scholarly journals Genome-wide association studies provide insights into the genetic determination of fruit traits of pear

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ming-Yue Zhang ◽  
Cheng Xue ◽  
Hongju Hu ◽  
Jiaming Li ◽  
Yongsong Xue ◽  
...  
Keyword(s):  
Fruit Quality ◽  
Molecular Breeding ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Quality Traits ◽  
Fruit Traits ◽  
Stone Cell ◽  
Genome Wide ◽  
Fruit Quality Traits

AbstractPear is a major fruit tree crop distributed worldwide, yet its breeding is a very time-consuming process. To facilitate molecular breeding and gene identification, here we have performed genome-wide association studies (GWAS) on eleven fruit traits. We identify 37 loci associated with eight fruit quality traits and five loci associated with three fruit phenological traits. Scans for selective sweeps indicate that traits including fruit stone cell content, organic acid and sugar contents might have been under continuous selection during breeding improvement. One candidate gene, PbrSTONE, identified in GWAS, has been functionally verified to be involved in the regulation of stone cell formation, one of the most important fruit quality traits in pear. Our study provides insights into the complex fruit related biology and identifies genes controlling important traits in pear through GWAS, which extends the genetic resources and basis for facilitating molecular breeding in perennial trees.

scholarly journals Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach Genome

2021 ◽  
Vol 12 ◽  
Author(s):  
Cassia da Silva Linge ◽  
Lichun Cai ◽  
Wanfang Fu ◽  
John Clark ◽  
Margaret Worthington ◽  
...  
Keyword(s):  
Fruit Quality ◽  
The United States ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Quality Traits ◽  
Fresh Market ◽  
Breeding Programs ◽  
Genome Wide ◽  
Fruit Quality Traits ◽  
Peach Breeding

Peach is one of the most important fruit crops in the world, with the global annual production about 24.6 million tons. The United States is the fourth-largest producer after China, Spain, and Italy. Peach consumption has decreased over the last decade, most likely due to inconsistent quality of the fruit on the market. Thus, marker-assisted selection for fruit quality traits is highly desired in fresh market peach breeding programs and one of the major goals of the RosBREED project. The ability to use DNA information to select for desirable traits would enable peach breeders to efficiently plan crosses and select seedlings with desired quality traits early in the selection process before fruiting. Therefore, we assembled a multi-locus genome wide association study (GWAS) of 620 individuals from three public fresh market peach breeding programs (Arkansas, Texas, and South Carolina). The material was genotyped using 9K SNP array and the traits were phenotyped for three phenological (bloom date, ripening date, and days after bloom) and 11 fruit quality-related traits (blush, fruit diameter, fruit weight, adherence, fruit firmness, redness around pit, fruit texture, pit weight, soluble solid concentration, titratable acidity, and pH) over three seasons (2010, 2011, and 2012). Multi-locus association analyses, carried out using mrMLM 4.0 and FarmCPU R packages, revealed a total of 967 and 180 quantitative trait nucleotides (QTNs), respectively. Among the 88 consistently reliable QTNs detected using multiple multi-locus GWAS methods and/or at least two seasons, 44 were detected for the first time. Fruit quality hotspots were identified on chromosomes 1, 3, 4, 5, 6, and 8. Out of 566 candidate genes detected in the genomic regions harboring the QTN clusters, 435 were functionally annotated. Gene enrichment analyses revealed 68 different gene ontology (GO) terms associated with fruit quality traits. Data reported here advance our understanding of genetic mechanisms underlying important fruit quality traits and further support the development of DNA tools for breeding.

scholarly journals Genomic Prediction and Genome-Wide Association Studies of Flour Yield and Alveograph Quality Traits Using Advanced Winter Wheat Breeding Material

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 669 ◽  
Author(s):  
Peter S. Kristensen ◽  
Just Jensen ◽  
Jeppe R. Andersen ◽  
Carlos Guzmán ◽  
Jihad Orabi ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Genomic Prediction ◽  
Association Studies ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Quality Traits ◽  
Breeding Programs ◽  
Genome Wide ◽  
Flour Yield

