EiB marker example

Wheat Durable Disease Resistance Gene Complex

Gene Name: Lr34/Yr18/Pm38

Chromosome: 7DS

Linkage: Co-segregating with Lr34/Yr18/Pm38

Marker Haplotype Rating:  5

Assay type: Co-dominant

Assay Reproducibility: Very High

Background:

A large number of genes that confer race specific form of resistance to leaf rust, stripe (yellow) rust and powdery mildew have been identified in wheat.  In addition, a small number of genes that confer partial or durable resistance to these have also been identified (Sing & Huerta-Espino, 2003).  Due to the rapidly evolving nature of the pathogens, the resistance conferred by race specific genes may be short term in nature compared to the resistance conferred by genes with partial/durable resistance.  Availability of molecular markers would enable wheat breeders deploy the durable resistance genes in combination with race specific genes making wheat cultivars more sustainable under high disease pressure.   

Genetic Information

The gene complex that confer durable resistance to leaf rust (Lr34), yellow rust (Yr18), and powdery mildew (Pm38), located on the short arm of wheat chromosome 7D (7DS), has been recently characterized with functional co-dominant SNP markers (Krattinger et al., 2009: Lagudah et al., 2009). The broad-spectrum resistance complex of Lr34/Yr18/Pm38 has been reported to be controlled by a single gene which encodes a putative ATP-binding cassette transporter (Krattinger et al., 2009).  The KASP assay interrogates a three-base deletion (TCC) in exon 11 that is associated with the Lr34/Yr18/Pm38 gene complex (Krattinger et al., 2009; Lagudah et al., 2009).

SNP Name: Lr34_TCCIND

SNP ID: CIMwMAS0001

Intertek SNP ID: snpTA0023

KASP Primer

Sequence

Haplotype

Phenotype

Controls

FAM

GGTATGCCATTTAACATAATCATGAA

Ins

Lr34/Yr18/Pm38-

Susceptible

Pavon76*, Pastor*

VIC

GGTATGCCATTTAACATAATCATGAT

-:-

Lr34/Yr18/Pm38+

Durable Resistance

Parula*, Tonichi*

Common

TACTATATGGGAGCATTATTTTTTTCC

 

 

 

* CIMMYT Spring wheat cultivars

Consensus sequence:

TACTATATGGGAGCATTATTTTTTTCCATC[TTC]ATGATTATGTTAAATGGCATACCAG

Supporting figures:

The genomic region containing Lr34/Yr18/Pm38 gene complex is indicated in Fig 1 and Fig 2.

SNP viewer image of the assay with the two main genotypic allele classes – FAM (blue), VIC (red) and the heterozygotes (green) is in Fig. 3.

---------------------------------------------------------------------------------------------------------

Wheat Fusarium Head Blight Resistance

Gene Name: Fhb1

Chromosome: 3BS

Linkage: Tight linkage with Fhb1

Marker Haplotype Rating:  4

Assay type: Co-dominant

Assay Reproducibility: Very High

Background:

Fusarium head blight (FHB) caused mainly by Fusarium graminarum is an important disease that affects wheat in warm and humid wheat growing regions that reduces grain yield and quality resulting in mycotoxin accumulation in the grain. Mycotoxins such as deoxynivalenol (DON), accumulated in grains affected by F. granminarum, can be harmful to human and animal health. Resistance to FHB is quantitatively inherited and different methods of resistance such as a) Resistance to initial infection (Type I) and b) Resistance to spread of infection (Type II) have been described. Using markers associated with large effect FHB QTLs can be used to improve FHB resistance in bread and durum wheats (Zhou et al., 2002; Miedaner et al., 2017).

Genetic Information: 

The Chinese variety Sumai3 and its derivatives have demonstrated a high level of Type II resistance to FHB that has been deployed as a source of FHB resistance in numerous wheat breeding programs (Wilcoxson et al., 1992). A QTL with large effects, Fhb1, identified in Sumai 3 and its derivatives has been mapped to the short arm of wheat chromosome 3 (3BS). Although there are differences in the effects associated with Fhb1 based on genetic backgrounds, Fhb1 associated QTL can explain up to 50% of the phenotypic variation for Type II FHB resistance that also resulted in low DON accumulation in infected kernels (Bai et al., 1999; Zhou et al., 2002). 

SNP markers have been developed that can be used to identify Sumai 3 based Fhb1 resistance QTL (Bernado et al., 2012).

