scholarly journals Genome-Wide Association Analysis Identifies Candidate Genes Regulating Seed Number per Silique in Arabidopsis thaliana

Plants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 585
Author(s):  
Huan-Li Jiang ◽  
Jun Hong ◽  
Yu-Tong Jiang ◽  
Shi-Xia Yu ◽  
Yan-Jie Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Analysis ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Loss Of Function ◽  
Seed Number ◽  
Wild Type ◽  
Genome Wide Association Analysis ◽  
New Genes ◽  
Genome Wide

Seed weight and number ultimately determine seed yield. Arabidopsis seed number comprised of silique number and seed number per silique (SNS). Comparing seed development and weight, determinants of seed number remain largely uncharacterized. In this study, taking advantage of 107 available Arabidopsis accessions, genome-wide association analysis (GWAS) was employed to identify the candidate genes regulating SNS. GWAS-based genotype and phenotype association analysis identified 38 most significant SNPs marker sites that were mapped to specific chromosomal positions and allowed us to screen for dozens of candidate genes. One of them (PIN3) was selected for functional validation based on gene expression analysis. It is a positive regulator of Arabidopsis SNS. Although silique length of PIN3 loss of function mutant was not significantly changed, its SNS and seed density (SD) were significantly reduced as compared with the wild type. Notably, PIN3 overexpression lines driven by a placenta-specific promoter STK exhibited significantly shorter siliques, slightly reduced SNS, but significant increased SD compared with wild type, suggesting that PIN3 positively regulates SD through inducing ovule primordia initiation regardless of the placenta size. Ovule initiation determines the maximal possibility of SNS, and new genes and mechanism regulating SNS through modulating ovule initiation is worth further investigated.

scholarly journals Genome-wide association analysis of chickpea germplasms differing for salinity tolerance based on DArTseq markers

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260709
Author(s):  
Shaimaa Mahmoud Ahmed ◽  
Alsamman Mahmoud Alsamman ◽  
Abdulqader Jighly ◽  
Mohamed Hassan Mubarak ◽  
Khaled Al-Shamaa ◽  
...  
Keyword(s):  
Association Analysis ◽  
Salinity Tolerance ◽  
Field Experiments ◽  
Agricultural Research ◽  
Gene Annotation ◽  
Genome Wide Association ◽  
Grain Legume ◽  
Genome Wide Association Analysis ◽  
New Genes ◽  
Genome Wide

Soil salinity is significant abiotic stress that severely limits global crop production. Chickpea (Cicer arietinum L.) is an important grain legume that plays a substantial role in nutritional food security, especially in the developing world. This study used a chickpea population collected from the International Center for Agricultural Research in the Dry Area (ICARDA) genebank using the focused identification of germplasm strategy. The germplasm included 186 genotypes with broad Asian and African origins and genotyped with 1856 DArTseq markers. We conducted phenotyping for salinity in the field (Arish, Sinai, Egypt) and greenhouse hydroponic experiments at 100 mM NaCl concentration. Based on the performance in both hydroponic and field experiments, we identified seven genotypes from Azerbaijan and Pakistan (IGs: 70782, 70430, 70764, 117703, 6057, 8447, and 70249) as potential sources for high salinity tolerance. Multi-trait genome-wide association analysis (mtGWAS) detected one locus on chromosome Ca4 at 10618070 bp associated with salinity tolerance under hydroponic and field conditions. In addition, we located another locus specific to the hydroponic system on chromosome Ca2 at 30537619 bp. Gene annotation analysis revealed the location of rs5825813 within the Embryogenesis-associated protein (EMB8-like), while the location of rs5825939 is within the Ribosomal Protein Large P0 (RPLP0). Utilizing such markers in practical breeding programs can effectively improve the adaptability of current chickpea cultivars in saline soil. Moreover, researchers can use our markers to facilitate the incorporation of new genes into commercial cultivars.

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.

scholarly journals Genome-Wide Association Analysis Identifies Candidate Genes Associated with Iron Deficiency Chlorosis in Soybean

2011 ◽  
Vol 4 (3) ◽  
pp. 154-164 ◽  
Author(s):  
Sujan Mamidi ◽  
Shireen Chikara ◽  
R. Jay Goos ◽  
David L. Hyten ◽  
Deepti Annam ◽  
...  
Keyword(s):  
Iron Deficiency ◽  
Candidate Genes ◽  
Association Analysis ◽  
Genome Wide Association ◽  
Iron Deficiency Chlorosis ◽  
Genome Wide Association Analysis ◽  
Genome Wide
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