kb. These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs.
Full-text · Article · Oct 2009 · Theoretical and Applied Genetics