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1. Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize

Author:
Edward S. Buckler,   et al.   ; Guillaume P. Ramstein;     Show all 2 Author
Source:
Genome biology 2022 v.23 no.1 pp. 183
ISSN:
1474-760X
Subject:
bioinformatics; carbon metabolism; chromatin; corn; gene expression; gene ontology; genes; genomics; grain yield; mutation; prediction; prioritization; sequence analysis
Abstract:
... BACKGROUND: Crop improvement through cross-population genomic prediction and genome editing requires identification of causal variants at high resolution, within fewer than hundreds of base pairs. Most genetic mapping studies have generally lacked such resolution. In contrast, evolutionary approaches can detect genetic effects at high resolution, but they are limited by shifting selection, missing ...
DOI:
10.1186/s13059-022-02747-2

2. Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

Author:
Edward S. Buckler,   et al.   ; Travis Wrightsman; Alexandre P. Marand; Peter A. Crisp; Nathan M. Springer;     Show all 5 Authors
Source:
The plant genome 2022 v.15 no.3 pp. e20249
ISSN:
1940-3372
Subject:
DNA methylation; Zea mays; cell specificity; chromatin; corn; genes; leaves; models; transcription factors
Abstract:
... Accessible chromatin regions are critical components of gene regulation but modeling them directly from sequence remains challenging, especially within plants, whose mechanisms of chromatin remodeling are less understood than in animals. We trained an existing deep‐learning architecture, DanQ, on data from 12 angiosperm species to predict the chromatin accessibility in leaf of sequence windows wit ...
DOI:
10.1002/tpg2.20249

3. Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact

Author:
Edward S. Buckler,   et al.   ; Xiao Zhang; Yonghui Zhu; Karl A. G. Kremling; M. Cinta Romay; Robert Bukowski; Qi Sun; Shibin Gao; Fei Lu;     Show all 9 Authors
Source:
Theoretical and applied genetics 2022 v.135 no.1 pp. 273-290
ISSN:
0040-5752
Subject:
corn; gene expression; gene expression regulation; genes; genetic variation; genome-wide association study; genomics; phenotype; plant height; population structure; quantitative traits
Abstract:
... KEY MESSAGE: Two read depth methods were jointly used in next-generation sequencing data to identify deletions in maize population. GWAS by deletions were analyzed for gene expression pattern and classical traits, respectively. Many studies have confirmed that structural variation (SV) is pervasive throughout the maize genome. Deletion is one type of SV that may impact gene expression and cause ph ...
DOI:
10.1007/s00122-021-03965-1

4. Predicting phenotypes from genetic, environment, management, and historical data using CNNs

Author:
Edward S. Buckler,   et al.   ; Jacob D. Washburn; Emre Cimen; Guillaume Ramstein; Timothy Reeves; Patrick O’Briant; Greg McLean; Mark Cooper; Graeme Hammer;     Show all 9 Authors
Source:
Theoretical and applied genetics 2021 v.134 no.12 pp. 3997-4011
ISSN:
0040-5752
Subject:
data collection; genomics; medicine; prediction; surveys
Abstract:
... KEY MESSAGE: Convolutional Neural Networks (CNNs) can perform similarly or better than standard genomic prediction methods when sufficient genetic, environmental, and management data are provided. Predicting phenotypes from genetic (G), environmental (E), and management (M) conditions is a long-standing challenge with implications to agriculture, medicine, and conservation. Most methods reduce the ...
DOI:
10.1007/s00122-021-03943-7

5. A k-mer grammar analysis to uncover maize regulatory architecture

Author:
Edward S. Buckler,   et al.   ; María Katherine Mejía-Guerra;     Show all 2 Author
Source:
BMC plant biology 2019 v.19 no.1 pp. 103
ISSN:
1471-2229
Subject:
chromatin; corn; gene expression regulation; intergenic DNA; models; nucleotide sequences
Abstract:
... BACKGROUND: Only a small percentage of the genome sequence is involved in regulation of gene expression, but to biochemically identify this portion is expensive and laborious. In species like maize, with diverse intergenic regions and lots of repetitive elements, this is an especially challenging problem that limits the use of the data from one line to the other. While regulatory regions are rare, ...
DOI:
10.1186/s12870-019-1693-2
PubMed:
30876396
PubMed Central:
PMC6419808

