Relationships between maize and teosinte of Mexico and Guatemala: Numerical analysis of allozyme data

Electrophoresis revealed 153 variants at 19 enzyme loci among 77 accessions of annual teosinte, 1 accession of diploid perennial teosinte, 1 accession of tetraploid perennial teosinte, and 43 accessions of maize from Mexico and Guatemala. One hundred and thirty-three (87%) variants were found within teosinte, and 95 (61%) variants were found within maize. Seventy-four (48%) variants were distributed among both teosinte and maize, whereas 58 (38%) variants were found only in teosinte and 20 (13%) variants were found only in maize. The majority of alleles were found in low frequency. A single allele predominated across maize and teosinte at 11 loci, 3 loci showed similar trends and 5 loci showed greater variability for the predominant alleles among maize and teosinte. Principal components analysis revealed little overlap between maize and teosinte, involving a minority of maize collections and Balsas teosintes. No clear evidence could be seen suggesting recent introgression between maize and teosinte. The collections of maize and teosinte were seen to represent a rich and contrasted array of germplasm.     

A genetic map of tomato based on BC(1) Lycopersicon esculentum x Solanum lycopersicoides reveals overall synteny but suppressed recombination between these homeologous genomes

F(1) hybrids between the cultivated tomato (Lycopersicon esculentum) and the wild nightshade Solanum lycopersicoides are male sterile and unilaterally incompatible, breeding barriers that impede further crosses to tomato. Meiosis is disrupted in 2x hybrids, with reduced chiasma formation and frequent univalents, but is normal in allotetraploid hybrids, indicating the genomes are homeologous. In this study, a partially male-fertile F(1) was backcrossed to tomato, producing the first BC(1) population suitable for genetic mapping from this cross. BC(1) plants were genotyped at marker loci to study the transmission of wild alleles and to measure rates of homeologous recombination. The pattern of segregation distortion, in favor of homozygotes on chromosomes 2 and 5 and heterozygotes on chromosomes 6 and 9, suggested linkage to a small number of loci under selection on each chromosome. Genome ratios nonetheless fit Mendelian expectations. Resulting genetic maps were essentially colinear with existing tomato maps but showed an overall reduction in recombination of approximately 27%. Recombination suppression was observed for all chromosomes except 9 and 12, affected both proximal and distal regions, and was most severe on chromosome 10 (70% reduction). Recombination between markers on the long arm of this chromosome was completely eliminated, suggesting a lack of colinearity between S. lycopersicoides and L. esculentum homeologues in this region. Results are discussed with respect to phylogenetic relationships between the species and their potential use for studies of homeologous pairing and recombination in a diploid plant genome.     

Inheritance of the Morphological Differences between Maize and Teosinte: Comparison of Results for Two F(2) Populations

Molecular marker loci (MMLs) were employed to map quantitative trait loci (QTLs) in an F(2) population derived from a cross of maize (Zea mays ssp. mays) and its probable progenitor, teosinte (Z. mays ssp. parviglumis). A total of 50 significant associations (putative QTLs) between the MMLs and nine key traits that distinguish maize and teosinte were identified. Results from this analysis are compared with our previous analysis of an F(2) population derived from a cross of a different variety of maize and another subspecies of teosinte (Z. mays ssp. mexicana). For traits that measure the architectural differences between maize and teosinte, the two F(2) populations possessed similar suites of QTLs. For traits that measure components of yield, substantially different suites of QTLs were identified in the two populations. QTLs that control about 20% or more of the phenotypic variance for a trait in one population were detected in the other population 81% of the time, while QTLs that control less than 10% of the variance in one population were detected in the other population only 28% of the time. In our previously published analysis of the maize X ssp. mexicana population, we identified five regions of the genome that control most of the key morphological differences between maize and teosinte. These same five regions also control most of the differences in the maize X ssp. parviglumis population. Results from both populations support the hypothesis that a relatively small number of loci with large effects were involved in the early evolution of the key traits that distinguish maize and teosinte. It is suggested that loci with large effects on morphology may not be a specific feature of crop evolution, but rather a common phenomenon in plant evolution whenever a species invades a new niche with reduced competition.     

