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Huang X, Gao F, Zhou P, Ma C, Tan W, Ma Y, Li M, Ni Z, Shi T, Hayat F, Li Y, Gao Z. Allelic variation of PmCBF03 contributes to the altitude and temperature adaptability in Japanese apricot (Prunus mume Sieb. et Zucc.). PLANT, CELL & ENVIRONMENT 2024; 47:1379-1396. [PMID: 38221869 DOI: 10.1111/pce.14813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/26/2023] [Accepted: 12/31/2023] [Indexed: 01/16/2024]
Abstract
Japanese apricot is an important subtropical deciduous fruit tree in China, widely distributed in different altitude areas. How does it adapt to the different temperature environments in these areas? In this study, we identified a low-temperature transcription factor PmCBF03 on chromosome 7 through adaptive analysis of populations at different altitudes, which has an early termination single nucleotide polymorphism mutation. There were two different types of variation, PmCBF03A type in high-altitude areas and PmCBF03T type in low-altitude areas. PmCBF03A gene increased the survival rate, Fv/Fm values, antioxidant enzyme activity, and expression levels of antioxidant enzyme genes, and reducing electrolyte leakage and accumulation of reactive oxygen species in transgenic Arabidopsis under low temperature and freezing stress. Simultaneously, PmCBF03A gene promoted the dormancy of transgenic Arabidopsis seeds than wild-type. Biochemical analysis demonstrated that PmCBF03A directly bound to the DRE/CRT element in the promoters of the PmCOR413, PmDAM6 and PmABI5 genes, promoting their transcription and enhanced the cold resistance and dormancy of the overexpressing PmCBF03A lines. While PmCBF03T gene is unable to bind to the promoters of PmDAM6 and PmABI5 genes, leading to early release of dormancy to adapt to the problem of insufficient chilling requirement in low-altitude areas.
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Affiliation(s)
- Xiao Huang
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Feng Gao
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Pengyu Zhou
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Chengdong Ma
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Wei Tan
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yufan Ma
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Minglu Li
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhaojun Ni
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ting Shi
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Faisal Hayat
- Department of Pomology, College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Yongping Li
- Department of Special Fruit Tree Germplasm Resources, Yunnan Green Food Development Center, Kunming, Yunnan, China
| | - Zhihong Gao
- Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Tan W, Zhou P, Huang X, Liao R, Wang X, Wu Y, Ni Z, Shi T, Yu X, Zhang H, Ma C, Gao F, Ma Y, Bai Y, Hayat F, Omondi OK, Coulibaly D, Gao Z. Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot. HORTICULTURE RESEARCH 2024; 11:uhae103. [PMID: 38689698 PMCID: PMC11059810 DOI: 10.1093/hr/uhae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 03/31/2024] [Indexed: 05/02/2024]
Abstract
Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.
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Affiliation(s)
- Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengyu Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruyu Liao
- Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Xiaoan Wang
- Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yaoyao Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaqing Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huiqin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chengdong Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufan Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Faisal Hayat
- Department of Pomology, College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Ouma Kenneth Omondi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Crops, Horticulture and Soils, Faculty of Agriculture, Egerton University, P.O. Box 536, Egerton 20115, Kenya
| | - Daouda Coulibaly
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Agricultural Sciences and Techniques-Horticulture, Rural Polytechnic Institute for Training and Applied Research (IPR/IFRA) of Katibougou, Koulikoro B.P.224, Mali
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Numaguchi K, Kitamura Y, Kashiwamoto T, Morimoto T, Oe T. Genomic region and origin for selected traits during differentiation of small-fruit cultivars in Japanese apricot (Prunus mume). Mol Genet Genomics 2023; 298:1365-1375. [PMID: 37632570 DOI: 10.1007/s00438-023-02062-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023]
Abstract
The Japanese apricot (Prunus mume) is a popular fruit tree in Japan. However, the genetic factors associated with fruit trait variations are poorly understood. In this study, we investigated nine fruit-associated traits, including harvesting time, fruit diameter, fruit shape, fruit weight, stone (endocarp) weight, ratio of stone weight to fruit weight, and rate of fruit gumming, using 110 Japanese apricot accessions over four years. A genome-wide association study (GWAS) was performed for these traits and strong signals were detected on chromosome 6 for harvesting time and fruit diameters. These peaks were shown to undergo strong artificial selection during the differentiation of small-fruit cultivars. The genomic region defined by the GWAS and XP-nSL analyses harbored several candidate genes associated with plant hormone regulation. Furthermore, the alleles of small-fruit cultivars in this region were shown to have genetic proximity to some Chinese cultivars of P. mume. These results indicate that the small-fruit trait originated in China; after being introduced into Japan, it was preferred and selected by the Japanese people, resulting in the differentiation of small-fruit cultivars.
