scholarly journals Identification of Candidate Forage Yield Genes in Sorghum (Sorghum bicolor L.) Using Integrated Genome-Wide Association Studies and RNA-Seq

2022 ◽  
Vol 12 ◽  
Author(s):  
Lihua Wang ◽  
Yanlong Liu ◽  
Li Gao ◽  
Xiaocui Yang ◽  
Xu Zhang ◽  
...  
Keyword(s):  
Dna Repair ◽  
Candidate Genes ◽  
Association Studies ◽  
Critical Role ◽  
Forage Yield ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Yield Traits ◽  
Genome Wide ◽  
Blue Module

Genetic dissection of forage yield traits is critical to the development of sorghum as a forage crop. In the present study, association mapping was performed with 85,585 SNP markers on four forage yield traits, namely plant height (PH), tiller number (TN), stem diameter (SD), and fresh weight per plant (FW) among 245 sorghum accessions evaluated in four environments. A total of 338 SNPs or quantitative trait nucleotides (QTNs) were associated with the four traits, and 21 of these QTNs were detected in at least two environments, including four QTNs for PH, ten for TN, six for SD, and one for FW. To identify candidate genes, dynamic transcriptome expression profiling was performed at four stages of sorghum development. One hundred and six differentially expressed genes (DEGs) that were enriched in hormone signal transduction pathways were found in all stages. Weighted gene correlation network analysis for PH and SD indicated that eight modules were significantly correlated with PH and that three modules were significantly correlated with SD. The blue module had the highest positive correlation with PH and SD, and the turquoise module had the highest negative correlation with PH and SD. Eight candidate genes were identified through the integration of genome-wide association studies (GWAS) and RNA sequencing. Sobic.004G143900, an indole-3-glycerol phosphate synthase gene that is involved in indoleacetic acid biosynthesis, was down-regulated as sorghum plants grew in height and was identified in the blue module, and Sobic.003G375100, an SD candidate gene, encoded a DNA repair RAD52-like protein 1 that plays a critical role in DNA repair-linked cell cycle progression. These findings demonstrate that the integrative analysis of omics data is a promising approach to identify candidate genes for complex traits.

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

scholarly journals Identification of Novel Genome-Wide Associations for Oral Inflammatory Traits

2020 ◽  
Author(s):  
Yanjiao Jin ◽  
Jie Yang ◽  
Shuyue Zhang ◽  
Jin Li ◽  
Songlin Wang
Keyword(s):  
Candidate Genes ◽  
Immune Regulation ◽  
Functional Annotation ◽  
Inflammatory Diseases ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
Causal Variants

Abstract Background: Oral diseases impact the majority of the world’s population. The following traits are common in oral inflammatory diseases: mouth ulcers, painful gums, bleeding gums, loose teeth, and toothache. Despite the prevalence of genome-wide association studies, the associations between these traits and common genomic variants, and whether pleiotropic loci are shared by some of these traits remain poorly understood. Methods: In this work, we conducted multi-trait joint analyses based on the summary statistics of genome-wide association studies of these five oral inflammatory traits from the UK Biobank, each of which is comprised of over 10,000 cases and over 300,000 controls. We estimated the genetic correlations between the five traits. We conducted fine-mapping and functional annotation based on multi-omics data to better understand the biological functions of the potential causal variants at each locus. To identify the pathways in which the candidate genes were mainly involved, we applied gene-set enrichment analysis, and further performed protein-protein interaction (PPI) analyses.Results: We identified 39 association signals that surpassed genome-wide significance, including three that were shared between two or more oral inflammatory traits, consistent with a strong correlation. Among these genome-wide significant loci, two were novel for both painful gums and toothache. We performed fine-mapping and identified causal variants at each novel locus. Further functional annotation based on multi-omics data suggested IL10 and IL12A/TRIM59 as potential candidate genes at the novel pleiotropic loci, respectively. Subsequent analyses of pathway enrichment and protein-protein interaction networks suggested the involvement of candidate genes at genome-wide significant loci in immune regulation.Conclusions: Our results highlighted the importance of immune regulation in the pathogenesis of oral inflammatory diseases. Some common immune-related pleiotropic loci or genetic variants are shared by multiple oral inflammatory traits. These findings will be beneficial for risk prediction, prevention, and therapy of oral inflammatory diseases.

scholarly journals Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp)

2021 ◽  
Author(s):  
Dev Paudel ◽  
Rocheteau Dareus ◽  
Julia Rosenwald ◽  
Maria Munoz-Amatriain ◽  
Esteban Rios
Keyword(s):  
Flowering Time ◽  
Candidate Genes ◽  
Vigna Unguiculata ◽  
Association Studies ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Human Consumption ◽  
Phenotypic Variance ◽  
Genome Wide Association Studies ◽  
Genome Wide

