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

Authors: BEYER, SAVANNAH - Purdue University; DABA, SINTAYEHU - Purdue University; TYAGI, PRIYANKA - North Carolina State University; Bockelman, Harold; Brown-Guedira, Gina; MOHAMMADI, MOHSEN - Purdue University

Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/3/2018
Publication Date: 1/2/2019
Citation: Beyer, S., Daba, S., Tyagi, P., Bockelman, H.E., Brown Guedira, G.L., Mohammadi, M. 2019. Loci and candidate genes controlling root traits in wheat seedlings—a wheat root GWAS. Functional and Integrative Genomics. 19:91-107.

Interpretive Summary: Nearly all trait mapping and breeding efforts in wheat during the last century have focused on discovery and improvement of above-ground traits such as yield and end-use quality. Roots, the hidden half of the plant, received almost no direct consideration for selection and breeding; however, it is possible that indirect selection for traits such as nutrient uptake and drought tolerance has occurred. Given the importance of roots to plant growth and development, selection and breeding for favorable root traits represents a viable method to tap into an untouched pool of potential for wheat improvement. Having DNA markers linked to root traits can improve the efficiency of selection. 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. 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. DNA sequencing was used to identify single-nucleotide polymorphism (SNP) markers. A total of 20,881 polymorphic sites were used to perform association mapping. In total, we identified 7 markers associated with seminal axis root length (SAR), 24 markers for branching (BR), four for total seminal root length (TSR), eight for root dry matter (RDM), and 20 for root diameter (RD). We evaluated the effects of height-reducing Rht alleles on root traits and found presence of the Rht-B1 dwarfing allele decreased RDM, while presence of the Rht-D1 dwarfing allele increased TSR and decreased RD.

Technical 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 identified include chalcone synthase, aquaporin, and chymotrypsin inhibitor for SAR, MYB transcription factor and peroxidase for BR, zinc fingers and amino acid transporters for RDM, and cinnamoyl-CoA reductase for RD. We evaluated the effects of height-reducing Rht alleles and the 1B/1R translocation event on root traits and found presence of the Rht-B1b allele decreased RDM, while presence of the Rht-D1b allele increased TSR and decreased RD.