Genome-wide association studies revealed novel stripe rust resistance QTL in barley at seedling and adult-plant stages

Gyawali, Sanjaya; Mamidi, Sujan; Chao, Shiaoman; Bhardwaj, Subhash; Shekhawat, P. S.; Selvakumar, R.; Gangwar, O. P.; Verma, Ramesh Pal Singh

doi:10.1007/s10681-020-02728-1

Cited by 10 publications

(6 citation statements)

References 57 publications

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“…Plants 2023, 12, x FOR PEER REVIEW 3 of 12 36], adaptation traits [37][38][39], yield-related traits [40,41], grain components and quality traits [42][43][44], and resistance to diseases [45][46][47][48]. Novel PM resistance QTLs have been identified using GWAS in wheat [49,50], oat [51], rye [52], and, of course, barley [53][54][55][56].…”

Section: Pm Resistance and Its Correlation With Agronomic Traits In T...mentioning

confidence: 99%

“…Today, this method, along with traditional linkage mapping with bi-parental populations, is routinely used for the identification of QTLs in crops, including barley. During the last decade alone, GWAS in barley has been successfully used for the identification of QTLs for abiotic stress tolerance [ 34 , 35 , 36 ], adaptation traits [ 37 , 38 , 39 ], yield-related traits [ 40 , 41 ], grain components and quality traits [ 42 , 43 , 44 ], and resistance to diseases [ 45 , 46 , 47 , 48 ]. Novel PM resistance QTLs have been identified using GWAS in wheat [ 49 , 50 ], oat [ 51 ], rye [ 52 ], and, of course, barley [ 53 , 54 , 55 , 56 ].…”

Section: Introductionmentioning

confidence: 99%

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Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Spring Barley under Conditions of Southeastern Kazakhstan

Genievskaya

Затыбеков

Абугалиева

et al. 2023

Plants

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Barley (Hordeum vulgare L.) is one of the most produced cereal crops in the world. It has traditionally been used for the production of animal feed and for malting, as well as for human consumption. However, its production is highly affected by biotic stress factors, particularly the fungal pathogen Blumeria graminis (DC.) f. sp. hordei (Bgh), which causes powdery mildew (PM). In this study, a collection of 406 barley accessions from the USA, Kazakhstan, Europe, and Africa were assessed for resistance to PM over a 3-year period in southeastern Kazakhstan. The collection was grown in the field in 2020, 2021, and 2022 and was genotyped using the 9K SNP Illumina chip. A genome-wide association study (GWAS) was conducted to identify the quantitative trait loci (QTLs) associated with PM resistance. As a result, seven QTLs for PM resistance were detected on chromosomes 4H, 5H, and 7H (FDR p-values < 0.05). Genetic positions of two QTLs were similar to those of PM resistance QTLs previously reported in the scientific literature, suggesting that the five remaining QTLs are novel putative genetic factors for the studied trait. Haplotype analysis for seven QTLs revealed three haplotypes which were associated with total PM resistance and one haplotype associated with the high PM severity in the barley collection. Identified QTLs and haplotypes associated with the PM resistance of barley may be used for further analysis, trait pyramiding, and marker-assisted selection.

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Section: Pm Resistance and Its Correlation With Agronomic Traits In T...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Spring Barley under Conditions of Southeastern Kazakhstan

Genievskaya

Затыбеков

Абугалиева

et al. 2023

Plants

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“…With the development of high-throughput SNP sequencing technology, QTL mapping for complex quantitative traits based on natural populations using genome-wide association studies (GWAS) has been widely applied in rice [ 38 ], maize [ 39 ], wheat [ 40 ] and barley [ 41 ]. In addition, certain important QTLs have been identified by cross-validation based on the results of GWAS and linkage analysis in previous studies [ 42 , 43 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide meta-analysis of QTL for morphological related traits of flag leaf in bread wheat

Jia²,

Islam³

et al. 2022

PLoS ONE

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Flag leaf is an important organ for photosynthesis of wheat plants, and a key factor affecting wheat yield. In this study, quantitative trait loci (QTL) for flag leaf morphological traits in wheat reported since 2010 were collected to investigate the genetic mechanism of these traits. Integration of 304 QTLs from various mapping populations into a high-density consensus map composed of various types of molecular markers as well as QTL meta-analysis discovered 55 meta-QTLs (MQTL) controlling morphological traits of flag leaves, of which 10 MQTLs were confirmed by GWAS. Four high-confidence MQTLs (MQTL-1, MQTL-11, MQTL-13, and MQTL-52) were screened out from 55 MQTLs, with an average confidence interval of 0.82 cM and a physical distance of 9.4 Mb, according to the definition of hcMQTL. Ten wheat orthologs from rice (7) and Arabidopsis (3) that regulated leaf angle, development and morphogenesis traits were identified in the hcMQTL region using comparative genomics, and were speculated to be potential candidate genes regulating flag leaf morphological traits in wheat. The results from this study provides valuable information for fine mapping and molecular markers assisted selection to improve morphological characters in wheat flag leaf.

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“…The main objectives of GWAS are the identification of causative factors for the trait and/or the determination of the genetic architecture of the trait. Recently, many barley germplasm populations, including accessions from different regions of the world [35][36][37][38][39], were genotyped using the 9K SNP (single nucleotide polymorphism) Illumina Infinium iSelect array [40]. This array contains 7842 SNPs, of which 6094 SNPs have known physical positions, and it was also used in the current study.…”

Section: Introductionmentioning

confidence: 99%

Identification of SNP Markers Associated with Grain Quality Traits in a Barley Collection (Hordeum vulgare L.) Harvested in Kazakhstan

et al. 2022

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Barley (Hordeum vulgare L.) is a cereal crop traditionally used in animal feed, malting, and food production. In this study, a collection of barley was analyzed according to key grain quality traits, including protein content (GPC), starch content (GSC), extractivity (EX), and grain test weight per liter (TWL). A genome-wide association study (GWAS) was conducted to identify the quantitative trait loci (QTLs) associated with GPC, GSC, EX, and TWL using a collection of 658 barley accessions from the USA and Kazakhstan. The collection was grown at three breeding organizations in Kazakhstan in 2010 and 2011 and genotyped using the 9K SNP Illumina chip. As a result, 18 marker-trait associations (MTAs) for GPC, 19 MTAs for GSC, 12 MTAs for EX, and 27 MTAs for TWL were detected, resulting in 30 identified QTLs. It was shown that the genetic locations of 25 of these 30 QTLs were in similar positions to the QTLs and genes previously reported in the scientific literature, suggesting that the 5 remaining QTLs are novel putative genetic factors for the studied grain quality traits. Five of the most significant SNP markers (p < 2.6×10-5) for the studied quality traits identified in the GWAS were used for the development of reliable and informative competitive allele-specific PCR (KASP) genotyping assays. The effectiveness of two assays (ipbb_hv_6 and ipbb_hv_128) was confirmed via validation in a separate collection of barley breeding lines grown in large field plots in northern Kazakhstan. Therefore, these KASP assays can be efficiently used in a marker-assisted selection of grain quality traits in barley breeding.

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Genome-wide association studies revealed novel stripe rust resistance QTL in barley at seedling and adult-plant stages

Cited by 10 publications

References 57 publications

Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Spring Barley under Conditions of Southeastern Kazakhstan

Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Spring Barley under Conditions of Southeastern Kazakhstan

Genome-wide meta-analysis of QTL for morphological related traits of flag leaf in bread wheat

Identification of SNP Markers Associated with Grain Quality Traits in a Barley Collection (Hordeum vulgare L.) Harvested in Kazakhstan

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