scholarly journals GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

2020 ◽  
Author(s):  
Lunwen Qian ◽  
Min Yao ◽  
Mei Guan ◽  
Zhenqian Zhang ◽  
Yixin Cui ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Candidate Genes ◽  
Acid Content ◽  
Complex Traits ◽  
Snp Array ◽  
Oleic Acid Content ◽  
Crop Species ◽  
Genome Wide ◽  
A Genome ◽  
Chromosome Haplotype

Abstract Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We use the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes ( BnmtACP2-A02 , BnABCI13-A02 and BnECI1-A02 ) in the A02 chromosome haplotype region and two genes ( BnFAD8-C02 and BnSDP1-C02 ) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

scholarly journals GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

2020 ◽  
Author(s):  
Min Yao ◽  
Mei Guan ◽  
Zhenqian Zhang ◽  
Qiuping Zhang ◽  
Yixin Cui ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Candidate Genes ◽  
Acid Content ◽  
Complex Traits ◽  
Snp Array ◽  
Oleic Acid Content ◽  
Crop Species ◽  
Genome Wide ◽  
A Genome ◽  
Chromosome Haplotype

Abstract Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We use the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes ( BnmtACP2-A02 , BnABCI13-A02 and BnECI1-A02 ) in the A02 chromosome haplotype region and two genes ( BnFAD8-C02 and BnSDP1-C02 ) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

scholarly journals GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

2019 ◽  
Author(s):  
Lunwen Qian ◽  
Min Yao ◽  
Mei Guan ◽  
Zhenqian Zhang ◽  
Qiuping Zhang ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Candidate Genes ◽  
Acid Content ◽  
Complex Traits ◽  
Snp Array ◽  
Oleic Acid Content ◽  
Crop Species ◽  
Genome Wide ◽  
A Genome ◽  
Chromosome Haplotype

Abstract Abstract Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS in combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We used the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02 and C03. Additionally, whole-genome sequencing of 50 rapeseed lines revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

scholarly journals GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

2019 ◽  
Author(s):  
Lunwen Qian ◽  
Min Yao ◽  
Mei Guan ◽  
Zhenqian Zhang ◽  
Qiuping Zhang ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Candidate Genes ◽  
Acid Content ◽  
Complex Traits ◽  
Snp Array ◽  
Oleic Acid Content ◽  
Crop Species ◽  
Genome Wide ◽  
A Genome ◽  
Chromosome Haplotype

Abstract Abstract Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS in combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We used the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02 and C03. Additionally, whole-genome sequencing of 50 rapeseed lines revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

scholarly journals GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

2019 ◽  
Author(s):  
Lunwen Qian ◽  
Min Yao ◽  
Mei Guan ◽  
Zhenqian Zhang ◽  
Qiuping Zhang ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Candidate Genes ◽  
Acid Content ◽  
Complex Traits ◽  
Snp Array ◽  
Oleic Acid Content ◽  
Crop Species ◽  
Genome Wide ◽  
A Genome ◽  
Chromosome Haplotype

Abstract Abstract Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS in combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We used the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02 and C03. Additionally, whole-genome sequencing of 50 rapeseed lines revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

Genome-Wide association Study Identifies Candidate Genes Related to Oleic acid content of Soybean Seed

2020 ◽  
Author(s):  
Pi-wu Wang ◽  
Qin Di ◽  
Xiao-Yi Liu
Keyword(s):  
Oleic Acid ◽  
Candidate Genes ◽  
Acid Content ◽  
Genome Wide Association Study ◽  
Soybean Seed ◽  
Oleic Acid Content ◽  
Chromosome 4 ◽  
Chromosome 11 ◽  
High Oleic ◽  
Genome Wide

Abstract Background: Soybeans [Glycine max (L.) Merr] originated in China and has been cultivated for more than 3000 years. Soybean oil is a complex mixture of five fatty acids (palmitic, stearic, oleic, linoleic, and linolenic). Soybean oil with high oleic acid content is desirable because this monounsaturated fatty acid improves the oxidative stability of the oil. To investigate the genetic architecture of oleic acid in soybean seed. 260 Soybean germplasms from Northeast China were collected as the natural population. A genome-wide association study (GWAS) was conducted in a panel of 260 germplasm resources.Results: Phenotypic identification result showed that the content of oleic acid varied from 8.2% to 35.0%. 2,311,337 single nucleotide polymorphism (SNP) markers were obtained. GWAS analysis showed that there were many genes related to oleic acid content with contribution rate 7%. The candidate genes Glyma.11G229600.1 on chromosome 11 and Glyma.04G102900.1 on chromosome 4 were detected in a 2-year long GWAS. The candidate gene Glyma.11G229600.1 showed a positive correlation with the oleic acid content, and the correlation coefficient was 0.980, while Glyma.04G102900.1 showed a negative correlation with the oleic acid content. The correlation coefficient was -0.964.Conclusions: Glyma.04G102900.1 on chromosome 4 and Glyma.11G229600.1 on chromosome 11 were detected in both anaylsis (2018 and 2019). Glyma.04G102900.1 and Glyma.11G229600.1 are new key candidate genes related to oleic acid in soybean seeds.These results will be useful for High-oleic soybean breeding.

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.

scholarly journals Genome-Wide Association Study Reveals Candidate Genes Involved in Fruit Trait Variation in Persian Walnut (Juglans regia L.)

