scholarly journals Genome Wide Association Study of Seedling and Adult Plant Leaf Rust Resistance in Elite Spring Wheat Breeding Lines

PLoS ONE ◽  
2016 ◽  
Vol 11 (2) ◽  
pp. e0148671 ◽  
Author(s):  
Liangliang Gao ◽  
M. Kathryn Turner ◽  
Shiaoman Chao ◽  
James Kolmer ◽  
James A. Anderson
Keyword(s):  
Association Study ◽  
Spring Wheat ◽  
Rust Resistance ◽  
Genome Wide Association Study ◽  
Leaf Rust Resistance ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Adult Plant ◽  
Breeding Lines ◽  
Genome Wide

scholarly journals Genome-wide association study of leaf rust resistance in Russian spring wheat varieties

2020 ◽  
Vol 20 (S1) ◽  
Author(s):  
Irina N. Leonova ◽  
Ekaterina S. Skolotneva ◽  
Elena A. Salina
Keyword(s):  
Association Study ◽  
Leaf Rust ◽  
Spring Wheat ◽  
Marker Assisted Selection ◽  
Rust Resistance ◽  
Genome Wide Association Study ◽  
Leaf Rust Resistance ◽  
Genome Wide Association ◽  
Wheat Varieties ◽  
Genome Wide

Abstract Background Leaf rust (Puccinia triticina Eriks.) is one of the most dangerous diseases of common wheat worldwide. Three approaches: genome-wide association study (GWAS), marker-assisted selection (MAS) and phytopathological evaluation in field, were used for assessment of the genetic diversity of Russian spring wheat varieties on leaf rust resistance loci and for identification of associated molecular markers. Results The collection, consisting of 100 Russian varieties of spring wheat, was evaluated over three seasons for resistance to the native population of leaf rust specific to the West Siberian region of Russia. The results indicated that most cultivars showed high susceptibility to P. triticina, with severity ratings (SR) of 60S–90S, however some cultivars showed a high level of leaf rust resistance (SR < 20MR-R). Based on the results of genome-wide association studies (GWAS) performed using the wheat 15 K genotyping array, 20 SNPs located on chromosomes 6D, 6A, 6B, 5A, 1B, 2A, 2B and 7A were revealed to be associated with leaf rust resistance. Genotyping with markers developed for known leaf rust resistance genes showed that most of the varieties contain genes Lr1, Lr3a, Lr9, Lr10, Lr17a, Lr20, Lr26 and Lr34, which are not currently effective against the pathogen. In the genome of three wheat varieties, gene Lr6Ai = 2 inherited from Th. intermedium was detected, which provides complete protection against the rust pathogen. It has been suggested that the QTL mapped to the chromosome 5AS of wheat cultivar Tulaikovskaya-zolotistaya, Tulaikovskaya-10, Samsar, and Volgouralskaya may be a new, previously undescribed locus conferring resistance to leaf rust. Obtained results also indicate that chromosome 1BL of the varieties Sonata, Otrada-Sibiri, Tertsiya, Omskaya-23, Tulaikovskaya-1, Obskaya-14, and Sirena may contain an unknown locus that provides a resistance response to local population. Conclusions This study provides new insights into the genetic basis of resistance to leaf rust in Russian spring wheat varieties. The SNPs significantly associated with leaf rust resistance can be used for the development and application of diagnostic markers in marker-assisted selection schemes.

scholarly journals Identifying Loci Conferring Resistance to Leaf and Stripe Rusts in a Spring Wheat Population (Triticum aestivum) via Genome-Wide Association Mapping

2019 ◽  
Vol 109 (11) ◽  
pp. 1932-1940 ◽  
Author(s):  
Weizhen Liu ◽  
James Kolmer ◽  
Sheri Rynearson ◽  
Xianming Chen ◽  
Liangliang Gao ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Stripe Rust ◽  
Spring Wheat ◽  
Rust Resistance ◽  
Genome Wide Association Study ◽  
Leaf Rust Resistance ◽  
Genome Wide Association ◽  
Stripe Rust Resistance ◽  
Adult Plant ◽  
Genome Wide

