Association Mapping and Transcriptome Analysis Reveal the Genetic Architecture of Maize Kernel Size

Kernel length, kernel width, and kernel thickness are important traits affecting grain yield and product quality. Here, the genetic architecture of the three kernel size traits was dissected in an association panel of 309 maize inbred lines using four statistical methods. Forty-two significant single nucleotide polymorphisms (SNPs; p < 1.72E-05) and 70 genes for the three traits were identified under five environments. One and eight SNPs were co-detected in two environments and by at least two methods, respectively, and they explained 5.87–9.59% of the phenotypic variation. Comparing the transcriptomes of two inbred lines with contrasting seed size, three and eight genes identified in the association panel showed significantly differential expression between the two genotypes at 15 and 39 days after pollination, respectively. Ten and 17 genes identified by a genome-wide association study were significantly differentially expressed between the two development stages in the two genotypes. Combining environment−/method-stable SNPs and differential expression analysis, ribosomal protein L7, jasmonate-regulated gene 21, serine/threonine-protein kinase RUNKEL, AP2-EREBP-transcription factor 16, and Zm00001d035222 (cell wall protein IFF6-like) were important candidate genes for maize kernel size and development.

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Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS

International Journal of Molecular Sciences ◽

10.3390/ijms21165649 ◽

2020 ◽

Vol 21 (16) ◽

pp. 5649

Author(s):

Ali Muhammad ◽

Weicheng Hu ◽

Zhaoyang Li ◽

Jianguo Li ◽

Guosheng Xie ◽

...

Keyword(s):

Genetic Architecture ◽

Genome Wide Association Study ◽

Snp Array ◽

Significant Snps ◽

Kernel Weight ◽

Snp Markers ◽

Kernel Length ◽

A Genome ◽

Genetic Mechanisms ◽

Kernel Traits

Kernel morphology is one of the major yield traits of wheat, the genetic architecture of which is always important in crop breeding. In this study, we performed a genome-wide association study (GWAS) to appraise the genetic architecture of the kernel traits of 319 wheat accessions using 22,905 single nucleotide polymorphism (SNP) markers from a wheat 90K SNP array. As a result, 111 and 104 significant SNPs for Kernel traits were detected using four multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, and pLARmEB) and three single-locus models (FarmCPU, MLM, and MLMM), respectively. Among the 111 SNPs detected by the multi-locus models, 24 SNPs were simultaneously detected across multiple models, including seven for kernel length, six for kernel width, six for kernels per spike, and five for thousand kernel weight. Interestingly, the five most stable SNPs (RAC875_29540_391, Kukri_07961_503, tplb0034e07_1581, BS00074341_51, and BobWhite_049_3064) were simultaneously detected by at least three multi-locus models. Integrating these newly developed multi-locus GWAS models to unravel the genetic architecture of kernel traits, the mrMLM approach detected the maximum number of SNPs. Furthermore, a total of 41 putative candidate genes were predicted to likely be involved in the genetic architecture underlining kernel traits. These findings can facilitate a better understanding of the complex genetic mechanisms of kernel traits and may lead to the genetic improvement of grain yield in wheat.

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Identification of unique venous thromboembolism-susceptibility variants in African-Americans

Thrombosis and Haemostasis ◽

10.1160/th16-08-0652 ◽

2017 ◽

Vol 117 (04) ◽

pp. 758-768 ◽

Cited By ~ 16

Author(s):

Sebastian Armasu ◽

Bryan McCauley ◽

Iftikhar Kullo ◽

Hugues Sicotte ◽

Jyotishman Pathak ◽

...