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Affiliation(s)
- Koji Numaguchi
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan.
- Wakayama Fruit Tree Experiment Station, 751-1, Oki, Aridagawa-cho, Arida-gun, Wakayama, 643-0022, Japan.
| | - Yuto Kitamura
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
- Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Tomoaki Kashiwamoto
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
| | - Takuya Morimoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 74 Kitainayazuma, Seika-cho, Soraku-gun, Kyoto, 619-0244, Japan
| | - Takaaki Oe
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
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He Y, Qin H, Wen J, Cao W, Yan Y, Sun Y, Yuan P, Sun B, Fan S, Lu W, Li C. Characterization of Key Compounds of Organic Acids and Aroma Volatiles in Fruits of Different Actinidia argute Resources Based on High-Performance Liquid Chromatography (HPLC) and Headspace Gas Chromatography-Ion Mobility Spectrometry (HS-GC-IMS). Foods 2023; 12:3615. [PMID: 37835267 PMCID: PMC10572923 DOI: 10.3390/foods12193615] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Actinidia arguta, known for its distinctive flavor and high nutritional value, has seen an increase in cultivation and variety identification. However, the characterization of its volatile aroma compounds remains limited. This study aimed to understand the flavor quality and key volatile aroma compounds of different A. arguta fruits. We examined 35 A. arguta resource fruits for soluble sugars, titratable acids, and sugar-acid ratios. Their organic acids and volatile aroma compounds were analyzed using high-performance liquid chromatography (HPLC) and headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS). The study found that among the 35 samples tested, S12 had a higher sugar-acid ratio due to its higher sugar content despite having a high titratable acid content, making its fruit flavor superior to other sources. The A. arguta resource fruits can be classified into two types: those dominated by citric acid and those dominated by quinic acid. The analysis identified a total of 76 volatile aroma substances in 35 A. arguta resource fruits. These included 18 esters, 14 alcohols, 16 ketones, 12 aldehydes, seven terpenes, three pyrazines, two furans, two acids, and two other compounds. Aldehydes had the highest relative content of total volatile compounds. Using the orthogonal partial least squares discriminant method (OPLS-DA) analysis, with the 76 volatile aroma substances as dependent variables and different soft date kiwifruit resources as independent variables, 33 volatile aroma substances with variable importance in projection (VIP) greater than 1 were identified as the main aroma substances of A. arguta resource fruits. The volatile aroma compounds with VIP values greater than 1 were analyzed for odor activity value (OAV). The OAV values of isoamyl acetate, 3-methyl-1-butanol, 1-hexanol, and butanal were significantly higher than those of the other compounds. This suggests that these four volatile compounds contribute more to the overall aroma of A. arguta. This study is significant for understanding the differences between the fruit aromas of different A. arguta resources and for scientifically recognizing the characteristic compounds of the fruit aromas of different A. arguta resources.