CYTOGENETIC STUDIES OF ALLOTETRAPLOID HYBRIDS OF MAIZE AND PERENNIAL TEOSINTE

Shaver , Donald L. (Brookhaven Natl. Lab., Upton, New York.) Cytogenetic studies of allotetraploid hybrids of maize and perennial teosinte. Amer. Jour. Bot. 49(4): 348–354. Illus. 1962.—Euchlaena perennis (4n), “perennial teosinte,” was less fertile when pollinated with 4n Zea mays than when selfed. Cross fertility between the 2 genera was influenced by the particular maize stock involved. Chromosome numbers varied from 36 to 43 in a population of 4n maize maintained by interpollination without regard to chromosome number. In the 4n intergeneric hybrid, nearly every chromosome number from 29 to 44 was found. The expression of the perennial growth habit varied with the proportion of perennial teosinte germ plasm present. Triploid hybrids with 2 perennial teosinte genomes and 1 maize genome were usually perennial. Tetraploid hybrids having 2 genomes of each parent were usually not fully perennial. Tetraploid hybrids with only 1 perennial teosinte genome had no perennial tendency but had a strong tendency to tiller. As compared with autotetraploids of maize having the same genetic markers, intergeneric hybrids showed a highly significant degree of preferential segregation for each of the 12 marker genes studied. In the opinion of the author, these data may represent the best available measure of the relationship of maize to teosinte, and are considered to support the proposal of Reeves and Mangelsdorf that maize and teosinte are congeneric.     

Influence of genetic background and heterozygosity on meiotic recombination in Arabidopsis thaliana.

Plant breeding relies on genetic variability generated by meiotic recombination. Control of recombination frequencies is not yet possible, but would significantly extend the options for plant-breeding strategies. A prerequisite would be variability of recombination frequencies. In this study, 15 transgenic kanamycin (KR) and hygromycin (HR) resistance gene insertions mapping to the five Arabidopsis thaliana chromosomes were used as genetic markers. Recombination frequencies were determined from the frequencies of resistance phenotypes within populations segregating for linked KR and HR markers. Recombination frequencies of marker pairs were compared among these four ecotypes, among F1s in both reciprocal forms derived from these ecotypes, and between F1s and their parent lines. On average, the recombination frequencies in F1 crosses were substantially higher (up to 2-fold) than in the homozygous parental ecotypes. A strong negative correlation between genetic similarities of ecotypes and recombination frequencies was detected for two adjacent marker pairs located on the long arm of chromosome 3, but not for marker pairs in other genomic regions. Our results suggest that heterozygosity influences recombination in plant breeding, and cannot be ignored in genetic mapping of genomes.     

Linkage Relationships Reflecting Ancestral Tetraploidy in Salmonid Fish

Fifteen classical linkage groups were identified in two salmonid species (Salmo trutta and Salmo gairdneri) and three fertile, interspecific hybrids (S. gairdneri X Salmo clarki, Salvelinus fontinalis X Salvelinus namaycush and S. fontinalis X Salvelinus alpinus) by backcrossing multiply heterozygous individuals. These linkage relationships of electrophoretically detected, protein coding loci were highly conserved among species. The loci encoding the enzymes appeared to be randomly distributed among the salmonid chromosomes. Recombination frequencies were generally greater in females than in males. In males, certain linkage groups were pseudolinked with other linkage groups, presumably because of facultative multivalent pairing and directed disjunction of chromosomes. Five such pseudolinkage groups were identified and they also appeared to be common among species and hybrids. Duplicate loci were never classically linked with each other, although some exhibited pseudolinkage and some showed evidence of exchanging alleles. Gene-centromere recombination frequencies estimated from genotypic distributions of gynogenetic offspring were consistent with map locations inferred from female intergenic recombination frequencies. These linkage relationships support the contention that all extant salmonids arose from a common tetraploid progenitor and that this progenitor may have been a segmental allotetraploid.     

