Dataset Information

Detection and application of genome-wide variations in peach for association and genetic relationship analysis.

ABSTRACT: BACKGROUND:Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. RESULTS:In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. CONCLUSIONS:The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

SUBMITTER: Guan L

PROVIDER: S-EPMC6937647 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Detection and application of genome-wide variations in peach for association and genetic relationship analysis.

Guan Liping L Cao Ke K Li Yong Y Guo Jian J Xu Qiang Q Wang Lirong L

BMC genetics 20191230 1

<h4>Background</h4>Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited.<h4>Results</h4>In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion ...[more]

PMID: 31888445

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Project description: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.

Project description:Abstract Objectives Genetic variation contributes to individual differences in food preference, dietary habit, and nutrient intake, thus affecting nutritional status. Although studies which showed the relevance between genetic differences and the intake of nutrients such as carotenoid, vitamin E, and fat are available, more studies are needed for implementation of precision nutrition. Objective of the study was to investigate genetic variations that are associated with nutrient intake and taste sensitivity. Methods A total of 100 healthy adults (50 men and 50 women) aged 25–35 y who were free of diseases were recruited. Anthropometric measurements, clinical parameters including CBC, lipid profile, glucose level, and liver function tests, dietary intake data using 3-day food record, and taste sensitivity for salty and sweet tastes were determined. A total of 800,000 single nucleotide polymorphisms (SNPs) were analyzed by Theragen Etex using Theragen Precision Medicine Research Array (PMRA) chips. Results A total of 577,164 qualified SNPs were analyzed and three SNPs that might have significant relevance with energy intake (rs75052357, rs1125186, rs73471118) were identified. Carriers of the C allele in rs75052357 (C > T), which is identified in IQGAP1 loci, showed significantly higher fat mass (CC: 16.16 ± 3.52 kg, TC: 14.26 ± 3.58 kg, TT: 12.43 ± 3.83 kg) and higher % body fat (CC: 25.68 ± 5.40%, TC: 22.79 ± 6.10%, TT: 20.60 ± 7.52%) despite a lower energy intake (CC: 1782.2 ± 445.5 kcal, TC: 2212.5 ± 424.1 kcal, TT: 2315.0 ± 892.6 kcal). Carriers of G allele in rs1125186 (G > C) had significantly higher fat mass (CC: 13.34 ± 16.22 kg, CG: 16.22 ± 3.48 kg, GG: 15.67 ± 3.63 kg) in spite of lower energy intake compared with CC carriers (CC: 2222.5 ± 515.9 kcal, CG: 1927.9 ± 452.6 kcal, GG: 1745.7 ± 476.7 kcal). Carriers of T allele in rs73471118 (C > T) had significantly higher energy intake (CC: 1815.5 ± 445.0 kcal, TC: 2726.5 ± 490.6 kcal), while having lower threshold for sweet taste (CC: 8.94 ± 8.51 g/L TC: 0.40 ± 0.00 g/L). Conclusions Novel SNPs showing associations between energy consumption and fat mass or sugar taste sensitivity have been identified. This finding can help developing personalized recommendation for energy intake, however, further studies to delineate the mechanisms are needed. Funding Sources Supported by Seoul National University Research Grant in 2018.

Dataset Information

Detection and application of genome-wide variations in peach for association and genetic relationship analysis.

Publications

Detection and application of genome-wide variations in peach for association and genetic relationship analysis.

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