Genome-wide DArT and SNP scan for QTL associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in elite ICARDA wheat (Triticum aestivum L.) germplasm

Jighly, Abdulqader; Oyiga, Benedict Chijioke; Makdis, Farid; Nazari, K.; Youssef, Omran; Tadesse, Wuletaw; Abdalla, O.; Ogbonnaya, Francis C.

doi:10.1007/s00122-015-2504-2

Cited by 69 publications

(52 citation statements)

References 97 publications

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“…Genome-wide association studies (GWAS) provide dense genome coverage and allow for accurate identification of putative QTL in unstructured populations (Lorenz et al 2011). It has been routinely used to identify the genetic basis of simple and complexly inherited agronomic and adaptive traits (Jighly et al 2015; McCouch et al 2016; Sun et al 2017). …”

Section: Introductionmentioning

confidence: 99%

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat

Oyiga

Ogbonnaya

Sharma³

et al. 2018

Theor Appl Genet

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Key messageSNP alleles on chromosomes 4BL and 6AL are associated with sensitivity to salt tolerance in wheat and upon validation can be exploited in the development of salt-tolerant wheat varieties.AbstractThe dissection of the genetic and molecular components of salt stress response offers strong opportunities toward understanding and improving salt tolerance in crops. In this study, GWAS was employed to identify a total of 106 SNP loci (R2 = 0.12–63.44%) linked to salt stress response in wheat using leaf chlorophyll fluorescence, grain quality and shoot ionic (Na+ and K+ ions) attributes. Among them, 14 SNP loci individually conferred pleiotropic effects on multiple independent salinity tolerance traits including loci at 99.04 cM (R2 ≥ 14.7%) and 68.45 cM (R2 ≥ 4.10%) on chromosomes 6AL and 4BL, respectively, that influenced shoot Na+-uptake, shoot K+/Na+ ratio, and specific energy fluxes for absorption (ABS/RC) and dissipation (DIo/RC). Analysis of the open reading frame (ORF) containing the SNP markers revealed that they are orthologous to genes involved in photosynthesis and plant stress (salt) response. Further transcript abundance and qRT-PCR analyses indicated that the genes are mostly up-regulated in salt-tolerant and down-regulated in salt-sensitive wheat genotypes including NRAMP-2 and OPAQUE1 genes on 4BL and 6AL, respectively. Both genes showed highest differential expression between contrasting genotypes when expressions of all the genes within their genetic intervals were analyzed. Possible cis-acting regulatory elements and coding sequence variation that may be involved in salt stress response were also identified in both genes. This study identified genetic and molecular components of salt stress response that are associated with Na+-uptake, shoot Na+/K+ ratio, ABS/RC, DIo/RC, and grain quality traits and upon functional validation would facilitate the development of gene-specific markers that could be deployed to improve salinity tolerance in wheat.Electronic supplementary materialThe online version of this article (10.1007/s00122-018-3220-5) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat

Oyiga

Ogbonnaya

Sharma³

et al. 2018

Theor Appl Genet

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“…In addition to Yr2, we also postulated the presence of an additional unknown resistance gene or genes in these lines. Several minor-and major-effect stripe rust resistance genes have been introduced from wheat relatives and alien species for control of the disease ( Jighly et al, 2015;Maccaferri et al, 2015;Rosewarne et al, 2013). Additionally, the crossing and backrossing of these wheat-alien introgression lines to each other resulted in the pyramiding of resistance genes, leading to lines containing a combination of at least two or three Yr resistance genes (Forsström and Merker, 2001;Merker, 1984;Merker and Lantai, 1997).…”

Section: Discussionmentioning

confidence: 99%

“…To avoid contamination among Pst isolates, inoculated plants were individually covered with cellophane bags prior to sporulation (Sørensen et al, 2016) and then the Pst spores were harvested three or four times from 16 to 20 d after inoculation. The protocols used for assessing the resistance of seedling plants at Izmir were according to Jighly et al (2015). For ease of handling, each set of 34 pots (7 by 7 by 8 cm), including one susceptible control (Morocco or Cartago), was placed in a plastic tray.…”

Section: Seedling Resistance Specificity Towards Multiple Isolatesmentioning

confidence: 99%

“…Qualitative resistance is the result of a resistance reaction of a specific resistance gene or genes in the host towards a specific gene or genes for avirulence in the pathogen. Molecular markers closely linked to these resistance genes can greatly aid in developing cultivars with resistance gene pyramids (Jighly et al, 2015;Maccaferri et al, 2015). In contrast, quantitative resistance is often conferred by several minor effect genes that are collectively less prone to being overcome by changes in the pathogen population and hence are more durable (Singh et al, 2011).…”

