scholarly journals Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Xiujuan Su ◽  
Guozhong Zhu ◽  
Xiaohui Song ◽  
Haijiang Xu ◽  
Weixi Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Analysis ◽  
Fiber Quality ◽  
Gossypium Barbadense ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Fiber Quality Traits ◽  
Genome Wide Association Analysis ◽  
Genome Wide

scholarly journals Genome-Wide Association Analysis Reveals Loci and Candidate Genes Involved in Fiber Quality Traits Under Multiple Field Environments in Cotton (Gossypium hirsutum)

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaohui Song ◽  
Guozhong Zhu ◽  
Sen Hou ◽  
Yamei Ren ◽  
Muhammad Waqas Amjid ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fiber Length ◽  
Fiber Strength ◽  
Fiber Quality ◽  
Quality Parameters ◽  
Fiber Development ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Fiber Quality Traits ◽  
Genome Wide

Fiber length, fiber strength, and fiber micronaire are the main fiber quality parameters in cotton. Thus, mining the elite and stable loci/alleles related to fiber quality traits and elucidating the relationship between the two may accelerate genetic improvement of fiber quality in cotton. Here, genome-wide association analysis (GWAS) was performed for fiber quality parameters based on phenotypic data, and 56,010 high-quality single nucleotide polymorphisms (SNPs) using 242 upland cotton accessions under 12 field environments were obtained. Phenotypic analysis exhibited that fiber length (FL) had a positive correlation with fiber strength (FS) and had a negative correlation with fiber micronaire (Mic). Genetic analysis also indicated that FL, FS, and Mic had high heritability of more than 80%. A total of 67 stable quantitative trait loci (QTLs) were identified through GWAS analysis, including 31 for FL, 21 for FS, and 22 for Mic. Of them, three pairs homologous QTLs were detected between A and D subgenomes, and seven co-located QTLs with two fiber quality parameters were found. Compared with the reported QTLs, 34 co-located with previous studies, and 33 were newly revealed. Integrated with transcriptome analysis, we selected 256, 244, and 149 candidate genes for FL, FS, and Mic, respectively. Gene Ontology (GO) analysis showed that most of the genes located in QTLs interval of the three fiber quality traits were involved in sugar biosynthesis, sugar metabolism, microtubule, and cytoskeleton organization, which played crucial roles in fiber development. Through correlation analysis between haplotypes and phenotypes, three genes (GH_A05G1494, GH_D11G3097, and GH_A05G1082) predominately expressed in fiber development stages were indicated to be potentially responsible for FL, FS, and Mic, respectively. The GH_A05G1494 encoded a protein containing SGS-domain, which is related to tubulin-binding and ubiquitin-protein ligase binding. The GH_D11G3097 encoded 20S proteasome beta subunit G1, and was involved in the ubiquitin-dependent protein catabolic process. The GH_A05G1082 encoded RAN binding protein 1 with a molecular function of GTPase activator activity. These results provide new insights and candidate loci/genes for the improvement of fiber quality in cotton.

Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis

2022 ◽  
Author(s):  
Rongrong Ding ◽  
Zhanwei Zhuang ◽  
Yibin Qiu ◽  
Donglin Ruan ◽  
Jie Wu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Analysis ◽  
Large Scale ◽  
Major Gene ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Backfat Thickness ◽  
Lean Meat ◽  
Genome Wide Association Analysis ◽  
Genome Wide

Abstract Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT. In addition, 9 candidate genes, including a proven major gene MC4R, 3 important candidate genes (RYR1, HMGA1 and NUDT3) which were previously described as related to BFT, and 5 novel candidate genes (SIRT2, NKAIN2, AMH, SORCS1 and SORCS3) were found based on their potential functional roles in BFT. The functions of candidate genes and gene set enrichment analysis indicate that most important pathways are related to energy homeostasis and adipogenesis. Finally, our data suggests that most of the candidate genes can be directly used for genetic improvement through molecular markers, except that the MC4R gene has an antagonistic effect on growth rate and carcass lean meat percentage in breeding. Our results will advance our understanding of the complex genetic architecture of BFT traits, and laid the foundation for additional genetic studies to increase carcass lean meat percentage of pig through marker-assisted selection and/or genomic selection.

scholarly journals Plasticity of Medicago truncatula seed dormancy relates to large-scale environment variation

2019 ◽  
Author(s):  
Juan Pablo Renzi ◽  
Martin Duchoslav ◽  
Jan Brus ◽  
Iveta Hradilová ◽  
Vilém Pechanec ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Analysis ◽  
Medicago Truncatula ◽  
Seed Dormancy ◽  
Genome Wide Association ◽  
Dormancy Release ◽  
Bet Hedging ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
Plastic Responses

AbstractSeed dormancy and timing of its release is important developmental transition determining the survival of individual as well as population and species. We used Medicago truncatula as model to study legume seed dormancy in ecological and genomics context. The effect of oscillating temperatures as one of the dormancy release factor was tested over the period of 88 days on the set of 178 accessions originating from variable environmental conditions of Mediterranean basin. Phenotypic plasticity of final dormancy was significantly correlated with increased aridity, suggesting that plastic responses to external stimuli provide seeds with strong bet-hedging capacity and the potential to cope with high levels of environmental heterogeneity. Genome-wide association analysis identified candidate genes associated with dormancy release related to secondary metabolites synthesis, hormone regulation and modification of the cell wall likely mediating seed coat permeability and ultimately imbibition and germination.HighlightMedicago seed dormancy was correlated with increased aridity of the environment, suggesting that plastic responses provide seeds with a bet-hedging capacity. Genome-wide association analysis identified candidate genes associated with release from dormancy.

P5009 A genome-wide association analysis for carcass and meat quality traits in Duroc pigs

2016 ◽  
Vol 94 (suppl_4) ◽  
pp. 119-120 ◽  
Author(s):  
R. Gonzalez ◽  
P. G. Eusebi ◽  
R. Quintanilla ◽  
T. Figueiredo ◽  
A. Manunza ◽  
...  
Keyword(s):  
Meat Quality ◽  
Association Analysis ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Genome Wide Association Analysis ◽  
Meat Quality Traits ◽  
Genome Wide ◽  
A Genome
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