The precise detection of causal DNA mutations (deoxyribonucleic acid) is very crucial for forward... more The precise detection of causal DNA mutations (deoxyribonucleic acid) is very crucial for forward genetic studies. Several sources of errors contribute to false‐positive detections by current variant‐calling algorithms, which impact associating phenotypes with genotypes. To improve the accuracy of mutation detection, we implemented a binning method for the accurate detection of likely ethyl methanesulfonate (EMS)‐induced mutations in a sequenced mutant population. We also implemented a clustering algorithm for detecting likely false negatives with high accuracy. Sorghum bicolor is a very valuable crop species with tremendous potential for uncovering novel gene functions associated with highly desirable agronomical traits. We demonstrate the precision of the described approach in the detection of likely EMS‐induced mutations from the publicly available low‐cost sequencing of the M3 generation from 600 sorghum BTx623 mutants. The approach detected 3,274,606 single nucleotide polymorph...
We sequenced the genome of the cacao pathogen Moniliophthora roreri MCA2952, which harbors mating... more We sequenced the genome of the cacao pathogen Moniliophthora roreri MCA2952, which harbors mating type A1B1 and is first instance of the fungus identified in Mexico. This draft genome consists of 59.68 Mb on 254 scaffolds; it is 95.8% complete based on the analysis of Benchmarking Universal Single-Copy Orthologs (BUSCO v.2 with the Basidiomycota odb9 database), and it is by far the most contiguous genome generated for the genus Moniliophthora.
listed above contribute to the cost of publication of this Journal, but they are not owners or pu... more listed above contribute to the cost of publication of this Journal, but they are not owners or publishers and have no responsibility for its content or policies. Mathematical papers intended for publication in the Pacific Journal of Mathematics should be in typed form or offset-reproduced, (not dittoed), double spaced with large margins. Underline Greek letters in red, German in green, and script in blue. The first paragraph or two must be capable of being used separately as a synopsis of the entire paper. The editorial "we" must not be used in the synopsis, and items of the bibliography should not be cited there unless absolutely necessary, in which case they must be identified by author and Journal, rather than by item number. Manuscripts, in duplicate if possible, may be sent to any one of the four editors. Please classify according to the scheme of Math. Rev. Index to Vol.
Plant phenotypes are often descriptive, rather than predictive of crop performance. As a result, ... more Plant phenotypes are often descriptive, rather than predictive of crop performance. As a result, extensive testing is required in plant breeding programmes to develop varieties aimed at performance in the target environments. Crop models can improve this testing regime by providing a predictive framework to (i) augment field phenotyping data and derive hard-to-measure phenotypes and (ii) estimate performance across geographical regions using historical weather data. The goal of this study was to parameterize the Agricultural Production Systems sIMulator (APSIM) crop growth models with remote-sensing and ground-reference data to predict variation in phenology and yield-related traits in 18 commercial grain and biomass sorghum hybrids. Genotype parameters for each hybrid were estimated using remote-sensing measurements combined with manual phenotyping in West Lafayette, IN, in 2018. The models were validated in hybrid performance trials in two additional seasons at that site and again...
The reverse genetics detection of single base changes in genes of interest, whether induced or en... more The reverse genetics detection of single base changes in genes of interest, whether induced or endogenous, is an extremely powerful tool for func-tional genomics. Two major thrusts of research in the grasses are characterizing the function of all the genes in various genomes and then comparing those func-tions among species. Targeting Induced Local Lesions IN Genomes (TILLING) has proven to be a valuable methodology for finding these polymorphisms in a wide range of plant and animal species and providing mutants carrying them to the researcher. With the advent of NextGen sequencing, targeted evaluation of thousands of genes across mutagenized populations with thousands of individuals will becomemuchmore widely available, and for a wide range of grass species.