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Affiliation(s)
- Yanli He
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Hongyan Qin
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Jinli Wen
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Weiyu Cao
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Yiping Yan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Yining Sun
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Pengqiang Yuan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Bowei Sun
- Faculty of Agriculture, Yanbian University, Yanji 136200, China;
| | - Shutian Fan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Wenpeng Lu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Changyu Li
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
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Shi T, Bai Y, Wu X, Wang Y, Iqbal S, Tan W, Ni Z, Gao Z. PmAGAMOUS recruits polycomb protein PmLHP1 to regulate single-pistil morphogenesis in Japanese apricot. PLANT PHYSIOLOGY 2023; 193:466-482. [PMID: 37204822 DOI: 10.1093/plphys/kiad292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/31/2023] [Accepted: 04/12/2023] [Indexed: 05/20/2023]
Abstract
Japanese apricot (Prunus mume Sieb. et Zucc.) is a traditional fruit tree with a long history. Multiple pistils (MP) lead to the formation of multiple fruits, decreasing fruit quality and yield. In this study, the morphology of flowers was observed at 4 stages of pistil development: undifferentiated stage (S1), predifferentiation stage (S2), differentiation stage (S3), and late differentiation stage (S4). In S2 and S3, the expression of PmWUSCHEL (PmWUS) in the MP cultivar was significantly higher than that in the single-pistil (SP) cultivar, and the gene expression of its inhibitor, PmAGAMOUS (PmAG), also showed the same trend, indicating that other regulators participate in the regulation of PmWUS during this period. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) showed that PmAG could bind to the promoter and the locus of PmWUS, and H3K27me3 repressive marks were also detected at these sites. The SP cultivar exhibited an elevated level of DNA methylation in the promoter region of PmWUS, which partially overlapped with the region of histone methylation. This suggests that the regulation of PmWUS involves both transcription factors and epigenetic modifications. Also, the gene expression of Japanese apricot LIKE HETEROCHROMATIN PROTEIN (PmLHP1), an epigenetic regulator, in MP was significantly lower than that in SP in S2 to 3, contrary to the trend in expression of PmWUS. Our results showed that PmAG recruited sufficient PmLHP1 to maintain the level of H3K27me3 on PmWUS during the S2 of pistil development. This recruitment of PmLHP1 by PmAG inhibits the expression of PmWUS at the precise time, leading to the formation of 1 normal pistil primordium.
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Affiliation(s)
- Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinxin Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- College of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Yike Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shahid Iqbal
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL 32351, USA
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Zang F, Ma Y, Wu Q, Tu X, Xie X, Huang P, Tong B, Zheng Y, Zang D. Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways. BMC PLANT BIOLOGY 2023; 23:235. [PMID: 37142995 PMCID: PMC10158352 DOI: 10.1186/s12870-023-04244-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions. RESULTS A total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth. CONCLUSIONS The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.
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Affiliation(s)
- Fengqi Zang
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, P. R. China
| | - Yan Ma
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Qichao Wu
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Xiaolong Tu
- State Key Laboratory of Genetic Resources and Evolution, Center for excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, P. R. China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan, 650204, P. R. China
| | - Xiaoman Xie
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, P. R. China
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, P. R. China
| | - Boqiang Tong
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, P. R. China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, P. R. China.
| | - Dekui Zang
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China.
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Song Y, Li C, Liu L, Hu P, Li G, Zhao X, Zhou H. The population genomic analyses of chloroplast genomes shed new insights on the complicated ploidy and evolutionary history in Fragaria. FRONTIERS IN PLANT SCIENCE 2023; 13:1065218. [PMID: 36874917 PMCID: PMC9975502 DOI: 10.3389/fpls.2022.1065218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/30/2022] [Indexed: 06/18/2023]
Abstract
The genus Fragaria consists of a rich diversity of ploidy levels with diploid (2x), tetraploid (4x), pentaploid (5x), hexaploidy (6x), octoploid (8x) and decaploid (10x) species. Only a few studies have explored the origin of diploid and octoploid strawberry, and little is known about the roles of tetraploidy and hexaploidy during the evolution of octoploid strawberry. The chloroplast genome is usually a stable circular genome and is widely used in investigating the evolution and matrilineal identification. Here, we assembled the chloroplast genomes of F. x ananassa cv. 'Benihoppe' (8x) using Illumina and HiFi data seperately. The genome alignment results showed that more InDels were located in the chloroplast genomes based on the PacBio HiFi data than Illumina data. We obtain highly accurate chloroplast genomes assembled through GetOrganelle using Illumina reads. We assembled 200 chloroplast genomes including 198 Fragaria (21 species) and 2 Potentilla samples. Analyses of sequence variation, phylogenetic and PCA analyses showed that Fragaria was divided into five groups. F. iinumae, F. nilgerrensis and all octoploid accessions formed Group A, C and E separately. Species native to western China were clustered into Group B. Group D consisted of F. virdis, F. orientalis, F. moschata, and F. vesca. STRUCTURE and haplotype network confirmed that the diploid F. vesca subsp. bracteata was the last maternal donator of octoploid strawberry. The dN/dS ratio estimated for the protein-coding genes revealed that genes involved in ATP synthase and photosystem function were under positive selection. These findings demonstrate the phylogeny of totally 21 Fragaria species and the origin of octoploid species. F. vesca was the last female donator of octoploid, which confirms the hypothesis that the hexaploid species F. moschata may be an evolutionary intermediate between the diploids and wild octoploid species.
