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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Research Project #432487

Research Project: Dissect the Sea Wheatgrass Genome and Transfer Biotic Stress Resistance and Abiotic Stress Tolerance into Wheat

Location: Cereal Crops Research

Project Number: 3060-21000-038-07-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Mar 15, 2017
End Date: Mar 14, 2020

Objective:
1) Develop a draft sea wheatgrass (SWG, Thinopyrum junceiforme) genome assembly for genome-specific markers; 2) Construct a chromosome arm introgression library to dissect the SWG genome, and; 3) Transfer biotic stress resistance and abiotic stress tolerance from SWG into wheat via chromosome engineering.

Approach:
To achieve the proposed objectives, the project team will use the following approaches. For developing a draft genome assembly of sea wheatgrass (SWG, Thinopyrum junceiforme) in objective 1, we will sequence SWG accession PI 414667, the parent of the wheat-SWG amphiploids. To do so, we will construct four sequencing libraries, which will be pooled and sequenced using Illumina HiSeq4000. The clean reads will be used for a genome assembly with adequate quality to establish syntenic relationship between SWG and wheat chromosomes. For developing SWG-specific markers, the single copy genes will be sorted out and aligned with wheat homoeologous genes for detection of genic single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) using the SOAPindel program. These SNPs and indels will be targeted for development of PCR-based SNP markers using a newly developed STARP (thermal asymmetric reverse PCR) technique. For objective 2, we will develop a set of 14 J1- and J2-genome chromosome addition lines using backcross method facilitated with molecular marker and GISH analysis. We will then use the monosomic approach to induce compensating translocations involving the known alien chromosomes in the addition lines. The STARP marker and GISH will be further used to confirm compensating centromeric translocations (Robertsonian). For objective 3, a set of 28 Robertsonian translocations developed in objective 2 will be evaluated for resistance to WL and stem rust resistance. The resistant lines will be recurrently backcrossed to the ph1b mutant. The ph1bph1b homozygotes will be selected by use ph1b diagnostic markers and be subjected to waterlogging, solid stem, stem rust and wheat streak mosaic virus assay subsequently. The double positives will be backcrossed to Chinese Spring and elite wheat cultivars. The progenies will be genotyped by SWG- and wheat-specific markers of the cognate homoeologous group to screen for SWG/wheat recombinants, which will be tested for WL and stem rust resistance using the wheat parents as controls. The size and location of the SWG chromosome segments in the new recombinants will determine using GISH analysis.