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

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 - logP > 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.

Variation in Root and Shoot Growth in Response to Reduced Nitrogen

“…Highly correlative traits can be measured interchangeably to save time and effort. A previous experiment has shown a correlation of r = 0.8 between root dry matter and root length in wheat seedlings of 200 historical wheat accessions [30], which indicates that root dry matter can be used as indirect estimation of total root length. Root architecture refers to the spatial configuration of the root system within the soil and is characterized by vertical and horizontal extending and proliferation, usually by three-dimensional presentation and quantification of traits such as length and angles.…”

“…They found a~35-fold difference in root dry matter from 0.22 to 7.6 g. These results appear to verify the wide genetic diversity of root dry matter in spring wheat. Similarly, in two-week seedlings, Beyer et al [30] reported a range of 6-20 mg for root dry matter in 215 historical lines evaluated in a paper roll-supported hydroponic system. While there was genetic variation present in the seedling roots, it was smaller to the range observed at maturity, suggesting that the genetic potential for root traits was realized later in the development.…”

Ancient wheat varieties have a higher ability to interact with plant growth‐promoting rhizobacteria

“…Crop breeding has resulted in the development of thousands of genotypes, which show contrasted agro-morphological and metabolic features (Berry, Kendall, Rutterford, Orford, & Griffiths, 2015;Beyer, Daba, Tyagi, Bockelman, Brown-Guedira, IWGSC, & Mohammadi, 2019;Gotti et al, 2018;Shaposhnikov et al, 2016;Siddique, Belford, & Tennant, 1990;York et al, 2015;Zhang et al, 2013), as well as contrasted stress response patterns (Esmail, Eldessouky, Mahfouz, & El-Demardash, 2016;Khakwani, Dennett, & Munir, 2011;Ramshini, Mirzazadeh, Moghaddam, & Amiri, 2016). Crop genotypes can also differ in their ability to recruit soil bacteria (Bouffaud et al, 2012), induce gene expression in rhizobacteria (Notz et al, 2001;Vacheron et al, 2016), and respond to PGPR inoculation (Sasaki et al, 2010;Vacheron et al, 2016).…”

Genetic architecture of polyphenol oxidase activity in wheat flour by genome‐wide association study

“…To find the candidate genes linked to significant markers, we used the IWGSC RefSeq v1.0 database to retrieve high‐confidence annotated genes located ±250 kb proximal to each MTA, as described by Beyer et al. (2019). Survey sequences to which the SNPs were best hits were screened in a BLASTN (Nucleotide Basic Local Alignment Search Tool) search against the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov/) and European Nucleotide Archive (ENA) (http://www.ebi.ac.uk/ena) to confirm the gene annotations by evaluating orthologous genes in related species, such as Triticum urartu Thumanian ex Gandilyan, Aegilops tauschii Coss., and Hordeum vulgare L. The BLAST hits were filtered with an e value threshold of 10 −5 and sequence similarities >75%.…”