Underestimation of heritability using a mixed model with a polygenic covariance structure in a genome-wide association study for complex traits

Abstract Background There is a long-term interest in investigating the genetic basis of the horned/polled phenotype in domestic goats. Here, we report a genome-wide association study (GWAS) to detect the genetic loci affecting the polled phenotype in goats. Results We obtained a total of 13,980,209 biallelic SNPs, using the genotyping-by-sequencing data from 45 Jintang Black (JT) goats, which included 32 female and nine male goats, and four individuals with the polled intersex syndrome (PIS). Using a mixed-model based GWAS, we identified two association signals, which were located at 150,334,857–150,817,260 bp (P = 5.15 × 10− 119) and 128,286,704–131,306,537 bp (P = 2.74 × 10− 15) on chromosome 1. The genotype distributions of the 14 most significantly associated SNPs were completely correlated with horn status in goats, based on the whole-genome sequencing (WGS) data from JT and two other Chinese horned breeds. However, variant annotation suggested that none of the detected SNPs within the associated regions were plausible causal mutations. Via additional read-depth analyses and visual inspections of WGS data, we found a 10.1-kb deletion (CHI1:g. 129424781_129434939del) and a 480-kb duplication (CHI1:150,334,286–150,818,098 bp) encompassing two genes KCNJ15 and ERG in the associated regions of polled and PIS-affected goats. Notably, the 10.1-kb deletion also served as the insertion site for the 480-kb duplication, as validated by PCR and Sanger sequencing. Our WGS genotyping showed that all horned goats were homozygous for the reference alleles without either the structural variants (SVs), whereas the PIS-affected goats were homozygous for both the SVs. We also demonstrated that horned, polled, and PIS-affected individuals among 333 goats from JT and three other Chinese horned breeds can be accurately classified via PCR amplification and agarose gel electrophoresis of two fragments in both SVs. Conclusion Our results revealed that two genomic regions on chromosome 1 are major loci affecting the polled phenotypes in goats. We provided a diagnostic PCR to accurately classify horned, polled, and PIS-affected goats, which will enable a reliable genetic test for the early-in-life prediction of horn status in goats.

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Genome-Wide association study identifies new elements on the genetic basis of quality-related traits in wheat across multiple environments

10.21203/rs.3.rs-99775/v1 ◽

2020 ◽

Author(s):

Zhien Pu ◽

Xueling Ye ◽

Yang Li ◽

Zehou Liu ◽

Bingxin Shi ◽

...

Keyword(s):

Association Study ◽

Complex Traits ◽

Genome Wide Association Study ◽

Snp Array ◽

Mixed Linear Model ◽

Genome Wide Association ◽

Phenotypic Analysis ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

Abstract Backgrounds: Grain protein concentration (GPC), grain starch concentration (GSC), and wet gluten concentration (WGC) are complex traits that determine nutrient concentration, end-use quality, and yield in wheat. To identify the elite and stable loci or genomic regions conferring high GPC, GSC, and WGC, a genome-wide association study (GWAS) based on a mixed linear model (MLM) was performed using 55K single nucleotide polymorphism (SNP) array in a panel of 236 wheat accessions, including 160 commercial varieties and 76 landraces, derived from Sichuan Province, China. The panel was evaluated for GPC, GSC, and WGC at four different fields. Results: Phenotypic analysis showed variation in GPC, GSC, and WGC among the different genotypes and environments. GWAS identified 12 quantitative trait loci (QTL) (-log10(P) > 2.5) associated with these three quality traits in at least two environments and located on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 5D, and 7D; the phenotypic variation explained (PVE) by these QTL ranged from 4.2% to 10.7%. Among these, three, seven, and two QTL are associated with GPC, GSC, and WGC, respectively; five QTL (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were defined potentially novel Compared with the previously reported QTLs/genes by linkage or association mapping, 5 QTLs (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were potentially novel. Furthermore, 21 presumptive candidate genes, which are involved in the metabolism or transportation of all kinds of carbohydrates, photosynthesis, programmed cell death, the balance of abscisic acid and ethylene, within these potentially novel genomic regions were predicted. Conclusions: This study provided new genetic resources and valuable genetic information of nutritional quality to broaden the genetic background and laid the molecular foundation for marker-assisted selection in wheat quality breeding.

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opulation Structure Analysis and Genome-Wide Association Study of Rice Landraces from Qiandongnan, China, using Specific–Locus Amplified Fragment Sequencing

International Journal of Agriculture and Biology ◽

10.17957/ijab/15.1679 ◽

2021 ◽

Vol 25 (02) ◽

pp. 388-396

Author(s):

Yan Li

Keyword(s):

Association Study ◽

Complex Traits ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Genome Wide Association ◽

Rice Landraces ◽

Genome Wide ◽

Sequencing Method ◽

A Genome ◽

Specific Locus

Uncovering the genetic basis of rice landraces has important applications in breeding. In this study, the specific-locus amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) of the agronomic traits of 60 rice species in Southeast Guizhou. We obtained a total of 178,287,776 reads, 314,065 SLAFs, and 571,521 single nucleotide polymorphisms (SNPs). A neighbor-joining phylogenetic tree, admixture proportions, and principal component analyses revealed that the investigated landraces were divided into japonica (heterozygosity rate 0.062) and indica (heterozygosity rate 0.073) groups. The groupings were consistent with the local classifications of ―He‖ and ―Gu‖ based on the resistance to seed shattering, and the SNPs clustered in the qSH1 gene. The GWAS of eight agronomic traits revealed that the signal peaks at four locations were closely related to previously reported genes or gene regions. This study demonstrates that the SLAF sequencing method combined with a GWAS may be effective for investigating the evolution of rice and identifying genes regulating complex traits in rice landraces cultivated in relatively isolated regions. © 2021 Friends Science Publishers

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