Use of genetic markers and genomic prediction might improve genetic gain for quality traits in wheat breeding programs. Here, flour yield and Alveograph quality traits were inspected in 635 F6 winter wheat breeding lines from two breeding cycles. Genome-wide association studies revealed single nucleotide polymorphisms (SNPs) on chromosome 5D significantly associated with flour yield, Alveograph P (dough tenacity), and Alveograph W (dough strength). Additionally, SNPs on chromosome 1D were associated with Alveograph P and W, SNPs on chromosome 1B were associated with Alveograph P, and SNPs on chromosome 4A were associated with Alveograph L (dough extensibility). Predictive abilities based on genomic best linear unbiased prediction (GBLUP) models ranged from 0.50 for flour yield to 0.79 for Alveograph W based on a leave-one-out cross-validation strategy. Predictive abilities were negatively affected by smaller training set sizes, lower genetic relationship between lines in training and validation sets, and by genotype–environment (G×E) interactions. Bayesian Power Lasso models and genomic feature models resulted in similar or slightly improved predictions compared to GBLUP models. SNPs with the largest effects can be used for screening large numbers of lines in early generations in breeding programs to select lines that potentially have good quality traits. In later generations, genomic predictions might be used for a more accurate selection of high quality wheat lines.

scholarly journals Genome-wide association mapping of date palm fruit traits

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Khaled M. Hazzouri ◽  
Muriel Gros-Balthazard ◽  
Jonathan M. Flowers ◽  
Dario Copetti ◽  
Alain Lemansour ◽  
...  
Keyword(s):  
Association Studies ◽  
Fruit Color ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Fruit Traits ◽  
Sugar Composition ◽  
Palm Fruit ◽  
Date Palms ◽  
Evolutionary Diversification ◽  
Genome Wide

Abstract Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform genome-wide association studies (GWAS) of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor VIRESCENS gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crops, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.

P5018 Genome-wide association studies for dry-cured ham quality traits in Italian Large White and Italian Duroc pigs

2016 ◽  
Vol 94 (suppl_4) ◽  
pp. 124-124
Author(s):  
L. Fontanesi ◽  
G. Schiavo ◽  
G. Galimberti ◽  
S. Bovo ◽  
F. Bertolini ◽  
...  
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Quality Traits ◽  
Large White ◽  
Genome Wide ◽  
Dry Cured Ham

scholarly journals Identification of favorable SNP alleles related to fruit traits in diverse apple germplasm

2020 ◽  
Author(s):  
A Reum Han ◽  
Seon-Ae Kim ◽  
Gi Hoon Kim ◽  
Cheol Choi
Keyword(s):  
Fruit Quality ◽  
Skin Color ◽  
Association Studies ◽  
Fruit Tree ◽  
Chromosome 9 ◽  
Breeding Systems ◽  
Candidate Snps ◽  
Genome Wide Association Studies ◽  
Quality Traits ◽  
Fruit Quality Traits

Abstract Background: The Apple ( Malus × domestica Borkh.) is a valuable fruit crop worldwide, and receives considerable attention as one of the model plants of the Rosaceae family. The primary purpose of apple breeding programs is to generate novel apple cultivars with fruit quality traits that have high commercial value. To advance fruit-tree breeding systems, it is necessary to investigate the association between genomes and targeted traits. Genome-wide association studies (GWAS) are promising to analyze the associations between the genome and traits in fruit tree crops. Results: In this study, we evaluated 10 major fruit quality traits including titratable acidity (TA), soluble solids content (SSC), and skin color from 301 apple germplasms for four years (2015-2018). GWAS analysis was performed using SNP data generated via genotyping by sequencing (GBS) and identified SNPs significantly related to the fruit quality traits. For TA, significant association loci were detected on chromosome 16 and genes in the candidate regions related to malate transporter. The GWAS loci of SSC was found on chromosome 15, where genes related to sucrose synthase and transporter are located. Significant SNPs associated with fruit skin color were identified on genetic region near the MYB1 gene on chromosome 9, which regulates anthocyanin biosynthesis. SNPs identified by the GWAS and Linkage disequilibrium (LD) analysis were further confirmed with high resolution melting (HRM) analysis to discover specific polymorphisms in the melting curve. Conclusion: Overall, these results could identify several candidate genes and SNP markers associated with the fruit quality traits, thus validation of these SNPs enabled marker-assisted selection (MAS). The candidate SNPs and genes observed in this study will contribute to a better understanding of genetic basis for the important fruit quality traits and provide tools for generation of novel cultivars with the quality traits for advancement of apple industry.

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