scholarly journals Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population

2019 ◽  
Author(s):  
Sandeep R. Marla ◽  
Gloria Burow ◽  
Ratan Chopra ◽  
Chad Hayes ◽  
Marcus O. Olatoye ◽  
...  
Keyword(s):  
Association Mapping ◽  
20Th Century ◽  
Linkage Mapping ◽  
Genetic Architecture ◽  
Chilling Stress ◽  
Chilling Tolerance ◽  
Field Trials ◽  
Nested Association Mapping ◽  
Chilling Sensitivity ◽  
Temperate Climates

AbstractDissecting the genetic architecture of stress tolerance in crops is critical to understand and improve adaptation. In temperate climates, early planting of chilling-tolerant varieties could provide longer growing seasons and drought escape, but chilling tolerance (<15°) is generally lacking in tropical-origin crops. Here we developed a nested association mapping (NAM) population to dissect the genetic architecture of early-season chilling tolerance in the tropical-origin cereal sorghum (Sorghum bicolor [L.] Moench). The NAM resource, developed from reference line BTx623 and three chilling-tolerant Chinese lines, is comprised of 771 recombinant inbred lines genotyped by sequencing at 43,320 single nucleotide polymorphisms. We phenotyped the NAM population for emergence, seedling vigor, and agronomic traits (>75,000 data points from ∼16,000 plots) in multi-environment field trials in Kansas under natural chilling stress (sown 30–45 days early) and normal growing conditions. Joint linkage mapping with early-planted field phenotypes revealed an oligogenic architecture, with 5–10 chilling tolerance loci explaining 20–41% of variation. Surprisingly, several of the major chilling tolerance loci co-localize precisely with the classical grain tannin (Tan1 and Tan2) and dwarfing genes (Dw1 and Dw3) that were under strong directional selection in the US during the 20th century. These findings suggest that chilling sensitivity was inadvertently selected due to coinheritance with desired nontannin and dwarfing alleles. The characterization of genetic architecture with NAM reveals why past chilling tolerance breeding was stymied and provides a path for genomics-enabled breeding of chilling tolerance.Article SummaryChilling sensitivity limits productivity of tropical-origin crops in temperate climates, and remains poorly understood at a genetic level. We developed a nested association mapping resource in sorghum, a tropical-origin cereal, to understand the genetic architecture of chilling tolerance. Linkage mapping of growth traits from early-planted field trials revealed several major chilling tolerance loci, including some colocalized with genes that were selected in the origin of US grain sorghum. These findings suggest chilling sensitivity was inadvertently selected during 20th century breeding, but can be bypassed using a better understanding of the underlying genetic architecture.DisclaimerMention of a trademark, warranty, proprietary product, or vendor does not constitute a guarantee by the USDA and does not imply approval or recommendation of the product to the exclusion of others that may be suitable. USDA is an equal opportunity provider and employer.

scholarly journals Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population

2019 ◽  
Vol 9 (12) ◽  
pp. 4045-4057 ◽  
Author(s):  
Sandeep R. Marla ◽  
Gloria Burow ◽  
Ratan Chopra ◽  
Chad Hayes ◽  
Marcus O. Olatoye ◽  
...  
Keyword(s):  
Association Mapping ◽  
Genetic Architecture ◽  
Mapping Population ◽  
Chilling Tolerance ◽  
Nested Association Mapping ◽  
Nested Association Mapping Population ◽  
Association Mapping Population

scholarly journals Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat

2020 ◽  
Vol 13 (3) ◽  
Author(s):  
Ahmad H. Sallam ◽  
Fazal Manan ◽  
Prabin Bajgain ◽  
Matthew Martin ◽  
Tamas Szinyei ◽  
...  
Keyword(s):  
Association Mapping ◽  
Spring Wheat ◽  
Genetic Architecture ◽  
Mapping Population ◽  
Quality Traits ◽  
Nested Association Mapping ◽  
Nested Association Mapping Population ◽  
Association Mapping Population

scholarly journals Genetic Architecture of Nitrogen-Deficiency Tolerance in Wheat Seedlings Based on a Nested Association Mapping (NAM) Population

2018 ◽  
Vol 9 ◽  
Author(s):  
Deqiang Ren ◽  
Xiaojian Fang ◽  
Peng Jiang ◽  
Guangxu Zhang ◽  
Junmei Hu ◽  
...  
Keyword(s):  
Association Mapping ◽  
Genetic Architecture ◽  
Nitrogen Deficiency ◽  
Wheat Seedlings ◽  
Nested Association Mapping

scholarly journals Oxidative Stress and Chilling Tolerance in Tomato Seedlings

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 645b-645
Author(s):  
Kanogwan Kerdnaimongkol ◽  
Anju Bhatia ◽  
Robert J. Joly ◽  
William R. Woodson
Keyword(s):  
Oxidative Stress ◽  
Hydrogen Peroxide ◽  
Superoxide Dismutase ◽  
Diurnal Variation ◽  
Chilling Stress ◽  
Chilling Injury ◽  
Chilling Tolerance ◽  
Light Period ◽  
Tomato Seedlings ◽  
Chilling Sensitivity

