Dataset Information

Association Mapping of Seedling Resistance to Tan Spot (Pyrenophora tritici-repentis Race 1) in CIMMYT and South Asian Wheat Germplasm.

ABSTRACT: Tan spot caused by Pyrenophora tritici-repentis (Ptr) is an important disease of wheat in many wheat producing areas of the world. A genome wide association study (GWAS) was conducted using 11,401 SNP markers of the Illumina Infinium 15K Bead Chip with whole genome coverage to identify genomic regions associated with resistance to tan spot in a diverse panel of 184 wheat genotypes originating from South Asia and CIMMYT. The GWAS panel was phenotyped for seedling resistance to tan spot with Ptr race 1 in two greenhouse experiments. Besides CIMMYT germplasm, several lines from South Asia (India, Bangladesh and Nepal) showed good degree of resistance to tan spot. Association mapping was conducted separately for individual experiments and for pooled data using mixed linear model (MLM) and Fixed and random model Circulating Probability Unification (FarmCPU) model; no significant MTAs were recorded through the MLM model, whereas FarmCPU model reported nine significant MTAs located on chromosomes 1B, 2A, 2B, 3B, 4A, 5A, 5B, 6A, and 7D. The long arms of chromosomes 5A and 5B were consistent across both environments, in which the Vrn-A1 locus was found in identified region of chromosome 5A, and MTA at IACX9261 on 5BL appears to represent the resistance gene tsn 1. MTAs observed on chromosomes 1B, 2A, 2B, 3B, 4A, 6A, and 7D have not been reported previously and are likely novel.

SUBMITTER: Phuke RM

PROVIDER: S-EPMC7483578 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Association Mapping of Seedling Resistance to Tan Spot (Pyrenophora tritici-repentis Race 1) in CIMMYT and South Asian Wheat Germplasm.

Phuke Rahul Madhavrao RM He Xinyao X Juliana Philomin P Bishnoi Santosh Kumar SK Singh Gyanendra Pratap GP Kabir Muhammad Rezaul MR Roy Krishna Kanta KK Joshi Arun Kumar AK Singh Ravi Prakash RP Singh Pawan Kumar PK

Frontiers in plant science 20200828

Tan spot caused by Pyrenophora tritici-repentis (Ptr) is an important disease of wheat in many wheat producing areas of the world. A genome wide association study (GWAS) was conducted using 11,401 SNP markers of the Illumina Infinium 15K Bead Chip with whole genome coverage to identify genomic regions associated with resistance to tan spot in a diverse panel of 184 wheat genotypes originating from South Asia and CIMMYT. The GWAS panel was phenotyped for seedling resistance to tan s ...[more]

PMID: 32983199

Similar Datasets

Project description:Tan spot is a destructive foliar wheat disease worldwide and caused by the ascomycete fungus Pyrenophora tritici-repentis (Ptr); it has become more frequent in Tunisia over the last decade. In this study, the virulence of 73 single-spore isolates, collected from durum and bread wheat fields during 2017-2018 growing season, was evaluated on four differential wheat genotypes. This was followed by polymerase chain reaction tests with specific primers for the effector genes ToxA, ToxB, and toxb (ToxB-homolog). Sequence analysis to validate the identity of the amplified genes was followed, and ToxA amplicons from a subset of 22 isolates were analyzed to determine its haplotype identity. Ptr isolates from Tunisia were grouped in races 2, 4, 5, and 7, and 44% of the tested isolates did not fit under any known race, and were denoted here as atypical. These atypical isolates induced the same symptoms as race 7 isolates, extensive necrosis, and chlorosis on susceptible genotypes, but lacked the ToxA gene. ToxA is the only identified necrosis-inducing effector in Ptr, and was amplified in 51% of tested isolates, and shared identical sequence to previously identified haplotype (H15). ToxB and its homolog toxb were present in 97% and 93% of tested isolates, respectively. Ptr in Tunisia lacked Ptr ToxC activity, and none of the tested isolates induced the specific symptoms of that effector. Race 7 and the atypical isolates dominated the Tunisian Ptr population, while races 2, 4, and 5 were found at low percentages. In conclusion, ToxB and its homolog were the most dominant genes in Ptr from Tunisia, and the majority of the isolates induced necrosis and chlorosis on Ptr ToxA and Ptr ToxB susceptible wheat genotypes. However, only about half of that necrosis can be attributed to ToxA presence, this result necessitates further research to investigate the prevalence of additional necrotic effector(s). Terminology: in this paper, Pyrenophora tritici-repentis abbreviated as Ptr, the effectors are referred to by Ptr ToxA, Ptr ToxB and Ptr ToxC, and the genes coding for them are written in italic as ToxA, ToxB, and ToxC, respectively.

Project description:Key messageGenetic mapping of sensitivity to the Pyrenophora tritici-repentis effector ToxB allowed development of a diagnostic genetic marker, and investigation of wheat pedigrees allowed transmission of sensitive alleles to be tracked. Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis, is a major disease of wheat (Triticum aestivum). Secretion of the P. tritici-repentis effector ToxB is thought to play a part in mediating infection, causing chlorosis of plant tissue. Here, genetic analysis using an association mapping panel (n = 480) and a multiparent advanced generation intercross (MAGIC) population (n founders = 8, n progeny = 643) genotyped with a 90,000 feature single nucleotide polymorphism (SNP) array found ToxB sensitivity to be highly heritable (h2 ≥ 0.9), controlled predominantly by the Tsc2 locus on chromosome 2B. Genetic mapping of Tsc2 delineated a 1921-kb interval containing 104 genes in the reference genome of ToxB-insensitive variety 'Chinese Spring'. This allowed development of a co-dominant genetic marker for Tsc2 allelic state, diagnostic for ToxB sensitivity in the association mapping panel. Phenotypic and genotypic analysis in a panel of wheat varieties post-dated the association mapping panel further supported the diagnostic nature of the marker. Combining ToxB phenotype and genotypic data with wheat pedigree datasets allowed historic sources of ToxB sensitivity to be tracked, finding the variety 'Maris Dove' to likely be the historic source of sensitive Tsc2 alleles in the wheat germplasm surveyed. Exploration of the Tsc2 region gene space in the ToxB-sensitive line 'Synthetic W7984' identified candidate genes for future investigation. Additionally, a minor ToxB sensitivity QTL was identified on chromosome 2A. The resources presented here will be of immediate use for marker-assisted selection for ToxB insensitivity and the development of germplasm with additional genetic recombination within the Tsc2 region.

Dataset Information

Association Mapping of Seedling Resistance to Tan Spot (Pyrenophora tritici-repentis Race 1) in CIMMYT and South Asian Wheat Germplasm.

Publications

Association Mapping of Seedling Resistance to Tan Spot (<i>Pyrenophora tritici-repentis</i> Race 1) in CIMMYT and South Asian Wheat Germplasm.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets