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 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 TeoNAM: a nested association mapping population for domestication and agronomic trait analysis in maize

2019 ◽  
Author(s):  
Qiuyue Chen ◽  
Chin Jian Yang ◽  
Alessandra M. York ◽  
Wei Xue ◽  
Lora L. Daskalska ◽  
...  
Keyword(s):  
Association Mapping ◽  
Complex Traits ◽  
Agronomic Traits ◽  
Mapping Population ◽  
Allelic Variation ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Nested Association Mapping ◽  
Nested Association Mapping Population ◽  
Association Mapping Population

AbstractRecombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping population (TeoNAM), derived from crossing five teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTLs from JLM were identified with many of these mapping to known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in teosinte and maize. We detected multiple QTLs for flowering time and other traits for which the teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.

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 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 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.

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