Genome-Wide Association Mapping of Seedling Vigor and Regrowth Vigor in Winter Wheat

Drought is a major constraint in wheat (Triticum aestivum L.) grain yield. The present work aimed to identify quantitative trait nucleotides (QTNs)/ candidate genes influencing drought tolerance-related traits at the seedling stage in 261 accessions of a diverse winter wheat panel. Seeds from three consecutive years were exposed to polyethylene glycol 12% (PEG-6000) and a control treatment (distilled water). The Farm-CPU method was used for the association analysis with 17,093 polymorphic SNPs. PEG treatment reduced shoot length (SL) (-36.3%) and root length (RL) (-11.3%) compared with control treatments, while the coleoptile length (CL) was increased by 11% under drought conditions, suggesting that it might be considered as an indicator of stress-tolerance. Interestingly, we revealed 70 stable QTN across 17 chromosomes. Eight QTNs related to more than one trait were detected on chromosomes 1B, 2A (2), 2B, 2D, 4B, 7A, and 7B and located nearby or inside candidate genes within the linkage disequilibrium (LD) interval. For instance, the QTN on chromosome 2D is located inside the gene TraesCS2D02G133900 that controls the variation of CL_S and SL_C. The allelic variation at the candidate genes showed significant influence on the associated traits, demonstrating their role in controlling the natural variation of multi-traits of drought stress tolerance. The gene expression of these candidate genes under different stress conditions validates their biological role in stress tolerance. Our findings offer insight into understanding the genetic factors and diverse mechanisms in response to water shortage conditions that are important for wheat improvement and adaptation at early developmental stages.

Section: Introductionmentioning

confidence: 95%

Association mapping unravels the genetics controlling seedling drought stress tolerance in winter wheat

Schierenbeck

Alqudah²,

Thabet³

et al. 2023

“…The literature reported the importance of this gene in influencing floral organ differentiation, cell wall biogenesis and degradation, and spike differentiation ( Zhu et al., 2016 ). A BLAST search revealed an association with a candidate gene, aminopeptidase M1-B , involved in plant developmental processes such as embryonic, vegetative, and reproductive development in agreement with Maulana et al. (2021) in wheat.…”

Section: Discussionmentioning

confidence: 94%

Meta-QTL analysis and candidate genes for quality traits, mineral content, and abiotic-related traits in wild emmer

Cabas-Lühmann,

Schwember,

Arriagada

et al. 2024

Wild emmer (Triticum turgidum ssp. dicoccoides) genotypes were studied for their high-nutritional value and good tolerance to various types of stress; for this reason, several QTL (quantitative trait loci) studies have been conducted to find favorable alleles to be introgressed into modern wheat cultivars. Given the complexity of the QTL nature, their interaction with the environment, and other QTLs, a small number of genotypes have been used in wheat breeding programs. Meta-QTL (MQTL) analysis helps to simplify the existing QTL information, identifying stable genomic regions and possible candidate genes for further allele introgression. The study aimed to identify stable QTL regions across different environmental conditions and genetic backgrounds using the QTL information of the past 14 years for different traits in wild emmer based upon 17 independent studies. A total of 41 traits were classified as quality traits (16), mineral composition traits (11), abiotic-related traits (13), and disease-related traits (1). The analysis revealed 852 QTLs distributed across all 14 chromosomes of wild emmer, with an average of 61 QTLs per chromosome. Quality traits had the highest number of QTLs (35%), followed by mineral content (33%), abiotic-related traits (28%), and disease-related traits (4%). Grain protein content (GPC) and thousand kernel weight (TKW) were associated with most of the QTLs detected. A total of 43 MQTLs were identified, simplifying the information, and reducing the average confidence interval (CI) from 22.6 to 4.78 cM. These MQTLs were associated with multiple traits across different categories. Nine candidate genes were identified for several stable MQTLs, potentially contributing to traits such as quality, mineral content, and abiotic stress resistance. These genes play essential roles in various plant processes, such as carbohydrate metabolism, nitrogen assimilation, cell wall biogenesis, and cell wall extensibility. Overall, this study underscores the importance of considering MQTL analysis in wheat breeding programs, as it identifies stable genomic regions associated with multiple traits, offering potential solutions for improving wheat varieties under diverse environmental conditions.

“…Most of these studies were conducted at reproductive stages. However, the number of studies identifying MTAs for seedling drought stress tolerance are scarce ( Ayalew et al., 2017 ; Ma et al., 2020 ; Maulana et al., 2020 , Maulana et al., 2021 ; Ahmed et al., 2022 ; Schierenbeck et al., 2023 ). Therefore, in the present study, we carried GWAS using 12,511 SNPs and identified 39 MTAs associated with seedling characteristics under controlled and drought stress.…”

Section: Discussionmentioning

confidence: 99%

“…Since wheat seedlings are crucial in determining plant stand and grain yield, researchers are now prioritizing their studies at seedling stage. For instance, multiple GWAS studies identified the significant MTAs associated with germination percentage (GP), shoot length (SL) ( Maulana et al., 2020 ), root length (RL) ( Ayalew et al., 2017 ), coleoptile length (CL) ( Ma et al., 2020 ), seedling vigour (SV) ( Maulana et al., 2021 ), and drought tolerance index (DTI) ( Schierenbeck et al., 2023 ) under drought stress. These studies identified the candidate genomic regions associated with seedling drought stress tolerance.…”

Section: Introductionmentioning

confidence: 99%

Deciphering the genetic landscape of seedling drought stress tolerance in wheat (Triticum aestivum L.) through genome-wide association studies

Gudi,

Halladakeri,

Singh

et al. 2024

Wheat is an important cereal crop constrained by several biotic and abiotic stresses including drought stress. Understating the effect of drought stress and the genetic basis of stress tolerance is important to develop drought resilient, high-yielding wheat cultivars. In this study, we investigated the effects of drought stress on seedling characteristics in an association panel consisting of 198 germplasm lines. Our findings revealed that drought stress had a detrimental effect on all the seedling characteristics under investigation with a maximum effect on shoot length (50.94% reduction) and the minimum effect on germination percentage (7.9% reduction). To gain a deeper understanding, we conducted a genome-wide association analysis using 12,511 single nucleotide polymorphisms (SNPs), which led to the identification of 39 marker-trait associations (MTAs). Of these 39 MTAs, 13 were particularly noteworthy as they accounted for >10% of the phenotypic variance with a LOD score >5. These high-confidence MTAs were further utilized to extract 216 candidate gene (CGs) models within 1 Mb regions. Gene annotation and functional characterization identified 83 CGs with functional relevance to drought stress. These genes encoded the WD40 repeat domain, Myb/SANT-like domain, WSD1-like domain, BTB/POZ domain, Protein kinase domain, Cytochrome P450, Leucine-rich repeat domain superfamily, BURP domain, Calmodulin-binding protein60, Ubiquitin-like domain, etc. Findings from this study hold significant promise for wheat breeders as they provide direct assistance in selecting lines harboring favorable alleles for improved drought stress tolerance. Additionally, the identified SNPs and CGs will enable marker-assisted selection of potential genomic regions associated with enhanced drought stress tolerance in wheat.