scholarly journals Genome-Wide Association Analysis for Tuber Dry Matter and Oxidative Browning in Water Yam (Dioscorea alata L.)

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 969 ◽  
Author(s):  
Cobes Gatarira ◽  
Paterne Agre ◽  
Ryo Matsumoto ◽  
Alex Edemodu ◽  
Victor Adetimirin ◽  
...  
Keyword(s):  
Association Analysis ◽  
Dry Matter ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Enzymatic Oxidation ◽  
Dioscorea Alata ◽  
Quality Traits ◽  
Genome Wide ◽  
Tuber Dry Matter ◽  
Water Yam

Yam (Dioscorea spp.) is a nutritional and medicinal staple tuber crop grown in the tropics and sub-tropics. Among the food yam species, water yam (Dioscorea alata L.) is the most widely distributed and cultivated species worldwide. Tuber dry matter content (DMC) and oxidative browning (OxB) are important quality attributes that determine cultivar acceptability in water yam. This study used a single nucleotide polymorphism (SNP) assay from a diversity arrays technology (DArT) platform for a genome-wide association study (GWAS) of the two quality traits in a panel of 100 water yam clones grown in three environments. The marker–trait association analysis identified significant SNPs associated with tuber DMC on chromosomes 6 and 19 and with OxB on chromosome 5. The significant SNPs cumulatively explained 45.87 and 12.74% of the total phenotypic variation for the tuber DMC and OxB, respectively. Gene annotation for the significant SNP loci identified important genes associated in the process of the proteolytic modification of carbohydrates in the dry matter accumulation pathway as well as fatty acid β-oxidation in peroxisome for enzymatic oxidation. Additional putative genes were also identified in the peak SNP sites for both tuber dry matter and enzymatic oxidation with unknown functions. The results of this study provide valuable insight for further dissection of the genetic architecture of tuber dry matter and enzymatic oxidation in water yam. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving food quality traits in water yam.

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

scholarly journals Genome-wide association mapping for agronomic and quality traits in foxtail millet

2019 ◽  
Author(s):  
Yanhong Lou ◽  
Yun Chen ◽  
Zhihao Liu ◽  
Mingjie Sun ◽  
Fei Han ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Foxtail Millet ◽  
Significant Snps ◽  
Genomic Variation ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Genome Wide ◽  
A Genome

Abstract Background: Foxtail millet [Setaria italica (L.) P. Beauv.] is a particularly important cereal and fodder crop in arid and semi-arid regions. The genomic variation and alleles underpinning agronomic and quality traits are important for foxtail millet improvement. To better understand the diversity of foxtail millet and facilitate the genetic dissection of its agronomic and quality traits, we used high-quality single nucleotide polymorphisms (SNPs) to perform a genome-wide association study (GWAS). Results: Using genotyping-by-sequencing, 107 foxtail millet accessions were sequenced, and further analysis revealed 72,181 high-quality SNPs, of which 53 were significantly associated with 15 agronomic and quality traits. These SNPs were distributed across the nine chromosomes of foxtail millet; 44 were located in intergenic regions, whereas one and eight SNPs were located in exon and intron regions, respectively. The GWAS revealed that 28 SNPs were associated with a single trait. Conclusions: For some of the significant SNPs, favourable genotypes showed pyramiding effects for several traits. The 53 loci identified in this study will therefore be useful for breeding programs aimed at foxtail millet improvement.

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 Studies for Sex Determination and Cross-Compatibility in Water Yam (Dioscorea alata L.)

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1412
Author(s):  
Jean M. Mondo ◽  
Paterne A. Agre ◽  
Robert Asiedu ◽  
Malachy O. Akoroda ◽  
Asrat Asfaw
Keyword(s):  
Sex Determination ◽  
Association Studies ◽  
Genome Wide Association ◽  
Dioscorea Alata ◽  
Genome Wide Association Studies ◽  
Chromosome 11 ◽  
Putative Gene ◽  
Genome Wide ◽  
Cross Compatibility ◽  
Water Yam

Yam (Dioscorea spp.) species are predominantly dioecious, with male and female flowers borne on separate individuals. Cross-pollination is, therefore, essential for gene flow among and within yam species to achieve breeding objectives. Understanding genetic mechanisms underlying sex determination and cross-compatibility is crucial for planning a successful hybridization program. This study used the genome-wide association study (GWAS) approach for identifying genomic regions linked to sex and cross-compatibility in water yam (Dioscorea alata L.). We identified 54 markers linked to flower sex determination, among which 53 markers were on chromosome 6 and one on chromosome 11. Our result ascertained that D. alata is characterized by the male heterogametic sex determination system (XX/XY). The cross-compatibility indices, average crossability rate (ACR) and percentage high crossability (PHC), were controlled by loci on chromosomes 1, 6 and 17. Of the significant loci, SNPs located on chromosomes 1 and 17 were the most promising for ACR and PHC, respectively, and should be validated for use in D. alata hybridization activities to predict cross-compatibility success. A total of 61 putative gene/protein families with direct or indirect influence on plant reproduction were annotated in chromosomic regions controlling the target traits. This study provides valuable insights into the genetic control of D. alata sexual reproduction. It opens an avenue for developing genomic tools for predicting hybridization success in water yam breeding programs.

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