We utilized maize (Zea mays L.) lines expressing the salmon silk (sm) phenotype, quantitative tra... more We utilized maize (Zea mays L.) lines expressing the salmon silk (sm) phenotype, quantitative trait locus analysis, and analytical chemistry of flavone compounds to establish the order of undefined steps in the synthesis of the flavone maysin in maize silks. In addition to the previously described sm1 gene, we identified a second sm locus, which we designate sm2, located on the long arm of maize chromosome 2. Our data indicate that the sm1 gene encodes or controls a glucose modification enzyme and sm2 encodes or controls a rhamnosyl transferase. The order of intermediates in the late steps of maysin synthesis was established as luteolin! isoorientin! rhamnosylisoorientin! maysin. In maize (Zea mays L.), ‘‘the genetics of pigment control is more fully elaborated than that of any other character’ ’ (Coe et al. 1988). However, in contrast to the extensive research that has been conducted using the anthocyanin pathway in maize, our understanding of the enzymatic steps involved in the sy...
Genotyping by sequencing (GBS) provides a robust and cost-effective means to genotype large numbe... more Genotyping by sequencing (GBS) provides a robust and cost-effective means to genotype large numbers of individuals at high density by targeting sequence adjacent to restriction enzyme cut sites. We genetically mapped (binomial p-value <0.001) 589,002 segregating 64-base ApeKI GBS tags as presence/absence markers in the maize IBM population relative to a new, high density map of 239 IBM lines based on the Illumina MaizeSNP50 Genotyping BeadChip. Using a high stringency (p<10-7) subset of these genetically mapped tags, we found that, of the GBS tags that segregated with B73, only 0.4% genetically mapped to a chromosome different from the one to which they physically align on B73 RefGen_v2. In contrast, for tags that segregated with Mo17, the comparable proportion was 9.3%. This difference likely results from structural variation combined with the ancient polyploidization that occurred in maize. We have also used the GBS tag segregation data to genetically map (1) contigs from ch...
Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have r... more Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution 1, 2, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines 3. We find ...
Whereas breeders have exploited diversity in maize for yield improvements, there has been limited... more Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are ...
We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed... more We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available fo...
We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed... more We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available fo...
In wheat-rye hybrids the nucleolus organizer regions (NORs), the sites of ribosomal RNA genes, fr... more In wheat-rye hybrids the nucleolus organizer regions (NORs), the sites of ribosomal RNA genes, from rye are suppressed. Wheat and wheat-rye hybrid genetic stocks containing different numbers of wheat and rye nucleolus organizers, as well as addition lines and rye-barley hybrids, were used in Southern hybridization experiments to determine the cause of nucleolar dominance and suppression in cereal hybrids. Based on the use of restriction endonucleases that cleave near the ends of the spacer unit and an additional, methylation-sensitive enzyme, HpaII, which does not recognize the CCGG restriction site if the internal C is methylated, an indirect method of assaying NOR expression was established. The results indicated that cleavage by the HpaII enzyme of the rye NOR sequences, is reduced when major NORs from other cereals were present. The reduction in the number of rye rRNA genes containing an unmethylated CCGG site in the promoter was associated with the suppression of the rye nucleolus. These results are consistent with a model in which promoter and upstream regulatory repeats of ribosomal RNA genes compete for limited concentrations of regulatory proteins, and genes that are methylated at key binding sites fail to engage these regulatory proteins and thus remain inactive.
We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed... more We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available fo...
We utilized maize (Zea mays L.) lines expressing the salmon silk (sm) phenotype, quantitative tra... more We utilized maize (Zea mays L.) lines expressing the salmon silk (sm) phenotype, quantitative trait locus analysis, and analytical chemistry of flavone compounds to establish the order of undefined steps in the synthesis of the flavone maysin in maize silks. In addition to the previously described sm1 gene, we identified a second sm locus, which we designate sm2, located on the long arm of maize chromosome 2. Our data indicate that the sm1 gene encodes or controls a glucose modification enzyme and sm2 encodes or controls a rhamnosyl transferase. The order of intermediates in the late steps of maysin synthesis was established as luteolin! isoorientin! rhamnosylisoorientin! maysin. In maize (Zea mays L.), ‘‘the genetics of pigment control is more fully elaborated than that of any other character’ ’ (Coe et al. 1988). However, in contrast to the extensive research that has been conducted using the anthocyanin pathway in maize, our understanding of the enzymatic steps involved in the sy...
Genotyping by sequencing (GBS) provides a robust and cost-effective means to genotype large numbe... more Genotyping by sequencing (GBS) provides a robust and cost-effective means to genotype large numbers of individuals at high density by targeting sequence adjacent to restriction enzyme cut sites. We genetically mapped (binomial p-value <0.001) 589,002 segregating 64-base ApeKI GBS tags as presence/absence markers in the maize IBM population relative to a new, high density map of 239 IBM lines based on the Illumina MaizeSNP50 Genotyping BeadChip. Using a high stringency (p<10-7) subset of these genetically mapped tags, we found that, of the GBS tags that segregated with B73, only 0.4% genetically mapped to a chromosome different from the one to which they physically align on B73 RefGen_v2. In contrast, for tags that segregated with Mo17, the comparable proportion was 9.3%. This difference likely results from structural variation combined with the ancient polyploidization that occurred in maize. We have also used the GBS tag segregation data to genetically map (1) contigs from ch...
Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have r... more Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution 1, 2, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines 3. We find ...
Whereas breeders have exploited diversity in maize for yield improvements, there has been limited... more Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are ...
We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed... more We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available fo...
We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed... more We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available fo...
In wheat-rye hybrids the nucleolus organizer regions (NORs), the sites of ribosomal RNA genes, fr... more In wheat-rye hybrids the nucleolus organizer regions (NORs), the sites of ribosomal RNA genes, from rye are suppressed. Wheat and wheat-rye hybrid genetic stocks containing different numbers of wheat and rye nucleolus organizers, as well as addition lines and rye-barley hybrids, were used in Southern hybridization experiments to determine the cause of nucleolar dominance and suppression in cereal hybrids. Based on the use of restriction endonucleases that cleave near the ends of the spacer unit and an additional, methylation-sensitive enzyme, HpaII, which does not recognize the CCGG restriction site if the internal C is methylated, an indirect method of assaying NOR expression was established. The results indicated that cleavage by the HpaII enzyme of the rye NOR sequences, is reduced when major NORs from other cereals were present. The reduction in the number of rye rRNA genes containing an unmethylated CCGG site in the promoter was associated with the suppression of the rye nucleolus. These results are consistent with a model in which promoter and upstream regulatory repeats of ribosomal RNA genes compete for limited concentrations of regulatory proteins, and genes that are methylated at key binding sites fail to engage these regulatory proteins and thus remain inactive.
We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed... more We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available fo...
Uploads
Papers by K. Houchins