Genome-wide association mapping of fruit-quality traits using genotyping-by-sequencing approach in citrus landraces, modern cultivars, and breeding lines in Japan

2018 ◽  
Vol 14 (2) ◽  
Author(s):  
A. Imai ◽  
K. Nonaka ◽  
T. Kuniga ◽  
T. Yoshioka ◽  
T. Hayashi
Keyword(s):  
Association Mapping ◽  
Fruit Quality ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Breeding Lines ◽  
Genome Wide ◽  
Fruit Quality Traits

Genome-wide association-mapping for fruit quality traits in tomato

Euphytica ◽  
2015 ◽  
Vol 207 (2) ◽  
pp. 439-451 ◽  
Author(s):  
Jing Zhang ◽  
Jiantao Zhao ◽  
Yan Liang ◽  
Zhirong Zou
Keyword(s):  
Association Mapping ◽  
Fruit Quality ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Genome Wide ◽  
Fruit Quality Traits

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 Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Mai F. Minamikawa ◽  
Keisuke Nonaka ◽  
Eli Kaminuma ◽  
Hiromi Kajiya-Kanegae ◽  
Akio Onogi ◽  
...  
Keyword(s):  
Association Study ◽  
Fruit Quality ◽  
Genomic Prediction ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Genome Wide ◽  
Fruit Quality Traits

scholarly journals Genome‐Wide Association Mapping of Fusarium Head Blight Resistance in Wheat using Genotyping‐by‐Sequencing

2016 ◽  
Vol 9 (1) ◽  
Author(s):  
Marcio P. Arruda ◽  
Patrick Brown ◽  
Gina Brown‐Guedira ◽  
Allison M. Krill ◽  
Carrie Thurber ◽  
...  
Keyword(s):  
Association Mapping ◽  
Fusarium Head Blight ◽  
Fusarium Head Blight Resistance ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Blight Resistance ◽  
Head Blight ◽  
Genome Wide

scholarly journals Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits

PLoS ONE ◽  
2017 ◽  
Vol 12 (1) ◽  
pp. e0169234 ◽  
Author(s):  
Elisa Biazzi ◽  
Nelson Nazzicari ◽  
Luciano Pecetti ◽  
E. Charles Brummer ◽  
Alberto Palmonari ◽  
...  
Keyword(s):  
Association Mapping ◽  
Medicago Sativa ◽  
Genomic Selection ◽  
Forage Quality ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Genome Wide ◽  
Selection For

scholarly journals Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

2019 ◽  
Author(s):  
Jaime Osorio ◽  
Gina Garzón ◽  
Paola Delgadillo ◽  
Silvio Bastidas ◽  
Leidy Moreno ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Oil Palm ◽  
Plant Architecture ◽  
Elaeis Guineensis ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis , Elaeis oleifera , genotyping-by-sequencing, plant architecture, yield.

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