6. Breaking the curse of dimensionality to identify causal variants in Breeding 4

Author:
Edward S. Buckler,   et al.   ; Guillaume P. Ramstein; Sarah E. Jensen;     Show all 3 Authors
Source:
Theoretical and applied genetics 2019 v.132 no.3 pp. 559-567
ISSN:
0040-5752
Subject:
DNA; artificial intelligence; cultivars; gene editing; genome; genotype; loci; nucleotide sequences; phenotype; plant breeding; plant morphology; quantitative genetics
Abstract:
... In the past, plant breeding has undergone three major transformations and is currently transitioning to a new technological phase, Breeding 4. This phase is characterized by the development of methods for biological design of plant varieties, including transformation and gene editing techniques directed toward causal loci. The application of such technologies will require to reliably estimate the ...
DOI:
10.1007/s00122-018-3267-3
PubMed:
30547185
PubMed Central:
PMC6439136

7. Tripsacum De novo Transcriptome Assemblies Reveal Parallel Gene Evolution with Maize after Ancient Polyploidy

Author:
Edward S. Buckler,   et al.   ; Christine M. Gault; Karl A. Kremling;     Show all 3 Authors
Source:
The plant genome 2018 v.11 no.3 pp. e180012
ISSN:
1940-3372
Subject:
Tripsacum dactyloides; Zea mays; corn; duplicate genes; evolution; gene deletion; gene expression; genomics; polyploidy; pseudogenes; transcriptome
Abstract:
... Plant genomes reduce in size following a whole‐genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize (Zea mays L.) and its sister genus, Tripsacum, share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for Tripsacum exist, it is unknown whether Tri ...
DOI:
10.3835/plantgenome2018.02.0012

8. Quantitative Genetics of the Maize Leaf Microbiome

Author:
Edward S. Buckler,   et al.   ; Jason G. Wallace; Karl A. Kremling; Lynsey L. Kovar;     Show all 4 Authors
Source:
Phytobiomes journal 2018 v.2 no.4 pp. 208-224
ISSN:
2471-2906
Subject:
bacteria; biochemical pathways; carbon metabolism; corn; environmental factors; genetic traits; genome-wide association study; genotype; habitats; heritability; leaves; loci; metagenomics; microbial communities; microbiome; phytobiome; secretion
Abstract:
... The degree to which the genotype of an organism can affect the composition of its associated microbial communities (“microbiome”) varies by organism and habitat, and in many cases is unknown. We analyzed the metabolically active bacteria of maize leaves across 300 diverse maize lines growing in a common environment. We performed comprehensive heritability analysis for 49 community diversity metric ...
DOI:
10.1094/PBIOMES-02-18-0008-R

9. Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn

Author:
Edward S. Buckler,   et al.   ; Matheus Baseggio; Matthew Murray; Maria Magallanes‐Lundback; Nicholas Kaczmar; James Chamness; Margaret E. Smith; Dean DellaPenna; William F. Tracy; Michael A. Gore;     Show all 10 Authors
Source:
The plant genome 2020 v.13 no.1 pp. e20008
ISSN:
1940-3372
Subject:
Zea mays; alleles; biochemical pathways; color; corn; endosperm; genome-wide association study; genomics; haplotypes; lutein; lycopene; mutation; prediction; sweetcorn; zeaxanthin
Abstract:
... Sweet corn (Zea mays L.) is highly consumed in the United States, but does not make major contributions to the daily intake of carotenoids (provitamin A carotenoids, lutein and zeaxanthin) that would help in the prevention of health complications. A genome‐wide association study of seven kernel carotenoids and twelve derivative traits was conducted in a sweet corn inbred line association panel ran ...
DOI:
10.1002/tpg2.20008

