Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

Abstract Congenital stationary night blindness (CSNB), in the complete form, is caused by dysfunctions in ON-bipolar cells (ON-BCs) which are secondary neurons of the retina. We describe the first disease causative variant associated with CSNB in the dog. A genome-wide association study using 12 cases and 11 controls from a research colony determined a 4.6 Mb locus on canine chromosome 32. Subsequent whole-genome sequencing identified a 1 bp deletion in LRIT3 segregating with CSNB. The canine mutant LRIT3 gives rise to a truncated protein with unaltered subcellular expression in vitro. Genetic variants in LRIT3 have been associated with CSNB in patients although there is limited evidence regarding its apparently critical function in the mGluR6 pathway in ON-BCs. We determine that in the canine CSNB retina, the mutant LRIT3 is correctly localized to the region correlating with the ON-BC dendritic tips, albeit with reduced immunolabelling. The LRIT3-CSNB canine model has direct translational potential enabling studies to help understand the CSNB pathogenesis as well as to develop new therapies targeting the secondary neurons of the retina.

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Genome-wide association study for longevity with whole-genome sequencing in 3 cattle breeds

Journal of Dairy Science ◽

10.3168/jds.2015-10697 ◽

2016 ◽

Vol 99 (9) ◽

pp. 7289-7298 ◽

Cited By ~ 14

Author(s):

Qianqian Zhang ◽

Bernt Guldbrandtsen ◽

Jørn Rind Thomasen ◽

Mogens Sandø Lund ◽

Goutam Sahana

Keyword(s):

Association Study ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Whole Genome ◽

Cattle Breeds ◽

Genome Wide

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Genome-Wide Association Study Using Whole-Genome Sequencing Identifies a Genomic Region on Chromosome 6 Associated With Comb Traits in Nandan-Yao Chicken

Frontiers in Genetics ◽

10.3389/fgene.2021.682501 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhuliang Yang ◽

Leqin Zou ◽

Tiantian Sun ◽

Wenwen Xu ◽

Linghu Zeng ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Improvement ◽

Genome Wide Association Study ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Chromosome 6 ◽

Whole Genome ◽

Genome Wide

Comb traits have potential economic value in the breeding of indigenous chickens in China. Identifying and understanding relevant molecular markers for comb traits can be beneficial for genetic improvement. The purpose of this study was to utilize genome-wide association studies (GWAS) to detect promising loci and candidate genes related to comb traits, namely, comb thickness (CT), comb weight (CW), comb height, comb length (CL), and comb area. Genome-wide single-nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs) in 300 Nandan-Yao chickens were detected using whole-genome sequencing. In total, we identified 134 SNPs and 25 INDELs that were strongly associated with the five comb traits. A remarkable region spanning from 29.6 to 31.4 Mb on chromosome 6 was found to be significantly associated with comb traits in both SNP- and INDEL-based GWAS. In this region, two lead SNPs (6:30,354,876 for CW and CT and 6:30,264,318 for CL) and one lead INDEL (a deletion from 30,376,404 to 30,376,405 bp for CL and CT) were identified. Additionally, two genes were identified as potential candidates for comb development. The nearby gene fibroblast growth factor receptor 2 (FGFR2)—associated with epithelial cell migration and proliferation—and the gene cytochrome b5 reductase 2 (CYB5R2)—identified on chromosome 5 from INDEL-based GWAS—are significantly correlated with collagen maturation. The findings of this study could provide promising genes and biomarkers to accelerate genetic improvement of comb development based on molecular marker-assisted breeding in Nandan-Yao chickens.

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A chemical genetic roadmap to improved tomato flavor

Science ◽

10.1126/science.aal1556 ◽

2017 ◽

Vol 355 (6323) ◽

pp. 391-394 ◽

Cited By ~ 212

Author(s):

Denise Tieman ◽

Guangtao Zhu ◽

Marcio F. R. Resende ◽

Tao Lin ◽

Cuong Nguyen ◽

...

Keyword(s):

Association Study ◽

Genome Sequencing ◽

Molecular Breeding ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Whole Genome ◽

Chemical Genetic ◽

Genome Wide ◽

A Genome ◽

Wild Accessions

Modern commercial tomato varieties are substantially less flavorful than heirloom varieties. To understand and ultimately correct this deficiency, we quantified flavor-associated chemicals in 398 modern, heirloom, and wild accessions. A subset of these accessions was evaluated in consumer panels, identifying the chemicals that made the most important contributions to flavor and consumer liking. We found that modern commercial varieties contain significantly lower amounts of many of these important flavor chemicals than older varieties. Whole-genome sequencing and a genome-wide association study permitted identification of genetic loci that affect most of the target flavor chemicals, including sugars, acids, and volatiles. Together, these results provide an understanding of the flavor deficiencies in modern commercial varieties and the information necessary for the recovery of good flavor through molecular breeding.

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Genome-wide association study of agronomic traits in rice cultivated in temperate regions

BMC Genomics ◽

10.1186/s12864-018-5086-y ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 6

Author(s):

Juan L Reig-Valiente ◽

Luis Marqués ◽

Manuel Talón ◽

Concha Domingo

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Genome Wide Association ◽

Genome Wide

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Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken

Scientific Reports ◽

10.1038/s41598-018-34364-0 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 8

Author(s):

Gabriel Costa Monteiro Moreira ◽

Clarissa Boschiero ◽

Aline Silva Mello Cesar ◽

James M. Reecy ◽

Thaís Fernanda Godoy ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Association Studies ◽

Fat Deposition ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Whole Genome ◽

Genome Wide

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A genome‐wide association study identifies new genes associated with developmental dysplasia of the hip

Clinical Genetics ◽

10.1111/cge.13483 ◽

2019 ◽

Vol 95 (3) ◽

pp. 345-355 ◽

Cited By ~ 4

Author(s):

Wenjin Yan ◽

Zheng Hao ◽

Shuyan Tang ◽

Jin Dai ◽

Liming Zheng ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Developmental Dysplasia ◽

Genome Wide Association ◽

New Genes ◽

Genome Wide ◽

A Genome ◽

Dysplasia Of The Hip

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Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

10.21203/rs.2.17481/v1 ◽

2019 ◽

Author(s):

Waltram Ravelombola ◽

Jun Qin ◽

Ainong Shi ◽

Fengmin Wang ◽

Yan Feng ◽

...

Keyword(s):

Association Study ◽

Genomic Selection ◽

Candidate Genes ◽

Plant Height ◽

Seed Weight ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Snp Markers ◽

Genome Wide Association ◽

Genome Wide

Abstract Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to evaluate maturity, plant height, seed weight, and yield in a diverse soybean accession panel, to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy. Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci ( E2 , E4 , and Dt1 ) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900 , Glyma.19g200800 , Glyma.09g196700 , and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent. Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits through marker-assisted selection (MAS) and GS in soybean breeding programs. After validation, the candidate genes can be transferred to new cultivars using SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

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