RETRACTED ARTICLE: An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines

This study analyzes population structure and linkage disequilibrium (LD) among 187 commonly used Chinese maize inbred lines, representing the genetic diversity among public, commercial and historically important lines for corn breeding. Seventy SSR loci, evenly distributed over 10 chromosomes, were assayed for polymorphism. The identified 290 alleles served to estimate population structure and analyze the genome-wide LD. The population of lines was highly structured, showing 6 subpopulations: BSSS (American BSSS including Reid), PA (group A germplasm derived from modern U.S. hybrids in China), PB (group B germplasm derived from modern U.S. hybrid in China), Lan (Lancaster Surecrop), LRC (derivative lines from Lvda Reb Cob, a Chinese landrace) and SPT (derivative lines from Si-ping-tou, a Chinese landrace). Forty lines, which formerly had an unknown and/or miscellaneous origin and pedigree record, were assigned to the appropriate group. Relationship estimates based on SSR marker data were quantified in a Q matrix, and this information will inform breeder’s decisions regarding crosses. Extensive inter- and intra-chromosomal LD was detected between 70 microsatellite loci for the investigated maize lines (2109 loci pairs in LD with D′ > 0.1 and 93 out of them at P < 0.01).This suggests that rapidly evolving microsatellites may track recent population structure. Interlocus LD decay among the diverse maize germplasm indicated that association studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations since most of the LD blocks were broken between diverse germplasm. The defined population structure and the LD analysis present the basis for future association mapping. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Analysis of linkage relationships between genetic markers around the fragile X locus with special reference to the daughters of normal transmitting males

Summary Genetic linkage data from loci around the fragile X locus at Xq27.3 are analysed in the light of the hypothesis of Pembrey et al. (1985) concerning the generation of the fragile X mutation. Recombination between the four loci 52A, F9, fragile X, and ST14 is significantly decreased in meioses giving rise to the affected grandsons of normal transmitting males, when compared to families where there are no apparent normal transmitting males. There are at least two possible explanations for this phenomenon. Either the established fragile site at Xq27.3 promotes increased recombination in the distal part of the X chromosome as a secondary event, unrelated to the mechanism of formation of the fragile site itself, or an event involving recombination at or around Xq27.3 is the mechanism of formation of the full fragile X mutation, and the decreased recombination seen amongst flanking marker loci in meioses giving rise to the affected grandsons of normal transmitting males is the result of interference.     

Cis-effects on meiotic recombination across distinct a1-sh2 intervals in a common Zea genetic background

Genetic distances across the a1-sh2 interval varied threefold in three near-isogenic stocks that carry structurally distinct teosinte A1 Sh2 haplotypes (from Z. mays spp. mexicana Chalco, Z. mays spp. parviglumis, and Z. luxurians) and a common maize a1::rdt sh2 haplotype. In each haplotype >85% of recombination events resolved in the proximal 10% of the approximately 130-kb a1-sh2 interval. Even so, significant differences in the distributions of recombination breakpoints were observed across subintervals among haplotypes. Each of the three previously detected recombination hot spots was detected in at least one of the three teosinte haplotypes and two of these hot spots were not detected in at least one teosinte haplotype. Moreover, novel hot spots were detected in two teosinte haplotypes. Due to the near-isogenic nature of the three stocks, the observed variation in the distribution of recombination events is the consequence of cis-modifications. Although generally negatively correlated with rates of recombination per megabase, levels of sequence polymorphisms do not fully account for the nonrandom distribution of recombination breakpoints. This study also suggests that estimates of linkage disequilibrium must be interpreted with caution when considering whether a gene has been under selection.     

Experimental evaluation of the potential of tropical germplasm for temperate maize improvement

 Commercial maize (Zea mays L.) in the USA has a restricted genetic base as newer hybrids are largely produced from crosses among elite inbred lines representing a small sample (predominantly about 6- to 8-base inbreds) of the Stiff stalk and Lancaster genetic backgrounds. Thus, expansion of genetic diversity in maize has been a continuous challenge to breeders. Tropical germplasm has been viewed as a useable source of diversity, although the integration of tropical germplasm into existing inbred line and hybrid development is laborious. The present study is an evaluation of the potential of tropical germplasm for temperate maize improvement. All possible single-, three-way-, and double-cross hybrids among three largely temperate and three temperate-adapted, all-tropical inbred lines were evaluated in yield-trial tests. Single-cross hybrids containing as much as 50–60% tropical germplasm produced 8.0 t ha^-1 of grain yield, equivalent to the mean yield of the commercial check hybrids. On the other hand, three-way and double-cross hybrids with the highest mean yield contained lower amounts of tropical germplasm, 10–19% and 34–44%, respectively. Overall, hybrids containing 10–60% tropical germplasm yielded within the range of the commercial hybrid checks. Hybrids with more than 60% tropical germplasm had significantly lower yields, and 100% tropical hybrids yielded the least among all hybrids evaluated. The results indicate that inbred lines containing tropical germplasm are not only a useful source to expand the genetic diversity of commercial maize hybrids, but they, also are competitive in crosses with temperate materials, producing high-yielding hybrids. These experimental hybrids exhibited good standability (comparable to the commercial check hybrids) but contained 1–2% higher grain moisture, leading to delayed maturity. Recurrent selection procedures are being conducted on derivatives of these materials to extract lines with superior yield, good standability, and reduced grain moisture which can be used for commercial exploitation. Received: 26 January 1998 / Accepted: 14 July 1998     

