Publications by authors named "Jeffrey C Glaubitz"

27 Publications

  • Page 1 of 1

Joint analysis of days to flowering reveals independent temperate adaptations in maize.

Heredity (Edinb) 2021 Jun 22;126(6):929-941. Epub 2021 Apr 22.

USDA-ARS, Ithaca, NY, USA.

Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from China, Europe (Dent and Flint) and the United States as well as in the Ames inbred diversity panel, using days to flowering as a proxy. Using cross-population prediction, where high prediction accuracy derives from overall genomic relatedness, shared genetic architecture, and sufficient diversity in the training population, we identify patterns in predictive ability across the five populations. To identify the source of temperate adapted alleles in these populations, we predict top associated genome-wide association study (GWAS) identified loci in a Random Forest Classifier using independent temperate-tropical North American populations based on lines selected from Hapmap3 as predictors. We find that North American populations are well predicted (AUC equals 0.89 and 0.85 for Ames and USNAM, respectively), European populations somewhat well predicted (AUC equals 0.59 and 0.67 for the Dent and Flint panels, respectively) and that the Chinese population is not predicted well at all (AUC is 0.47), suggesting an independent adaptation process for early flowering in China. Multiple adaptations for the complex trait days to flowering in maize provide hope for similar natural systems under climate change.
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http://dx.doi.org/10.1038/s41437-021-00422-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8178344PMC
June 2021

Genotyping by sequencing for SNP marker development in onion.

Genome 2020 Dec 27;63(12):607-613. Epub 2020 Aug 27.

Vegetable Crop Research Unit, United States Department of Agriculture, Agricultural Research Service, 1575 Linden Drive, Madison, WI 53706, USA.

Onion () is not highly tractable for development of molecular markers due to its large (16 gigabases per 1C) nuclear genome. Single nucleotide polymorphisms (SNPs) are useful for genetic characterization and marker-aided selection of onion because of codominance and common occurrence in elite germplasm. We completed genotyping by sequencing (GBS) to identify SNPs in onion using 46 F plants, parents of the F plants (Ailsa Craig 43 and Brigham Yellow Globe 15-23), two doubled haploid (DH) lines (DH2107 and DH2110), and plants from 94 accessions in the USDA National Plant Germplasm System (NPGS). SNPs were called using the TASSEL 3.0 Universal Network Enabled Analysis (UNEAK) bioinformatics pipeline. Sequences from the F and DH plants were used to construct a pseudo-reference genome against which genotypes from all accessions were scored. Quality filters were used to identify a set of 284 high quality SNPs, which were placed onto an existing genetic map for the F family. Accessions showed a moderate level of diversity (mean = 0.341) and evidence of inbreeding (mean = 0.592). GBS is promising for SNP discovery in onion, although lack of a reference genome required extensive custom scripts for bioinformatics analyses to identify high quality markers.
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http://dx.doi.org/10.1139/gen-2020-0011DOI Listing
December 2020

Genomic prediction across years in a maize doubled haploid breeding program to accelerate early-stage testcross testing.

Theor Appl Genet 2020 Oct 30;133(10):2869-2879. Epub 2020 Jun 30.

International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.

Key Message: Genomic selection with a multiple-year training population dataset could accelerate early-stage testcross testing by skipping the first-stage yield testing, which significantly saves the time and cost of early-stage testcross testing. With the development of doubled haploid (DH) technology, the main task for a maize breeder is to estimate the breeding values of thousands of DH lines annually. In early-stage testcross testing, genomic selection (GS) offers the opportunity of replacing expensive multiple-environment phenotyping and phenotypic selection with lower-cost genotyping and genomic estimated breeding value (GEBV)-based selection. In the present study, a total of 1528 maize DH lines, phenotyped in multiple-environment trials in three consecutive years and genotyped with a low-cost per-sample genotyping platform of rAmpSeq, were used to explore how to implement GS to accelerate early-stage testcross testing. Results showed that the average prediction accuracy estimated from the cross-validation schemes was above 0.60 across all the scenarios. The average prediction accuracies estimated from the independent validation schemes ranged from 0.23 to 0.32 across all the scenarios, when the one-year datasets were used as training population (TRN) to predict the other year data as testing population (TST). The average prediction accuracies increased to a range from 0.31 to 0.42 across all the scenarios, when the two-years datasets were used as TRN. The prediction accuracies increased to a range from 0.50 to 0.56, when the TRN consisted of two-years of breeding data and 50% of third year's data converted from TST to TRN. This information showed that GS with a multiple-year TRN set offers the opportunity to accelerate early-stage testcross testing by skipping the first-stage yield testing, which significantly saves the time and cost of early-stage testcross testing.
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http://dx.doi.org/10.1007/s00122-020-03638-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782462PMC
October 2020

High-Density Genetic Linkage Mapping of Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes.

