Multi-locus genome-wide association studies reveal novel genomic regions associated with vegetative stage salt tolerance in bread wheat (Triticum aestivum L.)

Chaurasia, Sundeep; Singh, Amit Kumar; Songachan, L. S.; Sharma, Axma Dutt; Bhardwaj, Rakesh; Singh, Kuldeep

doi:10.1016/j.ygeno.2020.08.006

Cited by 37 publications

(27 citation statements)

References 70 publications

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“…In contrast to the conventional QTL approach, the AM approach enables screening of a large number of alleles present in natural populations of species, thus providing greater resolution mapping of a target trait. In the past couple of years, AM has been widely applied to map traits in many crop species including wheat, rice, barley (Hordeum vulgare L.), maize and soybean (Glycine max L. Merril) [21,[24][25][26][27] with the availability of high-throughput genotyping and phenotyping platforms [22,23].…”

Section: Introductionmentioning

confidence: 99%

Genetic Dissection of Seedling Root System Architectural Traits in a Diverse Panel of Hexaploid Wheat through Multi-Locus Genome-Wide Association Mapping for Improving Drought Tolerance

Danakumara

Kumari

Singh

et al. 2021

IJMS

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Cultivars with efficient root systems play a major role in enhancing resource use efficiency, particularly water absorption, and thus in drought tolerance. In this study, a diverse wheat association panel of 136 wheat accessions including mini core subset was genotyped using Axiom 35k Breeders’ Array to identify genomic regions associated with seedling stage root architecture and shoot traits using multi-locus genome-wide association studies (ML-GWAS). The association panel revealed a wide variation of 1.5- to 50- fold and were grouped into six clusters based on 15 traits. Six different ML-GWAS models revealed 456 significant quantitative trait nucleotides (QTNs) for various traits with phenotypic variance in the range of 0.12–38.60%. Of these, 87 QTNs were repeatedly detected by two or more models and were considered reliable genomic regions for the respective traits. Among these QTNs, eleven were associated with average diameter and nine each for second order lateral root number (SOLRN), root volume (RV) and root length density (RLD). A total of eleven genomic regions were pleiotropic and each controlled two or three traits. Some important candidate genes such as Formin homology 1, Ubiquitin-like domain superfamily and ATP-dependent 6-phosphofructokinase were identified from the associated genomic regions. The genomic regions/genes identified in this study could potentially be targeted for improving root traits and drought tolerance in wheat.

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Section: Introductionmentioning

confidence: 99%

Genetic Dissection of Seedling Root System Architectural Traits in a Diverse Panel of Hexaploid Wheat through Multi-Locus Genome-Wide Association Mapping for Improving Drought Tolerance

Danakumara

Kumari

Singh

et al. 2021

IJMS

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“…In rice, the extent of LD decay was found to be nearly 75-150 kb, which is slightly higher than that of mungbean [76]. However, in wheat, the extent of LD was 2.1 Mb for subgenome A, 4.2 Mb for subgenome D, and 5.9 Mb for subgenome B, which is very much higher when compared to mungbean [77]. Population structure analysis revealed the presence of five subpopulations, which were further confirmed by PCA and un-rooted phylogenetic tree formation.…”

Section: Discussionmentioning

confidence: 82%

“…The VRADI07G06240 is a zinc finger CCCH domain-containing protein that is found to be expressed under short-term P-deprivation conditions in soybean leaves [77]. Whereas the VRADI08G11310 gene encodes a bHLH domain-containing protein, that may be involved in root hair formation and thereby increasing the P uptake under P starvation conditions [78].…”

Section: Discussionmentioning

confidence: 99%

Genetic Dissection of Phosphorous Uptake and Utilization Efficiency Traits Using GWAS in Mungbean