Diurnal variation in the chilling sensitivity of tomato seedlings was examined. Sensitivity to chilling in tomato seedlings is a response to light and not under the control of a circadian rhythm. Chilling sensitivity is highest in seedlings chilled at the end of the dark period, and these seedlings become more resistant to chilling injury upon exposure to the light. Diurnal variation in chilling sensitivity was associated with changes in catalase and superoxide dismutase activities. The results show an increase in catalase and superoxide dismutase activities at the end of the light period. The recovery of the net photosynthesis rate following chilling was faster in seedlings chilled at the end of the light period. It is suggested that an increase in catalase and superoxide dismutase activities at the end of light period before the chilling plays a role in the resistance to chilling stress in tomato seedlings. Forty-eight hours of 14°C acclimation or hydrogen peroxide pretreatment conferred chilling tolerance to tomato seedlings and were correlated with elevated catalase activity. Acclimated seedlings still exhibited diurnal variation in chilling sensitivity while hydrogen peroxide treated seedlings showed little evidence of a diurnal variation in chilling sensitivity. Transgenic tomato plants expressing an antisense catalase gene were generated. A several-fold decrease in total catalase has been detected in the leaf extracts of transformants. Preliminary analysis of these plants indicated that modification of reactive oxygen species scavenging in plant system can lead to change in oxidative stress tolerance.

scholarly journals Dissecting adaptive traits with nested association mapping: Genetic architecture of inflorescence morphology in sorghum

2019 ◽  
Author(s):  
Marcus O. Olatoye ◽  
Sandeep R. Marla ◽  
Zhenbin Hu ◽  
Sophie Bouchet ◽  
Ramasamy Perumal ◽  
...  
Keyword(s):  
Association Mapping ◽  
Genetic Architecture ◽  
Regulatory Networks ◽  
Allelic Variation ◽  
Recombinant Inbred Lines ◽  
Branch Length ◽  
Lower Branch ◽  
Nested Association Mapping ◽  
Inflorescence Morphology ◽  
Significant Enrichment

ABSTRACTIn the cereal crop sorghum (Sorghum bicolor) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. Here we characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter). Trait correlations suggest that lower and upper branch length are under largely independent genetic control, while lower branch length and rachis diameter are pleiotropic. Joint linkage and genome-wide association mapping revealed an oligogenic architecture with 1–22 QTL per trait, each explaining 0.1%–5.0% of variation across the entire NAM population. Overall, there is a significant enrichment (2.4-fold) of QTL colocalizing with homologs of grass inflorescence genes, notably with orthologs of maize (Ramosa2) and rice (Aberrant Panicle Organization1, TAWAWA1) inflorescence regulators. In global georeferenced germplasm, allelic variation at the major inflorescence morphology QTL is significantly associated with precipitation gradients, consistent with a role for these QTL in adaptation to agroclimatic zones. The findings suggest that global inflorescence diversity in sorghum is largely controlled by oligogenic, epistatic, and pleiotropic variation in ancestral regulatory networks. This genotype-phenotype trait dissection in global germplasm provides a basis for genomics-enabled breeding of locally-adapted inflorescence morphology.

scholarly journals Modelling the genetic architecture of flowering time control in barley through nested association mapping

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Andreas Maurer ◽  
Vera Draba ◽  
Yong Jiang ◽  
Florian Schnaithmann ◽  
Rajiv Sharma ◽  
...  
Keyword(s):  
Association Mapping ◽  
Flowering Time ◽  
Genetic Architecture ◽  
Nested Association Mapping ◽  
Time Control ◽  
Flowering Time Control

scholarly journals Genetic Architecture of a Rice Nested Association Mapping Population

2017 ◽  
Vol 7 (6) ◽  
pp. 1913-1926 ◽  
Author(s):  
Christopher A. Fragoso ◽  
Maria Moreno ◽  
Zuoheng Wang ◽  
Christopher Heffelfinger ◽  
Lady J. Arbelaez ◽  
...  
Keyword(s):  
Association Mapping ◽  
Genetic Architecture ◽  
Mapping Population ◽  
Nested Association Mapping ◽  
Nested Association Mapping Population ◽  
Association Mapping Population

scholarly journals Dissecting Adaptive Traits with Nested Association Mapping: Genetic Architecture of Inflorescence Morphology in Sorghum