Front Plant Sci 2020 30;11:448. Epub 2020 Apr 30.

Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.

has been targeted for domestication as future oilseed and catch crop. Three hundred eighty plants comprising genotypes of , , and their interspecific F mapping population were genotyped using genotyping by sequencing (GBS), and the generated polymorphic markers were used for the construction of high-density genetic linkage map. TASSEL-GBS, a reference genome-based pipeline, was used for this analysis using a draft whole genome sequence. The analysis resulted in 120,438 biallelic single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) above 0.01. The construction of genetic linkage map was conducted using MSTMap based on phased SNPs segregating in 1:2:1 ratio for the F individuals, followed by genetic mapping of segregating contig tag haplotypes as dominant markers against the linkage map. The final linkage map consisted of eight linkage groups (s) containing 2,330 SNP markers and spanned 881 Kosambi cM. Contigs (10,302) were genetically mapped to the eight s, which were assembled into pseudomolecules that covered a total of ∼120.6 Mbp. The final size of the pseudomolecules ranged from 9.4 Mbp () to 20.4 Mpb (). The following major correspondence between the eight Lepidium s ( to ) and the five () chromosomes (-) was revealed through comparative genomics analysis: _, _-&, _, _&, _&, _, and _. This analysis revealed that at least 66% of the sequences of the s showed high collinearity with chromosomes. The sequence identity between the corresponding regions of the s and chromosomes ranged from 80.6% () to 86.4% () with overall mean of 82.9%. The map positions on of the homologs of 24 genes that regulate various traits in were also identified. The eight s revealed in this study confirm the previously reported (1) haploid chromosome number of eight in and and (2) chromosomal fusion, translocation, and inversion events during the evolution of = 8 karyotype in ancestral species shared by and to = 5 karyotype in . This study generated highly useful genomic tools and resources for that can be used to accelerate its domestication.
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http://dx.doi.org/10.3389/fpls.2020.00448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7204607PMC
April 2020

Species-Specific Duplication Event Associated with Elevated Levels of Nonstructural Carbohydrates in .

G3 (Bethesda) 2020 05 4;10(5):1511-1520. Epub 2020 May 4.

Advanced Plant Technology, Clemson University, Clemson, SC

Simple sugars are the essential foundation to plant life, and thus, their production, utilization, and storage are highly regulated processes with many complex genetic controls. Despite their importance, many of the genetic and biochemical mechanisms remain unknown or uncharacterized. Sorghum, a highly productive, diverse C grass important for both industrial and subsistence agricultural systems, has considerable phenotypic diversity in the accumulation of nonstructural sugars in the stem. We use this crop species to examine the genetic controls of high levels of sugar accumulation, identify genetic mechanisms for the accumulation of nonstructural sugars, and link carbon allocation with iron transport. We identify a species-specific tandem duplication event controlling sugar accumulation using genome-wide association analysis, characterize multiple allelic variants causing increased sugar content, and provide further evidence of a putative neofunctionalization event conferring adaptability in Comparative genomics indicate that this event is unique to sorghum which may further elucidate evolutionary mechanisms for adaptation and divergence within the Poaceae. Furthermore, the identification and characterization of this event was only possible with the continued advancement and improvement of the reference genome. The characterization of this region and the process in which it was discovered serve as a reminder that any reference genome is imperfect and is in need of continual improvement.
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http://dx.doi.org/10.1534/g3.119.400921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7202026PMC
May 2020

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.

Nat Commun 2020 01 21;11(1):413. Epub 2020 Jan 21.

USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA.

Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.
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http://dx.doi.org/10.1038/s41467-019-14280-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6972940PMC
January 2020

The genetic architecture of teosinte catalyzed and constrained maize domestication.