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Affiliation(s)
- Yanhong Song
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Chaochao Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Lifeng Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Panpan Hu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Gang Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xia Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Houcheng Zhou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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Evaluation of Dynamic Changes and Regularity of Volatile Flavor Compounds for Different Green Plum ( Prunus mume Sieb. et Zucc) Varieties during the Ripening Process by HS-GC-IMS with PLS-DA. Foods 2023; 12:foods12030551. [PMID: 36766079 PMCID: PMC9913901 DOI: 10.3390/foods12030551] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/29/2022] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
Headspace gas chromatography-ion mobility spectrometry and partial-least-squares discriminant analysis (PLS-DA) were adopted to analyze the rule of change in flavor substances for different varieties of green plums at different levels of maturity (S1-immature, S2-commercially mature, and S3-fully mature). The results showed that 68 kinds of volatile flavor substances were identified in all green plum samples. The types and contents of such volatile substances experienced a V-shaped trend with an increasing degree of green plum maturity. During the S1 and S2 stages, aldehydes, ketones, and a small amount of alcohols were the main volatile flavor substances in the green plum samples. During the S3 stage, esters and alcohols were the most important volatile flavor components in the green plum pulp samples, followed by terpenes and ketones. YS had the most types and highest contents of volatile flavor substances in three stages, followed by GC and DZ. By using the PLS-DA method, this study revealed the differences in flavor of the different varieties of green plums at different maturity stages, and it identified eight common characteristic volatile flavor substances, such as ethyl acetate, 3-methylbutan-1-ol, and 2-propanone, produced by the different green plum samples during the ripening process, as well as the characteristic flavor substances of green plums at each maturity stage (S1-S3).
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Li Y, Jian Y, Mao Y, Meng F, Shao Z, Wang T, Zheng J, Wang Q, Liu L. "Omics" insights into plastid behavior toward improved carotenoid accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:1001756. [PMID: 36275568 PMCID: PMC9583013 DOI: 10.3389/fpls.2022.1001756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Plastids are a group of diverse organelles with conserved carotenoids synthesizing and sequestering functions in plants. They optimize the carotenoid composition and content in response to developmental transitions and environmental stimuli. In this review, we describe the turbulence and reforming of transcripts, proteins, and metabolic pathways for carotenoid metabolism and storage in various plastid types upon organogenesis and external influences, which have been studied using approaches including genomics, transcriptomics, proteomics, and metabonomics. Meanwhile, the coordination of plastid signaling and carotenoid metabolism including the effects of disturbed carotenoid biosynthesis on plastid morphology and function are also discussed. The "omics" insight extends our understanding of the interaction between plastids and carotenoids and provides significant implications for designing strategies for carotenoid-biofortified crops.
