TreeBASE Search-Matrix 58020 of study 21219

@ARTICLE{TreeBASE2Ref27363, author = {Kebede Tadesse Muleta and Matthew N Rouse and Shery Rynearson and Xianming Chen and Bedada G Buta and Michael Pumphrey}, title = {Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions}, year = {2017}, keywords = {Bread wheat, stripe rust, stem rust, genetic resistance, genetic diversity, association mapping}, doi = {}, url = {http://}, pmid = {}, journal = {BMC Plant Biology}, volume = {}, number = {}, pages = {}, abstract = {Background: The narrow genetic basis of resistance in modern wheat cultivars and the strong selection response of pathogen populations have been responsible for periodic and devastating epidemics of the wheat rust diseases. Characterizing new sources of resistance and incorporating multiple genes into elite cultivars is the most widely accepted current mechanism to achieve durable varietal performance against changes in pathogen virulence. Here, we report a high-density molecular characterization and genome-wide association study (GWAS) of stripe rust and stem rust resistance in 190 Ethiopian bread wheat lines based on phenotypic data from multi-environment field trials and seedling resistance screening experiments. A total of 24,281 single nucleotide polymorphism (SNP) markers filtered from the wheat 90K iSelect genotyping assay was used to survey Ethiopian germplasm for population structure, genetic diversity and marker-trait associations. Results: Upon screening for field resistance to stripe rust in the Pacific Northwest of the United States and Ethiopia over multiple growing seasons; and against multiple races of stripe rust and stem rust at seedling stage, eight accessions displayed resistance to all tested races of stem rust and field resistance to stripe rust at all environments. Our GWAS results show 15 loci were significantly associated with seedling and adult plant resistance to stripe rust at false discovery rate (FDR)-adjusted probability (P) <0.10. GWAS also detected 9 additional genomic regions significantly associated (FDR-adjusted P <0.10) with seedling resistance to stem rust in the Ethiopian wheat accessions. Many of the identiﬁed resistance loci were mapped close to previously identiﬁed rust resistance genes; however, three on the short arms of chromosomes 5A and 7B for stripe rust resistance and two on chromosomes 3B and 7B for stem rust resistance may be novel. Conclusion: Our results demonstrate that considerable genetic variation resides within the landrace accessions that can be utilized to broaden the genetic base of rust resistance in wheat breeding germplasm. The molecular markers identified in this study should be useful in efficiently targeting the associated resistance loci in marker-assisted breeding for rust resistance in Ethiopia and other countries. } }

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Matrix 58020 of Study 21219

Citation title: "Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions".

Study name: "Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions".

This study is part of submission 21219 (Status: Published).