10. In‐Field Whole‐Plant Maize Architecture Characterized by Subcanopy Rovers and Latent Space Phenotyping

Author:
Edward S. Buckler,   et al.   ; Joseph L. Gage; Elliot Richards; Nicholas Lepak; Nicholas Kaczmar; Chinmay Soman; Girish Chowdhary; Michael A. Gore;     Show all 8 Authors
Source:
Plant phenome journal 2019 v.2 no.1 pp. 1-11
ISSN:
2578-2703
Subject:
Zea mays; automation; biomass; corn; data collection; genomics; hybrids; lidar; phenotype; plant architecture; plant biology; prediction; principal component analysis
Abstract:
... Core Ideas Subcanopy rovers enabled 3D characterization of thousands of hybrid maize plots. Machine learning produces heritable latent traits that describe plant architecture. Rover‐based phenotyping is far more efficient than manual phenotyping. Latent phenotypes from rovers are ready for application to plant biology and breeding. Collecting useful, interpretable, and biologically relevant phenot ...
DOI:
10.2135/tppj2019.07.0011

11. Diverse Chromosomal Locations of Quantitative Trait Loci for Tolerance to Maize chlorotic mottle virus in Five Maize Populations

Author:
Edward S. Buckler,   et al.   ; Mark W. Jones; Bryan W. Penning; Tiffany M. Jamann; Jeff C. Glaubitz; Cinta Romay; Margaret G. Redinbaugh;     Show all 7 Authors
Source:
Phytopathology 2018 v.108 no.6 pp. 748-758
ISSN:
0031-949X
Subject:
Maize chlorotic mottle virus; Sugarcane mosaic virus; chromosome mapping; corn; disease control; farmers; genotyping; hybrids; inbred lines; leaves; loci; marker-assisted selection; mixed infection; necrosis; phenotype; quantitative trait loci; viruses
Abstract:
... The recent rapid emergence of maize lethal necrosis (MLN), caused by coinfection of maize with Maize chlorotic mottle virus (MCMV) and a second virus usually from the family Potyviridae, is causing extensive losses for farmers in East Africa, Southeast Asia, and South America. Although the genetic basis of resistance to potyviruses is well understood in maize, little was known about resistance to ...
Handle:
10113/6224970
DOI:
10.1094/PHYTO-09-17-0321-R

12. Genome‐Wide Association and Genomic Prediction Models of Tocochromanols in Fresh Sweet Corn Kernels

Author:
Edward S. Buckler,   et al.   ; Matheus Baseggio; Matthew Murray; Maria Magallanes‐Lundback; Nicholas Kaczmar; James Chamness; Margaret E. Smith; Dean DellaPenna; William F. Tracy; Michael A. Gore;     Show all 10 Authors
Source:
The plant genome 2019 v.12 no.1 pp. e180038
ISSN:
1940-3372
Subject:
Zea mays; alleles; alpha-tocopherol; antioxidants; biosynthesis; corn; gamma-tocopherol; genetic analysis; genome-wide association study; genomics; human health; inbred lines; models; nutrition; quantitative genetics; seeds; starch; sweetcorn; tocopherol O-methyltransferase; tocopherol cyclase; tocotrienols
Abstract:
... Sweet corn (Zea mays L.), a highly consumed fresh vegetable in the United States, varies for tocochromanol (tocopherol and tocotrienol) levels but makes only a limited contribution to daily intake of vitamin E and antioxidants. We performed a genome‐wide association study of six tocochromanol compounds and 14 derivative traits across a sweet corn inbred line association panel to identify genes ass ...
DOI:
10.3835/plantgenome2018.06.0038

13. A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction

Author:
Edward S. Buckler,   et al.   ; Sarah E. Jensen; Jean Rigaud Charles; Kebede Muleta; Peter J. Bradbury; Terry Casstevens; Santosh P. Deshpande; Michael A. Gore; Rajeev Gupta; Daniel C. Ilut; Lynn Johnson; Roberto Lozano; Zachary Miller; Punna Ramu; Abhishek Rathore; M. Cinta Romay; Hari D. Upadhyaya; Rajeev K. Varshney; Geoffrey P. Morris; Gael Pressoir; Guillaume P. Ramstein;     Show all 21 Authors
Source:
The plant genome 2020 v.13 no.1 pp. e20009
ISSN:
1940-3372
Subject:
cost effectiveness; cultivars; data collection; databases; genome; genomics; genotyping by sequencing; haplotypes; marker-assisted selection; prediction
Abstract:
... Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome‐wide variants for 24 founders of the ...
DOI:
10.1002/tpg2.20009

