Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events
Bud sports occur in many plant species, including fruit trees. Although they are correlated with genetic variance in somatic cells, the mechanisms responsible for bud sports are mostly unknown. In this study, a peach bud sport whose fruit shape was transformed to round from flat was identified by ne...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2019.00592/full |
| _version_ | 1811342651778138112 |
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| author | Qiuping Tan Qiuping Tan Qiuping Tan Xiao Liu Xiao Liu Xiao Liu Hongru Gao Wei Xiao Wei Xiao Wei Xiao Xiude Chen Xiude Chen Xiude Chen Xiling Fu Xiling Fu Xiling Fu Ling Li Ling Li Ling Li Dongmei Li Dongmei Li Dongmei Li Dongsheng Gao Dongsheng Gao Dongsheng Gao |
| author_facet | Qiuping Tan Qiuping Tan Qiuping Tan Xiao Liu Xiao Liu Xiao Liu Hongru Gao Wei Xiao Wei Xiao Wei Xiao Xiude Chen Xiude Chen Xiude Chen Xiling Fu Xiling Fu Xiling Fu Ling Li Ling Li Ling Li Dongmei Li Dongmei Li Dongmei Li Dongsheng Gao Dongsheng Gao Dongsheng Gao |
| author_sort | Qiuping Tan |
| collection | DOAJ |
| description | Bud sports occur in many plant species, including fruit trees. Although they are correlated with genetic variance in somatic cells, the mechanisms responsible for bud sports are mostly unknown. In this study, a peach bud sport whose fruit shape was transformed to round from flat was identified by next generation sequencing (NGS), and we provide evidence that a long loss of heterozygosity (LOH) event may be responsible for this alteration in fruit shape. Moreover, compared to the reference genome, we identified 237,476 high quality single nucleotide polymorphisms (SNPs) in the wild-type and bud sport genomes. Using this SNP set, a long LOH event was identified at the distal end of scaffold Pp06 of the bud sport genome. Haplotypes from 155 additional peach accessions were phased, suggesting that the homozygous distal end of scaffold Pp06 of the bud sport was likely derived from only one haplotype of the wild-type flat peach. A genome-wide association study (GWAS) of 127 peach accessions was conducted to associate a SNP found at 26,924,482 bp of scaffold Pp06 to differences in fruit shape. All accessions with round-shaped fruit were found to have an A/A genotype, while those with A/T, or T/T genotypes had flat-shaped fruits. Finally, we also found that 236 peach accessions and 141 Prunus species with round-type fruit were found to have an A/A genotype at this SNP, while 22 flat peach accessions had an A/T genotype. Taken together, our results suggest that genes flanking this A/T polymorphism, and haplotyped carrying the T allele may determine flat fruit shape in this population. Furthermore, the LOH event resulting in the loss of the haplotype carrying the T allele may therefore be responsible for fruit shape alteration in wild-type flat peach. |
| first_indexed | 2024-04-13T19:14:34Z |
| format | Article |
| id | doaj.art-5a6663c99fbf4ddca4adf4137a771585 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T19:14:34Z |
| publishDate | 2019-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-5a6663c99fbf4ddca4adf4137a7715852022-12-22T02:33:42ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-05-011010.3389/fpls.2019.00592441346Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity EventsQiuping Tan0Qiuping Tan1Qiuping Tan2Xiao Liu3Xiao Liu4Xiao Liu5Hongru Gao6Wei Xiao7Wei Xiao8Wei Xiao9Xiude Chen10Xiude Chen11Xiude Chen12Xiling Fu13Xiling Fu14Xiling Fu15Ling Li16Ling Li17Ling Li18Dongmei Li19Dongmei Li20Dongmei Li21Dongsheng Gao22Dongsheng Gao23Dongsheng Gao24College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, ChinaState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, ChinaFruit Innovation of Modern Agricultural Industry Technology System in Shandong Province, Shandong Agricultural University, Tai’an, ChinaCollege of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, ChinaState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, ChinaFruit Innovation of Modern Agricultural Industry Technology System in Shandong Province, Shandong Agricultural University, Tai’an, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing, ChinaCollege of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, ChinaState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, ChinaFruit Innovation of Modern Agricultural Industry Technology System in Shandong Province, Shandong Agricultural