Gene mapping of isozyme loci in chum salmon

Recombination values were used to calculate the gene-centromere map distances for four electrophoretically detected loci, Aat3, Idh1, Idh4, and Mpi, in chum salmon (Oncorhynchus keta). We also report the results from 39 pairwise examinations for joint segregation for 10 loci in nine testcross families. Only two loci assorted nonrandomly--either Aat1 or Aat2 with Gpt. Gene-centromere distances for Aat3 and Mpi differed significantly from those reported previously for rainbow trout (Salmo gairdneri), a closely related species. This difference indicates either the presence of chromosome rearrangements or a different rate of recombination between the species. These results contrast with the conservation of linkage distances previously reported within and between other salmonid genera.     

4-way bred rats as experimental animals

The present study is an attempt to utilize hybrids among several inbred strains of rats as useful animals for the studies of effectiveness and toxicology on drugs., Four-way crosses were made among the LEW, WM, F344 and DRY strains of rats, and their characteristics were examined. From the breeding data of diallel crosses among these four strains and reciprocal crosses among their F1 hybrids, the mating type indicating the highest reproductivity was (LEW X WM) F1 X (F344 X DRY) F1. These four-way crosses were designated as LWFD. The reproductivity of this mating type was exceedingly higher than those of four strains. In order to examine the susceptibility to thiamine hydrochloride, the acute toxicity test was practiced in inbred strains, F1 hybrids and four-way crosses. As a result, in spite of highly heterogeneous population, the LWFD did not show a peculiar response in comparison with four strains and their F1 hybrids. Furthermore, hematological and clinico-biochemical values of the LWFD did not show a large variability as presumed. From these results, it is suggested that hybrids such as four-way crosses among inbred strains can be used as useful animals for the studies of effectiveness and toxicology on drugs.     

Pollination between maize and teosinte: an important determinant of gene flow in Mexico

Gene flow between maize [Zea mays (L.)] and its wild relatives does occur, but at very low frequencies. Experiments were undertaken in Tapachula, Nayarit, Mexico to investigate gene flow between a hybrid maize, landraces of maize and teosinte (Z. mays ssp. mexicana, races Chalco and Central Plateau). Hybridization, flowering synchrony, pollen size and longevity, silk elongation rates, silk and trichome lengths and tassel diameter and morphology were measured. Hybrid and open-pollinated maize ears produced a mean of 8 and 11 seeds per ear, respectively, when hand-pollinated with teosinte pollen, which is approximately 1–2% of the ovules normally produced on a hybrid maize ear. Teosinte ears produced a mean of 0.2–0.3 seeds per ear when pollinated with maize pollen, which is more than one-fold fewer seeds than produced on a maize ear pollinated with teosinte pollen. The pollination rate on a per plant basis was similar in the context of a maize plant with 400–500 seeds and a teosinte plant with 30–40 inflorescences and 9–12 fruitcases per inflorescence. A number of other factors also influenced gene-flow direction: (1) between 90% and 95% of the fruitcases produced on teosinte that was fertilized by maize pollen were sterile; (2) teosinte collections were made in an area where incompatibility systems that limit fertilization are present; (3) silk longevity was much shorter for teosinte than for maize (approx. 4 days vs. approx. 11 days); (4) teosinte produced more pollen on a per plant basis than the landraces and commercial hybrid maize; (5) teosinte frequently produced lateral branches with silks close to a terminal tassel producing pollen. Collectively these factors tend to favor crossing in the direction of teosinte to maize. Our results support the hypothesis that gene flow and the subsequent introgression of maize genes into teosinte populations most probably results from crosses where teosinte first pollinates maize. The resultant hybrids then backcross with teosinte to introgress the maize genes into the teosinte genome. This approach would slow introgression and may help explain why teosinte continues to co-exist as a separate entity even though it normally grows in the vicinity of much larger populations of maize.     

