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 Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Rubus Idaeus ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Red Raspberry ◽  
Genome Wide ◽  
A Genome ◽  
Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

Genetic dissection of 2-heptenal content in soybean (Glycine max) seed through genome-wide association study

2020 ◽  
Vol 71 (10) ◽  
pp. 884
Author(s):  
Zhikun Wang ◽  
Mingming Yang ◽  
Yuanzhuo Wang ◽  
Chao Yang ◽  
Xue Zhao ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Fatty Acid Content ◽  
Soybean Seed ◽  
Genome Wide Association ◽  
Quality Characteristic ◽  
Genome Wide ◽  
A Genome

Association analysis is an alternative to conventional, family-based methods for detecting the location of gene(s) or quantitative trait loci (QTLs), and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Flavour is an essential quality characteristic of soymilk; however, soymilk contains volatile compounds unacceptable to consumers. One of main constituents in the volatiles of normal soymilk is 2-heptenal, which is thought to be a degradative oxidation product of polyunsaturated acids. In this study, a genome-wide association study using 24651 single-nucleotide polymorphisms (SNPs) was performed to identify quantitative trait nucleotides (QTNs) controlling 2-heptenal content in soybean (Glycine max (L.) Merr.) seed from a natural population of 110 soybean germplasm accessions. We detected 62 significant QTNs located on 18 different chromosomes that are significantly associated with 2-heptenal content in soybean seed. Among these, 17 QTNs co-localised with QTLs previously found to be related to protein, oil and/or fatty acid content in soybean seed. We also identified some candidate genes involved in lipid metabolism. These findings further our understanding of the genetic basis of 2-heptenal content in soybean seed and the improvement of marker-assisted breeding efficiency, which will be important for breeding soybean cultivars with low 2-heptenal content.

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 A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content

2019 ◽  
Vol 20 (23) ◽  
pp. 5915 ◽  
Author(s):  
Tengfei Zhang ◽  
Tingting Wu ◽  
Liwei Wang ◽  
Bingjun Jiang ◽  
Caixin Zhen ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oil Content ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Soybean Seed ◽  
Snp Markers ◽  
Growth Stages ◽  
Breeding Programs ◽  
Genome Wide ◽  
Excellent Source

Soybean is an excellent source of vegetable protein and edible oil. Understanding the genetic basis of protein and oil content will improve the breeding programs for soybean. Linkage analysis and genome-wide association study (GWAS) tools were combined to detect quantitative trait loci (QTL) that are associated with protein and oil content in soybean. Three hundred and eight recombinant inbred lines (RILs) containing 3454 single nucleotide polymorphism (SNP) markers and 200 soybean accessions, including 94,462 SNPs and indels, were applied to identify QTL intervals and significant SNP loci. Intervals on chromosomes 1, 15, and 20 were correlated with both traits, and QTL qPro15-1, qPro20-1, and qOil5-1 reproducibly correlated with large phenotypic variations. SNP loci on chromosome 20 that overlapped with qPro20-1 were reproducibly connected to both traits by GWAS (p < 10−4). Twenty-five candidate genes with putative roles in protein and/or oil metabolisms within two regions (qPro15-1, qPro20-1) were identified, and eight of these genes showed differential expressions in parent lines during late reproductive growth stages, consistent with a role in controlling protein and oil content. The new well-defined QTL should significantly improve molecular breeding programs, and the identified candidate genes may help elucidate the mechanisms of protein and oil biosynthesis.

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.

scholarly journals Post-Genotyping Optimization of Dataset Formation Could Affect Genetic Diversity Parameters: An Example of Analyses with Alpine Goat Breeds

2020 ◽  
Author(s):  
Neža Pogorevc ◽  
Mojca Simčič ◽  
Negar Khayatzadeh ◽  
Johann Soelkner ◽  
Beate Berger ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Distances ◽  
Phylogenetic Study ◽  
European Alps ◽  
Global Context ◽  
Outlier Test ◽  
Snp Data ◽  
Genome Wide ◽  
A Genome

Abstract BackgroundLocal breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. One objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters.ResultsDistinct genetic origin of the Drežnica goat was demonstrated having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning.ConclusionsGenetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of the breeding and management programs and therefore important for preserving genetic variability and uniqueness of local rare breeds.

scholarly journals Enhanced NRT1.1/NPF6.3 expression in shoots improves growth under nitrogen deficiency stress in Arabidopsis

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yasuhito Sakuraba ◽  
Chaganzhana ◽  
Atsushi Mabuchi ◽  
Koh Iba ◽  
Shuichi Yanagisawa
Keyword(s):  
Plant Growth ◽  
Nitrate Uptake ◽  
Genome Wide Association Study ◽  
Nitrogen Deficiency ◽  
Breeding Programs ◽  
Promoter Sequences ◽  
Genome Wide ◽  
A Genome ◽  
N Deficiency ◽  
Low Nitrogen

