Genome-Wide Association Analysis for Liveweight Traits in Braunvieh Cattle

Abstract A genome-wide association study (GWAS) for liveweight traits of Braunvieh cattle was performed. The study included 300 genotyped animals by the GeneSeek® Genomic Profiler Bovine LDv.4 panel; after quality control, 22,734 SNP and 276 animals were maintained in the analysis. The examined phenotypic data considered birth, weaning, and yearling weights. The association analysis was performed using the principal components method via the egscore function of the GenABEL version 1.8-0 package in the R environment. The marker rs133262280 located in BTA 22 was associated with birth weight, and two SNPs were associated with weaning weight, rs43668789 (BTA 11) and rs136155567 (BTA 27). New QTL associated with these liveweight traits and four positional and functional candidate genes potentially involved in variations of the analyzed traits were identified. The most important genes in these genomic regions were MCM2 (minichromosome maintenance complex component 2), TPRA1 (transmembrane protein adipocyte associated 1), GALM (galactose mutarotase), and NRG1 (neuregulin 1), with relationships with embryonic cleavage, bone and tissue growth, cell adhesion, and organic development. This study is the first to present a GWAS conducted in Braunvieh cattle in Mexico and represents a basis for future research. Further analyses of found associated regions will clarify its contribution to the genetic basis of growth-related traits.

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European landrace diversity for common bean biofortification: a genome-wide association study

Scientific Reports ◽

10.1038/s41598-020-76417-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Leonardo Caproni ◽

Lorenzo Raggi ◽

Elise F. Talsma ◽

Peter Wenzl ◽

Valeria Negri

Keyword(s):

Common Bean ◽

Genome Wide Association Study ◽

Preliminary Evidence ◽

Snp Markers ◽

Genome Wide Association ◽

Future Research ◽

Balanced Diet ◽

Genome Wide ◽

Seed Content ◽

A Genome

AbstractMineral deficiencies represent a global challenge that needs to be urgently addressed. An adequate intake of iron and zinc results in a balanced diet that reduces chances of impairment of many metabolic processes that can lead to clinical consequences. In plants, bioavailability of such nutrients is reduced by presence of compounds such as phytic acid, that can chelate minerals and reduce their absorption. Biofortification of common bean (Phaseolus vulgaris L.) represents an important strategy to reduce mineral deficiencies, especially in areas of the world where this crop plays a key role in the diet. In this study, a panel of diversity encompassing 192 homozygous genotypes, was screened for iron, zinc and phytate seed content. Results indicate a broad variation of these traits and allowed the identification of accessions reasonably carrying favourable trait combinations. A significant association between zinc seed content and some molecular SNP markers co-located on the common bean Pv01 chromosome was detected by means of genome-wide association analysis. The gene Phvul001G233500, encoding for an E3 ubiquitin-protein ligase, is proposed to explain detected associations. This result represents a preliminary evidence that can foster future research aiming at understanding the genetic mechanisms behind zinc accumulation in beans.

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A genome-wide association study unravels cytokinin as a major component in the root defense responses against Ralstonia solanacearum

Journal of Experimental Botany ◽

10.1093/jxb/eraa610 ◽

2021 ◽

Author(s):

Alejandro Alonso-Díaz ◽

Santosh B Satbhai ◽

Roger de Pedro-Jové ◽

Hannah M Berry ◽

Christian Göschl ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Allelic Variation ◽

Defense Responses ◽

Genome Wide Association ◽

Root Growth Inhibition ◽

Future Research ◽

Cytokinin Signaling ◽

Genome Wide ◽

A Genome

Abstract Bacterial wilt caused by the soil-borne pathogen Ralstonia solancearum is economically devastating, with no effective methods to fight the disease. This pathogen invades plants through their roots and colonizes their xylem, clogging the vasculature and causing rapid wilting. Key to preventing colonization are the early defense responses triggered in the host’s root upon infection, which remain mostly unknown. Here, we have taken advantage of a high-throughput in vitro infection system to screen natural variability associated to the root growth inhibition phenotype caused by R. solanacearum in Arabidopsis during the first hours of infection. To analyze the genetic determinants of this trait, we have performed a Genome-Wide Association Study, identifying allelic variation at several loci related to cytokinin metabolism, including genes responsible for biosynthesis and degradation of cytokinin. Further, our data clearly demonstrate that cytokinin signaling is induced early during the infection process and cytokinin contributes to immunity against R. solanacearum. This study highlights a new role of cytokinin in root immunity, paving the way for future research that will help understanding the mechanisms underpinning root defenses.