The nuclear pore complex (NPC) regulates the movement of macromolecules between the nucleus and c... more The nuclear pore complex (NPC) regulates the movement of macromolecules between the nucleus and cytoplasm. Dysfunction of many components of the NPC results in human genetic diseases, including triple A syndrome (AAAS) as a result of mutations in ALADIN. Here, we report a nonsense mutation in the maize ortholog, aladin1 (ali1-1), at the orthologous amino acid residue of an AAAS allele from humans, alters plant stature, tassel architecture, and asymmetric divisions of subsidiary mother cells (SMCs). Crosses with the stronger nonsense allele ali1-2 identified complex allele interactions for plant height and aberrant SMC division. RNA-seq analysis of the ali1-1 mutant identified compensatory transcript accumulation for other NPC components as well as gene expression consequences consistent with conservation of ALADIN1 functions between humans and maize. These findings demonstrate that ALADIN1 is necessary for normal plant development, shoot architecture, and asymmetric cell division in...
To help high school students develop a deeper understanding of energy and matter flow in biologic... more To help high school students develop a deeper understanding of energy and matter flow in biological systems, a key goal of the Next Generation Science Standards (NGSS), we have designed a series of inquiry-driven modules that experimentally explore photosynthesis in the context of carbohydrate partitioning. Carbohydrate partitioning refers to the distribution of photosynthesis products from source organs, such as leaves, to growing or storage tissues. These cost- and time-effective modules help students develop a more integrated understanding of how energy flows from light into leaves before moving outward to other parts of the plant and ultimately into other organisms. Our approach of teaching carbohydrate partitioning along with photosynthesis greatly expands the number of NGSS core ideas and cross-cutting concepts in an integrated manner, empowers students to see how photosynthesis and carbohydrate partitioning are central to their existence, and provides a rich platform for expe...
ABSTRACTSorghum is a staple food for over 500 million people in Sub-Saharan Africa and Asia, howe... more ABSTRACTSorghum is a staple food for over 500 million people in Sub-Saharan Africa and Asia, however, sorghum proteins are poorly digested when wet-cooked. Three sorghum mutants were identified in a mutagenized population of the inbred line BTx623 that showed a 23-37% increase in wet-cooked protein digestibility compared to their unmutagenized parent. Furthermore, in comparison to the known high lysine, highly digestible sorghum mutant, P721Q, these mutants had 9% more protein overall that was 10% more digestible, had 12% more lysine, as well as better seed hardness. Using bulked segregant analysis based on whole genome sequencing data, we identified unique genomic regions on chromosome 5 of each EMS mutant that are associated with the increase in protein digestibility. Analyzing shared mutations in candidate genes, the high protein digestibility phenotype in one mutant is linked to a point mutation in a novel, ankyrin repeat protein. In another, the increase is associated with a mu...
Key message Seven novel alleles of SBEIIb and one allele of SSIIa co-segregated with the ASV phen... more Key message Seven novel alleles of SBEIIb and one allele of SSIIa co-segregated with the ASV phenotype and contributed to distinct starch quality traits important for food-processing applications. Abstract Sorghum is an important food crop for millions of people in Africa and Asia. Whole-genome re-sequencing of sorghum EMS mutants exhibiting an alkali spreading value (ASV) phenotype revealed candidate SNPs in Sobic.004G163700 and Sobic.010G093400. Comparative genomics identified Sobic.010G093400 as a starch synthase IIa and Sobic.004G163700 as a starch branching enzyme IIb. Segregation analyses showed that mutations in Sobic.010G093400 or Sobic.004G163700 co-segregated with the ASV phenotype. Mutants in SSIIa exhibited no change in amylose content but expressed lower final viscosity and lower starch gelatinization temperature (GT) than starches from non-mutant plants. The sbeIIb mutants exhibited significantly higher amylose levels and starch GT and lower viscosity compared to non-m...
The accurate detection of induced mutations is critical for both forward and reverse genetics stu... more The accurate detection of induced mutations is critical for both forward and reverse genetics studies. Experimental chemical mutagenesis induces relatively few single base changes per individual. In a complex eukaryotic genome, false positive detection of mutations can occur at or above this mutagenesis rate. We demonstrate here, using a population of ethyl methanesulfonate (EMS) treated Sorghum bicolor BTx623 individuals, that using replication to detect false positive induced variants in next-generation sequencing data permits higher throughput variant detection with greater accuracy. We used a lower sequence coverage depth (average of 7X) from 586 independently mutagenized individuals and detected 5,399,493 homozygous SNPs. Of these, 76% originated from only 57,872 genomic positions prone to false positive variant calling. These positions are characterized by high copy number paralogs where the error-prone SNP positions are at copies containing a variant at the SNP position. The ...