AbstractIdentification of genes and their alleles capable of improving plant growth under low nitrogen (N) conditions is key for developing sustainable agriculture. Here, we show that a genome-wide association study using Arabidopsis thaliana accessions suggested an association between different magnitudes of N deficiency responses and diversity in NRT1.1/NPF6.3 that encodes a dual-affinity nitrate transporter involved in nitrate uptake by roots. Various analyses using accessions exhibiting reduced N deficiency responses revealed that enhanced NRT1.1 expression in shoots rather than in roots is responsible for better growth of Arabidopsis seedlings under N deficient conditions. Furthermore, polymorphisms that increased NRT1.1 promoter activity were identified in the NRT1.1 promoter sequences of the accessions analyzed. Hence, our data indicated that polymorphism-dependent activation of the NRT1.1 promoter in shoots could serve as a tool in molecular breeding programs for improving plant growth in low N environments.

scholarly journals Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava

2020 ◽  
Author(s):  
Ismail Yusuf Rabbi ◽  
Siraj Ismail Kayondo ◽  
Guillaume Bauchet ◽  
Muyideen Yusuf ◽  
Cynthia Idhigu Aghogho ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Carotenoid Content ◽  
Cassava Mosaic Disease ◽  
International Institute ◽  
Dry Matter Content ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome

AbstractCassava (Manihot esculenta) is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. Genetic progress in this clonally propagated crop can be accelerated through the discovery of markers and candidate genes that could be used in cassava breeding programs. We carried out a genome-wide association study (GWAS) using a panel of 5,310 clones developed at the International Institute of Tropical Agriculture - Nigeria. The population was genotyped at more than 100,000 SNP markers via genotyping-by-sequencing (GBS). Genomic regions underlying genetic variation for 14 traits classified broadly into four categories: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type). We also included several agro-morphological traits related to leaves, stems and roots with high heritability. In total, 41 significant associations were uncovered. While some of the identified loci matched with those previously reported, we present additional association signals for the traits. We provide a catalogue of favourable alleles at the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in cassava breeding programs and candidate genes for functional validation.

scholarly journals Genome-wide association analysis permits characterization of Stagonospora nodorum blotch (SNB) resistance in hard winter wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rami AlTameemi ◽  
Harsimardeep S. Gill ◽  
Shaukat Ali ◽  
Girma Ayana ◽  
Jyotirmoy Halder ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Stagonospora Nodorum ◽  
Complex Nature ◽  
Breeding Programs ◽  
Stagonospora Nodorum Blotch ◽  
Genome Wide ◽  
A Genome

AbstractStagonospora nodorum blotch (SNB) is an economically important wheat disease caused by the necrotrophic fungus Parastagonospora nodorum. SNB resistance in wheat is controlled by several quantitative trait loci (QTLs). Thus, identifying novel resistance/susceptibility QTLs is crucial for continuous improvement of the SNB resistance. Here, the hard winter wheat association mapping panel (HWWAMP) comprising accessions from breeding programs in the Great Plains region of the US, was evaluated for SNB resistance and necrotrophic effectors (NEs) sensitivity at the seedling stage. A genome-wide association study (GWAS) was performed to identify single‐nucleotide polymorphism (SNP) markers associated with SNB resistance and effectors sensitivity. We found seven significant associations for SNB resistance/susceptibility distributed over chromosomes 1B, 2AL, 2DS, 4AL, 5BL, 6BS, and 7AL. Two new QTLs for SNB resistance/susceptibility at the seedling stage were identified on chromosomes 6BS and 7AL, whereas five QTLs previously reported in diverse germplasms were validated. Allele stacking analysis at seven QTLs explained the additive and complex nature of SNB resistance. We identified accessions (‘Pioneer-2180’ and ‘Shocker’) with favorable alleles at five of the seven identified loci, exhibiting a high level of resistance against SNB. Further, GWAS for sensitivity to NEs uncovered significant associations for SnToxA and SnTox3, co-locating with previously identified host sensitivity genes (Tsn1 and Snn3). Candidate region analysis for SNB resistance revealed 35 genes of putative interest with plant defense response-related functions. The QTLs identified and validated in this study could be easily employed in breeding programs using the associated markers to enhance the SNB resistance in hard winter wheat.

scholarly journals Genetic Architecture of Early Vigor Traits in Wild Soybean

2020 ◽  
Vol 21 (9) ◽  
pp. 3105
Author(s):  
Janice Kofsky ◽  
Hengyou Zhang ◽  
Bao-Hua Song
Keyword(s):  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Current Increase ◽  
Snp Data ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean ◽  
Early Vigor

A worldwide food shortage has been projected as a result of the current increase in global population and climate change. In order to provide sufficient food to feed more people, we must develop crops that can produce higher yields. Plant early vigor traits, early growth rate (EGR), early plant height (EPH), inter-node length, and node count are important traits that are related to crop yield. Glycine soja, the wild counterpart to cultivated soybean, Glycine max, harbors much higher genetic diversity and can grow in diverse environments. It can also cross easily with cultivated soybean. Thus, it holds a great potential in developing soybean cultivars with beneficial agronomic traits. In this study, we used 225 wild soybean accessions originally from diverse environments across its geographic distribution in East Asia. We quantified the natural variation of several early vigor traits, investigated the relationships among them, and dissected the genetic basis of these traits by applying a Genome-Wide Association Study (GWAS) with genome-wide single nucleotide polymorphism (SNP) data. Our results showed positive correlation between all early vigor traits studied. A total of 12 SNPs significantly associated with EPH were identified with 4 shared with EGR. We also identified two candidate genes, Glyma.07G055800.1 and Glyma.07G055900.1, playing important roles in influencing trait variation in both EGR and EPH in G. soja.

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