Keyword(s):

Gene Expression ◽

Venous Thromboembolism ◽

African Americans ◽

Differential Expression ◽

White Women ◽

Genome Wide Association Study ◽

Expression Data ◽

Significant Differential Expression ◽

Genome Wide ◽

A Genome

SummaryTo identify novel single nucleotide polymorphisms (SNPs) associated with venous thromboembolism (VTE) in African-Americans (AAs), we performed a genome-wide association study (GWAS) of VTE in AAs using the Electronic Medical Records and Genomics (eMERGE) Network, comprised of seven sites each with DNA biobanks (total ~39,200 unique DNA samples) with genome-wide SNP data (imputed to 1000 Genomes Project cosmopolitan reference panel) and linked to electronic health records (EHRs). Using a validated EHR-driven phenotype extraction algorithm, we identified VTE cases and controls and tested for an association between each SNP and VTE using unconditional logistic regression, adjusted for age, sex, stroke, site-platform combination and sickle cell risk genotype. Among 393 AA VTE cases and 4,941 AA controls, three intragenic SNPs reached genome-wide significance: LEMD3 rs138916004 (OR=3.2; p=1.3E-08), LY86 rs3804476 (OR=1.8; p=2E-08) and LOC100130298 rs142143628 (OR=4.5; p=4.4E-08); all three SNPs validated using internal cross-validation, parametric bootstrap and meta-analysis methods. LEMD3 rs138916004 and LOC100130298 rs142143628 are only present in Africans (1000G data). LEMD3 showed a significant differential expression in both NCBI Gene Expression Omnibus (GEO) and the Mayo Clinic gene expression data, LOC100130298 showed a significant differential expression only in the GEO expression data, and LY86 showed a significant differential expression only in the Mayo expression data. LEMD3 encodes for an antagonist of TGF-β-induced cell proliferation arrest. LY86 encodes for MD-1 which down-regulates the pro-inflammatory response to lipopolysaccharide; LY86 variation was previously associated with VTE in white women; LOC100130298 is a non-coding RNA gene with unknown regulatory activity in gene expression and epigenetics.Supplementary Material to this article is available online at www.thrombosis-online.com.

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Natural variations in the P-type ATPase heavy metal transporter ZmCd1 controlling cadmium accumulation in maize grains

10.1101/2021.01.13.426291 ◽

2021 ◽

Author(s):

Bin Tang ◽

Meijie Luo ◽

Yunxia Zhang ◽

Huanle Guo ◽

Jingna Li ◽

...

Keyword(s):

Heavy Metal ◽

Molecular Markers ◽

Genome Wide Association Study ◽

Inbred Lines ◽

Cd Accumulation ◽

A Genome ◽

Maize Varieties ◽

Natural Variations ◽

Maize Grain ◽

P Type

SummaryCadmium (Cd) accumulation in maize grains is detrimental to human health. Developing maize varieties with low-Cd contents via marker-assisted selection is important for ensuring the production of maize grains safe for consumption. However, the key gene controlling maize grain Cd accumulation has not been cloned. In this study, we identified two major loci for maize grain Cd accumulation (qCd1 and qCd2) on chromosome 2 during a genome-wide association study (GWAS). The qCd1 locus was analyzed by bulked segregant RNA-seq and fine mapping with a biparental segregating population of Jing724 (low-Cd line) and Mo17 (high-Cd line). The ZmCd1 candidate gene in the qCd1 locus encodes a vacuolar membrane-localized heavy metal P-type ATPase transporter, ZmHMA3, which is orthologous to the tonoplast Cd transporter OsHMA3. Genomic DNA sequence and transcript analyses suggested that a transposon in intron 1 of ZmCd1 is responsible for the abnormal amino acid sequence in Mo17. An EMS mutant analysis and an allelism test confirmed ZmCd1 influences maize grain Cd accumulation. The natural variations in ZmCd1 were used to develop four PCR-based molecular markers, which revealed five ZmCd1 haplotypes in the GWAS population. The molecular markers were also used to predict the grain Cd contents in commonly cultivated maize germplasms in China. The predicted Cd contents for 36 inbred lines and 13 hybrids were consistent with the measured Cd contents. Furthermore, several low-Cd elite inbred lines and hybrids were identified, including Jing2416, MC01, Jingnonke728, and Jingke968. Therefore, the molecular markers developed in this study are applicable for molecular breeding and developing maize varieties with low grain Cd contents.

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Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior

Science ◽

10.1126/science.aat7693 ◽

2019 ◽

Vol 365 (6456) ◽

pp. eaat7693 ◽

Cited By ~ 53

Author(s):

Andrea Ganna ◽

Karin J. H. Verweij ◽

Michel G. Nivard ◽

Robert Maier ◽

Robbee Wedow ◽

...

