[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.
[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: 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.
PLoS ONE 03/2012; 7(3):e32626. DOI:10.1371/journal.pone.0032626 · 3.23 Impact Factor
[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
[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.
Fuel and Energy Abstracts 10/2011; 124(1):37-45. DOI:10.1016/j.fcr.2011.06.003
[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.
PLoS ONE 09/2011; 6(9):e24861. DOI:10.1371/journal.pone.0024861 · 3.23 Impact Factor
[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.
American Journal of Botany 09/2011; 98(9):1537-48. DOI:10.3732/ajb.1100193 · 2.60 Impact Factor
[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.
[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.
[Show abstract][Hide abstract] ABSTRACT: CIMMYT is the source of improved maize (Zea mays L.) breeding material for a significant portion of the nontemperate maize growing world. Landraces which did not serve as sources for improved maize germplasm may contain untapped allelic variation useful for future breeding progress. Information regarding levels of diversity in different germplasm would help to identify sources for broadening Improved breeding pools and in seeking genes and alleles that have not been tapped in modern maize breeding. The objectives of this study were to examine the diversity in mate landraces, modern open pollinated varieties (OPVs), and inbred lines adapted to nontemperate growing areas to find unique sources of allelic diversity that may be used in maize improvement. Twenty-five simple sequence repeat markers were used to characterize 497 individuals from 24 landraces of maize from Mexico, 672 individuals from 23 CIMMYT improved breeding populations, and 261 CIMMYT inbred lines. Number of alleles, gene diversity per locus, unique alleles per locus, and population structure all differ between germplasm groups. The unique alleles found in each germplasm group represent a great reservoir of untapped genetic resources for maize improvement, and implications for hybrid breeding are discussed.
[Show abstract][Hide abstract] ABSTRACT: Mexican races of maize (Zea mays L.) represent a valuable genetic resource for breeding and genetic surveys. We applied simple sequence repeat (SSR) markers to characterize 25 accessions of races of maize from Mexico. Our objectives were to (1) study the molecular genetic diversity within and among these accessions and (2) examine their relationships as assumed previously on the basis of morphological data. A total of 497 individuals were fingerprinted with 25 SSR markers. We observed a high total number of alleles (7.84 alleles per locus) and total gene diversity (0.61), confirming the broad genetic base of the maize races from Mexico. In addition, the accessions were grouped into distinct racial complexes on the basis of a model-based clustering approach. The principal coordinate analyses of the four Modern Incipient hybrids corroborated the proposed parental races of Chalqueño, Cónico Norteño, Celaya, and Bolita on the basis of the morphological data. Consequently, for some of the accessions, hybridizations provide a clue that can further be used to explain the associations among the Mexican races of maize.
[Show abstract][Hide abstract] ABSTRACT: Core subsets can be formed on the basis of molecular markers and different sampling strategies. This research used genetic markers on three maize data sets for studying 24 stratified sampling strategies to investigate which strategy conserved the most diversity in the core subsetascomparedwiththeoriginalsample.Thestrategieswereformed by combining three factors: (i) two clustering methods (UPGMA and Ward), based on (ii) two initial genetic distance measures, and using (iii) sixallocationcriteria(two basedonthesizeofthecluster andfourbased on maximizing distances in the core (the D method) used with four diversity indices). The objectives were (i) to study the influence of these factorsandtheirinteractiononthediversityofthecoresubsetsand(ii)to compare the 24 stratified sampling strategies with the M strategy implemented in the MSTRAT algorithm. Success of each strategy was measured on the basis of maximizing genetic distances (Modified Roger and Cavalli-Sforza and Edwards distances) and genetic diversity indices (Shannon index, proportion of heterozygous loci, and number of effective alleles) in each core. Twenty independent stratified random samples were obtained for each strategy using a sampling intensity of 20% of the collection. For the three data sets, the UPGMA with D allocation methods produced core subsets with significantly more diversity than the other methods and were better than the M strategy for maximizing genetic distance. For most of the diversity indices, the M strategy outperformed the D method.
[Show abstract][Hide abstract] ABSTRACT: When forming core subsets, accessions from a collection are classified into clusters, and then samples are drawn from the clusters with the aim of maintaining the diversity of the collection. In a stratified sampling strategy, the allocation method provides a criterion for determining the number of accessions to be selected from each cluster. This paper proposes an allocation method (D method) and compares it with three other allocation methods (L, LD, and NY methods). In these allocation methods, the number of accessions sampled per cluster is proportional to (i) the mean of the Gower's distance between accessions within the cluster (D method), (ii) the logarithm of the cluster size (L method), (iii) the product of the cluster size times the mean Gower distance (NY method), and (iv) the product of the logarithm of the cluster size times the mean Gower distance (LD method). Five hundred independent stratified random samples with two sampling intensities (10 and 20%) were obtained from four datasets. The allocation methods were compared on the basis of three criteria: diversity of the samples, recovery of the range of variables in the sample, and variances of the samples. Results showed that the D method produced samples (i) with significantly more diversity than the other allocation methods, (ii) that recovered more of the range of the variables, (iii) with higher variances for the continuous variables than the other three methods, and (iv) with variances higher than the variance among accessions of the collection. A sampling intensity of 10% preserves the same or more variability than a sampling intensity of 20%.
