Genome-Wide Association Study Reveals Novel Genomic Regions Associated With High Grain Protein Content in Wheat Lines Derived From Wild Emmer Wheat

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 identified candidate genes for seed size and seed composition improvement in M. truncatula

Scientific Reports ◽

10.1038/s41598-021-83581-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Zhijuan Chen ◽

Vanessa Lancon-Verdier ◽

Christine Le Signor ◽

Yi-Min She ◽

Yun Kang ◽

...

Keyword(s):

Association Study ◽

Protein Content ◽

Seed Size ◽

Seed Protein ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Strong Positive Correlation ◽

Seed Composition ◽

Seed Traits ◽

Genome Wide

AbstractGrain legumes are highly valuable plant species, as they produce seeds with high protein content. Increasing seed protein production and improving seed nutritional quality represent an agronomical challenge in order to promote plant protein consumption of a growing population. In this study, we used the genetic diversity, naturally present in Medicago truncatula, a model plant for legumes, to identify genes/loci regulating seed traits. Indeed, using sequencing data of 162 accessions from the Medicago HAPMAP collection, we performed genome-wide association study for 32 seed traits related to seed size and seed composition such as seed protein content/concentration, sulfur content/concentration. Using different GWAS and postGWAS methods, we identified 79 quantitative trait nucleotides (QTNs) as regulating seed size, 41 QTNs for seed composition related to nitrogen (i.e. storage protein) and sulfur (i.e. sulfur-containing amino acid) concentrations/contents. Furthermore, a strong positive correlation between seed size and protein content was revealed within the selected Medicago HAPMAP collection. In addition, several QTNs showed highly significant associations in different seed phenotypes for further functional validation studies, including one near an RNA-Binding Domain protein, which represents a valuable candidate as central regulator determining both seed size and composition. Finally, our findings in M. truncatula represent valuable resources to be exploitable in many legume crop species such as pea, common bean, and soybean due to its high synteny, which enable rapid transfer of these results into breeding programs and eventually help the improvement of legume grain production.

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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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Genome-Wide Association Study Uncovers Novel Genomic Regions Associated With Coleoptile Length in Hard Winter Wheat

Frontiers in Genetics ◽

10.3389/fgene.2019.01345 ◽

2020 ◽

Vol 10 ◽

Cited By ~ 2

Author(s):

Jagdeep Singh Sidhu ◽

Dilkaran Singh ◽

Harsimardeep Singh Gill ◽

Navreet Kaur Brar ◽

Yeyan Qiu ◽

...

Keyword(s):

Winter Wheat ◽

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Coleoptile Length ◽

Genome Wide ◽

Genomic Regions

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Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet

Scientific Reports ◽

10.1038/s41598-020-76230-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Mahesh Pujar ◽

S. Gangaprasad ◽

Mahalingam Govindaraj ◽

Sunil S. Gangurde ◽

A. Kanatti ◽

...

Keyword(s):

Association Study ◽

Protein Content ◽

Pearl Millet ◽

Genome Wide Association Study ◽

Breeding Strategy ◽

Genome Wide Association ◽

Late Embryogenesis Abundant Protein ◽

Pentatricopeptide Repeat ◽

Genome Wide ◽

Population Structure Analysis

Abstract Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.

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