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Seedling and Adult Plant Stripe Rust Resistance in Diverse Wheat–Alien Introgression Lines

Rahmatov

Hovmøller

Nazari³

et al. 2017

Crop Science

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Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Eriks., is an important foliar disease of wheat (Triticum aestivum L.) worldwide. The use of genetic diversity, particularly from wild relatives, has made a significant contribution to improving wheat productivity. To identify new sources of seedling and adult plant resistance, we evaluated 263 wheat–alien introgression derivatives from Secale cereale L., Leymus mollis (Trin.) Plig., Leymus racemosus (Lam.) Tzevlev, and Thinopyrum junceiforme (Á.Löve & D.Löve) Á. Löve. Three resistance genes, Yr1+, Yr2+, and Yr9+ were postulated to be present in 7, 19, and 12% of wheat–alien introgression lines, respectively. In addition, the results suggested the gene combinations of Yr1–Yr2 (1%), Yr1–Yr32 (2%), Yr2–Yr9 (5.4%), Yr1–Yr2–Yr32 (11%), and the additional unknown resistance gene(s) being present in these materials in the respective percentages. The molecular markers Xwmc364 for Yr2 (36%), Xscm9 and Xiag95 for Yr9 (17%), and Xwmc198 for Yr32 (13%) were used to validate the presence of these Yr genes. Ninety‐eight (37%) of the lines possess unknown resistance genes that could not be determined with the isolates used in this study and six (2.3%) of the lines showed seedling resistance to all isolates. The lines with the putative new resistance gene(s) will be crossed to the adapted genotypes to develop a mapping population for determining the underlying genetic basis of resistance. If these resistance genes are validated as being new, they will enhance the genetic diversity for stripe rust resistance in wheat.

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“…Yrq2 was mapped on chromosome 3AS in wheat line Xichang 76-9 but confers slow rusting , and therefore should be different from YrTye. Through genome-wide association mapping, Jighly et al (2015) reported a QTL on 3AS to confer seedling resistance, but neither the gene nor its location has been validated. Because of no any formally named Yr gene was previously located on chromosome 3AS (McIntosh et al 2014), we named YrTye as Yr76.…”

Section: Discussionmentioning

confidence: 99%

Molecular Mapping of Stripe Rust Resistance Gene Yr76 in Winter Club Wheat Cultivar Tyee

et al. 2016

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Tyee, one of the wheat cultivars used to differentiate races of Puccinia striiformis f. sp. tritici in the United States, was identified to have a single gene for all-stage resistance, tentatively named YrTye. To map the gene, Tyee was crossed with ‘Avocet Susceptible’ (AvS). Genetic analysis of the F1, F2, F2:3, and BC1 progenies confirmed a single dominant gene for resistance to race PSTv-37 that is avirulent to YrTye. A mapping population of 135 F2 plants was phenotyped with PSTv-37 and the derived F2:3 lines were tested with races PSTv-37, PSTv-40, and PSTv-79. The F2 mapping population was genotyped with simple sequence repeat (SSR) markers. A genetic map comprising 13 SSR markers located YrTye in chromosome 3AS flanked distally by SSR marker wmc11 and proximally by wmc532 at 2.6 and 3.4 cM, respectively. Amplification of Chinese Spring 3A deletion lines placed the gene in the distal bin 3AS4-0.45 to 1.00. Because YrTye is different from all formally named Yr genes in chromosomal location, we permanently name the gene Yr76. A near-isogenic line of spring common wheat was developed and selected by testing F3 lines derived from a AvS*4/Tyee cross with Tyee-avirulent and virulent races and the flanking markers. The specific SSR alleles flanking Yr76 were validated using cultivars and breeding lines with and without the gene, and showed high polymorphisms. The specificity of Yr76 is useful in differentiating P. striiformis f. sp. tritici races, and its tightly linked markers will be useful in developing resistant cultivars when combining the gene with other genes for resistance to stripe rust.

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Genome-wide DArT and SNP scan for QTL associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in elite ICARDA wheat (Triticum aestivum L.) germplasm

Cited by 69 publications

References 97 publications

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat

Seedling and Adult Plant Stripe Rust Resistance in Diverse Wheat–Alien Introgression Lines

Molecular Mapping of Stripe Rust Resistance Gene Yr76 in Winter Club Wheat Cultivar Tyee

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