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Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

Frontiers in Plant Science ◽

10.3389/fpls.2021.770434 ◽

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.

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Approximate conditional phenotype analysis based on genome wide association summary statistics

Scientific Reports ◽

10.1038/s41598-021-82000-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Peitao Wu ◽

Biqi Wang ◽

Steven A. Lubitz ◽

Emelia J. Benjamin ◽

James B. Meigs ◽

...

Keyword(s):

Large Scale ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Summary Statistics ◽

Phenotypic Data ◽

Individual Level ◽

Genome Wide ◽

Level Data ◽

A Genome ◽

Phenotype Analysis

AbstractBecause single genetic variants may have pleiotropic effects, one trait can be a confounder in a genome-wide association study (GWAS) that aims to identify loci associated with another trait. A typical approach to address this issue is to perform an additional analysis adjusting for the confounder. However, obtaining conditional results can be time-consuming. We propose an approximate conditional phenotype analysis based on GWAS summary statistics, the covariance between outcome and confounder, and the variant minor allele frequency (MAF). GWAS summary statistics and MAF are taken from GWAS meta-analysis results while the traits covariance may be estimated by two strategies: (i) estimates from a subset of the phenotypic data; or (ii) estimates from published studies. We compare our two strategies with estimates using individual level data from the full GWAS sample (gold standard). A simulation study for both binary and continuous traits demonstrates that our approximate approach is accurate. We apply our method to the Framingham Heart Study (FHS) GWAS and to large-scale cardiometabolic GWAS results. We observed a high consistency of genetic effect size estimates between our method and individual level data analysis. Our approach leads to an efficient way to perform approximate conditional analysis using large-scale GWAS summary statistics.

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Genome-wide association analysis identified molecular markers associated with important tea flavor-related metabolites

Horticulture Research ◽

10.1038/s41438-021-00477-3 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Kaixing Fang ◽

Zhiqiang Xia ◽

Hongjian Li ◽

Xiaohui Jiang ◽

Dandan Qin ◽

...

Keyword(s):

Molecular Markers ◽

Association Analysis ◽

Rank Order ◽

Tea Plant ◽

Genome Wide Association ◽

Future Research ◽

Candidate Snps ◽

Genome Wide Association Analysis ◽

Genome Wide ◽

A Genome

AbstractThe characteristic secondary metabolites in tea (theanine, caffeine, and catechins) are important factors contributing to unique tea flavors. However, there has been relatively little research on molecular markers related to these metabolites. Thus, we conducted a genome-wide association analysis of the levels of these tea flavor-related metabolites in three seasons. The theanine, caffeine, and catechin levels in Population 1 comprising 191 tea plant germplasms were examined, which revealed that their heritability exceeded 0.5 in the analyzed seasons, with the following rank order (highest to lowest heritabilities): (+)-catechin > (−)-gallocatechin gallate > caffeine = (−)-epicatechin > (−)-epigallocatechin-3-gallate > theanine > (−)-epigallocatechin > (−)-epicatechin-3-gallate > catechin gallate > (+)-gallocatechin. The SNPs detected by amplified-fragment SNP and methylation sequencing divided Population 1 into three groups and seven subgroups. An association analysis yielded 307 SNP markers related to theanine, caffeine, and catechins that were common to all three seasons. Some of the markers were pleiotropic. The functional annotation of 180 key genes at the SNP loci revealed that FLS, UGT, MYB, and WD40 domain-containing proteins, as well as ATP-binding cassette transporters, may be important for catechin synthesis. KEGG and GO analyses indicated that these genes are associated with metabolic pathways and secondary metabolite biosynthesis. Moreover, in Population 2 (98 tea plant germplasm resources), 30 candidate SNPs were verified, including 17 SNPs that were significantly or extremely significantly associated with specific metabolite levels. These results will provide a foundation for future research on important flavor-related metabolites and may help accelerate the breeding of new tea varieties.

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Rapid Identification of QTL for Mesocotyl Length in Rice Through Combining QTL-seq and Genome-Wide Association Analysis

Frontiers in Genetics ◽

10.3389/fgene.2021.713446 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yamei Wang ◽

Jindong Liu ◽

Yun Meng ◽

Hongyan Liu ◽

Chang Liu ◽

...

