There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postdomestication gene flow from teosinte into maize.

/pdf/a-single-domestication-for-maize-shown-by-multilocus-iv327rf58a.pdf

A single domestication for maize shown by multilocus microsatellite genotyping

Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.

https://www.genetics.org/content/genetics/165/4/2117.full.pdf

Genetic Structure and Diversity Among Maize Inbred Lines as Inferred From DNA Microsatellites

Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (c) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. Our study was based on 1,537 elite maize inbred lines genotyped with 359 SSR and 8,244 SNP markers. The average number of alleles per locus, of group specific alleles, and the gene diversity (D) were higher for SSRs than for SNPs. Modified Roger's distance (MRD) estimates and membership probabilities of the STRUCTURE matrices were higher for SSR than for SNP markers but the germplasm organization in four heterotic pools was consistent with STRUCTURE results based on SSRs and SNPs. MRD estimates calculated for the two marker systems were highly correlated (0.87). Our results suggested that the same conclusions regarding the structure and the diversity of heterotic pools could be drawn from both markers types. Furthermore, although our results suggested that the ratio of the number of SSRs and SNPs required to obtain MRD or D estimates with similar precision is not constant across the various precision levels, we propose that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity.

/pdf/population-structure-and-genetic-diversity-in-a-commercial-39zhoafu33.pdf

Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers

The objectives of this study were (i) to assess the level of genetic diversity in elite sterility-maintaining (B) and fertility-restoring (R) sorghum [Sorghum bicolor (L.) Moench] lines as compared with a group of exotic and converted germplasm (IS) from the World Collection, (ii) to compare the classification of germplasm on the basis of estimates of genetic similarities obtained by means of AFLP and microsatellite (SSR) markers, and (iii) to compare the classification of germplasm obtained by different classes of molecular markers. A set of 100 SSRs, 1318 EcoRI/Msel AFLP, and 496 PstI/MseI AFLP markers with known map positions were utilized to determine the genetic similarity in a group of B, R, and IS public inbreds. Cluster analysis of genetic similarity estimates (GS ij ) revealed that the classification of sorghum inbreds is based on the sorghum working groups, Zera-zera, Kafir, Kafir-Milo, Durra, and Feterita. Cluster analyses failed to give a clear differentiation between B- and R-lines, suggesting that R- and B-lines do not represent well-defined heterotic groups in this set of public lines. By comparing the different classes of molecular markers (SSRs, AFLPs, combinations of SSRs and AFLPs), we determined that the distribution of the markers and the coverage of the genome by the markers did affect the classification of genotypes. Dendrograms of genetic similarity (GS) based on PstI/MseI AFLP markers, or a set of markers spaced at 1- to 2-cM intervals across the genome, produced clusters that were in better agreement with pedigree information than the analysis based solely on the EcoRI/ Msel AFLP or SSR markers used in this study.

/pdf/genetic-diversity-of-public-inbreds-of-sorghum-determined-by-19hrgss732.pdf

Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers.

Since the advent of modern plant breeding in the 1930s, North American maize has undergone a dramatic adaptation to high-input agriculture. Despite the importance of genetic contributions to historical yield increases, little is known about the underlying genomic changes. Here we use high-density SNP genotyping to characterize a set of North American maize lines spanning the history of modern breeding. We provide a unique analysis of genome-wide developments in genetic diversity, ancestry, and selection. The genomic history of maize is marked by a steady increase in genetic differentiation and linkage disequilibrium, whereas allele frequencies in the total population have remained relatively constant. These changes are associated with increasing genetic separation of breeding pools and decreased diversity in the ancestry of individual lines. We confirm that modern heterotic groups are the product of ongoing divergence from a relatively homogeneous landrace population, but show that differential landrace ancestry remains evident. Using a recent association approach, we characterize signals of directional selection throughout the genome, identifying a number of candidate genes of potential agronomic relevance. However, overall we find that selection has had limited impact on genome-wide patterns of diversity and ancestry, with little evidence for individual lines contributing disproportionately to the accumulation of favorable alleles in today's elite germplasm. Our data suggest breeding progress has mainly involved selection and recombination of relatively common alleles, contributed by a representative but limited set of ancestral lines.

https://www.pnas.org/content/pnas/109/31/12420.full.pdf

Historical genomics of North American maize

The genetic relationship between inbreds i and j can be estimated from pedigree or from molecular marker data. The objectives of this study were to: (1) determine whether pedigree, restriction fragment length polymorphism (RFLP), and simple sequence repeat (SSR) data give similar estimates of parental contribution and coefficient of coancestry (f

 ij
 ) among a set of maize (Zea mays L.) inbreds, and (2) compare the usefulness of RFLP and SSR markers for estimating genetic relationship. We studied 13 maize inbreds with known pedigrees. The inbreds were genotyped using 124 RFLP and 195 SSR markers. For each type of marker, parental contributions were estimated from marker similarity among an inbred and both of its parents, and were subsequently used to estimate f

 ij
 . Estimates of parental contribution differed significantly (α<0.05) between pedigree data and either type of marker, but not between the marker systems. The RFLP estimates of parental contribution failed to sum to 1.0, reflecting a higher frequency of non-parental bands with RFLP than with SSR markers. The f

 ij
 estimated from pedigree, RFLP, and SSR data were highly correlated (r=0.87–0.97), although significant differences were found among the three sets of f

 ij
 estimates. We concluded that pedigree and marker data often lead to different estimates of parental contribution and f

 ij
 , and that SSR markers are superior to RFLP markers for estimating genetic relationship. A relevant question is whether or not the inbreds previously genotyped with an older marker system (e.g., RFLP) need to be re-analyzed with a newer marker system (e.g., SSR) for the purpose of estimating genetic relationship. Such re-analysis seems unnecessary if data for the same type of marker are available for a given inbred and both of its parents.

Parental contribution and coefficient of coancestry among maize inbreds: Pedigree, RFLP, and SSR data

The objectives of this study were the examination of genetic similarities in a diverse group of maize inbreds and an investigation of the incidence of shared haplotypes within closely related groups. Size polymorphisms from 218 mapped simple-sequence repeats (SSR) for 57 entries were detected with the ABI377 Prism system and scored with Genotyper software. The standard error for the estimated size of identical PCR products was 0.13 base pairs. Size estimates were used to examine genetic relationships among the Iodent, flint, corn belt dent, sweet corn and popcorn groups in Zea mays L. inbreds. Cluster analysis of SSR distance data from 57 entries showed similarity between the European flints (F2, F7 and EP1), CO109 and the su1 sweet corns developed in the United States. The inbred F64 from Argentina was distinct from all other entries. Close examination of two sources of B37 revealed that the Purdue University version of B37 contains a set of alleles characteristic of B73. Five groups (Iodents, European flints, the B73 group of corn belt dents, su1 sweet corn, popcorn) show persistent within-group haplotypes.

G. Hookstra

Papers

Parental contribution and coefficient of coancestry among maize inbreds: Pedigree, RFLP, and SSR data

Pedigree analysis and haplotype sharing within diverse groups of Zea mays L. inbreds