University, Tai’an, ChinaCollege of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, ChinaState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, ChinaFruit Innovation of Modern Agricultural Industry Technology System in Shandong Province, Shandong Agricultural University, Tai’an, ChinaCollege of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, ChinaState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, ChinaFruit Innovation of Modern Agricultural Industry Technology System in Shandong Province, Shandong Agricultural University, Tai’an, ChinaCollege of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, ChinaState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, ChinaFruit Innovation of Modern Agricultural Industry Technology System in Shandong Province, Shandong Agricultural University, Tai’an, ChinaCollege of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, ChinaState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, ChinaFruit Innovation of Modern Agricultural Industry Technology System in Shandong Province, Shandong Agricultural University, Tai’an, ChinaCollege of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, ChinaState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, ChinaFruit Innovation of Modern Agricultural Industry Technology System in Shandong Province, Shandong Agricultural University, Tai’an, ChinaBud sports occur in many plant species, including fruit trees. Although they are correlated with genetic variance in somatic cells, the mechanisms responsible for bud sports are mostly unknown. In this study, a peach bud sport whose fruit shape was transformed to round from flat was identified by next generation sequencing (NGS), and we provide evidence that a long loss of heterozygosity (LOH) event may be responsible for this alteration in fruit shape. Moreover, compared to the reference genome, we identified 237,476 high quality single nucleotide polymorphisms (SNPs) in the wild-type and bud sport genomes. Using this SNP set, a long LOH event was identified at the distal end of scaffold Pp06 of the bud sport genome. Haplotypes from 155 additional peach accessions were phased, suggesting that the homozygous distal end of scaffold Pp06 of the bud sport was likely derived from only one haplotype of the wild-type flat peach. A genome-wide association study (GWAS) of 127 peach accessions was conducted to associate a SNP found at 26,924,482 bp of scaffold Pp06 to differences in fruit shape. All accessions with round-shaped fruit were found to have an A/A genotype, while those with A/T, or T/T genotypes had flat-shaped fruits. Finally, we also found that 236 peach accessions and 141 Prunus species with round-type fruit were found to have an A/A genotype at this SNP, while 22 flat peach accessions had an A/T genotype. Taken together, our results suggest that genes flanking this A/T polymorphism, and haplotyped carrying the T allele may determine flat fruit shape in this population. Furthermore, the LOH event resulting in the loss of the haplotype carrying the T allele may therefore be responsible for fruit shape alteration in wild-type flat peach.https://www.frontiersin.org/article/10.3389/fpls.2019.00592/fullPrunus persicafruit shapebud sportgenome-wide association studynext generation sequencing |
| spellingShingle | Qiuping Tan Qiuping Tan Qiuping Tan Xiao Liu Xiao Liu Xiao Liu Hongru Gao Wei Xiao Wei Xiao Wei Xiao Xiude Chen Xiude Chen Xiude Chen Xiling Fu Xiling Fu Xiling Fu Ling Li Ling Li Ling Li Dongmei Li Dongmei Li Dongmei Li Dongsheng Gao Dongsheng Gao Dongsheng Gao Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events Frontiers in Plant Science Prunus persica fruit shape bud sport genome-wide association study next generation sequencing |
| title | Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events |
| title_full | Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events |
| title_fullStr | Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events |
| title_full_unstemmed | Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events |
| title_short | Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events |
| title_sort | comparison between flat and round peaches genomic evidences of heterozygosity events |
| topic | Prunus persica fruit shape bud sport genome-wide association study next generation sequencing |
| url | https://www.frontiersin.org/article/10.3389/fpls.2019.00592/full |
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