Loci and candidate genes controlling root traits in wheat seedlings-a wheat root GWAS

Functional & Integrative Genomics
Savannah BeyerMohsen Mohammadi

Abstract

Two hundred one hexaploid wheat accessions, representing 200 years of selection and breeding history, were sampled from the National Small Grains Collection in Aberdeen, ID, and evaluated for five root traits at the seedling stage. A paper roll-supported hydroponic system was used for seedling growth. Replicated roots samples were analyzed by WinRHIZO. We observed accessions with nearly no branching and accessions with up to 132 cm of branching. Total seminal root length ranged from 70 to 248 cm, a 3.5-fold difference. Next-generation sequencing was used to produce single-nucleotide polymorphism (SNP) markers and genomic libraries that were aligned to the wheat reference genome IWGSCv1 and were called single-nucleotide polymorphism (SNP) markers. After filtering and imputation, a total of 20,881 polymorphic sites were used to perform association mapping in TASSEL. Gene annotations were conducted for identified marker-trait associations (MTAs) with - log10P > 3.5 (p value < 0.003). In total, we identified 63 MTAs with seven for seminal axis root length (SAR), 24 for branching (BR), four for total seminal root length (TSR), eight for root dry matter (RDM), and 20 for root diameter (RD). Putative proteins of interest that we ident...Continue Reading

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Citations

Oct 4, 2019·Genome Génome / Conseil National De Recherches Canada·Ting LiXiu-Jin Lan
Sep 12, 2019·Plant, Cell & Environment·Jordan ValenteClaire Prigent-Combaret
Jan 21, 2020·Journal of Experimental Botany·Agnieszka Deja-MuylleTom Beeckman
Jun 19, 2020·International Journal of Molecular Sciences·Alicja Macko-PodgórniDariusz Grzebelus
Jan 26, 2020·Plants·Seth Tolley, Mohsen Mohammadi
Jun 30, 2019·International Journal of Molecular Sciences·Ahmed SallamAndreas Börner
Mar 17, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jingjing JinJun Ma

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Methods Mentioned

BETA
transgenic
genotyping
PCR
allelic
Assay
Hi-Seq
PCA
gene knockout

Software Mentioned

TASSEL ( Trait Analysis by aSSociation , Evolution , and Linka...
qqman
TASSEL
R Development Core Team
STRUCTURE
Ensembl
lme4
WinRHIZO
R

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