[Show abstract][Hide abstract] ABSTRACT: A major objective when regenerating germ plasm collections is to maintain as many genes (or alleles) as possible. Two stages, sampling and propagating, can be identified in any regeneration cycle. A rare allele can be lost at either stage, when a cross-pollinated population is being regenerated. The objectives of this study were (i) to derive the theoretical probability that one or a few rare alleles will be retained after one regeneration cycle and (ii) to determine, through computer simulation, the average number of alleles lost after a certain number of regeneration cycles. The effects of four mating methods commonly used on cross-pollinated crops (i.e., random pollen pollination, chain cross, paired cross, and self-pollination) were compared. If more than five seeds are harvested from each regenerated plant, the probability that an allele will be lost during Stage 2 can be ignored. However, harvesting and maintaining more seeds than are required for subsequent regeneration cycles will have some negative effects on the retention of genetic diversity. Self-pollination is the best mating strategy for retaining rare alleles only if the germination rate is 100% and all the reserved seeds are regenerated. It can be used for species where inbreeding depression is not serious and the seeds of individual plants from an accession can be stored separately. Paired cross without reciprocal is recommended for regenerating cross-pollinated species, as it results in the same genetic consequence as paired cross with reciprocal or chain cross, but requires only half the number of labor-intensive crosses.
[Show abstract][Hide abstract] ABSTRACT: Classification methods are used in genetic resource conservation and plant breeding. The two-stage Ward-Modified Location Model (Ward-MLM) clustering strategy defines initial groups by the Ward method and the MLM is then used to improve those groups. The three-way clustering strategy considers the same trait measured in different environments as different variables (environment-trait combination), so that the resulting clusters of cultivars have a small group x environment interaction (GEI) for all the traits included in the study. An important component of the GEI is the imperfect genotypic correlation or crossover interaction (COI). This study used the three-way Ward-MLM clustering strategy in three different data sets with the objectives of (i) evaluating the ability of the Ward-MLM methodology for clustering cultivars into groups with low COI, (ii) obtaining a graphical representation of the variables in a low dimensional scatter plot produced by the multidimensional scaling method (MDS) in which the GEI of continuous and categorical traits and environments can be visualized, and (iii) studying how the relationship between a pair of traits changes across environments. The three-way Ward-MLM strategy produced groups of cultivars with low levels of COI. The increment of the correlation coefficient values between groups with respect to the total correlation coefficients indicated that the groups formed by the three-way Ward-MLM strategy comprised subsets of individuals that had similar trait responses across environments.
[Show abstract][Hide abstract] ABSTRACT: On-farm conservation is recognized as a key component of a comprehensive strategy to conserve crop genetic resources. A fundamental problem faced by any on-farm conservation project is the identification of crop populations on which efforts should be focused. This paper describes a method to identify a subset of landraces for further conservation efforts from a larger collection representing the diversity found in the Central Valleys of Oaxaca, Mexico. Mexico is a center of origin and diversity for maize (Zea mays L.). The 17 landraces selected from an initial collection of 152 satisfy two criteria. First, they represent the diversity present in the larger collection. Second, they appear to serve the interests of farmers in the region. Data for applying the method were elicited through participatory as well as conventional techniques. They incorporate the complementary perspectives of both men and women members of farm households, and of plant breeders and social scientists.
[Show abstract][Hide abstract] ABSTRACT: When evaluating genetic resources and forming core subsets, gene bank accessions are classified into homogeneous and well-separated groups. The modified location model (MLM) is used in the context of a two-stage clustering strategy in which initial groups are first defined using a hierarchical clustering method (such as Ward) and then the MLM is applied to the groups that are formed (Ward-MLM). The MLM allows assuming correlations (between attributes) and variances (of the attributes) among subpopulations (SPs) to be equal (homogeneous, HOM) or different (heterogeneous, HET). The objectives of this study were (i) to compare the effect of assuming homogeneity with the effect of assuming heterogeneity of variance-covariance matrices on the classification of two simulated data sets using the Ward-MLM strategy; and (ii) to make the same type of comparison using data from maize (Zea mays L.) accessions from nine countries. When simulated HOM data were analyzed with the HOM model and the simulated HET data were analyzed with the HET model, some of the original SPs were represented in the resulting clusters but others changed and formed more separated groups. The HET model always formed the most compact and separated clusters, even for HOM data. Classification of 10 real data sets showed that the HET model produced more compact and well-separated groups than the HOM model. However, only the HOM model identified and grouped a small number of observations with very peculiar attributes. Although the HET model may suffice in most situations, the recommended strategy when classifying genetic resources would be to use both models.