2020 ◽  
Vol 10 (5) ◽  
pp. 1785-1796
Author(s):  
Marcus O. Olatoye ◽  
Sandeep R. Marla ◽  
Zhenbin Hu ◽  
Sophie Bouchet ◽  
Ramasamy Perumal ◽  
...  
Keyword(s):  
Association Mapping ◽  
Genetic Architecture ◽  
Regulatory Networks ◽  
Linear Models ◽  
Allelic Variation ◽  
Recombinant Inbred Lines ◽  
Branch Length ◽  
Lower Branch ◽  
Nested Association Mapping ◽  
Inflorescence Morphology

In the cereal crop sorghum (Sorghum bicolor) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. We characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter). Trait correlations suggest that lower and upper branch length are under somewhat independent control, while lower branch length and rachis diameter are highly pleiotropic. Joint linkage and genome-wide association mapping revealed an oligogenic architecture with 1–22 QTL per trait, each explaining 0.1–5.0% of variation across the entire NAM population. There is a significant enrichment (2.twofold) of QTL colocalizing with grass inflorescence gene homologs, notably with orthologs of maize Ramosa2 and rice Aberrant Panicle Organization1 and TAWAWA1. Still, many QTL do not colocalize with inflorescence gene homologs. In global georeferenced germplasm, allelic variation at the major inflorescence QTL is geographically patterned but only weakly associated with the gradient of annual precipitation. Comparison of NAM with diversity panel association suggests that naive association models may capture some true associations not identified by mixed linear models. Overall, the findings suggest that global inflorescence diversity in sorghum is largely controlled by oligogenic, epistatic, and pleiotropic variation in ancestral regulatory networks. The findings also provide a basis for genomics-enabled breeding of locally-adapted inflorescence morphology.

scholarly journals A Nested Association Mapping Panel in Arabidopsis thaliana for Mapping and Characterizing Genetic Architecture

2020 ◽  
Vol 10 (10) ◽  
pp. 3701-3708 ◽  
Author(s):  
Marcus T. Brock ◽  
Matthew J. Rubin ◽  
Dean DellaPenna ◽  
Cynthia Weinig
Keyword(s):  
Arabidopsis Thaliana ◽  
Association Mapping ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Recurrent Parent ◽  
Linkage Maps ◽  
Nucleotide Polymorphisms ◽  
Nested Association Mapping ◽  
Mapping Panel ◽  
Genotype By Sequencing

Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred line populations (RILs) of Arabidopsis thaliana, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in individual RIL populations indicate that our GBS markers have improved power to detect small effect QTL and enhanced resolution of QTL support intervals in comparison to original linkage maps. Using these robust linkage maps, we imputed a common set of publicly available parental SNPs into each RIL linkage map, generating overlapping markers across all populations. Though ultimately depending on allele frequencies at causal loci, simulations of the NAM panel suggest that surveying between 4 to 7 of the 14 RIL populations provides high resolution of the genetic architecture of complex traits, relative to a single mapping population.

scholarly journals A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations

2021 ◽  
Vol 11 ◽  
Author(s):  
Suhong Bu ◽  
Weiren Wu ◽  
Yuan-Ming Zhang
Keyword(s):  
Association Mapping ◽  
Linkage Mapping ◽  
Complex Traits ◽  
Association Studies ◽  
New Method ◽  
Genome Wide Association Studies ◽  
Single Family ◽  
Association Model ◽  
Model Framework ◽  
Nested Association Mapping

Nested association mapping (NAM) has been an invaluable approach for plant genetics community and can dissect the genetic architecture of complex traits. As the most popular NAM analysis strategy, joint multifamily mapping can combine all information from diverse genetic backgrounds and increase population size. However, it is influenced by the genetic heterogeneity of quantitative trait locus (QTL) across various subpopulations. Multi-locus association mapping has been proven to be powerful in many cases of QTL mapping and genome-wide association studies. Therefore, we developed a multi-locus association model of multiple families in the NAM population, which could discriminate the effects of QTLs in all subpopulations. A series of simulations with a real maize NAM genomic data were implemented. The results demonstrated that the new method improves the statistical power in QTL detection and the accuracy in QTL effect estimation. The new approach, along with single-family linkage mapping, was used to identify QTLs for three flowering time traits in the maize NAM population. As a result, most QTLs detected in single family linkage mapping were identified by the new method. In addition, the new method also mapped some new QTLs with small effects, although their functions need to be identified in the future.

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