Keyword(s):

Association Analysis ◽

Genome Wide Association Study ◽

Seedling Emergence ◽

Rapid Identification ◽

Vital Role ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Direct Seeded ◽

Phenotypic Variations

Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct seeding cultivation. In this study, QTL sequencing (QTL-seq) applied to 12 F2 populations identified 14 QTL for ML, which were distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9 based on the Δ(SNP-index) or G-value statistics. Besides, a genome-wide association study (GWAS) using two diverse panels identified five unique QTL on chromosomes 1, 8, 9, and 12 (2), respectively, explaining 5.3–14.6% of the phenotypic variations. Among these QTL, seven were in the regions harboring known genes or QTLs, whereas the other 10 were potentially novel. Six of the QTL were stable across two or more populations. Eight high-confidence candidate genes related to ML were identified for the stable loci based on annotation and expression analyses. Association analysis revealed that two PCR gel-based markers for the loci co-located by QTL-seq and GWAS, Indel-Chr1:18932318 and Indel-Chr7:15404166 for loci qML1.3 and qML7.2 respectively, were significantly associated with ML in a collection of 140 accessions and could be used as breeder-friendly markers in further breeding.

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Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron

Plants ◽

10.3390/plants10040798 ◽

2021 ◽

Vol 10 (4) ◽

pp. 798

Author(s):

Reunreudee Kaewcheenchai ◽

Phanchita Vejchasarn ◽

Kousuke Hanada ◽

Kazumasa Shirai ◽

Chatchawan Jantasuriyarat ◽

...

Keyword(s):

Association Study ◽

Chlorophyll Content ◽

Genome Wide Association Study ◽

Indica Rice ◽

Genome Wide Association ◽

Shoot Biomass ◽

Future Research ◽

Shoot Height ◽

Genome Wide ◽

A Genome

Excess soluble iron in acidic soil is an unfavorable environment that can reduce rice production. To better understand the tolerance mechanism and identify genetic loci associated with iron toxicity (FT) tolerance in a highly diverse indica Thai rice population, a genome-wide association study (GWAS) was performed using genotyping by sequencing and six phenotypic data (leaf bronzing score (LBS), chlorophyll content, shoot height, root length, shoot biomass, and root dry weight) under both normal and FT conditions. LBS showed a high negative correlation with the ratio of chlorophyll content and shoot biomass, indicating the FT-tolerant accessions can regulate cellular homeostasis when encountering stress. Sixteen significant single nucleotide polymorphisms (SNPs) were identified by association mapping. Validation of candidate SNP using other FT-tolerant accessions revealed that SNP:2_21262165 might be associated with tolerance to FT; therefore, it could be used for SNP marker development. Among the candidate genes controlling FT tolerance, RAR1 encodes an innate immune responsive protein that links to cellular redox homeostasis via interacting with abiotic stress-responsive Hsp90. Future research may apply the knowledge obtained from this study in the molecular breeding program to develop FT-tolerant rice varieties.

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Genome-wide association study of vegetarianism in UK Biobank identifies association with VRK2

Wellcome Open Research ◽

10.12688/wellcomeopenres.16396.1 ◽

2020 ◽

Vol 5 ◽

pp. 291

Author(s):

Georgina K. Fensom ◽

Karl Smith-Byrne ◽

Colm D. Andrews ◽

Tim J. Key ◽

Ruth C. Travis

Keyword(s):

Association Study ◽

Fluid Intelligence ◽

Genome Wide Association Study ◽

Genetic Correlations ◽

Genome Wide Association ◽

Future Research ◽

Age At Menarche ◽

Uk Biobank ◽

Genome Wide ◽

A Genome

Prospective studies have observed differences in risks for several health outcomes when comparing meat-eaters and vegetarians, but the mechanisms underlying these differences remain uncertain. Identifying genetic factors related to vegetarianism may be valuable for assessing causality. We report a genome-wide association study (GWAS) of vegetarianism in 367,198 participants from UK Biobank. We identified one locus, rs10189138, near the vaccinia related kinase 2 (VRK2) gene, significantly associated with vegetarianism (β=0.153, p=3x10-8). The associations between rs10189138 and 40 traits were calculated, and the rs10189138 T allele (MAF=0.12) was found to be significantly associated with greater height, after controlling the false discovery rate (FDR). Correlations between genetically predicted vegetarianism and 855 other genetically predicted traits were also calculated, and vegetarianism had significant positive genetic correlations with fluid intelligence and age at menarche, after controlling the FDR. Future research on an independent sample is needed to see if this GWAS result can be replicated.

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