Genome wide association study identifies novel single nucleotide polymorphic loci and candidate genes involved in soybean sudden death syndrome resistance

Genetic technologies used in breeding of small ruminants requires searching for new molecular markers of productive traits. The most effective for this is genome-wide association study (GWAS) of single nucleotide polymorphisms (SNP) with economically valuable traits. The paper presents results of study of associations of the frequency of single nucleotide polymorphisms with a rank assessment according to complex of productive traits (super-elite) in Romanov sheep using DNA biochips Ovine Infinium HD BeadChip 600K. Eleven SNPs have been found having significant correlation with the animals belonging to the “super-elite” group. Five substitutions are located in the genes introns, six are related to intergenic polymorphisms. The highest reliability of association with productivity was observed in substitution rs410516628 (р = 3,14 · 10-9) located on the 3rd chromosome. Substitution rs422028000 on 2nd chromosome differs with the fact that in the “super-elite” group it was found in 90 % of haplotypes. Polymorphisms rs411162754 (1st chromosome) and rs417281100 (10th chromosome) in our study turned out to be the rarest – only in “super-elite” group and only in a quarter of haplotypes. The genes located near the identified SNPs are mainly associated with metabolic and regulatory processes. Our study has identified several new candidate genes with polymorphism probably associated with the ranking in terms of productivity in Romanov sheep: LTBP1, KCNH8, LMX1B, ZBTB43, MSRA, CHPF, PID1 and DNER. The results obtained create a theoretical basis for further study of candidate genes affecting implementation of phenotypic traits in Romanov sheep. The revealed polymorphisms associated with the productive traits of sheep can be used in practical breeding as molecular and genetic markers for selection of parental pairs.

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Candidate genes screening for plant height and the first branch height based on QTL mapping and genome-wide association study in rapessed (<italic>Brassica napus</italic> L.)

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2020.94067 ◽

2019 ◽

Vol 46 (2) ◽

pp. 214-227

Author(s):

Cun-Min QU ◽

Jia-Na LI ◽

Zhi-You CHEN ◽

Kun LU ◽

Qiang HUO ◽

...

Keyword(s):

Brassica Napus ◽

Qtl Mapping ◽

Association Study ◽

Candidate Genes ◽

Plant Height ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽

10.3390/agriculture11040318 ◽

2021 ◽

Vol 11 (4) ◽

pp. 318

Author(s):

Tae-Ho Ham ◽

Yebin Kwon ◽

Yoonjung Lee ◽

Jisu Choi ◽

Joohyun Lee

Keyword(s):

Association Study ◽

Candidate Genes ◽

Cold Tolerance ◽

Genome Wide Association Study ◽

Seedling Stage ◽

Genome Wide Association ◽

Matrix Analysis ◽

Rice Seedlings ◽

Genome Wide ◽

A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

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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 Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽

10.3390/genes12050718 ◽

2021 ◽

Vol 12 (5) ◽

pp. 718

Author(s):

Bingxin Meng ◽

Tao Wang ◽

Yi Luo ◽

Deze Xu ◽

Lanzhi Li ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Association Analysis ◽

Genome Wide Association Study ◽

Flag Leaf ◽

Genome Wide Association ◽

Lodging Resistance ◽

Leaf Type ◽

Stem Strength ◽

Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

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Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep

Genetics Selection Evolution ◽

10.1186/s12711-021-00649-8 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Bingru Zhao ◽

Hanpeng Luo ◽

Xixia Huang ◽

Chen Wei ◽

Jiang Di ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Genetic Improvement ◽

Genome Wide Association Study ◽

Growth Traits ◽

Fibre Diameter ◽

Single Step ◽

Genome Wide Association ◽

Six Traits ◽

Genome Wide

Abstract Background Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). Results Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from − 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. Conclusions Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.

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