Genome-Wide Association Mapping for Yield and Related Traits Under Drought Stressed and Non-stressed Environments in Wheat

Rabbi, Smha; Kumar, Ajay; Naraghi, Sepehr Mohajeri; Şimşek, Şenay; Sapkota, Suraj; Solanki, Shyam; Alamri, Mohammed S.; Elias, Elias M.; Kianian, Shahryar F.; Missaoui, Ali; Mohamed, Maryati

doi:10.3389/fgene.2021.649988

Cited by 16 publications

(10 citation statements)

References 46 publications

(85 reference statements)

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“…The traditional QTL mapping method usually involves the hybrid population of two parents and the detection of target trait loci via linkage mapping ( Bettgenhaeuser and Krattinger, 2019 ). The limitation of this method is that relatively few recombination events occur during artificial hybridization, which leads to low resolution ( Rabbi et al, 2021 ). Fine mapping requires the investment of considerable time, labor, and resources to develop many recombinant populations.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study Reveals the Genetic Basis of Five Quality Traits in Chinese Wheat

et al. 2022

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Bread wheat is a highly adaptable food crop grown extensively around the world and its quality genetic improvement has received wide attention. In this study, the genetic loci associated with five quality traits including protein content (PC), gluten content (GC), baking value (BV), grain hardness (HA), and sedimentation value (SV) in a population of 253 Chinese wheat grown in Inner Mongolia were investigated through genome wide association mapping. A total of 103 QTL containing 556 SNPs were significantly related to the five quality traits based on the phenotypic data collected from three environments and BLUP data. Of these QTL, 32 QTL were continuously detected under at least two experiments. Some QTL such as qBV3D.2/qHA3D.2 on 3D, qPC5A.3/qGC5A on 5A, qBV5D/qHA5D on 5D, qBV6B.2/qHA6B.3 on 6B, and qBV6D/qHA6D.1 on 6D were associated with multiple traits. In addition, distribution of favorable alleles of the stable QTL in the association panel and their effects on five quality traits were validated. Analysis of existing transcriptome data revealed that 34 genes were specifically highly expressed in grains during reproductive growth stages. The functions of these genes will be characterized in future experiments. This study provides novel insights into the genetic basis of quality traits in wheat.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study Reveals the Genetic Basis of Five Quality Traits in Chinese Wheat

et al. 2022

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“…In this study, MTAs were also detected, adding to the previous list of candidate genes and markers. In spite of this, aligning our results with earlier studies is challenging due to different reference genome models than IWGSC Ref.Seq, inaccurate genomic locations, or combining different markers (GBS-derived SNP versus SSR and DART) 62 – 65 . Of course, detecting MTAs on the same chromosome as previous projects increase their assurance.…”

Section: Discussionmentioning

confidence: 66%

“…Numerous efforts have been made so far to locate QTLs and genes affecting wheat traits in order to facilitate marker-assisted breeding for wheat 62 , 63 . In this study, MTAs were also detected, adding to the previous list of candidate genes and markers.…”

Section: Discussionmentioning

confidence: 99%

Genetic analyses and prediction for lodging‑related traits in a diverse Iranian hexaploid wheat collection

Rabieyan,

Darvishzadeh,

Alipour

2024

Sci Rep

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Lodging is one of the most important limiting environmental factors for achieving the maximum yield and quality of grains in cereals, including wheat. However, little is known about the genetic foundation underlying lodging resistance (LR) in wheat. In this study, 208 landraces and 90 cultivars were phenotyped in two cropping seasons (2018–2019 and 2019–2020) for 19 LR-related traits. A genome-wide association study (GWAS) and genomics prediction were carried out to dissect the genomic regions of LR. The number of significant marker pairs (MPs) was highest for genome B in both landraces (427,017) and cultivars (37,359). The strongest linkage disequilibrium (LD) between marker pairs was found on chromosome 4A (0.318). For stem lodging-related traits, 465, 497, and 478 marker-trait associations (MTAs) and 45 candidate genes were identified in year 1, year 2, and pooled. Gene ontology exhibited genomic region on Chr. 2B, 6B, and 7B control lodging. Most of these genes have key roles in defense response, calcium ion transmembrane transport, carbohydrate metabolic process, nitrogen compound metabolic process, and some genes harbor unknown functions that, all together may respond to lodging as a complex network. The module associated with starch and sucrose biosynthesis was highlighted. Regarding genomic prediction, the GBLUP model performed better than BRR and RRBLUP. This suggests that GBLUP would be a good tool for wheat genome selection. As a result of these findings, it has been possible to identify pivotal QTLs and genes that could be used to improve stem lodging resistance in Triticum aestivum L.