14. A Low‐Cost Automated System for High‐Throughput Phenotyping of Single Oat Seeds

Author:
Edward S. Buckler V,   et al.   ; James W. Clohessy; Duke Pauli; Kevin M. Kreher; Paul R. Armstrong; Tingting Wu; Owen A. Hoekenga; Jean‐Luc Jannink; Mark E. Sorrells; Michael A. Gore;     Show all 10 Authors
Source:
Plant phenome journal 2018 v.1 no.1 pp. 1-13
ISSN:
2578-2703
Subject:
Avena sativa; automation; breeding programs; cameras; color; colorimetry; cost effectiveness; crops; data collection; genetic improvement; genotype; hulling; identity preservation; image analysis; morphometry; near-infrared spectroscopy; oats; phenotype; plant breeding; reflectance; screening; seed color; seeds
Abstract:
... Efforts focused on the genetic improvement of seed morphometric and color traits would greatly benefit from efficient and reliable quantitative phenotypic assessment in a nondestructive manner. Although several seed phenotyping systems exist, none of them combine the cost effectiveness, identity preservation, throughput, and accuracy needed for implementation in plant breeding. We integrated an im ...
DOI:
10.2135/tppj2018.07.0005

15. Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers

Author:
Edward S. Buckler,   et al.   ; Chunhui Li; Yongxiang Li; Yunsu Shi; Yanchun Song; Dengfeng Zhang; Zhiwu Zhang; Yu Li; Tianyu Wang;     Show all 9 Authors
Source:
Theoretical and applied genetics 2016 v.129 no.9 pp. 1775-1784
ISSN:
0040-5752
Subject:
Zea mays; chromosome mapping; corn; epistasis; gametophytes; genes; genetic recombination; genetic variation; inbred lines; molecular cloning; plant breeding; quantitative trait loci; segregation distortion; China; United States
Abstract:
... KEY MESSAGE : Using two nested association mapping populations and high-density markers, some important genomic regions controlling recombination frequency and segregation distortion were detected. Understanding the maize genomic features would be useful for the study of genetic diversity and evolution and for maize breeding. Here, we used two maize nested association mapping (NAM) populations sep ...
DOI:
10.1007/s00122-016-2739-6

16. Non‐Mendelian Single‐Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop

Author:
Edward S. Buckler,   et al.   ; Dong Zhang; Katherine A. Easterling; Nicholi J. Pitra; Mark C. Coles; Hank W. Bass; Paul D. Matthews;     Show all 7 Authors
Source:
The plant genome 2017 v.10 no.3 pp. eplantgenome2017.04.0032
ISSN:
1940-3372
Subject:
Humulus lupulus; autosomes; bitter acids; bitterness; breeding programs; cultivars; cytogenetic analysis; disease resistance; drought tolerance; genome; genome-wide association study; genomics; genotyping by sequencing; landraces; loci; meiosis; natural history; odors; phenotypic variation; phylogeny; plant breeding; prophase; segregation distortion; sex ratio; single nucleotide polymorphism
Abstract:
... Hop (Humulus lupulus L.) breeding programs seek to exploit genetic resources for bitter flavor, aroma, and disease resistance. However, these efforts have been thwarted by segregation distortion including female‐biased sex ratios. To better understand the transmission genetics of hop, we genotyped 4512 worldwide accessions of hop, including cultivars, landraces, and over 100 wild accessions using ...
DOI:
10.3835/plantgenome2017.04.0032