Keyword(s):

Sexual Behavior ◽

Genetic Architecture ◽

Large Scale ◽

Genome Wide Association Study ◽

Same Sex ◽

Genome Wide ◽

A Genome ◽

Number Of Sexual Partners ◽

Opposite Sex ◽

Males And Females

Twin and family studies have shown that same-sex sexual behavior is partly genetically influenced, but previous searches for specific genes involved have been underpowered. We performed a genome-wide association study (GWAS) on 477,522 individuals, revealing five loci significantly associated with same-sex sexual behavior. In aggregate, all tested genetic variants accounted for 8 to 25% of variation in same-sex sexual behavior, only partially overlapped between males and females, and do not allow meaningful prediction of an individual’s sexual behavior. Comparing these GWAS results with those for the proportion of same-sex to total number of sexual partners among nonheterosexuals suggests that there is no single continuum from opposite-sex to same-sex sexual behavior. Overall, our findings provide insights into the genetics underlying same-sex sexual behavior and underscore the complexity of sexuality.

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Genetic architecture of bone quality variation in layer chickens revealed by a genome-wide association study

Scientific Reports ◽

10.1038/srep45317 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 9

Author(s):

Jun Guo ◽

Congjiao Sun ◽

Liang Qu ◽

Manman Shen ◽

Taocun Dou ◽

...

Keyword(s):

Association Study ◽

Bone Quality ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Layer Chickens ◽

Quality Variation

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Expanding the Genetic Architecture of Nicotine Dependence and its Shared Genetics with Multiple Traits: Findings from the Nicotine Dependence GenOmics (iNDiGO) Consortium

10.1101/2020.01.15.898858 ◽

2020 ◽

Author(s):

Bryan C. Quach ◽

Michael J. Bray ◽

Nathan C. Gaddis ◽

Mengzhen Liu ◽

Teemu Palviainen ◽

...

Keyword(s):

Nicotine Dependence ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

African Ancestry ◽

Multiple Traits ◽

Expression Of Genes ◽

Genome Wide ◽

A Genome ◽

The Uk ◽

Smoking Index

AbstractCigarette smoking is the leading cause of preventable morbidity and mortality. Knowledge is evolving on genetics underlying initiation, regular smoking, nicotine dependence (ND), and cessation. We performed a genome-wide association study using the Fagerström Test for ND (FTND) in 58,000 smokers of European or African ancestry. Five genome-wide significant loci, including two novel loci MAGI2/GNAI1 (rs2714700) and TENM2 (rs1862416) were identified, and loci reported for other smoking traits were extended to ND. Using the heaviness of smoking index (HSI) in the UK Biobank (N=33,791), rs2714700 was consistently associated, but rs1862416 was not associated, likely reflecting ND features not captured by the HSI. Both variants were cis-eQTLs (rs2714700 for MAGI2-AS3 in hippocampus, rs1862416 for TENM2 in lung), and expression of genes spanning ND-associated variants was enriched in cerebellum. SNP-based heritability of ND was 8.6%, and ND was genetically correlated with 17 other smoking traits (rg=0.40–0.95) and co-morbidities. Our results emphasize the FTND as a composite phenotype that expands genetic knowledge of smoking, including loci specific to ND.

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Genome-Wide Association Study Reveals Novel Genetic Loci for Quantitative Resistance to Septoria Tritici Blotch in Wheat (Triticum aestivum L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.671323 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tilahun Mekonnen ◽

Clay H. Sneller ◽

Teklehaimanot Haileselassie ◽

Cathrine Ziyomo ◽

Bekele G. Abeyo ◽

...

Keyword(s):

Genome Wide Association Study ◽

Agronomic Traits ◽

Defense Responses ◽

Septoria Tritici Blotch ◽

Septoria Tritici ◽

Adult Plant ◽

Putative Qtls ◽

Association Panel ◽

A Genome ◽

Trait Associations

Septoria tritici blotch, caused by the fungus Zymoseptoria titici, poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant (p ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26–105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7–13.2% of the total phenotypic variation. Seven of the QTLs (R2 = 2.7–10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.

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