Genome-wide association mapping and candidate gene analysis for seed shape in soybean (Glycine max)

2019 ◽  
Vol 70 (8) ◽  
pp. 684 ◽  
Author(s):  
Xue Zhao ◽  
Wenjing Li ◽  
Xiaoyue Zhao ◽  
Jinyang Wang ◽  
Zhiyang Liu ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Analysis ◽  
Quantitative Trait ◽  
Molecular Mechanisms ◽  
Environmental Stability ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Seed Shape ◽  
Genome Wide ◽  
Genomic Regions

Seed shape (SS) of soybean (Glycine max (L.) Merr.) is an important morphological trait that significantly affects the quality of marketable seed. Study of the genetic architecture of SS is important and basic to soybean molecular breeding. In the present study, a natural soybean population of 202 diverse accessions mainly from China was used to analyse the genetic basis of SS via genome-wide association analysis (GWAS), which was based on single-nucleotide polymorphisms (SNP) generated by specific-locus amplified fragment sequencing method. In total, 27335 SNPs were finally identified with minor allele frequencies >5%. By using GWAS, 14 quantitative trait nucleotides (QTNs) were identified to be associated with seed length, 13 with seed width and 21 with seed thickness in four tested environments. Among these QTNs, 21 QTNs overlapped or were located in the linked genomic regions of the reported quantitative trait loci related to SS or seed weight; and the other 27 QTNs were novel loci for SS. Ten QTNs showed environmental stability and were detected under at least two environments. In total, 83 genes were predicted in the 200-kbp flanking region of six stable QTNs that could be detected under >three environments. Gene-based association analysis was performed by using 38 accessions of diverse SS; 778 SNPs were found in the 83 genes based on 38 accessions, and 270 SNPs from 41 genes were found significantly associated with SS. Twenty-eight genes were environmentally stable and/or pleiotropic in controlling two or more SS-related traits at the same time. The identified loci along with the candidate genes could be of great value for studying the molecular mechanisms underlying SS and improving the potential seed yield of soybean.

A genome-wide association study of hexanal content related to soymilk off-flavours in seed of soybean (Glycine max)

2020 ◽  
Vol 71 (6) ◽  
pp. 552 ◽  
Author(s):  
Zhikun Wang ◽  
Gege Bao ◽  
Chao Yang ◽  
Mingming Yang ◽  
Xue Zhao ◽  
...  
Keyword(s):  
Glycine Max ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Molecular Mechanisms ◽  
Fatty Acid Content ◽  
Soybean Seed ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Hexanal Content

Flavour is an essential quality characteristic of soymilk; however, it contains volatile compounds unacceptable to consumers. Hexanal is the most important flavour compound that gives a sensory beany, grassy flavour in the soymilk. An effective way to reduce hexanal content in soymilk is to screen for and utilise cultivars of soybean (Glycine max (L.) Merr.) with lower hexanal content. The objective of the present study was to dissect the genetic basis of hexanal content in soybean seed by using genome-wide association analysis (GWAS), thereby providing guidance for the selection and breeding of soybean varieties with low hexanal content. We used 24651 single-nucleotide polymorphisms (SNPs) and screened seeds from 111 cultivated soybean accessions to identify quantitative trait nucleotides (QTNs) affecting hexanal content. We discovered 14 novel QTNs located on five different chromosomes that are significantly associated with hexanal content in soybean seed. Among these, 11 QTNs co-localised with quantitative trait loci previously found in linkage or association mapping studies related to protein, oil and/or fatty acid content in soybean seed. We also identified some candidate genes involved in amino acid metabolism, protein content, lipid metabolism and hormone metabolism. Six cultivars with low hexanal content were identified by screening. This is the first GWAS study on hexanal content in soybean seed, and a number of QTNs and candidate genes were identified. Some of these may be useful to breeders for the improvement of marker-assisted breeding efficiency for low hexanal content and may be useful for exploring possible molecular mechanisms underlying hexanal content in soybean seed.

scholarly journals Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

2021 ◽  
Vol 7 (11) ◽  
pp. eabd1239
Author(s):  
Mark Simcoe ◽  
Ana Valdes ◽  
Fan Liu ◽  
Nicholas A. Furlotte ◽  
David M. Evans ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Color Variation ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Melanin Pigmentation ◽  
Eye Color ◽  
Human Eye ◽  
Genome Wide ◽  
Genomic Regions

Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human 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 Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

2021 ◽  
Vol 12 ◽  
Author(s):  
Kelechi Uchendu ◽  
Damian Ndubuisi Njoku ◽  
Agre Paterne ◽  
Ismail Yusuf Rabbi ◽  
Daniel Dzidzienyo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome ◽  
Breeding Programmes ◽  
Vegetables And Fruits ◽  
Genomic Regions

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

scholarly journals The ABO blood group locus and a chromosome 3 gene cluster associate with SARS-CoV-2 respiratory failure in an Italian-Spanish genome-wide association analysis

2020 ◽  
Author(s):  
David Ellinghaus ◽  
Frauke Degenhardt ◽  
Luis Bujanda ◽  
Maria Buti ◽  
Agustín Albillos ◽  
...  
Keyword(s):  
Respiratory Failure ◽  
Blood Group ◽  
Association Analysis ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Group Locus

ABSTRACTBackgroundRespiratory failure is a key feature of severe Covid-19 and a critical driver of mortality, but for reasons poorly defined affects less than 10% of SARS-CoV-2 infected patients.MethodsWe included 1,980 patients with Covid-19 respiratory failure at seven centers in the Italian and Spanish epicenters of the SARS-CoV-2 pandemic in Europe (Milan, Monza, Madrid, San Sebastian and Barcelona) for a genome-wide association analysis. After quality control and exclusion of population outliers, 835 patients and 1,255 population-derived controls from Italy, and 775 patients and 950 controls from Spain were included in the final analysis. In total we analyzed 8,582,968 single-nucleotide polymorphisms (SNPs) and conducted a meta-analysis of both case-control panels.ResultsWe detected cross-replicating associations with rs11385942 at chromosome 3p21.31 and rs657152 at 9q34, which were genome-wide significant (P<5×10−8) in the meta-analysis of both study panels, odds ratio [OR], 1.77; 95% confidence interval [CI], 1.48 to 2.11; P=1.14×10−10 and OR 1.32 (95% CI, 1.20 to 1.47; P=4.95×10−8), respectively. Among six genes at 3p21.31, SLC6A20 encodes a known interaction partner with angiotensin converting enzyme 2 (ACE2). The association signal at 9q34 was located at the ABO blood group locus and a blood-group-specific analysis showed higher risk for A-positive individuals (OR=1.45, 95% CI, 1.20 to 1.75, P=1.48×10−4) and a protective effect for blood group O (OR=0.65, 95% CI, 0.53 to 0.79, P=1.06×10−5).ConclusionsWe herein report the first robust genetic susceptibility loci for the development of respiratory failure in Covid-19. Identified variants may help guide targeted exploration of severe Covid-19 pathophysiology.

Genome-wide association analysis identifies quantitative trait loci for growth in a Landrace purebred population

2014 ◽  
Vol 45 (3) ◽  
pp. 442-444 ◽  
Author(s):  
E. J. Jung ◽  
H. B. Park ◽  
J. B. Lee ◽  
C. K. Yoo ◽  
B. M. Kim ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Association Analysis ◽  
Quantitative Trait ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
Trait Loci
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