Proc Natl Acad Sci U S A 2019 03 6;116(12):5643-5652. Epub 2019 Mar 6.

Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706;

The process of evolution under domestication has been studied using phylogenetics, population genetics-genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between teosinte and maize landrace genetic variance-covariance matrices (G-matrices). While the structure of G-matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace G-matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory.
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http://dx.doi.org/10.1073/pnas.1820997116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431195PMC
March 2019

Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population.

Plant J 2016 06 20;86(5):391-402. Epub 2016 Jun 20.

Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China.

Flowering time is one of the major adaptive traits in domestication of maize and an important selection criterion in breeding. To detect more maize flowering time variants we evaluated flowering time traits using an extremely large multi- genetic background population that contained more than 8000 lines under multiple Sino-United States environments. The population included two nested association mapping (NAM) panels and a natural association panel. Nearly 1 million single-nucleotide polymorphisms (SNPs) were used in the analyses. Through the parallel linkage analysis of the two NAM panels, both common and unique flowering time regions were detected. Genome wide, a total of 90 flowering time regions were identified. One-third of these regions were connected to traits associated with the environmental sensitivity of maize flowering time. The genome-wide association study of the three panels identified nearly 1000 flowering time-associated SNPs, mainly distributed around 220 candidate genes (within a distance of 1 Mb). Interestingly, two types of regions were significantly enriched for these associated SNPs - one was the candidate gene regions and the other was the approximately 5 kb regions away from the candidate genes. Moreover, the associated SNPs exhibited high accuracy for predicting flowering time.
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http://dx.doi.org/10.1111/tpj.13174DOI Listing
June 2016

Independent Molecular Basis of Convergent Highland Adaptation in Maize.

Genetics 2015 Aug 15;200(4):1297-312. Epub 2015 Jun 15.

Department of Plant Sciences, University of California, Davis, California 95616 The Center for Population Biology and the Genome Center, University of California, Davis, California 95616

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.
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http://dx.doi.org/10.1534/genetics.115.178327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571994PMC
August 2015

High-resolution genetic mapping of maize pan-genome sequence anchors.

Nat Commun 2015 Apr 16;6:6914. Epub 2015 Apr 16.

1] Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA [2] United States Department of Agriculture/Agricultural Research Service, Ithaca, New York 14850, USA.

In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a 'pan-genome', which is essential to fully understand the genetic control of phenotypes. However, the pan-genome's complexity hinders its accurate assembly via sequence alignment. Here we demonstrate an approach to facilitate pan-genome construction in maize. By performing 18 trillion association tests we map 26 million tags generated by reduced representation sequencing of 14,129 maize inbred lines. Using machine-learning models we select 4.4 million accurately mapped tags as sequence anchors, 1.1 million of which are presence/absence variations. Structural variations exhibit enriched association with phenotypic traits, indicating that it is a significant source of adaptive variation in maize. The ability to efficiently map ultrahigh-density pan-genome sequence anchors enables fine characterization of structural variation and will advance both genetic research and breeding in many crops.
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http://dx.doi.org/10.1038/ncomms7914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411285PMC
April 2015

Recombination in diverse maize is stable, predictable, and associated with genetic load.

Proc Natl Acad Sci U S A 2015 Mar 9;112(12):3823-8. Epub 2015 Mar 9.

Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; US Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853; and.

Among the fundamental evolutionary forces, recombination arguably has the largest impact on the practical work of plant breeders. Varying over 1,000-fold across the maize genome, the local meiotic recombination rate limits the resolving power of quantitative trait mapping and the precision of favorable allele introgression. The consequences of low recombination also theoretically extend to the species-wide scale by decreasing the power of selection relative to genetic drift, and thereby hindering the purging of deleterious mutations. In this study, we used genotyping-by-sequencing (GBS) to identify 136,000 recombination breakpoints at high resolution within US and Chinese maize nested association mapping populations. We find that the pattern of cross-overs is highly predictable on the broad scale, following the distribution of gene density and CpG methylation. Several large inversions also suppress recombination in distinct regions of several families. We also identify recombination hotspots ranging in size from 1 kb to 30 kb. We find these hotspots to be historically stable and, compared with similar regions with low recombination, to have strongly differentiated patterns of DNA methylation and GC content. We also provide evidence for the historical action of GC-biased gene conversion in recombination hotspots. Finally, using genomic evolutionary rate profiling (GERP) to identify putative deleterious polymorphisms, we find evidence for reduced genetic load in hotspot regions, a phenomenon that may have considerable practical importance for breeding programs worldwide.
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http://dx.doi.org/10.1073/pnas.1413864112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378432PMC
March 2015

TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.

