Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat

Mourad, Amira M. I.; Sallam, Ahmed; Belamkar, Vikas; Wegulo, Stephen N.; Bowden, Robert L.; Jin, Yue; Mahdy, E.E.; Bakheit, B. R.; El-Wafaa, Atif Abo; Poland, Jesse; Baenziger, P. Stephen

doi:10.3389/fpls.2018.00380

Cited by 66 publications

(61 citation statements)

References 36 publications

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“…The only drawback of breeding research is the cost and time consuming to achieve its goals. The recent advances in DNA technology and genomics paved the way to identify genomic regions controlling important traits such as drought tolerance in crops (Sandhu et al 2014;Hussain et al 2017;Eltaher et al 2018;Mourad et al 2018). These technologies provide DNA markers that can be combined with phenotypic data to identify genomic regions associated with target traits using genetic association analyses such as genome-wide association study, QTL mapping, single-marker analysis, etc.…”

Section: Introductionmentioning

confidence: 99%

Utilize of genetic diversity and marker-trait association to improve drought tolerance in rice (Oryza sativa L.)

Sallam

2020

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Drought stress in one of the main problems for rice crop as it reduces the production and productivity of the grain yield significantly. In Egypt, many restrictions were made on the cultivation of rice due to its high water demand. Producing promising drought-tolerant rice cultivars in a combination with high yielding is one of the main targets for rice breeders. To address this challenge, a set of 22 highly diverse rice genotypes were evaluated under normal and drought conditions. Morphological, physiological, yield traits were recorded on each genotype. Drought susceptibility index (DSI) was estimated for six yield traits to identify the most drought-tolerant rice genotypes. High genetic variation was found among genotypes tested in the experiment. Under normal conditions, the highest phenotypic correlation was found between grain yield (GY) and sterility percentage (SP) (- 0.73**), while, it was among GY and chlorophyll content (CC) (0.82**) under drought conditions. To identify quantitative trait loci (QTL) controlling yielding traits under drought and normal, single marker analysis was performed between all yield traits under both condition and a set of 106 simple sequence repeat (SSR) marker alleles. The genetic association analysis revealed 14 and 17 QTL under drought and normal conditions, respectively. The most drought-tolerant genotypes were selected based on DSI, the number of QTL in each selected genotypes, and the level of genetic diversity. As a result, five genotypes (Giza 178, IET1444, GZ1368-S-5-4, Nahda, Giza 14) were identified as the most promising drought-tolerant rice genotypes. Eight QTL controlling drought tolerance were identified in Giza 178, Nahda, and GZ1368-S-5-4, while, four QTL were found in IET1444. The number of different QTLs were estimated among the five selected genotypes. Giza 178 and GZ1368-S-5-4 shared the same QTLs. Seven different QTLs were found among Nahda, IET1444, GZ1368-S-5-4, and Giza 14. Combining information from phenotypic traits, genetic diversity analysis, and QTL identification was very useful in identifying the true drought-tolerant rice genotypes that can be used for crossing in the future breeding program.

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Section: Introductionmentioning

confidence: 99%

Utilize of genetic diversity and marker-trait association to improve drought tolerance in rice (Oryza sativa L.)

Sallam

2020

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“…GWAS is a powerful approach that identi es novel alleles associated with complex traits by utilizing linkage disequilibrium and examine marker-trait associations [17][18][19]. It has been applied successfully to study the genetic architecture of disease resistance in different crops such as rice [20], maize [21], grain sorghum [22], and wheat [23][24][25][26]. Maccaferri et al, (2015) reported association mapping of the resistance to the American race of P. striiformis using a world-wide collection of spring wheat genotyped by DArT markers.…”

Section: Introductionmentioning

confidence: 99%

Genomic Regions Associated With Stripe Rust Resistance Against the Egyptian Race Revealed by Genome-Wide Association Study

Mohamed

Mourad

2020

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Background: Wheat stripe rust (caused by Puccinia striiformis f. sp. Tritici), is a major disease that causes huge yield damage. New pathogen races appeared in the last few years and caused a broke down in the resistant genotypes. In Egypt, some of the resistant genotypes began to be susceptible to stripe rust in recent years. This situation increases the need to produce new genotypes with durable resistance. Besides, looking for a new resistant source from the available wheat genotypes all over the world help in enhancing the breeding programs. Results: In the recent study, a set of 103-spring wheat genotypes from different fourteen countries were evaluated to their field resistant to stripe rust for two years. These genotypes included 17 Egyptian genotypes from the old and new cultivars. The 103-spring wheat genotypes were reported to be well adapted to the Egyptian environmental conditions. Out of the tested genotypes, eight genotypes from four different countries were found to be resistant in both years. Genotyping was carried out using genotyping-by-sequencing and a set of 26,703 SNPs were used in the genome-wide association study. Five SNP markers, located on chromosomes 2A and 4A, were found to be significantly associated with the resistance in both years. Three gene models associated with disease resistance and underlying these significant SNPs were identified. One immune Iranian genotype, with the highest number of different alleles from the most resistant Egyptian genotypes, was detected. Conclusion: the high variation among the tested genotypes in their resistance to the Egyptian stripe rust race confirming the possible improvement of stripe rust resistance in the Egyptian wheat genotypes. The identified five SNP markers are stable and could be used in marker-assisted selection after validation in different genetic backgrounds. Crossing between the immune Iranian genotype and the Egyptian genotypes will improve stripe rust resistance in Egypt.

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“…SSR markers are characterized with high polymorphisms, good repeatability, co-dominance, and distribution throughout whole genome, and favored for QTL mapping and molecular breeding in wheat [8][9][10]. With rapid advancements in sequencing technology, high-throughput sequencing or chipbased SNP genotyping platforms have been used for QTL mapping [11][12][13][14]. Additionally, the wheat reference genome was assembled and released recently [15].…”

Section: Introductionmentioning

confidence: 99%

Rapid identification and characterization of genetic loci for defective kernel in bread wheat

Tian

et al. 2019

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Background Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential. Results Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78 - 18.17%, 16.61 - 21.83% and 19.08 - 28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were determined according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0. Conclusions Overall, we achieved a rapid QTL mapping and reasonable predication of causal genes for Dek, laying foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat.

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Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat

Cited by 66 publications

References 36 publications

Utilize of genetic diversity and marker-trait association to improve drought tolerance in rice (Oryza sativa L.)

Utilize of genetic diversity and marker-trait association to improve drought tolerance in rice (Oryza sativa L.)

Genomic Regions Associated With Stripe Rust Resistance Against the Egyptian Race Revealed by Genome-Wide Association Study

Rapid identification and characterization of genetic loci for defective kernel in bread wheat

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