2021 ◽  
Vol 11 ◽  
Author(s):  
Anthony Bernard ◽  
Julie Crabier ◽  
Armel S. L. Donkpegan ◽  
Annarita Marrano ◽  
Fabrice Lheureux ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Fruit Quality ◽  
Genome Wide Association Study ◽  
Juglans Regia ◽  
Snp Array ◽  
Germplasm Collection ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Elucidating the genetic determinants of fruit quality traits in walnut is essential to breed new cultivars meeting the producers and consumers’ needs. We conducted a genome-wide association study (GWAS) using multi-locus models in a panel of 170 accessions of Juglans regia from the INRAE walnut germplasm collection, previously genotyped using the AxiomTMJ. regia 700K SNP array. We phenotyped the panel for 25 fruit traits related to morphometrics, shape, volume, weight, ease of cracking, and nutritional composition. We found more than 60 marker-trait associations (MTAs), including a highly significant SNP associated with nut face diameter, nut volume and kernel volume on chromosome 14, and 5 additional associations were detected for walnut weight. We proposed several candidate genes involved in nut characteristics, such as a gene coding for a beta-galactosidase linked to several size-related traits and known to be involved in fruit development in other species. We also confirmed associations on chromosomes 5 and 11 with nut suture strength, recently reported by the University of California, Davis. Our results enhance knowledge of the genetic control of important agronomic traits related to fruit quality in walnut, and pave the way for the development of molecular markers for future assisted selection.

scholarly journals A genome-wide association study explores the genetic determinism of host resistance to Salmonella pullorum infection in chickens

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Xinghua Li ◽  
Changsheng Nie ◽  
Yuchen Liu ◽  
Yu Chen ◽  
Xueze Lv ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Carrier State ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Challenge Experiment ◽  
Salmonella Pullorum

Abstract Background Salmonella infection is a serious concern in poultry farming because of its impact on both economic loss and human health. Chicks aged 20 days or less are extremely vulnerable to Salmonella pullorum (SP), which causes high mortality. Furthermore, an outbreak of SP infection can result in a considerable number of carriers that become potential transmitters, thus, threatening fellow chickens and offspring. In this study, we conducted a genome-wide association study (GWAS) to detect potential genomic loci and candidate genes associated with two disease-related traits: death and carrier state. Methods In total, 818 birds were phenotyped for death and carrier state traits through a SP challenge experiment, and genotyped by using a 600 K high-density single nucleotide polymorphism (SNP) array. A GWAS using a single-marker linear mixed model was performed with the GEMMA software. RNA-sequencing on spleen samples was carried out for further identification of candidate genes. Results We detected a region that was located between 33.48 and 34.03 Mb on chicken chromosome 4 and was significantly associated with death, with the most significant SNP (rs314483802) accounting for 11.73% of the phenotypic variation. Two candidate genes, FBXW7 and LRBA, were identified as the most promising genes involved in resistance to SP. The expression levels of FBXW7 and LRBA were significantly downregulated after SP infection, which suggests that they may have a role in controlling SP infections. Two other significant loci and related genes (TRAF3 and gga-mir-489) were associated with carrier state, which indicates a different polygenic determinism compared with that of death. In addition, genomic inbreeding coefficients showed no correlation with resistance to SP within each breed in our study. Conclusions The results of this GWAS with a carefully organized Salmonella challenge experiment represent an important milestone in understanding the genetics of infectious disease resistance, offer a theoretical basis for breeding SP-resistant chicken lines using marker-assisted selection, and provide new information for salmonellosis research in humans and other animals.

scholarly journals Genome-Wide Association Study of Leaf Chlorophyll Content Using High-Density SNP Array in Peanuts (Arachis hypogaea L.)

Agronomy ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 152
Author(s):  
Kunyan Zou ◽  
Ki-Seung Kim ◽  
Dongwoo Kang ◽  
Min-Cheol Kim ◽  
Jungmin Ha ◽  
...  
Keyword(s):  
Association Study ◽  
Chlorophyll Content ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Genome Wide Association ◽  
Crop Species ◽  
Leaf Chlorophyll Content ◽  
Leaf Chlorophyll ◽  
Genome Wide ◽  
A Genome

The content of chlorophyll, a fundamental component required for photosynthesis in plants, has been widely studied across crop species. In this study, we aimed to evaluate the genetic diversity of 453 peanut accessions. We evaluated the evolutionary relationships using a genome-wide association study (GWAS) of leaf color data based on chlorophyll content analysis using the Axiom_Arachis array containing 58K single-nucleotide polymorphisms (SNPs). We identified seven SNPs as being significantly associated with leaf chlorophyll content on the chromosomes Aradu.A02, Aradu.A08, Araip.B02, Araip.B05, Araip.B06, and Araip.B08 in a GAPIT analysis. The SNP AX-176820297 on Araip.B05 was significantly linked with leaf chlorophyll content across the seasons. The Arahy.SDG4EV gene was detected to be in linkage disequilibrium (LD) with the significant SNPs, and its expression was significantly correlated with leaf chlorophyll content. The results of the current study provide useful and fundamental information with which to assess genetic variations in chlorophyll content and can be utilized for further genetic and genomic studies and breeding programs in peanuts.

Sign in / Sign up

Export Citation Format

Share Document