PLoS One 2014 28;9(2):e90346. Epub 2014 Feb 28.

Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America ; USDA Agricultural Research Service, Ithaca, New York, United States of America.

Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers. Herein we describe a bioinformatics pipeline, TASSEL-GBS, designed for the efficient processing of raw GBS sequence data into SNP genotypes. The TASSEL-GBS pipeline successfully fulfills the following key design criteria: (1) Ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8-16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished "pseudo-reference" consisting of numerous contigs. We describe the TASSEL-GBS pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (Zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based SNP filters. Overall, the GBS assay and the TASSEL-GBS pipeline provide robust tools for studying genomic diversity.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090346PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3938676PMC
October 2014

Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map.

Theor Appl Genet 2014 Jan 27;127(1):73-84. Epub 2013 Sep 27.

Department of Plant Breeding, Cornell University, Ithaca, NY, 14853, USA.

Improved efficacy and durability of powdery mildew resistance can be enhanced via knowledge of the genetics of resistance and susceptibility coupled with the development of high-resolution maps to facilitate the stacking of multiple resistance genes and other desirable traits. We studied the inheritance of powdery mildew (Erysiphe necator) resistance and susceptibility of wild Vitis rupestris B38 and cultivated V. vinifera 'Chardonnay', finding evidence for quantitative variation. Molecular markers were identified using genotyping-by-sequencing, resulting in 16,833 single nucleotide polymorphisms (SNPs) based on alignment to the V. vinifera 'PN40024' reference genome sequence. With an average density of 36 SNPs/Mbp and uniform coverage of the genome, this 17K set was used to identify 11 SNPs on chromosome 7 associated with a resistance locus from V. rupestris B38 and ten SNPs on chromosome 9 associated with a locus for susceptibility from 'Chardonnay' using single marker association and linkage disequilibrium analysis. Linkage maps for V. rupestris B38 (1,146 SNPs) and 'Chardonnay' (1,215 SNPs) were constructed and used to corroborate the 'Chardonnay' locus named Sen1 (Susceptibility to Erysiphe necator 1), providing the first insight into the genetics of susceptibility to powdery mildew from V. vinifera. The identification of markers associated with a susceptibility locus in a V. vinifera background can be used for negative selection among breeding progenies. This work improves our understanding of the nature of powdery mildew resistance in V. rupestris B38 and 'Chardonnay', while applying next-generation sequencing tools to advance grapevine genomics and breeding.
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http://dx.doi.org/10.1007/s00122-013-2202-xDOI Listing
January 2014

Comprehensive genotyping of the USA national maize inbred seed bank.

Genome Biol 2013 Jun 11;14(6):R55. Epub 2013 Jun 11.

Background: Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.

Results: The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits.

Conclusions: The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.
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http://dx.doi.org/10.1186/gb-2013-14-6-r55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707059PMC
June 2013

Population genomic and genome-wide association studies of agroclimatic traits in sorghum.

Proc Natl Acad Sci U S A 2013 Jan 24;110(2):453-8. Epub 2012 Dec 24.

Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.

Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized ~265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic conditions. Using this genome-wide SNP map, we have characterized population structure with respect to geographic origin and morphological type and identified patterns of ancient crop diffusion to diverse agroclimatic regions across Africa and Asia. To better understand the genomic patterns of diversification in sorghum, we quantified variation in nucleotide diversity, linkage disequilibrium, and recombination rates across the genome. Analyzing nucleotide diversity in landraces, we find evidence of selective sweeps around starch metabolism genes, whereas in landrace-derived introgression lines, we find introgressions around known height and maturity loci. To identify additional loci underlying variation in major agroclimatic traits, we performed genome-wide association studies (GWAS) on plant height components and inflorescence architecture. GWAS maps several classical loci for plant height, candidate genes for inflorescence architecture. Finally, we trace the independent spread of multiple haplotypes carrying alleles for short stature or long inflorescence branches. This genome-wide map of SNP variation in sorghum provides a basis for crop improvement through marker-assisted breeding and genomic selection.
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http://dx.doi.org/10.1073/pnas.1215985110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545811PMC
January 2013

Comparative population genomics of maize domestication and improvement.

