Abstract
Key messageThe pleiotropic SNPs/haplotypes, overlapping genes (metal ion binding, photosynthesis), and homozygous/biallelic SNPs and transcription factors (HTH myb-type and BHLH) hold great potential for improving wheat yield potential on sodic-dispersive soils.Sodic-dispersive soils have multiple subsoil constraints including poor soil structure, alkaline pH and subsoil toxic elemental ion concentration, affecting growth and development in wheat. Tolerance is required at all developmental stages to enhance wheat yield potential on such soils. An in-depth investigation of genome-wide associations was conducted using a field phenotypic data of 206 diverse Focused Identification of Germplasm Strategy (FIGS) wheat lines for two consecutive years from different sodic and non-sodic plots and the exome targeted genotyping by sequencing (tGBS) assay. A total of 39 quantitative trait SNPs (QTSs), including 18 haplotypes were identified on chromosome 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 5A, 5D, 6B, 7A, 7B, 7D for yield and yield-components tolerance. Among these, three QTSs had common associations for multiple traits, indicating pleiotropism and four QTSs had close associations for multiple traits, within 32.38 Mb. The overlapping metal ion binding (Mn, Ca, Zn and Al) and photosynthesis genes and transcription factors (PHD-, Dof-, HTH myb-, BHLH-, PDZ_6-domain) identified are known to be highly regulated during germination, maximum stem elongation, anthesis, and grain development stages. The homozygous/biallelic SNPs having allele frequency above 30% were identified for yield and crop establishment/plants m−2. These SNPs correspond to HTH myb-type and BHLH transcription factors, brassinosteroid signalling pathway, kinase activity, ATP and chitin binding activity. These resources are valuable in haplotype-based breeding and genome editing to improve yield potential on sodic-dispersive soils.
Highlights
Wheat is one of the most important cereals in human diets and plays a significant role in feeding global population, which is expected to increase by 30% (United Nations 2019) in 2050
Dispersion index was 12 times higher in sodic compared to nonsodic site, and pH was above 9.0 at 30–70 cm depth
Within-year variance comparison for plants m −2 (PM) and heads m −2 (HM) showed opposite trends in both years albeit in opposite order; the variance of PM was less than HM on non-sodic than sodic site in 2018 and the vice versa in 2019
Summary
Wheat is one of the most important cereals in human diets and plays a significant role in feeding global population, which is expected to increase by 30% (United Nations 2019) in 2050. The dense structure causes poor movement of air and water infiltration, resulting in low oxygen availability and waterlogging, respectively. These soils have neutral to strong alkalinity (pH 7–12), high content of sodic clay (18%) resulting in high dispersion index Sodic soils severely constrain crop production in Australia and worldwide and ESP as low as 2 can cause notable yield reduction (Sharma 2017). Yield reductions of 70% under sodicity have been reported (Rengasamy 2002) These scenarios highlight the significant loss to agricultural production and the requirement of wheat genetic enhancements to improve yield potential on sodicdispersive soils
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