... References. ↵ Buckler, ES 2001 . Molecular diversity, structure and domestication of grasses.... more ... References. ↵ Buckler, ES 2001 . Molecular diversity, structure and domestication of grasses. Genet. Res. 77:213–218. [View Article]. ↵ Caldwell, DG 2004 . A structured mutant population for forward and reverse genetics in barley (Hordeum vulgare L.). Plant J. 40:143–150. ...
Plants form their gametes late in somatic development and, as a result, often pass somatic mutati... more Plants form their gametes late in somatic development and, as a result, often pass somatic mutations on to their progeny. Classic examples of this process are the germinal revertants of unstable, Ac/Ds transposon-induced kernel mutations in maize: frequent and early reversion events during somatic development are generally correlated with a high frequency of revertant gametes. We have characterized a Ds allele of the maize waxy (wx) gene, wx-m5:CS7, for which the correlation between somatic and germinal reversion frequencies no longer holds. The ability of wx-m5:CS7 (CS7) to produce revertant gametes is suppressed approximately 100-fold in comparison with a second Ds allele, wx-m5:CS8 (CS8), which has an identical insertion at Wx and the same frequent and early somatic reversion pattern in endosperm. The excision of Ds from wx is not reduced 100-fold in the somatic tissues of CS7 plants as compared with CS8 plants. Suppressed formation of CS7 revertant gametes is independent of the Ac transposase source and is heritably passed to the embryos of progeny kernels; however, frequent and early somatic reversion is observed again in endosperms of these progeny kernels. This suppression appears to be caused by a dominant mutation in a trans-acting product that can suppress the germinal reversion of other Ds-induced alleles as well; the mutation is tightly linked to Wx but is not in the CS7 Ds itself. Taken together, the data suggest a novel mode of developmental control of Ac/Ds elements by the host plant, suppressing element excision in the shoot meristem.
The precise detection of causal DNA mutations (deoxyribonucleic acid) is very crucial for forward... more The precise detection of causal DNA mutations (deoxyribonucleic acid) is very crucial for forward genetic studies. Several sources of errors contribute to false‐positive detections by current variant‐calling algorithms, which impact associating phenotypes with genotypes. To improve the accuracy of mutation detection, we implemented a binning method for the accurate detection of likely ethyl methanesulfonate (EMS)‐induced mutations in a sequenced mutant population. We also implemented a clustering algorithm for detecting likely false negatives with high accuracy. Sorghum bicolor is a very valuable crop species with tremendous potential for uncovering novel gene functions associated with highly desirable agronomical traits. We demonstrate the precision of the described approach in the detection of likely EMS‐induced mutations from the publicly available low‐cost sequencing of the M3 generation from 600 sorghum BTx623 mutants. The approach detected 3,274,606 single nucleotide polymorph...
We sequenced the genome of the cacao pathogen Moniliophthora roreri MCA2952, which harbors mating... more We sequenced the genome of the cacao pathogen Moniliophthora roreri MCA2952, which harbors mating type A1B1 and is first instance of the fungus identified in Mexico. This draft genome consists of 59.68 Mb on 254 scaffolds; it is 95.8% complete based on the analysis of Benchmarking Universal Single-Copy Orthologs (BUSCO v.2 with the Basidiomycota odb9 database), and it is by far the most contiguous genome generated for the genus Moniliophthora.
listed above contribute to the cost of publication of this Journal, but they are not owners or pu... more listed above contribute to the cost of publication of this Journal, but they are not owners or publishers and have no responsibility for its content or policies. Mathematical papers intended for publication in the Pacific Journal of Mathematics should be in typed form or offset-reproduced, (not dittoed), double spaced with large margins. Underline Greek letters in red, German in green, and script in blue. The first paragraph or two must be capable of being used separately as a synopsis of the entire paper. The editorial "we" must not be used in the synopsis, and items of the bibliography should not be cited there unless absolutely necessary, in which case they must be identified by author and Journal, rather than by item number. Manuscripts, in duplicate if possible, may be sent to any one of the four editors. Please classify according to the scheme of Math. Rev. Index to Vol.