Nat Genet 2012 Jun 3;44(7):808-11. Epub 2012 Jun 3.

Department of Plant Sciences, University of California, Davis, California, USA.

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, 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. We find evidence of recovery of diversity after domestication, likely introgression from wild relatives, and evidence for stronger selection during domestication than improvement. We identify a number of genes with stronger signals of selection than those previously shown to underlie major morphological changes. Finally, through transcriptome-wide analysis of gene expression, we find evidence both consistent with removal of cis-acting variation during maize domestication and improvement and suggestive of modern breeding having increased dominance in expression while targeting highly expressed genes.
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http://dx.doi.org/10.1038/ng.2309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5531767PMC
June 2012

Maize HapMap2 identifies extant variation from a genome in flux.

Nat Genet 2012 Jun 3;44(7):803-7. Epub 2012 Jun 3.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

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 pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.
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http://dx.doi.org/10.1038/ng.2313DOI Listing
June 2012

Megabase-scale inversion polymorphism in the wild ancestor of maize.

Genetics 2012 Jul 27;191(3):883-94. Epub 2012 Apr 27.

Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA.

Chromosomal inversions are thought to play a special role in local adaptation, through dramatic suppression of recombination, which favors the maintenance of locally adapted alleles. However, relatively few inversions have been characterized in population genomic data. On the basis of single-nucleotide polymorphism (SNP) genotyping across a large panel of Zea mays, we have identified an ∼50-Mb region on the short arm of chromosome 1 where patterns of polymorphism are highly consistent with a polymorphic paracentric inversion that captures >700 genes. Comparison to other taxa in Zea and Tripsacum suggests that the derived, inverted state is present only in the wild Z. mays subspecies parviglumis and mexicana and is completely absent in domesticated maize. Patterns of polymorphism suggest that the inversion is ancient and geographically widespread in parviglumis. Cytological screens find little evidence for inversion loops, suggesting that inversion heterozygotes may suffer few crossover-induced fitness consequences. The inversion polymorphism shows evidence of adaptive evolution, including a strong altitudinal cline, a statistical association with environmental variables and phenotypic traits, and a skewed haplotype frequency spectrum for inverted alleles.
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http://dx.doi.org/10.1534/genetics.112.138578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389981PMC
July 2012

A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.

PLoS One 2011 May 4;6(5):e19379. Epub 2011 May 4.

Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America.

Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019379PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087801PMC
May 2011

Genetic signals of origin, spread, and introgression in a large sample of maize landraces.

Proc Natl Acad Sci U S A 2011 Jan 28;108(3):1088-92. Epub 2010 Dec 28.

Department of Plant Sciences, University of California, Davis, CA 95616, USA.

The last two decades have seen important advances in our knowledge of maize domestication, thanks in part to the contributions of genetic data. Genetic studies have provided firm evidence that maize was domesticated from Balsas teosinte (Zea mays subspecies parviglumis), a wild relative that is endemic to the mid- to lowland regions of southwestern Mexico. An interesting paradox remains, however: Maize cultivars that are most closely related to Balsas teosinte are found mainly in the Mexican highlands where subspecies parviglumis does not grow. Genetic data thus point to primary diffusion of domesticated maize from the highlands rather than from the region of initial domestication. Recent archeological evidence for early lowland cultivation has been consistent with the genetics of domestication, leaving the issue of the ancestral position of highland maize unresolved. We used a new SNP dataset scored in a large number of accessions of both teosinte and maize to take a second look at the geography of the earliest cultivated maize. We found that gene flow between maize and its wild relatives meaningfully impacts our inference of geographic origins. By analyzing differentiation from inferred ancestral gene frequencies, we obtained results that are fully consistent with current ecological, archeological, and genetic data concerning the geography of early maize cultivation.
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http://dx.doi.org/10.1073/pnas.1013011108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024656PMC
January 2011

Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis).

Mol Ecol 2010 Mar 15;19(6):1162-73. Epub 2010 Feb 15.

Department of Plant Sciences, University of California, Davis, CA 95616, USA.