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“…First, a RIL population has few recombination events and can only be used to detect genes that show a significant difference between parental lines (Korte and Farlow 2013 ). Second, a large proportion of the studies have been based on low-resolution molecular maps consisting of only 100–1000 SSRs, EST-STS, and DArT markers, insufficient to saturate the large 17 giga-base-pair wheat genome (Rabbi et al 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study of drought tolerance in wheat (Triticum aestivum L.) identifies SNP markers and candidate genes

Nouraei,

Mia,

Liu

et al. 2024

Mol Genet Genomics

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Drought stress poses a severe threat to global wheat production, necessitating an in-depth exploration of the genetic basis for drought tolerance associated traits. This study employed a 90 K SNP array to conduct a genome-wide association analysis, unravelling genetic determinants of key traits related to drought tolerance in wheat, namely plant height, root length, and root and shoot dry weight. Using the mixed linear model (MLM) method on 125 wheat accessions subjected to both well-watered and drought stress treatments, we identified 53 SNPs significantly associated with stress susceptibility (SSI) and tolerance indices (STI) for the targeted traits. Notably, chromosomes 2A and 3B stood out with ten and nine associated markers, respectively. Across 17 chromosomes, 44 unique candidate genes were pinpointed, predominantly located on the distal ends of 1A, 1B, 1D, 2A, 3A, 3B, 4A, 6A, 6B, 7A, 7B, and 7D chromosomes. These genes, implicated in diverse functions related to plant growth, development, and stress responses, offer a rich resource for future investigation. A clustering pattern emerged, notably with seven genes associated with SSI for plant height and four genes linked to both STI of plant height and shoot dry weight, converging on specific regions of chromosome arms of 2AS and 3BL. Additionally, shared genes encoding polygalacturonase, auxilin-related protein 1, peptide deformylase, and receptor-like kinase underscored the interconnectedness between plant height and shoot dry weight. In conclusion, our findings provide insights into the molecular mechanisms governing wheat drought tolerance, identifying promising genomic loci for further exploration and crop improvement strategies. Graphical Abstract (1) A diverse panel of wheat genotypes was cultivated under both well-watered and drought stress conditions; (2) Phenotyping involved washing, scanning, drying and weighing plants to evaluate the stress susceptibility (SSI) and stress tolerance (STI) indices for four drought tolerance-related traits; (3) Genotyping was performed by extracting DNA and using the wheat 90 K Illumina iSelect array; (4) Phenotypic and genotypic data were utilized in a genome-wide association analysis (GWAS) using a mixed linear model (MLM); (5) Population structure assessment, principal component analysis (PCA), and kinship analysis were conducted; (6) Candidate genes were identified, and (7) their molecular functions were analysed and discussed.

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Genome-Wide Association Mapping for Yield and Related Traits Under Drought Stressed and Non-stressed Environments in Wheat

Cited by 16 publications

References 46 publications

Genome-Wide Association Study Reveals the Genetic Basis of Five Quality Traits in Chinese Wheat

Genome-Wide Association Study Reveals the Genetic Basis of Five Quality Traits in Chinese Wheat

Genetic analyses and prediction for lodging‑related traits in a diverse Iranian hexaploid wheat collection

Genome-wide association study of drought tolerance in wheat (Triticum aestivum L.) identifies SNP markers and candidate genes

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