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Affiliation(s)
- Yuanyuan Li
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yue Jian
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yuanyu Mao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Fanliang Meng
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Zhiyong Shao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Tonglin Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Jirong Zheng
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Lihong Liu
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
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Huang X, Coulibaly D, Tan W, Ni Z, Shi T, Li H, Hayat F, Gao Z. The analysis of genetic structure and characteristics of the chloroplast genome in different Japanese apricot germplasm populations. BMC PLANT BIOLOGY 2022; 22:354. [PMID: 35864441 PMCID: PMC9306182 DOI: 10.1186/s12870-022-03731-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/04/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Chloroplast (cp) genomes are generally considered to be conservative and play an important role in population diversity analysis in plants, but the characteristics and diversity of the different germplasm populations in Japanese apricot are still not clear. RESULTS A total of 146 cp genomes from three groups of wild, domesticated, and bred accessions of Japanese apricot were sequenced in this study. The comparative genome analysis revealed that the 146 cp genomes were divided into 41 types, and ranged in size from 157,886 to 158,167 bp with a similar structure and composition to those of the genus Prunus. However, there were still minor differences in the cp genome that were mainly caused by the contraction and expansion of the IR region, and six types of SSR in which mono-nucleotide repeats were the most dominant type of repeats in the cp genome. The genes rpl33 and psbI, and intergenic regions of start-psbA, rps3-rpl22, and ccsA-ndhD, showed the highest nucleotide polymorphism in the whole cp genome. A total of 325 SNPs were detected in the 146 cp genomes, and more than 70% of the SNPs were in region of large single-copy (LSC). The SNPs and haplotypes in the cp genome indicated that the wild group had higher genetic diversity than the domesticated and bred groups. In addition, among wild populations, Southwest China, including Yunnan, Tibet, and Bijie of Guizhou, had the highest genetic diversity. The genetic relationship of Japanese apricot germplasm resources in different regions showed a degree of correlation with their geographical distribution. CONCLUSION Comparative analysis of chloroplast genomes of 146 Japanese apricot resources was performed to analyze the used to explore the genetic relationship and genetic diversity among Japanese apricot resources with different geographical distributions, providing some reference for the origin and evolution of Japanese apricot.
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Affiliation(s)
- Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Daouda Coulibaly
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Hantao Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Faisal Hayat
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
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Ni X, Ni Z, Ouma KO, Gao Z. Mutations in PmUFGT3 contribute to color variation of fruit skin in Japanese apricot (Prunus mume Sieb. et Zucc.). BMC PLANT BIOLOGY 2022; 22:304. [PMID: 35751035 PMCID: PMC9229503 DOI: 10.1186/s12870-022-03693-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/14/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Japanese apricot (Prunus mume Sieb. et Zucc.) is popular for both ornamental and processing value, fruit color affects the processing quality, and red pigmentation is the most obvious phenotype associated with fruit color variation in Japanese apricot, mutations in structural genes in the anthocyanin pathway can disrupt the red pigmentation, while the formation mechanism of the red color trait in Japanese apricot is still unclear. RESULTS: One SNP marker (PmuSNP_27) located within PmUFGT3 gene coding region was found highly polymorphic among 44 different fruit skin color cultivars and relative to anthocyanin biosynthesis in Japanese apricot. Meantime, critical mutations were identified in two alleles of PmUFGT3 in the green-skinned type is inactivated by seven nonsense mutations in the coding region, which leads to seven amino acid substitution, resulting in an inactive UFGT enzyme. Overexpression of the PmUFGT3 allele from red-skinned Japanese apricot in green-skinned fruit lines resulted in greater anthocyanin accumulation in fruit skin. Expression of same allele in an Arabidopsis T-DNA mutant deficient in anthocyanidin activity the accumulation of anthocyanins. In addition, using site-directed mutagenesis, we created a single-base substitution mutation (G to T) of PmUFGT3 isolated from green-skinned cultivar, which caused an E to D amino acid substitution and restored the function of the inactive allele of PmUFGT3 from a green-skinned individual. CONCLUSION This study confirms the function of PmUFGT3, and provides insight into the mechanism underlying fruit color determination in Japanese apricot, and possible approaches towards genetic engineering of fruit color.
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Affiliation(s)
- Xiaopeng Ni
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 China
| | - Kenneth Omondi Ouma
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095 China
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