Plant phenotypes are often descriptive, rather than predictive of crop performance. As a result, ... more Plant phenotypes are often descriptive, rather than predictive of crop performance. As a result, extensive testing is required in plant breeding programmes to develop varieties aimed at performance in the target environments. Crop models can improve this testing regime by providing a predictive framework to (i) augment field phenotyping data and derive hard-to-measure phenotypes and (ii) estimate performance across geographical regions using historical weather data. The goal of this study was to parameterize the Agricultural Production Systems sIMulator (APSIM) crop growth models with remote-sensing and ground-reference data to predict variation in phenology and yield-related traits in 18 commercial grain and biomass sorghum hybrids. Genotype parameters for each hybrid were estimated using remote-sensing measurements combined with manual phenotyping in West Lafayette, IN, in 2018. The models were validated in hybrid performance trials in two additional seasons at that site and again...
The reverse genetics detection of single base changes in genes of interest, whether induced or en... more The reverse genetics detection of single base changes in genes of interest, whether induced or endogenous, is an extremely powerful tool for func-tional genomics. Two major thrusts of research in the grasses are characterizing the function of all the genes in various genomes and then comparing those func-tions among species. Targeting Induced Local Lesions IN Genomes (TILLING) has proven to be a valuable methodology for finding these polymorphisms in a wide range of plant and animal species and providing mutants carrying them to the researcher. With the advent of NextGen sequencing, targeted evaluation of thousands of genes across mutagenized populations with thousands of individuals will becomemuchmore widely available, and for a wide range of grass species.
The nuclear pore complex (NPC) regulates the movement of macromolecules between the nucleus and c... more The nuclear pore complex (NPC) regulates the movement of macromolecules between the nucleus and cytoplasm. Dysfunction of many components of the NPC results in human genetic diseases, including triple A syndrome (AAAS) as a result of mutations in ALADIN. Here, we report a nonsense mutation in the maize ortholog, aladin1 (ali1-1), at the orthologous amino acid residue of an AAAS allele from humans, alters plant stature, tassel architecture, and asymmetric divisions of subsidiary mother cells (SMCs). Crosses with the stronger nonsense allele ali1-2 identified complex allele interactions for plant height and aberrant SMC division. RNA-seq analysis of the ali1-1 mutant identified compensatory transcript accumulation for other NPC components as well as gene expression consequences consistent with conservation of ALADIN1 functions between humans and maize. These findings demonstrate that ALADIN1 is necessary for normal plant development, shoot architecture, and asymmetric cell division in...
To help high school students develop a deeper understanding of energy and matter flow in biologic... more To help high school students develop a deeper understanding of energy and matter flow in biological systems, a key goal of the Next Generation Science Standards (NGSS), we have designed a series of inquiry-driven modules that experimentally explore photosynthesis in the context of carbohydrate partitioning. Carbohydrate partitioning refers to the distribution of photosynthesis products from source organs, such as leaves, to growing or storage tissues. These cost- and time-effective modules help students develop a more integrated understanding of how energy flows from light into leaves before moving outward to other parts of the plant and ultimately into other organisms. Our approach of teaching carbohydrate partitioning along with photosynthesis greatly expands the number of NGSS core ideas and cross-cutting concepts in an integrated manner, empowers students to see how photosynthesis and carbohydrate partitioning are central to their existence, and provides a rich platform for expe...
ABSTRACTSorghum is a staple food for over 500 million people in Sub-Saharan Africa and Asia, howe... more ABSTRACTSorghum is a staple food for over 500 million people in Sub-Saharan Africa and Asia, however, sorghum proteins are poorly digested when wet-cooked. Three sorghum mutants were identified in a mutagenized population of the inbred line BTx623 that showed a 23-37% increase in wet-cooked protein digestibility compared to their unmutagenized parent. Furthermore, in comparison to the known high lysine, highly digestible sorghum mutant, P721Q, these mutants had 9% more protein overall that was 10% more digestible, had 12% more lysine, as well as better seed hardness. Using bulked segregant analysis based on whole genome sequencing data, we identified unique genomic regions on chromosome 5 of each EMS mutant that are associated with the increase in protein digestibility. Analyzing shared mutations in candidate genes, the high protein digestibility phenotype in one mutant is linked to a point mutation in a novel, ankyrin repeat protein. In another, the increase is associated with a mu...