17. Joint‐linkage mapping and GWAS reveal extensive genetic loci that regulate male inflorescence size in maize

Author:
Edward S. Buckler,   et al.   ; Xun Wu; Yongxiang Li; Yunsu Shi; Yanchun Song; Dengfeng Zhang; Chunhui Li; Yu Li; Zhiwu Zhang; Tianyu Wang;     Show all 10 Authors
Source:
Plant biotechnology journal 2016 v.14 no.7 pp. 1551-1562
ISSN:
1467-7644
Subject:
DNA-binding proteins; Zea mays; breeding; chromosome mapping; corn; crop yield; genes; genotyping; inbred lines; inflorescences; loci; males; microarray technology; mutants; nucleotides; probability; quantitative trait loci; quantitative traits; transporters; zinc; China; United States
Abstract:
... Both insufficient and excessive male inflorescence size leads to a reduction in maize yield. Knowledge of the genetic architecture of male inflorescence is essential to achieve the optimum inflorescence size for maize breeding. In this study, we used approximately eight thousand inbreds, including both linkage populations and association populations, to dissect the genetic architecture of male inf ...
DOI:
10.1111/pbi.12519
PubMed:
26801971
PubMed Central:
PMC5066742

18. The Genetic Makeup of a Global Barnyard Millet Germplasm Collection

Author:
Edward S. Buckler,   et al.   ; Jason G. Wallace; Hari D. Upadhyaya; M. Vetriventhan; C. Tom Hash; Punna Ramu;     Show all 6 Authors
Source:
The plant genome 2015 v.8 no.1 pp. -
ISSN:
1940-3372
Subject:
Echinochloa frumentacea; case studies; drought tolerance; gene banks; genome; genomics; genotyping by sequencing; germplasm; germplasm conservation; phylogeny; population structure; research institutions; spatial data; East Asia
Abstract:
... Barnyard millet (Echinochloa spp.) is an important crop for many smallholder farmers in southern and eastern Asia. It is valued for its drought tolerance, rapid maturation, and superior nutritional qualities. Despite these characteristics there are almost no genetic or genomic resources for this crop in either cultivated species [E. colona (L.) Link and E. crus-galli (L.) P. Beauv.]. Recently, a c ...
DOI:
10.3835/plantgenome2014.10.0067

19. Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots

Author:
Edward S. Buckler,   et al.   ; Shaoqun Zhou; Ying K. Zhang; Karl A. Kremling; Yezhang Ding; John S. Bennett; Justin S. Bae; Dean K. Kim; Hayley H. Ackerman; Michael V. Kolomiets; Eric A. Schmelz; Frank C. Schroeder; Georg Jander;     Show all 13 Authors
Source:
new phytologist 2019 v.221 no.4 pp. 2096-2111
ISSN:
0028-646X
Subject:
Fusarium graminearum; Zea mays; corn; disease resistance; ethylene; fungi; genes; genetic engineering; metabolism; metabolites; metabolomics; pathogens; quantitative trait loci; roots; seedlings; transcriptomics
Abstract:
... The production and regulation of defensive specialized metabolites play a central role in pathogen resistance in maize (Zea mays) and other plants. Therefore, identification of genes involved in plant specialized metabolism can contribute to improved disease resistance. We used comparative metabolomics to identify previously unknown antifungal metabolites in maize seedling roots, and investigated ...
DOI:
10.1111/nph.15520

20. Genome-wide association mapping of provitamin A carotenoid content in cassava

Author:
Edward S. Buckler,   et al.   ; Williams Esuma; Liezel Herselman; Maryke Tine Labuschagne; Punna Ramu; Fei Lu; Yona Baguma; Robert Sezi Kawuki;     Show all 8 Authors
Source:
Euphytica 2016 v.212 no.1 pp. 97-110
ISSN:
0014-2336
Subject:
plant breeding; vitamin A; marker-assisted selection; loci; cassava; vitamin A deficiency; genetic improvement; genome-wide association study; single nucleotide polymorphism; chromosome mapping; genes; genotype; nucleotide sequences; roots; Manihot esculenta
Abstract:
... Global efforts are underway to develop staple crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency, which is widespread among resource-poor farmers in the developing world. As a staple crop for more than 500 million people in sub-Saharan Africa, cassava (Manihot esculenta Crantz) enriched with provitamin A carotenoids could have immense nutritional imp ...
DOI:
10.1007/s10681-016-1772-5