Shared Genetic Control of Root System Architecture between
| Autor: | Zihao, Zheng, Stefan, Hey, Talukder, Jubery, Huyu, Liu, Yu, Yang, Lisa, Coffey, Chenyong, Miao, Brandi, Sigmon, James C, Schnable, Frank, Hochholdinger, Baskar, Ganapathysubramanian, Patrick S, Schnable |
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| Rok vydání: | 2019 |
| Předmět: |
Genotype
Quantitative Trait Loci food and beverages Plant Roots Polymorphism Single Nucleotide Zea mays Phenotype Biological Variation Population Databases Genetic Image Processing Computer-Assisted Gene Regulatory Networks Genetic Association Studies Software Sorghum Research Articles Genome-Wide Association Study |
| Zdroj: | Plant physiology. 182(2) |
| ISSN: | 1532-2548 |
| Popis: | Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed Core Root Excavation using Compressed-air (CREAMD), a high-throughput pipeline for the cleaning of field-grown roots, and Core Root Feature Extraction (COFE), a semiautomated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize (Zea mays) and sorghum (Sorghum bicolor), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from >3,300 maize roots and >1,470 sorghum roots. Single nucleotide polymorphism (SNP)-based GWAS identified 87 TAS (trait-associated SNPs) in maize, representing 77 genes and 115 TAS in sorghum. An additional 62 RSA-associated maize genes were identified via expression read depth GWAS. Among the 139 maize RSA-associated genes (or their homologs), 22 (16%) are known to affect RSA in maize or other species. In addition, 26 RSA-associated genes are coregulated with genes previously shown to affect RSA and 51 (37% of RSA-associated genes) are themselves transe–quantitative trait locus for another RSA-associated gene. Finally, the finding that RSA-associated genes from maize and sorghum included seven pairs of syntenic genes demonstrates the conservation of regulation of morphology across taxa. |
| Databáze: | OpenAIRE |
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