Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach Genome
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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-02-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.644799/full |
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| author | Cassia da Silva Linge Lichun Cai Lichun Cai Wanfang Fu John Clark Margaret Worthington Zena Rawandoozi David H. Byrne Ksenija Gasic |
| author_facet | Cassia da Silva Linge Lichun Cai Lichun Cai Wanfang Fu John Clark Margaret Worthington Zena Rawandoozi David H. Byrne Ksenija Gasic |
| author_sort | Cassia da Silva Linge |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-13T02:15:34Z |
| format | Article |
| id | doaj.art-53f4cd5e84c644e486144be3ddeb9776 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-13T02:15:34Z |
| publishDate | 2021-02-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-53f4cd5e84c644e486144be3ddeb97762022-12-22T00:02:53ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-02-011210.3389/fpls.2021.644799644799Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach GenomeCassia da Silva Linge0Lichun Cai1Lichun Cai2Wanfang Fu3John Clark4Margaret Worthington5Zena Rawandoozi6David H. Byrne7Ksenija Gasic8Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesDepartment of Horticulture, Michigan State University, East Lansing, MI, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesDepartment of Horticulture, University of Arkansas, Fayetteville, AR, United StatesDepartment of Horticulture, University of Arkansas, Fayetteville, AR, United StatesDepartment of Horticultural Sciences, Texas A&M University, College Station, TX, United StatesDepartment of Horticultural Sciences, Texas A&M University, College Station, TX, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesPeach 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.https://www.frontiersin.org/articles/10.3389/fpls.2021.644799/fullFarmCPUmrMLM 4.0candidate gene analysesSNP arrayRosBREEDQTN |
| spellingShingle | Cassia da Silva Linge Lichun Cai Lichun Cai Wanfang Fu John Clark Margaret Worthington Zena Rawandoozi David H. Byrne Ksenija Gasic Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach Genome Frontiers in Plant Science FarmCPU mrMLM 4.0 candidate gene analyses SNP array RosBREED QTN |
| title | Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach Genome |
| title_full | Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach Genome |
| title_fullStr | Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach Genome |
| title_full_unstemmed | Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach Genome |
| title_short | Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach Genome |
| title_sort | multi locus genome wide association studies reveal fruit quality hotspots in peach genome |
| topic | FarmCPU mrMLM 4.0 candidate gene analyses SNP array RosBREED QTN |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.644799/full |
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