GWAS, KASP-SNP markers and haplotype-based pre-breeding for improving yield potential on sodic-dispersive soils in wheat (Triticum aestivum L.)

Document Type

Conference Proceeding

Publication Date

28-8-2022

Conference Title

Wheat Breeding Assembly 2022

Place of Publication

Narrabri, NSW

Disciplines

Agricultural Science | Agronomy and Crop Sciences

Abstract

Sodic-dispersive soils have multiple subsoil constraints including poor soil structure, high pH ( > 7), salinity, high subsoil toxic elemental ion concentration (boron, aluminium), and water-logging, affecting growth and development in wheat. Dispersive soils are common in the Australian agricultural landscapes and wheat growing regions around the world. Recent estimates show about 8-10 % soils in Western Australian grain belt to be dispersive leading to heavy losses in production and grower income. 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 two-year field phenotypic data of 206 diverse. Focused Identification of Germplasm Strategy (FIGS) wheat lines 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 to soil sodicity. 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 were identified for yield and crop establishment/plants m-2. These SNPs correspond to HTH myb-type and BHLH transcription factors, brassinosteroid signaling pathway, kinase activity, ATP, and chitin binding activity (Published, 10.1007/s00122-021-04021-8). Further, the variants (SNPs and InDel) identified are functionally annotated and characterized using snpEff pipeline. The characterized variants are analyzed for their effects on protein based on type of impact (high, low, moderate and modifier) using the wheat genome binary database. The functional SNPs having higher phenotypic variation and allele frequency greater than five percent is now being converted to KASP-SNP markers and the rapid KASP-SNP assay will be validated in FIGS and double haploid populations. These resources are valuable in haplotype-based breeding and genome editing to improve yield potential on sodic-dispersive soils.

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