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 367 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

scholarly journals Current knowledge in hypertension genetics: mosaic theory, candidate genes and genome-wide association studies

2020 ◽  
Vol 26 (5) ◽  
pp. 490-500
Author(s):  
A. O. Konradi
Keyword(s):  
Candidate Genes ◽  
High Performance ◽  
New Technologies ◽  
Current Knowledge ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Modern Approach ◽  
Genome Wide

The article reviews monogenic forms of hypertension, data on the role of heredity of essential hypertension and candidate genes, as well as genome-wide association studies. Modern approach for the role of genetics is driven by implementation of new technologies and their productivity. High performance speed of new technologies like genome-wide association studies provide data for better knowledge of genetic markers of hypertension. The major goal nowadays for research is to reveal molecular pathways of blood pressure regulation, which can help to move from populational to individual level of understanding of pathogenesis and treatment targets.

scholarly journals Genome-Wide Association Studies of 39 Seed Yield-Related Traits in Sesame (Sesamum indicum L.)

2018 ◽  
Vol 19 (9) ◽  
pp. 2794 ◽  
Author(s):  
Rong Zhou ◽  
Komivi Dossa ◽  
Donghua Li ◽  
Jingyin Yu ◽  
Jun You ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Seed Yield ◽  
Association Studies ◽  
Oil Quality ◽  
Genome Wide Association ◽  
Oilseed Crop ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Highly Correlated ◽  
Capsule Size

Sesame is poised to become a major oilseed crop owing to its high oil quality and adaptation to various ecological areas. However, the seed yield of sesame is very low and the underlying genetic basis is still elusive. Here, we performed genome-wide association studies of 39 seed yield-related traits categorized into five major trait groups, in three different environments, using 705 diverse lines. Extensive variation was observed for the traits with capsule size, capsule number and seed size-related traits, found to be highly correlated with seed yield indexes. In total, 646 loci were significantly associated with the 39 traits (p < 10−7) and resolved to 547 quantitative trait loci QTLs. We identified six multi-environment QTLs and 76 pleiotropic QTLs associated with two to five different traits. By analyzing the candidate genes for the assayed traits, we retrieved 48 potential genes containing significant functional loci. Several homologs of these candidate genes in Arabidopsis are described to be involved in seed or biomass formation. However, we also identified novel candidate genes, such as SiLPT3 and SiACS8, which may control capsule length and capsule number traits. Altogether, we provided the highly-anticipated basis for research on genetics and functional genomics towards seed yield improvement in sesame.

Genome‐wide association studies revealed candidate genes for tail fat deposition and body size in the Hulun Buir sheep

2019 ◽  
Vol 136 (5) ◽  
pp. 362-370 ◽  
Author(s):  
Tongyu Zhang ◽  
Hongding Gao ◽  
Goutam Sahana ◽  
Yanjun Zan ◽  
Hongying Fan ◽  
...  
Keyword(s):  
Body Size ◽  
Candidate Genes ◽  
Association Studies ◽  
Fat Deposition ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Dissecting the Genetic Architecture of Seed Protein and Oil Content in Soybean from the Yangtze and Huaihe River Valleys Using Multi-Locus Genome-Wide Association Studies

2019 ◽  
Vol 20 (12) ◽  
pp. 3041 ◽  
Author(s):  
Li ◽  
Xu ◽  
Yang ◽  
Zhao
Keyword(s):  
Candidate Genes ◽  
Genetic Architecture ◽  
Oil Content ◽  
Seed Protein ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Huaihe River ◽  
Genome Wide ◽  
River Valleys

Soybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil. Seed protein and oil content are two valuable quality traits controlled by multiple genes in soybean. In this study, the restricted two-stage multi-locus genome-wide association analysis (RTM-GWAS) procedure was performed to dissect the genetic architecture of seed protein and oil content in a diverse panel of 279 soybean accessions from the Yangtze and Huaihe River Valleys in China. We identified 26 quantitative trait loci (QTLs) for seed protein content and 23 for seed oil content, including five associated with both traits. Among these, 39 QTLs corresponded to previously reported QTLs, whereas 10 loci were novel. As reported previously, the QTL on chromosome 20 was associated with both seed protein and oil content. This QTL exhibited opposing effects on these traits and contributed the most to phenotype variation. From the detected QTLs, 55 and 51 candidate genes were identified for seed protein and oil content, respectively. Among these genes, eight may be promising candidate genes for improving soybean nutritional quality. These results will facilitate marker-assisted selective breeding for soybean protein and oil content traits.

Sign in / Sign up

Export Citation Format

Share Document