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

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 using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

Nature Genetics ◽

10.1038/ng.3596 ◽

2016 ◽

Vol 48 (8) ◽

pp. 927-934 ◽

Cited By ~ 226

Author(s):

Kenji Yano ◽

Eiji Yamamoto ◽

Koichiro Aya ◽

Hideyuki Takeuchi ◽

Pei-ching Lo ◽

...

Keyword(s):

Association Study ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Genome Wide Association ◽

Whole Genome ◽

New Genes ◽

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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