Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (<i>Sorghum bicolor</i>)

Valluru, Ravi; Gazave, Élodie; Fernandes, Samuel B.; Ferguson, John N.; Lozano, Roberto; Hirannaiah, Pradeep; Zuo, Tao; Brown, Patrick J.; Leakey, Andrew D. B.; Gore, Michael A.; Buckler, Edward S.; Bandillo, Nonoy

doi:10.1534/genetics.118.301742

Cited by 52 publications

(68 citation statements)

References 90 publications

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“…Plant material, field experiments and phenotypic data In this study, we evaluated a biomass sorghum diversity panel consisting of 869 lines (Valluru et al 2018). The diversity panel was grown at three field locations only a few km from the main campus of the University of Illinois Urbana-Champaign in 2016 (Fisher and Energy Farms) and 2017 (Maxwell and Energy Farms).…”

Section: Methodsmentioning

confidence: 99%

Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum

Santos

Fernandes²,

McCoy

et al. 2020

G3 Genes|Genomes|Genetics

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The ability to connect genetic information between traits over time allow Bayesian networks to offer a powerful probabilistic framework to construct genomic prediction models. In this study, we phenotyped a diversity panel of 869 biomass sorghum (Sorghum bicolor (L.) Moench) lines, which had been genotyped with 100,435 SNP markers, for plant height (PH) with biweekly measurements from 30 to 120 days after planting (DAP) and for end-of-season dry biomass yield (DBY) in four environments. We evaluated five genomic prediction models: Bayesian network (BN), Pleiotropic Bayesian network (PBN), Dynamic Bayesian network (DBN), multi-trait GBLUP (MTr-GBLUP), and multi-time GBLUP (MTi-GBLUP) models. In fivefold cross-validation, prediction accuracies ranged from 0.46 (PBN) to 0.49 (MTr-GBLUP) for DBY and from 0.47 (DBN, DAP120) to 0.75 (MTi-GBLUP, DAP60) for PH. Forward-chaining cross-validation further improved prediction accuracies of the DBN, MTi-GBLUP and MTr-GBLUP models for PH (training slice: 30-45 DAP) by 36.4–52.4% relative to the BN and PBN models. Coincidence indices (target: biomass, secondary: PH) and a coincidence index based on lines (PH time series) showed that the ranking of lines by PH changed minimally after 45 DAP. These results suggest a two-level indirect selection method for PH at harvest (first-level target trait) and DBY (second-level target trait) could be conducted earlier in the season based on ranking of lines by PH at 45 DAP (secondary trait). With the advance of high-throughput phenotyping technologies, our proposed two-level indirect selection framework could be valuable for enhancing genetic gain per unit of time when selecting on developmental traits.

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Section: Methodsmentioning

confidence: 99%

Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum

Santos

Fernandes²,

McCoy

et al. 2020

G3 Genes|Genomes|Genetics

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“…A dataset of 107,421 SNPs (hereafter referred to as target set) scored using genotyping-by-sequencing was obtained from Fernandes et al [48] and Thurber et al [22]. In order to increase the marker density for the target panel, a whole-genome re-sequencing dataset (hereafter referred to as the reference genotype set) was used for imputing un-typed SNPs [49]. The reference set was composed of 239 individuals and 5,512,653 SNPs anchored to the Sorghum bicolor reference genome version 3.1 (https://phytozome.jgi.doe.gov) [50].…”

Section: Genotypingmentioning

confidence: 99%

Conserved defense responses between maize and sorghum to Exserohilum turcicum

et al. 2020

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Background: Exserohilum turcicum is an important pathogen of both sorghum and maize, causing sorghum leaf blight and northern corn leaf blight. Because the same pathogen can infect and cause major losses for two of the most important grain crops, it is an ideal pathosystem to study plant-pathogen evolution and investigate shared resistance mechanisms between the two plant species. To identify sorghum genes involved in the E. turcicum response, we conducted a genome-wide association study (GWAS). Results: Using the sorghum conversion panel evaluated across three environments, we identified a total of 216 significant markers. Based on physical linkage with the significant markers, we detected a total of 113 unique candidate genes, some with known roles in plant defense. Also, we compared maize genes known to play a role in resistance to E. turcicum with the association mapping results and found evidence of genes conferring resistance in both crops, providing evidence of shared resistance between maize and sorghum. Conclusions: Using a genetics approach, we identified shared genetic regions conferring resistance to E. turcicum in both maize and sorghum. We identified several promising candidate genes for resistance to leaf blight in sorghum, including genes related to R-gene mediated resistance. We present significant advancements in the understanding of host resistance to E. turcicum, which is crucial to reduce losses due to this important pathogen.

