scholarly journals Phenotypic Diversity and Association Mapping of Ascorbic Acid Content in Spinach

2022 ◽  
Vol 12 ◽  
Author(s):  
Dario Rueda ◽  
Henry O. Awika ◽  
Renesh Bedre ◽  
Devi R. Kandel ◽  
Kranthi K. Mandadi ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Linear Model ◽  
Genome Wide Association Study ◽  
Phenotypic Diversity ◽  
Ascorbic Acid Content ◽  
Bioinformatic Analysis ◽  
Mixed Linear Model ◽  
Nutritional Content ◽  
Breeding Programs ◽  
A Genome

Ascorbic acid (AsA), or vitamin C, is an essential nutrient for humans. In plants, AsA functions as an antioxidant during normal metabolism or in response to stress. Spinach is a highly nutritious green leafy vegetable that is consumed fresh, cooked or as a part of other dishes. One current goal in spinach breeding programs is to enhance quality and nutritional content. However, little is known about the diversity of nutritional content present in spinach germplasm, especially for AsA content. In this study, a worldwide panel of 352 accessions was screened for AsA content showing that variability in spinach germplasm is high and could be utilized for cultivar improvement. In addition, a genome-wide association study for marker-trait association was performed using three models, and associated markers were searched in the genome for functional annotation analysis. The generalized linear model (GLM), the compressed mixed linear model (CMLM) based on population parameters previously determined (P3D) and the perMarker model together identified a total of 490 significant markers distributed across all six spinach chromosomes indicating the complex inheritance of the trait. The different association models identified unique and overlapping marker sets, where 27 markers were identified by all three models. Identified high AsA content accessions can be used as parental lines for trait introgression and to create segregating populations for further genetic analysis. Bioinformatic analysis indicated that identified markers can differentiate between high and low AsA content accessions and that, upon validation, these markers should be useful for breeding programs.

scholarly journals Genetic analysis of sucrose concentration in soybean seeds using a historical soybean genomic panel

2021 ◽  
Author(s):  
Alexandra Ficht ◽  
Robert W. Bruce ◽  
Davoud Torkamaneh ◽  
Christopher Grainger ◽  
Milad Eskandari ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genome Wide Association Study ◽  
Sucrose Concentration ◽  
Soybean Seed ◽  
Breeding Programs ◽  
Snp Data ◽  
Genome Wide ◽  
A Genome ◽  
Important Trait ◽  
Genotype By Sequencing

Abstract Soybean (Glycine max (L.) Merr) is a crop of global importance for both human and animal consumption, which was domesticated in China more than 6000 years ago. A concern about losing genetic diversity as a result of decades of breeding has been expressed by soybean researchers. In order to develop new cultivars, it is critical for breeders to understand the genetic variability present for traits of interest in their program germplasm. Sucrose concentration is becoming an increasingly important trait for the production of soy-food products. The objective of this study was to use a genome-wide association study (GWAS) to identify putative QTL for sucrose concentration in soybean seed. A GWAS panel consisting of 266 historic and current soybean accessions was genotyped with 76k genotype-by-sequencing (GBS) SNP data and phenotyped in four field locations in Ontario (Canada) from 2015 to 2017. Seven putative QTL were identified on chromosomes 1, 6, 8, 9, 10, 13 and 14. A key gene related to sucrose synthase (Glyma.06g182700) was found to be associated with the QTL found on chromosome 6. This information will facilitate efforts to increase the available genetic variability for sucrose concentration in soybean breeding programs and develop new and improved high-sucrose soybean cultivars suitable for the soy-food industry.

scholarly journals Diurnal Variations in Physiological Characteristics, Photoassimilates, and Total Ascorbate in Early and Late Sown Indian Wheat Cultivars under Exposure to Elevated Ozone

Atmosphere ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1568
Author(s):  
Durgesh Singh Yadav ◽  
Bhavna Jaiswal ◽  
Shashi Bhushan Agrawal ◽  
Madhoolika Agrawal
Keyword(s):  
Ascorbic Acid ◽  
Ascorbic Acid Content ◽  
Triticum Aestivum L ◽  
Diurnal Changes ◽  
Wheat Cultivars ◽  
Negative Effects ◽  
Breeding Programs ◽  
Elevated O3 ◽  
Elevated Ozone ◽  
Selection Of