et al. 2021

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Mungbean (Vignaradiata L. Wilczek) is an early maturing legume grown predominantly in Asia for its protein-rich seeds. P deficiency can lead to several physiological disorders which ultimately result in a low grain yield in mungbean. The genetic dissection of PUpE (Puptake efficiency) and PUtE (P utilization efficiency) traits are essential for breeding mungbean varieties with a high P uptake and utilization efficiency. The study involves an association mapping panel consisting of 120 mungbean genotypes which were phenotyped for total dry weight, P concentration, total P uptake, and P utilization efficiency under low P (LP) and normal P (NP) conditions in a hydroponic system. A genotyping-by-sequencing (GBS) based genome-wide association study (GWAS) approach was employed to dissect the complexity of PUpE and PUtE traits at the genetic level in mungbean. This has identified 116 SNPs in 61 protein-coding genes and of these, 16 have been found to enhance phosphorous uptake and utilization efficiency in mungbeans. We identified six genes with a high expression (VRADI01G04370, VRADI05G20860, VRADI06G12490, VRADI08G20910, VRADI08G00070 and VRADI09G09030) in root, shoot apical meristem and leaf, indicating their role in the regulation of P uptake and utilization efficiency in mungbean. The SNPs present in three genes have also been validated using a Sanger sequencing approach.

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“…Each K was run 3 times from K2 to K10 and based on results, the K7 estimate was selected and used in association. The signi cance of the tested molecular marker main effect at P≤0.0001 was considered as an indicator for the signi cance of the marker-trait association (Chaurasia et al 2020). Phenotypic data under either the control or stressed conditions were used to perform genome wide association analysis.…”

Section: Genome-wide Association and Structure Analysesmentioning

confidence: 99%

“…which may allow (Abou-Elwafa et al 2019; Fleury et al 2010). GWAS has proven as a useful approach for uncovering the complex genetic mechanisms governing tolerance to abiotic stress in several crop plants (Long et al 2013;Turki et al 2015 (Chaurasia et al 2020). Using 395675 SNP markers in a diversity panel of 323 wheat accessions, (Li et al 2020) identi ed 269 signi cant associations between phenotypic traits and SNP markers, from which 22 are overlapping with QTLs identi ed by bi-parental QTL mapping.…”

Section: Introductionmentioning

confidence: 99%

Identification of genomic regions associated with agronomical traits of bread wheat under two levels of salinity using GWAS

Alotaibi

Al-Qthanin

Aljabri

et al. 2021

Preprint

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Soil salinity is a major environmental stress that adversely impacts the growth, development, productivity and quality of crop species, in particular, in arid and semi-arid regions. Identification of chromosomal regions associated with agronomic traits under salinity stress is crucial for improving salinity tolerance in wheat. GWAS and structure analyses were employed to evaluate 289 elite lines of the Wheat Association Mapping Initiative (WAMI) population under low (LS) and high (HS) salinity conditions using 15,737 SNP markers and seven agronomical traits. Evaluated genotypes responded differently to the different environments in all measured phenotypic traits, highlighting genetic diversity within the WAMI population in response to salt stress. Heritability degree ranged from moderate (37%) to high (88%). GWAS identified 118 and 120 significant associations between SNP markers and seven evaluated phenotypic traits under LS and HS conditions, respectively. Significant association of some markers with more than one phenotypic trait was observed, indicating possible pleiotropic or indirect effects. A high degree of significant linkage disequilibrium (> 52%) was observed among SNP markers on different chromosomes indicating epistatic interaction. The salt stress index (STI) exhibited a positive significant correlation to grain yield per plant (GYP) under both LS and HS conditions (R2 = 0.851–0.856). A linear regression between STI and GYP under HS conditions (GYPs) was identified, suggest that STI is the best tolerance index for predicting high yielding-genotypes. The results present the WAMI population as a valuable source for improving yield potential for salt tolerance in wheat. Furthermore, our findings emphasize that GWAS is a powerful tool in promoting wheat breeding through accurate identification of molecular markers significantly associated with agronomic traits, which is essential for marker-assisted breeding.

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Multi-locus genome-wide association studies reveal novel genomic regions associated with vegetative stage salt tolerance in bread wheat (Triticum aestivum L.)

Cited by 37 publications

References 70 publications

Genetic Dissection of Seedling Root System Architectural Traits in a Diverse Panel of Hexaploid Wheat through Multi-Locus Genome-Wide Association Mapping for Improving Drought Tolerance

Genetic Dissection of Seedling Root System Architectural Traits in a Diverse Panel of Hexaploid Wheat through Multi-Locus Genome-Wide Association Mapping for Improving Drought Tolerance

Genetic Dissection of Phosphorous Uptake and Utilization Efficiency Traits Using GWAS in Mungbean

Identification of genomic regions associated with agronomical traits of bread wheat under two levels of salinity using GWAS

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