A previous genome-wide association study (GWAS) for leaf rust (caused by Puccinia triticina) resistance identified 46 resistance quantitative trait loci (QTL) in an elite spring wheat leaf rust resistance diversity panel. With the aim of characterizing the pleiotropic resistance sources to both leaf rust and stripe rust (caused by P. striiformis f. sp. tritici), stripe rust responses were tested in five U.S. environments at the adult-plant stage and to five U.S. races at the seedling stage. The data revealed balanced phenotypic distributions in this population except for the seedling response to P. striiformis f. sp. tritici race PSTv-37. GWAS for stripe rust resistance discovered a total of 21 QTL significantly associated with all-stage or field resistance on chromosomes 1B, 1D, 2B, 3B, 4A, 5A, 5B, 5D, 6A, 6B, 7A, and 7B. Previously documented pleiotropic resistance genes Yr18/Lr34 and Yr46/Lr67 and tightly linked genes Yr17-Lr37 and Yr30-Sr2-Lr27 were also detected in this population. In addition, stripe rust resistance QTL Yrswp-2B.1, Yrswp-3B, and Yrswp-7B colocated with leaf rust resistance loci 2B_3, 3B_t2, and 7B_4, respectively. Haplotype analysis uncovered that Yrswp-3B and 3B_t2 were either tightly linked genes or the same gene for resistance to both stripe and leaf rusts. Single nucleotide polymorphism markers IWB35950, IWB74350, and IWB72134 for the 3B QTL conferring resistance to both rusts should be useful in incorporating the resistance allele(s) in new cultivars.

scholarly journals The Genetic Architecture of Grain Yield in Spring Wheat Based on Genome-Wide Association Study

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuyao Li ◽  
Jingquan Tang ◽  
Wenlin Liu ◽  
Wenyi Yan ◽  
Yan Sun ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Spring Wheat ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

Uncovering the genetic architecture for grain yield (GY)–related traits is important for wheat breeding. To detect stable loci for GY-related traits, a genome-wide association study (GWAS) was conducted in a diverse panel, which included 251 elite spring wheat accessions mainly from the Northeast of China. In total, 52,503 single nucleotide polymorphisms (SNPs) from the wheat 55 K SNP arrays were used. Thirty-eight loci for GY-related traits were detected and each explained 6.5–16.7% of the phenotypic variations among which 12 are at similar locations with the known genes or quantitative trait loci and 26 are likely to be new. Furthermore, six genes possibly involved in cell division, signal transduction, and plant development are candidate genes for GY-related traits. This study provides new insights into the genetic architecture of GY and the significantly associated SNPs and accessions with a larger number of favorable alleles could be used to further enhance GY in breeding.

Genome-wide association study for agronomic and physiological traits in spring wheat evaluated in a range of heat prone environments

2017 ◽  
Vol 130 (9) ◽  
pp. 1819-1835 ◽  
Author(s):  
Francis C. Ogbonnaya ◽  
Awais Rasheed ◽  
Emeka C. Okechukwu ◽  
Abdulqader Jighly ◽  
Farid Makdis ◽  
...  
Keyword(s):  
Association Study ◽  
Spring Wheat ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Physiological Traits ◽  
Genome Wide

scholarly journals Genome-Wide Association Study of Spot Form of Net Blotch Resistance in the Upper Midwest Barley Breeding Programs

2017 ◽  
Vol 107 (1) ◽  
pp. 100-108 ◽  
Author(s):  
R. R. Burlakoti ◽  
S. Gyawali ◽  
S. Chao ◽  
K. P. Smith ◽  
R. D. Horsley ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
The United States ◽  
Genome Wide Association ◽  
Net Blotch ◽  
Upper Midwest ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Barley Breeding ◽  
Genome Wide

Pyrenophora teres f. maculata, the causal agent of spot form of net blotch (SFNB), is an emerging pathogen of barley in the United States and Australia. Compared with net form of net blotch (NFNB), less is known in the U.S. Upper Midwest barley breeding programs about host resistance and quantitative trait loci (QTL) associated with SFNB in breeding lines. The main objective of this study was to identify QTL associated with SFNB resistance in the Upper Midwest two-rowed and six-rowed barley breeding programs using a genome-wide association study approach. A total of 376 breeding lines of barley were evaluated for SFNB resistance at the seedling stage in the greenhouse in Fargo in 2009. The lines were genotyped with 3,072 single nucleotide polymorphism (SNP) markers. Phenotypic evaluation showed a wide range of variability among populations from the four breeding programs and the two barley-row types. The two-rowed barley lines were more susceptible to SFNB than the six-rowed lines. Continuous distributions of SFNB severity indicate the quantitative nature of SFNB resistance. The mixed linear model (MLM) analysis, which included both population structure and kinship matrices, was used to identify significant SNP-SFNB associations. Principal component analysis was used to control false marker-trait association. The linkage disequilibrium (LD) estimates varied among chromosomes (10 to 20 cM). The MLM analysis identified 10 potential QTL in barley: SFNB-2H-8-10, SFNB-2H-38.03, SFNB-3H-58.64, SFNB-3H-78.53, SFNB-3H-91.88, SFNB-3H-117.1, SFNB-5H-155.3, SFNB-6H-5.4, SFNB-6H-33.74, and SFNB-7H-34.82. Among them, four QTL (SFNB-2H-8-10, SFNB-2H-38.03 SFNB-3H-78.53, and SFNB-3H-117.1) have not previously been published. Identification of SFNB resistant lines and QTL associated with SFNB resistance in this study will be useful in the development of barley genotypes with better SFNB resistance.

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