Rising tropospheric ozone (O3) in the atmosphere is detrimental to crop’s productivity and is one of the reasons for a warmer climate. The present study describes diurnal changes in gaseous exchange, chlorophyll fluorescence, ascorbic acid, and photoassimilate parameters in flag leaves of four Indian wheat (Triticum aestivum L.) cultivars (two early sown and two late sown cultivars) under ambient and elevated O3 treatments, using the open-top chambers (OTCs). Results showed that the diurnal pattern of photosynthetic rate (Ps), sucrose, and ascorbic acid content varied according to changes in photosynthetically active radiation (PAR) and O3 concentrations during the daytime and were maximum between 10:00 to 12:00. The present study suggested that elevated O3 caused more negative effects on photosystem II in early sown compared to late sown cultivars. The greater loss of photosynthesis led to lower production of photoassimilates in early sown cultivars, which utilized more assimilates in ascorbic acid formation for detoxification of ROS formed due to elevated O3. This work will also help to identify the robustness of physiological machinery in different wheat cultivars under elevated levels of O3, and may be used for selection of suitable cultivars during future breeding programs.

scholarly journals Genetics of Germination and Seedling Traits under Drought Stress in a MAGIC Population of Maize

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1786
Author(s):  
Soumeya Rida ◽  
Oula Maafi ◽  
Ana López-Malvar ◽  
Pedro Revilla ◽  
Meriem Riache ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Genome Wide Association Study ◽  
Genetic Regulation ◽  
Breeding Programs ◽  
Seedling Traits ◽  
Genome Wide ◽  
A Genome ◽  
Positive Correlations ◽  
Genomic Regions ◽  
Magic Population

Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance.

scholarly journals MULTI-TRAIT MODELS FOR GENOMIC REGIONS ASSOCIATED WITH MAL DE RÍO CUARTO AND BACTERIAL DISEASE IN MAIZE

2021 ◽  
Vol 32 (Issue 1) ◽  
pp. 25-33
Author(s):  
M. Ruiz ◽  
E.A. Rossi ◽  
N.C. Bonamico ◽  
M.G. Balzarini
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Bacterial Disease ◽  
Maize Germplasm ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Maize (Zea Mays L.) production has been greatly benefited from the improvement of inbred lines in regard to the resistance to diseases. However, the absence of resistant genotypes to bacteriosis is remarkable. The aim of the study was to identify genomic regions for resistance to Mal de Río Cuarto (MRC) and to bacterial disease (BD) in a diverse maize germplasm evaluated in the Argentinian region where MRC virus is endemic. A maize diverse population was assessed for both diseases during the 2019-2020 crop season. Incidence and severity of MRC and BD were estimated for each line and a genome wide association study (GWAS) was conducted with 78,376 SNP markers. A multi-trait mixed linear model was used for simultaneous evaluation of resistance to MRC and BD in the scored lines. The germplasm showed high genetic variability for both MRC and BD resistance. No significant genetic correlation was observed between the response to both diseases. Promising genomic regions for resistance to MRC and BD were identified and will be confirmed in further trials. Key words: maize disease; genome wide association study; SNP; multi-trait model

scholarly journals MULTI-TRAIT MODELS FOR GENOMIC REGIONS ASSOCIATED WITH MAL DE RÍO CUARTO AND BACTERIAL DISEASE IN MAIZE

2021 ◽  
Vol 32 (Issue 1) ◽  
pp. 25-33
Author(s):  
M. Ruiz ◽  
E.A. Ross ◽  
N.C. Bonamico ◽  
M.G. Balzarini
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Bacterial Disease ◽  
Maize Germplasm ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Maize (Zea Mays L.) production has been greatly benefited from the improvement of inbred lines in regard to the resistance to diseases. However, the absence of resistant genotypes to bacteriosis is remarkable. The aim of the study was to identify genomic regions for resistance to Mal de Río Cuarto (MRC) and to bacterial disease (BD) in a diverse maize germplasm evaluated in the Argentinian region where MRC virus is endemic. A maize diverse population was assessed for both diseases during the 2019-2020 crop season. Incidence and severity of MRC and BD were estimated for each line and a genome wide association study (GWAS) was conducted with 78,376 SNP markers. A multi-trait mixed linear model was used for simultaneous evaluation of resistance to MRC and BD in the scored lines. The germplasm showed high genetic variability for both MRC and BD resistance. No significant genetic correlation was observed between the response to both diseases. Promising genomic regions for resistance to MRC and BD were identified and will be confirmed in further trials. Key words: maize disease; genome wide association study; SNP; multi-trait model

scholarly journals Genome-wide association study uncovers major genetic loci associated with seed flooding tolerance in soybean

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ripa Akter Sharmin ◽  
Benjamin Karikari ◽  
Fangguo Chang ◽  
G.M. Al Amin ◽  
Mashiur Rahman Bhuiyan ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Linear Model ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Mixed Linear Model ◽  
Genome Wide Association ◽  
Flooding Tolerance ◽  
Genome Wide ◽  
Germination Stage