Genetic basis of kernel nutritional traits during maize domestication and improvement

The nutritional traits of maize kernels are important for human and animal nutrition, and these traits have undergone selection to meet the diverse nutritional needs of humans. However, our knowledge of the genetic basis of selecting for kernel nutritional traits is limited. Here, we identified both single and epistatic quantitative trait loci (QTLs) that contributed to the differences of oil and carotenoid traits between maize and teosinte. Over half of teosinte alleles of single QTLs increased the values of the detected oil and carotenoid traits. Based on the pleiotropism or linkage information of the identified single QTLs, we constructed a trait–locus network to help clarify the genetic basis of correlations among oil and carotenoid traits. Furthermore, the selection features and evolutionary trajectories of the genes or loci underlying variations in oil and carotenoid traits revealed that these nutritional traits produced diverse selection events during maize domestication and improvement. To illustrate more, a mutator distance–relative transposable element (TE) in intron 1 of DXS2, which encoded a rate‐limiting enzyme in the methylerythritol phosphate pathway, was identified to increase carotenoid biosynthesis by enhancing DXS2 expression. This TE occurs in the grass teosinte, and has been found to have undergone selection during maize domestication and improvement, and is almost fixed in yellow maize. Our findings not only provide important insights into evolutionary changes in nutritional traits, but also highlight the feasibility of reintroducing back into commercial agricultural germplasm those nutritionally important genes hidden in wild relatives.     

Evaluating Tripsacum‐introgressed maize germplasm after infestation with western corn rootworms (Coleoptera: Chrysomelidae)

Maize (Zea mays L.) is a valuable commodity throughout the world, but corn rootworms (Chrysomelidae: Diabrotica spp.) often cause economic damage and increase production costs. Current rootworm management strategies have limitations, and in order to create viable management alternatives, researchers have been developing novel maize lines using Eastern gamagrass (Tripsacum dactyloides L.) germplasm, a wild relative of maize that is resistant to rootworms. Ten maize Tripsacum‐introgressed inbred lines derived from recurrent selection of crosses with gamagrass and teosinte (Zea diploperennis Iltis) recombinants and two public inbred lines were assessed for susceptibility to western corn rootworm (Diabrotica virgifera virgifera LeConte) and yield in a two‐year field study. Two experimental maize inbred lines, SDG11 and SDG20, had mean root damage ratings that were significantly lower than the susceptible public line B73. Two other experimental maize inbred lines, SDG12 and SDG6, appeared tolerant to rootworm damage because they exhibited yield increases after rootworm infestation in both years. In the majority of cases, mean yield per plant of experimental maize lines used in yield analyses was equal to or exceeded that of the public inbred lines B73 and W64A. Our study indicates that there is potential to use Tripsacum‐introgressed maize germplasm in breeding programs to enhance plant resistance and/or tolerance to corn rootworms, although further research on insect resistance and agronomic potential of this germplasm needs to be conducted in F₁ hybrids.     

Analysis and Optimization of Bulk DNA Sampling with Binary Scoring for Germplasm Characterization

The strategy of bulk DNA sampling has been a valuable method for studying large numbers of individuals through genetic markers. The application of this strategy for discrimination among germplasm sources was analyzed through information theory, considering the case of polymorphic alleles scored binarily for their presence or absence in DNA pools. We defined the informativeness of a set of marker loci in bulks as the mutual information between genotype and population identity, composed by two terms: diversity and noise. The first term is the entropy of bulk genotypes, whereas the noise term is measured through the conditional entropy of bulk genotypes given germplasm sources. Thus, optimizing marker information implies increasing diversity and reducing noise. Simple formulas were devised to estimate marker information per allele from a set of estimated allele frequencies across populations. As an example, they allowed optimization of bulk size for SSR genotyping in maize, from allele frequencies estimated in a sample of 56 maize populations. It was found that a sample of 30 plants from a random mating population is adequate for maize germplasm SSR characterization. We analyzed the use of divided bulks to overcome the allele dilution problem in DNA pools, and concluded that samples of 30 plants divided into three bulks of 10 plants are efficient to characterize maize germplasm sources through SSR with a good control of the dilution problem. We estimated the informativeness of 30 SSR loci from the estimated allele frequencies in maize populations, and found a wide variation of marker informativeness, which positively correlated with the number of alleles per locus.     

