Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-12-30

AUTHORS

Rohit Mago, Linda Tabe, Sonia Vautrin, Hana Šimková, Marie Kubaláková, Narayana Upadhyaya, Hélène Berges, Xiuying Kong, James Breen, Jaroslav Doležel, Rudi Appels, Jeffrey G Ellis, Wolfgang Spielmeyer

ABSTRACT

BackgroundThe adult plant stem rust resistance gene Sr2 was introgressed into hexaploid wheat cultivar (cv) Marquis from tetraploid emmer wheat cv Yaroslav, to generate stem rust resistant cv Hope in the 1920s. Subsequently, Sr2 has been widely deployed and has provided durable partial resistance to all known races of Puccinia graminis f. sp. tritici. This report describes the physical map of the Sr2-carrying region on the short arm of chromosome 3B of cv Hope and compares the Hope haplotype with non-Sr2 wheat cv Chinese Spring.ResultsSr2 was located to a region of 867 kb on chromosome 3B in Hope, which corresponded to a region of 567 kb in Chinese Spring. The Hope Sr2 region carried 34 putative genes but only 17 were annotated in the comparable region of Chinese Spring. The two haplotypes differed by extensive DNA sequence polymorphisms between flanking markers as well as by a major insertion/deletion event including ten Germin-Like Protein (GLP) genes in Hope that were absent in Chinese Spring. Haplotype analysis of a limited number of wheat genotypes of interest showed that all wheat genotypes carrying Sr2 possessed the GLP cluster; while, of those lacking Sr2, some, including Marquis, possessed the cluster, while some lacked it. Thus, this region represents a common presence-absence polymorphism in wheat, with presence of the cluster not correlated with presence of Sr2. Comparison of Hope and Marquis GLP genes on 3BS found no polymorphisms in the coding regions of the ten genes but several SNPs in the shared promoter of one divergently transcribed GLP gene pair and a single SNP downstream of the transcribed region of a second GLP.ConclusionPhysical mapping and sequence comparison showed major haplotype divergence at the Sr2 locus between Hope and Chinese Spring. Candidate genes within the Sr2 region of Hope are being evaluated for the ability to confer stem rust resistance. Based on the detailed mapping and sequencing of the locus, we predict that Sr2 does not belong to the NB-LRR gene family and is not related to previously cloned, race non-specific rust resistance genes Lr34 and Yr36. More... »

PAGES

379

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12870-014-0379-z

DOI

http://dx.doi.org/10.1186/s12870-014-0379-z

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1032751380

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25547135


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26 schema:description BackgroundThe adult plant stem rust resistance gene Sr2 was introgressed into hexaploid wheat cultivar (cv) Marquis from tetraploid emmer wheat cv Yaroslav, to generate stem rust resistant cv Hope in the 1920s. Subsequently, Sr2 has been widely deployed and has provided durable partial resistance to all known races of Puccinia graminis f. sp. tritici. This report describes the physical map of the Sr2-carrying region on the short arm of chromosome 3B of cv Hope and compares the Hope haplotype with non-Sr2 wheat cv Chinese Spring.ResultsSr2 was located to a region of 867 kb on chromosome 3B in Hope, which corresponded to a region of 567 kb in Chinese Spring. The Hope Sr2 region carried 34 putative genes but only 17 were annotated in the comparable region of Chinese Spring. The two haplotypes differed by extensive DNA sequence polymorphisms between flanking markers as well as by a major insertion/deletion event including ten Germin-Like Protein (GLP) genes in Hope that were absent in Chinese Spring. Haplotype analysis of a limited number of wheat genotypes of interest showed that all wheat genotypes carrying Sr2 possessed the GLP cluster; while, of those lacking Sr2, some, including Marquis, possessed the cluster, while some lacked it. Thus, this region represents a common presence-absence polymorphism in wheat, with presence of the cluster not correlated with presence of Sr2. Comparison of Hope and Marquis GLP genes on 3BS found no polymorphisms in the coding regions of the ten genes but several SNPs in the shared promoter of one divergently transcribed GLP gene pair and a single SNP downstream of the transcribed region of a second GLP.ConclusionPhysical mapping and sequence comparison showed major haplotype divergence at the Sr2 locus between Hope and Chinese Spring. Candidate genes within the Sr2 region of Hope are being evaluated for the ability to confer stem rust resistance. Based on the detailed mapping and sequencing of the locus, we predict that Sr2 does not belong to the NB-LRR gene family and is not related to previously cloned, race non-specific rust resistance genes Lr34 and Yr36.
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32 schema:keywords Chinese Spring
33 DNA sequence polymorphisms
34 GLP
35 GLP genes
36 Lr34
37 Marquis
38 NB-LRR gene family
39 Puccinia graminis f.
40 SNPs
41 Sr2
42 Yaroslav
43 Yr36
44 ability
45 analysis
46 arm
47 candidate genes
48 chromosome 3B
49 clusters
50 comparable regions
51 comparison
52 deletion events
53 detailed mapping
54 divergence
55 downstream
56 durable partial resistance
57 events
58 f.
59 family
60 gene Lr34
61 gene family
62 gene pairs
63 genes
64 genotypes
65 germin-like protein genes
66 graminis f.
67 haplotype analysis
68 haplotype divergence
69 haplotypes
70 hope
71 insertion/deletion events
72 interest
73 kb
74 limited number
75 loci
76 mapping
77 maps
78 markers
79 number
80 pairs
81 partial resistance
82 physical map
83 polymorphism
84 presence
85 presence of Sr2
86 presence-absence polymorphism
87 promoter
88 protein gene
89 putative genes
90 race
91 region
92 report
93 resistance
94 resistance gene Lr34
95 resistance loci
96 rust resistance
97 rust resistance loci
98 sequence comparison
99 sequence polymorphisms
100 sequencing
101 short arm
102 spring
103 stem rust resistance
104 stem rust resistance gene Sr2
105 stem rust resistance locus
106 transcribed region
107 wheat
108 wheat genotypes
109 schema:name Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus
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