SNP Name: snp3BS-8

SNP ID: wMAS000008

Intertek SNP ID: snpTA0037

KASP Primers

Sequence

Haplotype

Phenotype

Controls

FAM

CACATGCATTTGCAAGGTTGTTATCC

C

Fhb1- (susceptible)

Chinese Spring, Pastor*

VIC

CACATGCATTTGCAAGGTTGTTATCG

G

Fhb1+ (partial resistance)

Sumai 3, Ning 7840

Common

CAAAGCAGCCTTAGGTCAATAGTTTGAAA

 

 

 

* CIMMYT origin

Consensus sequence: AACTCTGAAACAAAGCAGCCTTAGGTCAATAGTTTGAAATTTTCATATCAACACAA[G/C]GATAACAACCTTGCA

AATGCATGTGCATTATAATGGCAGACTACAATCTTGGGCAACTAAAATTGAGTCGACTCGCTTGTCCCGGTGG

GCCGATGGTGACAGCTCTCTTGACCCAATTTTCTTATGAAGCCAACCCAGAAGACCCATCGGCCTTGAAATTA

TGGGCTGGACCAATGTCCCAATGGGTAACATCGGCCCATTCCCATCGGGACTCTCACACGATCTAGCTTCCA

CCACCTCCCTCATATGCCACTTTGGACAGAAACGTGAAGAACCGAAGGAAACCAAGATTTCAATTGTTCAGTT

TTGGATGAAAAATTGAAGAACCGTANGTAACTTTTTTTGTAATTATTGATGAACCTTTTGTCCTCTCTTGGAAGT

TGGAACCTTTTCTATTTAGGGTGATAACTGGGGCACCTCTCTATGTATGGAATTGATCAACATGAATTTTTTATAT

ATCTGGATTGAACTTCTCACCTCTGTAC

Supporting figures:

The genomic region representing Fhb1 QTL is indicated in Fig 1.

SNP viewer image of the KASP assay is given in Fig. 2.

------------------------------------------------------------------------------------------------------------------------------------------------------

Wheat Gene Cluster with Multiple Rust Resistance Genes

Gene Name:  Lr37-Yr17-Sr38

Chromosome: 2AS

Linkage: Co-segregating with Lr37/Yr17/Sr38

Marker Haplotype Rating:  5

Assay type: Co-dominant

Assay Reproducibility: High

Background:

The gene cluster known as VPM1 containing Yr17, Lr37 and Sr39 rust resistance genes that confer resistances to leaf rust, yellow (stripe) rust and stem rust respectively has been introgressed from Triticum ventricosum into cultivated wheat (Seah et al., 2000).  The introgressed chromosome segment is located in the T. ventricosum translocation known as 2NS/2AS. Although rust races that have developed virulence to Yr17 and Lr37 have been reported (Robert et al., 1999), this gene cluster is known to provide resistance to a wide range of races and is useful in breeding in combination with other rust resistance genes (Helguera et al., 2003).

Genetic Information: 

The gene complex present in the translocated chromosome segment from Triticum ventricosum into the short arm of wheat chromosome 2A (2AS) is inherited as a block of genes with little chance of recombination.  Wheat breeders would be able to deploy the gene cluster into multiple wheat backgrounds using the SNP markers presented.

SNP Name:  VPM_SNP

SNP ID:  CIMwMAS0004

Intertek SNP ID:  snpTA0025

KASP Primers

Sequence

Haplotype

Phenotype

Controls

FAM

CGCCGTTCCGAAYACGAGA

T

Lr37/Yr17/Sr38+

(resistant)

Milan, Reedling

 

VIC

CGCCGTTCCGAAYACGAGG

C

Lr37/Yr17/Sr38-

(susceptible)

Parula*, Pavon76*

Common

CCCTGGCTTGCACCTTCGACAA

 

 

 

 

 

 

 

 

* CIMMYT origin

Note: Some false positives among CIMMYT synthetic wheats have been observed.

Consensus Sequence: GGTCGCCCTGGCTTGCACCTTCGACAAGGGGCTACTGACCAARGC[C/T]CTCGTRTTCGGAACGGCGAGAA

GGTTTGCAGGACCAGGAAGRAGATAGGAACCAAACATCNNNNNNNNNNNNNNNATGCCAYGCRCATTYRTT

CCGATGCACAACCGAGCGAC

Supporting figures:

The genomic region containing the T. ventricosum chromosome segment in 2NS/2AS translocation is indicated in Fig 1.

SNP viewer image of the assay is in Fig. 2.