Genome-wide association study reveals complex genetic architecture of cadmium and mercury accumulation and tolerance traits in Medicago truncatula

Heavy metals are an increasing problem due to contamination from human sources that and can enter the food chain by being taken up by plants. Understanding the genetic basis of accumulation and tolerance in plants is important for reducing the uptake of toxic metals in crops and crop relatives, as well as for removing heavy metals from soils by means of phytoremediation. Following exposure of Medicago truncatula seedlings to cadmium (Cd) and mercury (Hg), we conducted a genome-wide association study using relative root growth (RRG) and leaf accumulation measurements. Cd and Hg accumulation and RRG had heritability ranging 0.44 - 0.72 indicating high genetic diversity for these traits. The Cd and Hg trait associations were broadly distributed throughout the genome, indicated the traits are polygenic and involve several quantitative loci. For all traits, candidate genes included several membrane associated ATP-binding cassette transporters, P-type ATPase transporters, several oxidative stress response genes and stress related UDP-glycosyltransferases. The P-type ATPase transporters and ATP-binding cassette protein-families have roles in vacuole transport of heavy metals, and our findings support their wide use in physiological plant responses to heavy metals and abiotic stresses. We also found associations between Cd RRG with the genes CAX3 and PDR3, two linked adjacent genes, and leaf accumulation of Hg associated with the genes NRAMP6 and CAX9. When plant genotypes with the most extreme phenotypes were compared, we found significant divergence in genomic regions using population genomics methods that contained metal transport and stress response gene ontologies. Several of these genomic regions show high linkage disequilibrium (LD) among candidate genes suggesting they have evolved together. Minor allele frequency (MAF) and effect size of the most significant SNPs was negatively correlated with large effect alleles being most rare. This is consistent with purifying selection against alleles that increase toxicity and abiotic stress. Conversely, the alleles with large affect that had higher frequencies that were associated with the exclusion of Cd and Hg. Overall, macroevolutionary conservation of heavy metal and stress response genes is important for improvement of forage crops by harnessing wild genetic variants in gene banks such as the Medicago HapMap collection.

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

Science Advances ◽

10.1126/sciadv.abd1239 ◽

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.

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Large-scale integration of meta-QTL and genome-wide association study discovers the genomic regions and candidate genes for yield and yield-related traits in bread wheat

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03881-4 ◽

2021 ◽

Author(s):

Yang Yang ◽

Aduragbemi Amo ◽

Di Wei ◽

Yongmao Chai ◽

Jie Zheng ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Bread Wheat ◽

Large Scale ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

Large Scale Integration ◽

Scale Integration ◽

Genomic Regions

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Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

Rice ◽

10.1186/s12284-020-00433-0 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Leila Nayyeripasand ◽

Ghasem Ali Garoosi ◽

Asadollah Ahmadikhah

Keyword(s):

Association Study ◽

Candidate Gene ◽

Candidate Genes ◽

Salinity Tolerance ◽

Genome Wide Association Study ◽

Dry Weight ◽

Genome Wide Association ◽

Vegetative Stage ◽

Genome Wide ◽

Genomic Regions

Abstract Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. Conclusion Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.

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Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight

Genetics Selection Evolution ◽

10.1186/s12711-015-0142-4 ◽

2015 ◽

Vol 47 (1) ◽

Cited By ~ 40

Author(s):

Hawlader A. Al-Mamun ◽

Paul Kwan ◽

Samuel A. Clark ◽

Mohammad H. Ferdosi ◽

Ross Tellam ◽

...

Keyword(s):

Body Weight ◽

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Orthologous Region ◽

Merino Sheep ◽

Genome Wide ◽

Genomic Regions ◽

Australian Merino

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Genome‐Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High‐Quality Rice

The Plant Genome ◽

10.3835/plantgenome2017.08.0076 ◽

2018 ◽

Vol 11 (3) ◽

pp. 170076 ◽

Cited By ~ 6

Author(s):

Gastón Quero ◽

Lucía Gutiérrez ◽

Eliana Monteverde ◽

Pedro Blanco ◽

Fernando Pérez de Vida ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

High Quality ◽

Breeding Populations ◽

Genome Wide ◽

Genomic Regions

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Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax

International Journal of Molecular Sciences ◽

10.3390/ijms19082303 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2303 ◽

Cited By ~ 18

Author(s):

Frank You ◽

Jin Xiao ◽

Pingchuan Li ◽

Zhen Yao ◽

Gaofeng Jia ◽

...

Keyword(s):

Association Study ◽

Seed Yield ◽

Phenotypic Variation ◽

Genome Wide Association Study ◽

Oil Quality ◽

Genome Wide Association ◽

Selection Signatures ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19× using the Illumina Hi-Seq platform. Phenotypic data for 11 seed yield and oil quality traits were collected in eight year/location environments. A total of 17,288 single nucleotide polymorphisms were identified, which explained more than 80% of the phenotypic variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO) and linolenic (LIN) acid contents. Twenty-three unique genomic regions associated with 33 quantitative trait loci (QTL) for the studied traits were detected, thereby validating four genomic regions previously identified. The 33 QTL explained 48–73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN but only 8–14% for plant height, DTM and seed yield. A genome-wide selective sweep scan for selection signatures detected 114 genomic regions that accounted for 7.82% of the flax pseudomolecule and overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for 11 traits. The results demonstrate the utility of GWAS combined with selection signatures for dissection of the genetic structure of traits and for pinpointing genomic regions for breeding improvement.

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