Differential Mismatch Repair Can Explain the Disproportionalities between Physical Distances and Recombination Frequencies of Cyc1 Mutations in Yeast

Recombination rates have been examined in two-point crosses of various defined cyc1 mutations that cause the loss or nonfunction of iso-1-cytochrome c in the yeast Saccharomyces cerevisiae. Recombinants arising by three different means were investigated, including X-ray induced mitotic recombination, spontaneous mitotic recombination, and meiotic recombination. Heteroallelic diploid strains were derived by crossing cyc1 mutants containing a series of alterations at or near the same site to cyc1 mutants containing alterations at various distances. Marked disproportionalities between physical distances and recombination frequencies were observed with certain cyc1 mutations, indicating that certain mismatched bases can significantly affect recombination. The marker effects were more pronounced when the two mutational sites of the heteroalleles were within about 20 base pairs, but separated by at least 4 base pairs. Two alleles, cyc1-163 and cyc1-166, which arose by G.C----C.G transversions at nucleotide positions 3 and 194, respectively, gave rise to especially high rates of recombination. Other mutations having different substitutions at the same nucleotide positions were not associated with abnormally high recombination frequencies. We suggest that these marker effects are due to the lack of repair of either G/G or C/C mismatched base pairs, while the other mismatched base pair of the heteroallele undergoes substantial repair. Furthermore, we suggest that diminished recombination frequencies are due to the concomitant repair of both mismatches within the same DNA tract.     

Suppression of recombination in wide hybrids of Petunia hybrida as revealed by genetic mapping of marker transgenes

In the course of a heterologous transposon tagging experiment in Petunia hybrida (n=7), 135 independent T-DNA loci were tested for linkage to the target genes Hf1 and Fl, which are located on the two largest chromosomes. Approximately one-third (47) of these T-DNA loci were linked to one of these two markers. Of these 47 linkedloci, 19 mapped within 1 cM of its marker, indicating a highly non-random genetic distribution of introduced loci. However, rather than non-random integration within both of the marked chromosomes, this probably reflects a suppression of recombination around these marker loci in the particular wide hybrids used for mapping. This hypothesis was tested by measuring recombination between linked T-DNAs in an inbred background. Inbred recombination levels were found to be at least 3-fold higher around the Hf1 locus and 12-fold higher around Fl compared to the wide hybrids. These findings may reflect the origin of P. hybrida by hybridization of wild species, and while relevant to genetic mapping in petunia in particular they may also have more general significance for any mapping strategies involving the use of wide hybrids in other species.     

Genetic Analysis of the Morphological Differences between Maize and Teosinte

Molecular marker loci were used to investigate the inheritance of morphological traits that distinguish maize (Zea mays ssp. mays) from a closely related wild relative, teosinte (Z. mays ssp. mexicana). Regression and interval mapping analyses gave largely congruent results concerning the numbers of loci controlling the morphological traits and the magnitudes of their effects; however, interval mapping tended to give larger estimates for the magnitudes of the effects of the morphological trait loci. This tendency was exaggerated for traits that were non-normally distributed. Variation for most inflorescence traits is controlled by one or two regions of the genome with large effects plus several other regions with relatively small effects. As such, the data are congruent with a mode of inheritance for most traits involving one or two major loci plus several minor loci. Regions of the genome with large effects on one trait consistently had smaller effects on several other traits, possibly as a result of pleiotropy. Most of the variation for the dramatic differences in inflorescence morphology between maize and teosinte is explained by five restricted regions of the genome. One of these regions encompasses a previously described gene, tb1 (teosinte branched), and the effects of this region on inflorescence architecture are similar to the known effects of tb1. Implications of this work for the genetic basis of morphological evolution in plants are discussed.