Matrices

Title: Herpotrichiellaceae - ITS alignment

Rows

Taxon Label	Row Segments	Characters 1?–30
Capronia dactylotricha NR_137136_DAOM_208471	(none)	-CCGAGTTAGGGTC-T-----------CC-
Capronia epimyces AF050245_DAOM_216386	(none)	-CAGAGTTAGGGTC-T-----------TC-
Capronia fungicola NR_121261_ATCC_42523	(none)	-CAGAGTTAGGGTC-T-----------TC-
Capronia kleinmondensis EU552107_CPC_13182	(none)	-CCGAGTTAGGGTC-T-----------TC-
Capronia leucadendri EU552108_CPC_13181	(none)	-CCGAGTCAGGGTC-T-----------TC-
Capronia munkii NR_121263_DAOM_216390	(none)	-AAGAGTTAGGGTC-T-----------TC-
Capronia parasitica NR_121264_CBS_123.88	(none)	-TCGAGTTAGGGTC-T-----------TC-
Capronia pulcherrima NR_121266_DAOM_216384	(none)	-AAGAGTTAGGGTC-T-----------TC-
Capronia sp. CBS 164.92 AF050240 CBS 164.92	(none)	-ATGAGTTAGGGTC-T-----------TC-
Capronia sp. CSN1167 ITS5 CS32	(none)	-CCGAGTTAGGGTC-T-----------TC-
Capronia sp. CSN1168 ITS5 CS014	(none)	------------------------------
Capronia sp. CSN1172 ITS5 consensus	(none)	-CCGAGTTAGGGTC-T-----------TC-
Cladophialophora boppii NR_131297_CBS_126.86	(none)	AAGAAGTTAGGGTT-T-----------TC-
Cladophialophora devriesii NR_111279_CBS_147.84	(none)	-ACGAGTAAGGGTC-T-----------CT-
Cladophialophora humicola EU035408_CBS_117536_BBA_65570	(none)	-ATGAGTTAGGGTC-T-----------TC-
Cladophialophora minourae AY251087_CBS_556.83	(none)	-AAGAGTTAGGGTC-TCCT--------CC-
Cladophialophora minutissima NR_137550_Pj1_R1	(none)	-ATGAGTTAGGGTC-T-----------TC-
Cladophialophora mycetomatis NR_111364_CBS_122637	(none)	---------------T-----------CT-
Cladophialophora proteae NR_132819_CBS_111667_CPC_1514_	(none)	-CCGAGTTAGGGTC-C-----------TGC
Cladophialophora pucciniophila NR_137769_KACC_43957	(none)	-CCGAGTTGAGGGTCTG-----CGTCCTTA
Cladophialophora subtilis NR_111363_CBS_122642	(none)	-ACGAGTTAGGGTC-T-----------TC-
Cladophialophora sylvestris NR_132820_CBS_350.83	(none)	-ATGAGTTAGGGTT-T-----------TC-
Cyphellophora europaea NR_120101_CBS_101466	(none)	-CCGAGTTAGGGTG-C-----------CTA
Cyphellophora oxyspora NR_132883_CBS_698.73	(none)	-CCGAGTTAGGGTG-T-----------CAA
Cyphellophora pauciseptata NR_132868_CBS_284.85	(none)	-CCGAGTTAGGGTG-C-----------TT-
Exophiala angulospora NR_111625_CBS_482.92	(none)	-AAGAGTTAGGGTC-T-----------TC-
Exophiala aquamarina NR_111626_CBS_119918	(none)	-ACGAGTAAGGGTC-T-----------CT-
Exophiala asiatica NR_111332_CBS_122847	(none)	-ATGAGTTAGGGTT-C-----------TTT
Exophiala bergeri NR_111245_CBS_353.52	(none)	------------------------------
Exophiala bonariae NR_144964_CCFEE_5792	(none)	-CCGAGTTAGGGTC-T-----------CA-
Exophiala cancerae NR_137766_CBS_120420	(none)	-ACGAGTTAGGGTC-T-----------CA-
Exophiala capensis NR_121493_CBS_128771	(none)	-ACGAGTTAGGGTC-T-----------TC-
Exophiala castellanii NR_121460_CBS_158.58	(none)	-ACGAGTTAGGGTC-T-----------TC-
Exophiala dermatitidis NR_121268_CBS_207.35	(none)	-ACGAGTTAGGGTC-T-----------TC-
Exophiala equina NR_111627_CBS_119.23	(none)	-ACGAGTTAGGGTC-T-----------CT-
Exophiala eucalypti KY173411_CPC_27630	(none)	-AAGAGTTAGGGTC-T-----------TC-
Exophiala eucalyptorum NR_132882_CBS_121638	(none)	-CTGAGTTAGGGTC-T-----------TC-
Exophiala exophialae NR_111130_CBS_668.76	(none)	-CCGAGTTAGGGTC-C-----------TCA
Exophiala hongkongensis NR_111671_HKU_32	(none)	-ACGAGTTAGGGTT-CC-----G----TC-
Exophiala jeanselmei NR_111129_CBS_507.90	(none)	-CCGAGTTAGGGTC-C-----------TCA
Exophiala lacus NR_111629_CBS_117497	(none)	-CCGAGTTAGGGTC-T-----------CA-
Exophiala lecanii corni_NR_145351_CBS_123.33	(none)	-ACGAGTTAGGGTC-T-----------TTT
Exophiala mesophila NR_121461_CBS_402.95	(none)	-ACGAGTTAGGGTC-T-----------TC-
Exophiala moniliae NR_111448_CBS_520.76	(none)	-AAGAGTAAGGGTC-T-----------TC-
Exophiala nishimurae NR_137092_CBS_101538	(none)	-ACGAGTTAGGGTT-T-----------CCG