Analysis of fine scale genetic structure in continuous populations of outcrossing plant species has traditionally been limited by the availability of sufficient markers. We used a set of 468 SNPs to characterize fine-scale genetic structure within and between two dense stands of the wild ancestor of maize, teosinte (Zea mays ssp. parviglumis). Our analyses confirmed that teosinte is highly outcrossing and showed little population structure over short distances. We found that the two populations were clearly genetically differentiated, although the actual level of differentiation was low. Spatial autocorrelation of relatedness was observed within both sites but was somewhat stronger in one of the populations. Using principal component analysis, we found evidence for significant local differentiation in the population with stronger spatial autocorrelation. This differentiation was associated with pronounced shifts in the first two principal components along the field. These shifts corresponded to changes in allele frequencies, potentially due to local topographical features. There was little evidence for selection at individual loci as a contributing factor to differentiation. Our results demonstrate that significant local differentiation may, but need not, co-occur with spatial autocorrelation of relatedness. The present study represents one of the most detailed analyses of local genetic structure to date and provides a benchmark for future studies dealing with fine scale patterns of genetic diversity in natural plant populations.
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http://dx.doi.org/10.1111/j.1365-294X.2010.04559.xDOI Listing
March 2010

Genetic properties of the maize nested association mapping population.

Science 2009 Aug;325(5941):737-40

United States Department of Agriculture-Agriculture Research Service (USDA-ARS), USA.

Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. We crossed 25 diverse inbred maize lines to the B73 reference line, capturing a total of 136,000 recombination events. Variation for recombination frequencies was observed among families, influenced by local (cis) genetic variation. We identified evidence for numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated a limited role for genes with large effects and epistatic interactions on fitness. We observed excess residual heterozygosity in pericentromeric regions, which suggested that selection in inbred lines has been less efficient in these regions because of reduced recombination frequency. This implies that pericentromeric regions may contribute disproportionally to heterosis.
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http://dx.doi.org/10.1126/science.1174320DOI Listing
August 2009

The genetic architecture of maize flowering time.

Science 2009 Aug;325(5941):714-8

U.S. Department of Agriculture (USDA)-Agricultural Research Service (USDA-ARS), USA.

Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis.
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http://dx.doi.org/10.1126/science.1174276DOI Listing
August 2009

Population structure and genetic diversity of New World maize races assessed by DNA microsatellites.

Am J Bot 2008 Oct;95(10):1240-53

Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706 USA.

Because of the economic importance of maize and its scientific importance as a model system for studies of domestication, its evolutionary history is of general interest. We analyzed the population genetic structure of maize races by genotyping 964 individual plants, representing almost the entire set of ∼350 races native to the Americas, with 96 microsatellites. Using Bayesian clustering, we detected four main clusters consisting of highland Mexican, northern United States (US), tropical lowland, and Andean races. Phylogenetic analysis indicated that the southwestern US was an intermediary stepping stone between Mexico and the northern US. Furthermore, southeastern US races appear to be of mixed northern flint and tropical lowland ancestry, while lowland middle South American races are of mixed Andean and tropical lowland ancestry. Several cases of post-Columbian movement of races were detected, most notably from the US to South America. Of the four main clusters, the highest genetic diversity occurs in highland Mexican races, while diversity is lowest in the Andes and northern US. Isolation by distance appears to be the main factor underlying the historical diversification of maize. We identify highland Mexico and the Andes as potential sources of genetic diversity underrepresented among elite lines used in maize breeding programs.
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http://dx.doi.org/10.3732/ajb.0800097DOI Listing
October 2008

Panzea: an update on new content and features.

Nucleic Acids Res 2008 Jan 19;36(Database issue):D1041-3. Epub 2007 Nov 19.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

Panzea (http://www.panzea.org), the public web site of the project 'Molecular and Functional Diversity in the Maize Genome', has expanded over the past two years in data content, display tools and informational sections. The most significant data content expansions occurred for the single nucleotide polymorphism (SNP), sequencing, isozyme and phenotypic data types. We have enhanced our existing web display tools and have launched a number of new tools for data display and analysis. For example, we have implemented one that allows users to find polymorphisms between two accessions, a geographic map tool to visualize the geographic distribution of SNPs, simple sequence repeats (SSRs) and isozyme alleles and a graphical view of the placement of Panzea markers and genes/loci on genetic and physical maps. One goal of the informatics component of our project has been to generate code that can be used by other groups. We have enhanced our existing code base and have made our new tools available. Finally, we have also made available new informational sections as part of our educational and outreach efforts.
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http://dx.doi.org/10.1093/nar/gkm1022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238995PMC
January 2008

Prospects for inferring pairwise relationships with single nucleotide polymorphisms.

Mol Ecol 2003 Apr;12(4):1039-47

Purdue University, Department of Forestry & Natural Resources, 195 Marsteller St, West Lafayette, Indiana 47907-2033, USA.

An extraordinarily large number of single nucleotide polymorphisms (SNPs) are now available in humans as well as in other model organisms. Technological advancements may soon make it feasible to assay hundreds of SNPs in virtually any organism of interest. One potential application of SNPs is the determination of pairwise genetic relationships in populations without known pedigrees. Although microsatellites are currently the marker of choice for this purpose, the number of independently segregating microsatellite markers that can be feasibly assayed is limited. Thus, it can be difficult to distinguish reliably some classes of relationship (e.g. full-sibs from half-sibs) with microsatellite data alone. We assess, via Monte Carlo computer simulation, the potential for using a large panel of independently segregating SNPs to infer genetic relationships, following the analytical approach of Blouin et al. (1996). We have explored a 'best case scenario' in which 100 independently segregating SNPs are available. For discrimination among single-generation relationships or for the identification of parent-offspring pairs, it appears that such a panel of moderately polymorphic SNPs (minor allele frequency of 0.20) will provide discrimination power equivalent to only 16-20 independently segregating microsatellites. Although newly available analytical methods that can account for tight genetic linkage between markers will, in theory, allow improved estimation of relationships using thousands of SNPs in highly dense genomic scans, in practice such studies will only be feasible in a handful of model organisms. Given the comparable amount of effort required for the development of both types of markers, it seems that microsatellites will remain the marker of choice for relationship estimation in nonmodel organisms, at least for the foreseeable future.
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http://dx.doi.org/10.1046/j.1365-294x.2003.01790.xDOI Listing
April 2003

Effects of native forest regeneration practices on genetic diversity in Eucalyptus consideniana.

Theor Appl Genet 2003 Aug 14;107(3):422-31. Epub 2003 May 14.

CSIRO Forestry and Forest Products, PO Box E4008, Kingston, ACT 2604, Australia.

Impacts of forest harvesting and regeneration practices on genetic diversity in the Australian native forest species Eucalyptus consideniana Maiden (yertchuk) were examined using 29 Mendelian DNA markers (18 RFLPs and 11 microsatellites). Two replicate logging coupes were studied from each of the two most commonly employed silvicultural treatments: clear felling with aerial re-sowing and the seed tree system. For each coupe, genetic diversity measures were compared between a sample of the sapling regeneration and a corresponding control sample from bordering unharvested trees. When calculations were performed over all 29 loci, significant reductions of allelic richness (AR), effective number of alleles (AE) and/or expected heterozygosity (HE) were detected on one or both of seed tree coupes, but on neither of the clear falls. When calculations were performed over the 11 microsatellites alone, all three measures, AR, AE and HE, were significantly reduced on both of the seed replicates but on neither of the two clear falls. In contrast, when the RFLPs were examined separately, there were no significant reductions of diversity on either of the two seed tree coupes or on the two clear falls. These results suggest that genetic erosion is more likely under the seed tree system than under clear-felling with aerial re-sowing and that there is greater statistical power to detect it with microsatellites than with RFLPs. A Monte Carlo simulation to test the statistical significance of the number of apparently lost or gained alleles showed that significant losses of alleles above specified threshold frequencies occurred only in the two seed tree replicates. Three of the four control and regeneration population pairs were significantly differentiated, as indicated by exact tests or by pairwise FST estimates. Comparisons of CONTML dendrograms, constructed for the regeneration populations only versus the control populations only, indicated that genetic drift was significantly promoted under forest management. No significant decreases in observed heterozygosity, or increases in the panmictic index (f), were observed in any of the comparisons suggesting that inbreeding was not promoted by a single rotation of forest management.
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http://dx.doi.org/10.1007/s00122-003-1262-8DOI Listing
August 2003
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