Abstract Background Seed flooding stress is one of the threatening environmental stressors that adversely limits soybean at the germination stage across the globe. The knowledge on the genetic basis underlying seed-flooding tolerance is limited. Therefore, we performed a genome-wide association study (GWAS) using 34,718 single nucleotide polymorphism (SNPs) in a panel of 243 worldwide soybean collections to identify genetic loci linked to soybean seed flooding tolerance at the germination stage. Results In the present study, GWAS was performed with two contrasting models, Mixed Linear Model (MLM) and Multi-Locus Random-SNP-Effect Mixed Linear Model (mrMLM) to identify significant SNPs associated with electrical conductivity (EC), germination rate (GR), shoot length (ShL), and root length (RL) traits at germination stage in soybean. With MLM, a total of 20, 40, 4, and 9 SNPs associated with EC, GR, ShL and RL, respectively, whereas in the same order mrMLM detected 27, 17, 13, and 18 SNPs. Among these SNPs, two major SNPs, Gm_08_11971416, and Gm_08_46239716 were found to be consistently connected with seed-flooding tolerance related traits, namely EC and GR across two environments. We also detected two SNPs, Gm_05_1000479 and Gm_01_53535790 linked to ShL and RL, respectively. Based on Gene Ontology enrichment analysis, gene functional annotations, and protein-protein interaction network analysis, we predicted eight candidate genes and three hub genes within the regions of the four SNPs with Cis-elements in promoter regions which may be involved in seed-flooding tolerance in soybeans and these warrant further screening and functional validation. Conclusions Our findings demonstrate that GWAS based on high-density SNP markers is an efficient approach to dissect the genetic basis of complex traits and identify candidate genes in soybean. The trait associated SNPs could be used for genetic improvement in soybean breeding programs. The candidate genes could help researchers better understand the molecular mechanisms underlying seed-flooding stress tolerance in soybean.

scholarly journals Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
João Vitor Maldonado dos Santos ◽  
Everton Geraldo Capote Ferreira ◽  
André Luiz de Lima Passianotto ◽  
Bruna Bley Brumer ◽  
Adriana Brombini Dos Santos ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Major Gene ◽  
Cost Effective ◽  
Stem Canker ◽  
Snp Marker ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
A Genome ◽  
Marker Assay

Abstract Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. Results We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. Conclusions Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.

scholarly journals Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Şakir Burak Bükücü ◽  
Mehmet Sütyemez ◽  
Sina Kefayati ◽  
Aibibula Paizila ◽  
Abdulqader Jighly ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Juglans Regia ◽  
Genotypic Variation ◽  
Phenotypic Traits ◽  
Juvenile Period ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome ◽  
Major Qtl

Abstract Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2 between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.

Genome-Wide association study identifies new elements on the genetic basis of quality-related traits in wheat across multiple environments

2020 ◽  
Author(s):  
Zhien Pu ◽  
Xueling Ye ◽  
Yang Li ◽  
Zehou Liu ◽  
Bingxin Shi ◽  
...  
Keyword(s):  
Association Study ◽  
Complex Traits ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Mixed Linear Model ◽  
Genome Wide Association ◽  
Phenotypic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Abstract Backgrounds: Grain protein concentration (GPC), grain starch concentration (GSC), and wet gluten concentration (WGC) are complex traits that determine nutrient concentration, end-use quality, and yield in wheat. To identify the elite and stable loci or genomic regions conferring high GPC, GSC, and WGC, a genome-wide association study (GWAS) based on a mixed linear model (MLM) was performed using 55K single nucleotide polymorphism (SNP) array in a panel of 236 wheat accessions, including 160 commercial varieties and 76 landraces, derived from Sichuan Province, China. The panel was evaluated for GPC, GSC, and WGC at four different fields. Results: Phenotypic analysis showed variation in GPC, GSC, and WGC among the different genotypes and environments. GWAS identified 12 quantitative trait loci (QTL) (-log10(P) > 2.5) associated with these three quality traits in at least two environments and located on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 5D, and 7D; the phenotypic variation explained (PVE) by these QTL ranged from 4.2% to 10.7%. Among these, three, seven, and two QTL are associated with GPC, GSC, and WGC, respectively; five QTL (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were defined potentially novel Compared with the previously reported QTLs/genes by linkage or association mapping, 5 QTLs (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were potentially novel. Furthermore, 21 presumptive candidate genes, which are involved in the metabolism or transportation of all kinds of carbohydrates, photosynthesis, programmed cell death, the balance of abscisic acid and ethylene, within these potentially novel genomic regions were predicted. Conclusions: This study provided new genetic resources and valuable genetic information of nutritional quality to broaden the genetic background and laid the molecular foundation for marker-assisted selection in wheat quality breeding.

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