Exophiala oligosperma NR_111134_CBS_725.88	(none)	-CCGAGTTAGGGTC-C-----------TCA
Exophiala pisciphila NR_121269_CBS_537.73	(none)	-ACGAGTTAGGGTC-C-----------CT-
Exophiala placitae EU040215_CPC_13707	(none)	-CCGAGTTAGGGCC-C-----------CCC
Exophiala psychrophila NR_145371_CBS_191.87	(none)	-ACGAGTTAGGGTC-T-----------CA-
Exophiala salmonis NR_121270_CBS_157.67	(none)	-ACGAGTTAGGGTT-C-----------CC-
Exophiala sideris NR_111553_CBS_121818	(none)	--AGGAATACGGTC-T-----------TC-
Exophiala sp. CSN1190 ITS4 CS025	(none)	-ACGAGTTAGGGTC-T-----------TC-
Exophiala sp. CSN1921 ITSds	(none)	-ACGAGTTAGGGTC-T-----------TC-
Exophiala spinifera NR_111131_CBS_899.68	(none)	-CCGAGTTAGGGTC-C-----------TCA
Exophiala xenobiotica CSN1930_ITS4_CS30	(none)	-CCGAGTTAGGGTC-C-----------AT-
Exophiala xenobiotica NR_111203_CBS_118157	(none)	-CCGAGTTAGGGTC-C-----------AT-
Fonsecaea multimorphosa NR_111612_CBS_980.96	(none)	-ACGAGTTAGGGTC-T-----------CC-
Fonsecaea nubica NR_111333_CBS_269.64	(none)	-ATGAGTTAGGGTC-T-----------TC-
Herpotrichiellaceae sp. CSN1170 ITS5 consensus	(none)	-ACGAGTTAAGGTC-T-----------TT-
Herpotrichiellaceae sp. CSN1211 ITS5 CS32	(none)	-TTGAGATAGGGTC-T-----------TT-
Herpotrichiellaceae sp. CSN995 ITS5 CS29	(none)	-ACGAGTTAGGGTCTT-----------TT-
Knufia cryptophialidica NR_121501_DAOM_216555	(none)	-CCGAGCTAGGGTT-G-----------CCC
Knufia endospora NR_111634_UAMH_10396	(none)	-CCGAGTTAGGGTT-G-----------CCC
Knufia epidermidis NR_111330_CBS_120353	(none)	-CCGAGTTAGGGTT-C---------GCTTC
Knufia karalitana NR_145018_CCFEE_5656	(none)	-CCGAGTTAGGGTT-T-------GCCCCTC
Knufia marmoricola NR_145016_CCFEE_5895	(none)	-CCGAGTAAGGGTC-T--------CCCTCA
Knufia mediterranea NR_145019_CCFEE_5738	(none)	-CCGAGTTAGGGTG-CGCCGTATCCAATCG
Knufia perforans NR_121502_CBS_885.95	(none)	-CCGAGTTAGGGTC-T-------TCCCCTC
Knufia petricola NR_111871_CBS_726.95	(none)	-CCGAGTTAGGGTT-T--------CCCCTC
Knufia tsunedae NR_132842_FMR_10621	(none)	-CCGAGTTAGGGTT-T---------CGTCT
Knufia vaticanii NR_145017_CCFEE_5939	(none)	-CCGAGTTAGGGTT-T-------TTCCTTG
Neophaeococcomyces aloes NR_132069_CPC_21873	(none)	-CCGAGATCAGGAC-C--------CGCTCA
Neophaeococcomyces catenatus NR_111635_UAMH_4357	(none)	-CCGAGTTAGGGCC-C-----------TCG
Periconiella levispora NR_137687_CBS_873.73	(none)	-CAGAGTGCGGGCC----------------
Phaeoannellomyces elegans KF928443_CBS_101597	(none)	--CGAGTTAGGGTC-T-----------TC-
Phialophora macrospora NR_146235_MUCL_9760	(none)	-ACGAGTTAGGGTC-TC----------TC-
Phialophora verrucosa NR_146242_CBS_140325	(none)	-ACGAGTTAGGGTC-TC----------TC-
Ramichloridium apiculatum NR_145091_CBS_156.59	(none)	CCAGAAGCCGCGTC--G-----G----CC-
Ramichloridium cerophilum NR_145092_CBS_103.59	(none)	-CTGAGTGAGGGTC-T-----------CC-
Ramichloridium punctatum NR_120081_CPC_18974	(none)	CCAGAAGCCGCGTC--G-----G----CC-
Rhinocladiella anceps NR_111275_CBS_181.65	(none)	-CTGAGCTTGGGTC-T-----------TT-
Rhinocladiella aquaspersa NR_119760_CBS_313.73	(none)	-ACGAGTTAGGGTC-T-----------CA-
Rhinocladiella basitona NR_111135_CBS_101460	(none)	-TCGAGTTAGGGTC-C-----------TCA
Rhinocladiella fasciculata NR_145356_CBS_132.86	(none)	-CCGAGTTAGGGTC-T-----------TT-
Rhinocladiella mackenziei NR_111185_CBS_650.93	(none)	-ACGAGTTAGGGTC-T-----------TC-
Rhinocladiella phaeophora NR_103592_CBS_496.78	(none)	-ACGAGTTAGGGTC-T-----------CA-
Rhinocladiella similis NR_111244_CBS_111763	(none)	------------------------------
Thysanorea papuana NR_111276_CBS_212.96	(none)	-CAGAGTTAGGGTC-T-----------CT-
Veronaea botryosa NR_103593_CBS_254.57	(none)	-ACGAGTTAGGGTC-T-----------CC-
Veronaea compacta NR_077176_CBS_268.75	(none)	-ACGAGTTAGGGTC-T-----------CC-
Veronaea japonica NR_111277_CBS_776.83	(none)	-ACGAGTTAGGGTC-T-----------CC-

Columns

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