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“…To allow for a comparative analysis, genomic evolution and amino acid conservation modeling 24,25 was used to catalog candidate deleterious variants across both the sorghum and maize genomes. Genomic evolutionary rate profiling (GERP) 26 of the exonic SNPs in maize were annotated as deleterious.…”

Section: Main Textmentioning

confidence: 99%

“…GERP (Genomic evolutionary rate profiling): Sorghum GERP 26 scores were estimated from the alignment of six species including Zea mays , Oryza sativa , Setaria italica , Brachypodium distachyon , Hordeum vulgare and Musa acuminate 46 . For further information, please refer to Valluru et al 25 . We used maize GERP scores calculated previously by Rodgers-Melnick et al 52 .…”

Section: Convolutional Neural Network Modelmentioning

confidence: 99%

Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize

Lozano

Gazave

Santos

et al. 2019

Preprint

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Sorghum and maize share a close evolutionary history that can be explored through comparative genomics. To perform a large-scale comparison of the genomic variation between these two species, we analyzed 13 million variants identified from whole genome resequencing of 468 sorghum lines together with 25 million variants previously identified in 1,218 maize lines.Deleterious mutations in both species were prevalent in pericentromeric regions, enriched in non-syntenic genes, and present at low allele frequencies. A comparison of deleterious burden between sorghum and maize revealed that sorghum, in contrast to maize, departed from the "domestication cost" hypothesis that predicts a higher deleterious burden among domesticates compared to wild lines. Additionally, sorghum and maize population genetic summary statistics were used to predict a gene deleterious index with an accuracy higher than 0.5. This research represents a key step towards understanding the evolutionary dynamics of deleterious variants in sorghum and provides a comparative genomics framework to start prioritizing them for removal through genome editing and breeding. 2 Main text: Sorghum ( Sorghum bicolor L. Moench) and maize ( Zea mays L.) are both members of the Poaceae family and often serve as a model system for comparative plant genomics. Their common Poaceae ancestor underwent a whole-genome duplication (WGD) event ~96 million years ago 1 , and a second WGD in maize corresponds closely with its divergence 12 million years ago from sorghum 2 . The role of polyploidization in maize diversification 1 makes the sorghum-maize system particularly powerful for comparative studies.A rchaeobotanical studies support a single sorghum domestication event around 3000 BC in Eastern Sudan 3 , with genetic studies supporting a potential second independent domestication center in west Africa 4,5 . Maize, in contrast, was domesticated once from teosinte in the Balsas river valley in central Mexico around 9000 years ago 6,7 . While some orthologs between these two species experienced parallel selection during domestication 8 , most domestication related genes appear to be drawn from a non-overlapping set 9 . It is well established that maize experienced a decline in effective population size due to a domestication bottleneck 10,11 that increased the burden of deleterious alleles in the domesticate compared to teosinte 12,13 .Evidence for reduced nucleotide diversity in landraces from a genetic bottleneck 5 or population size decline 14 has also been reported for sorghum.Sorghum has a hermaphroditic inflorescence, contributing to its predominantly self-pollinating nature. Domesticated sorghum has an estimated outcrossing rate of only 7 to 20% 9,15 , while the outcrossing rate tends to be higher (up to 70% 16 ) for weedy and wild sorghum. In contrast, maize and its wild progenitor teosinte are monoecious and generally outcrossing at a rate of over 90% 17 . In this study, we performed a joint analysis of functional variation in sorghum and 3 maize lines that span th...

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Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (Sorghum bicolor)

Cited by 52 publications

References 90 publications

Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum

Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum

Conserved defense responses between maize and sorghum to Exserohilum turcicum

Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize

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