Key message Seven novel alleles of SBEIIb and one allele of SSIIa co-segregated with the ASV phen... more Key message Seven novel alleles of SBEIIb and one allele of SSIIa co-segregated with the ASV phenotype and contributed to distinct starch quality traits important for food-processing applications. Abstract Sorghum is an important food crop for millions of people in Africa and Asia. Whole-genome re-sequencing of sorghum EMS mutants exhibiting an alkali spreading value (ASV) phenotype revealed candidate SNPs in Sobic.004G163700 and Sobic.010G093400. Comparative genomics identified Sobic.010G093400 as a starch synthase IIa and Sobic.004G163700 as a starch branching enzyme IIb. Segregation analyses showed that mutations in Sobic.010G093400 or Sobic.004G163700 co-segregated with the ASV phenotype. Mutants in SSIIa exhibited no change in amylose content but expressed lower final viscosity and lower starch gelatinization temperature (GT) than starches from non-mutant plants. The sbeIIb mutants exhibited significantly higher amylose levels and starch GT and lower viscosity compared to non-m...
The accurate detection of induced mutations is critical for both forward and reverse genetics stu... more The accurate detection of induced mutations is critical for both forward and reverse genetics studies. Experimental chemical mutagenesis induces relatively few single base changes per individual. In a complex eukaryotic genome, false positive detection of mutations can occur at or above this mutagenesis rate. We demonstrate here, using a population of ethyl methanesulfonate (EMS) treated Sorghum bicolor BTx623 individuals, that using replication to detect false positive induced variants in next-generation sequencing data permits higher throughput variant detection with greater accuracy. We used a lower sequence coverage depth (average of 7X) from 586 independently mutagenized individuals and detected 5,399,493 homozygous SNPs. Of these, 76% originated from only 57,872 genomic positions prone to false positive variant calling. These positions are characterized by high copy number paralogs where the error-prone SNP positions are at copies containing a variant at the SNP position. The ...
... References. ↵ Buckler, ES 2001 . Molecular diversity, structure and domestication of grasses.... more ... References. ↵ Buckler, ES 2001 . Molecular diversity, structure and domestication of grasses. Genet. Res. 77:213–218. [View Article]. ↵ Caldwell, DG 2004 . A structured mutant population for forward and reverse genetics in barley (Hordeum vulgare L.). Plant J. 40:143–150. ...
Plants form their gametes late in somatic development and, as a result, often pass somatic mutati... more Plants form their gametes late in somatic development and, as a result, often pass somatic mutations on to their progeny. Classic examples of this process are the germinal revertants of unstable, Ac/Ds transposon-induced kernel mutations in maize: frequent and early reversion events during somatic development are generally correlated with a high frequency of revertant gametes. We have characterized a Ds allele of the maize waxy (wx) gene, wx-m5:CS7, for which the correlation between somatic and germinal reversion frequencies no longer holds. The ability of wx-m5:CS7 (CS7) to produce revertant gametes is suppressed approximately 100-fold in comparison with a second Ds allele, wx-m5:CS8 (CS8), which has an identical insertion at Wx and the same frequent and early somatic reversion pattern in endosperm. The excision of Ds from wx is not reduced 100-fold in the somatic tissues of CS7 plants as compared with CS8 plants. Suppressed formation of CS7 revertant gametes is independent of the Ac transposase source and is heritably passed to the embryos of progeny kernels; however, frequent and early somatic reversion is observed again in endosperms of these progeny kernels. This suppression appears to be caused by a dominant mutation in a trans-acting product that can suppress the germinal reversion of other Ds-induced alleles as well; the mutation is tightly linked to Wx but is not in the CS7 Ds itself. Taken together, the data suggest a novel mode of developmental control of Ac/Ds elements by the host plant, suppressing element excision in the shoot meristem.
Uploads
Papers by Clifford Weil