Genome-wide superior alleles, haplotypes and candidate genes associated with tolerance on sodic-dispersive soils in wheat (Triticum aestivum L.)

Authors

Darshan L. Sharma, Department of Primary Industries and Regional DevelopmentFollow
Roopali Bhoite, Department of Primary Industries and Regional DevelopmentFollow
Karyn Reeves, Department of Primary Industries and Regional DevelopmentFollow
Kerrie Forrest, Agriculture Victoria
Rosemary Smith, Department of Primary Industries and Regional DevelopmentFollow
Mirza Dowla, Department of Primary Industries and Regional Development

Document Type

Article

Publication Date

1-5-2022

Journal Title

Theoretical and Applied Genetics

ISSN

Print: 0040-5752; Electronic: 1432-2242

Disciplines

Agricultural Science | Agriculture | Agronomy and Crop Sciences | Plant Breeding and Genetics

Abstract

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.

Recommended Citation

Sharma, D L, Bhoite, R, Reeves, K, Forrest, K, Smith, R, and Dowla, M. (2022), Genome-wide superior alleles, haplotypes and candidate genes associated with tolerance on sodic-dispersive soils in wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 135, 1113-1128.
https://library.dpird.wa.gov.au/fc_researchart/17