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Li B, Muhammad N, Zhang S, Lan Y, Yang Y, Han S, Liu M, Yang M. Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources. PLANTS (BASEL, SWITZERLAND) 2023; 12:2885. [PMID: 37571038 PMCID: PMC10421302 DOI: 10.3390/plants12152885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/23/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023]
Abstract
Jujube (Ziziphus jujuba Mill.) is a commercially important tree native to China, known for its high nutritional value and widespread distribution, as well as its diverse germplasm resources. Being resilient to harsh climatic conditions, the cultivation of jujube could provide a solution to food insecurity and income for people of arid and semi-arid regions in and outside of China. The evaluation of germplasm resources and genetic diversity in jujube necessitates the use of Simple Sequence Repeat (SSR) markers. SSR markers are highly polymorphic and can be used to evaluate the genetic diversity within and between cultivars of Chinese jujube, and are important for conservation biology, breeding programs, and the discovery of important traits for Chinese jujube improvement in China and abroad. However, traditional methods of SSR development are time-consuming and inadequate to meet the growing research demands. To address this issue, we developed a novel approach called Multiple-Genome-Based SSR identification (MGB-SSR), which utilizes the genomes of three jujube cultivars to rapidly screen for polymorphic SSRs in the jujube genome. Through the screening process, we identified 12 pairs of SSR primers, which were then used to successfully classify 249 jujube genotypes. Based on the genotyping results, a digital ID card was established, enabling the complete identification of all 249 jujube plants. The MGB-SSR approach proved efficient in rapidly detecting polymorphic SSRs within the jujube genome. Notably, this study represents the first successful differentiation of jujube germplasm resources using 12 SSR markers, with 4 markers successfully identifying triploid jujube genotypes. These findings offer valuable information for the classification of Chinese jujube germplasm, thereby providing significant assistance to jujube researchers and breeders in identifying unknown jujube germplasm.
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Affiliation(s)
- Bin Li
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Noor Muhammad
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Shufeng Zhang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Yunxin Lan
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Yihan Yang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Shoukun Han
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China
| | - Meng Yang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
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Sapkota D, Zhang D, Park S, Meinhardt LW, Yao S. Genotyping of Jujube ( Ziziphus spp.) Germplasm in New Mexico and Southwestern Texas. PLANTS (BASEL, SWITZERLAND) 2023; 12:2405. [PMID: 37446967 DOI: 10.3390/plants12132405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/15/2023]
Abstract
Since the early 19th century, a substantial amount of jujube (Ziziphus spp.) germplasm has been introduced from China and Europe into the United States. However, due to a lack of passport data, cultivar mislabeling is common and the genetic background of the introduced germplasm remains unknown. In the present study, a low-density SNP array was employed to genotype 204 jujube trees sampled from multiple locations in New Mexico, Texas, Missouri, and Kentucky. Multilocus matching of SNP profiles revealed a significant rate of genetic redundancy among these jujube samples. A total of 14 synonymous groups were detected, comprising 48 accessions. Bayesian clustering analysis and neighbor-joining tree partitioned the US jujube germplasm into two major clusters. The first cluster included cultivated genotypes (Ziziphus jujuba Mill.), whereas the other major cluster comprised the wild/sour jujube (Ziziphus spinosa Hu.). The results also revealed a unique jujube population at Fabens/Tornillo, Texas, and a semi-naturalized population at Tucumcari, NM. These findings will provide valuable guidance to jujube growers and researchers on the effective utilization of jujube germplasm in the horticultural industry.
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Affiliation(s)
- Dikshya Sapkota
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Sunchung Park
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Shengrui Yao
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
- Sustainable Agriculture Sciences Center, New Mexico State University, Alcalde, NM 87511, USA
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Zhi Y, Chuanjiang Z, Xinfang Y, Mengyi D, Zhenlei W, Fenfen Y, Cuiyun W, Jiurui W, Mengjun L, Minjuan L. Genetic analysis of mixed models of fruit sugar-acid fractions in a cross between jujube ( Ziziphus jujuba Mill.) and wild jujube ( Z. acido jujuba). FRONTIERS IN PLANT SCIENCE 2023; 14:1181903. [PMID: 37251778 PMCID: PMC10213531 DOI: 10.3389/fpls.2023.1181903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023]
Abstract
Chinese jujube (Ziziphus jujuba Mill.), an economically significant species in the Rhamnaceae family, is a popular fruit tree in Asia. The sugar and acid concentrations in jujube are considerably higher than those in other plants. Due to the low kernel rate, it is extremely difficult to establish hybrid populations. Little is known about jujube evolution and domestication, particularly with regard to the role of the sugar and acid components of jujube. Therefore, we used cover net control as a hybridization technique for the cross-breeding of Ziziphus jujuba Mill and 'JMS2' and (Z. acido jujuba) 'Xing16' to obtain an F1 population (179 hybrid progeny). The sugar and acid levels in the F1 and parent fruit were determined by HPLC. The coefficient of variation ranged from 28.4 to 93.9%. The sucrose and quinic acid levels in the progeny were higher than those in the parents. The population showed continuous distributions with transgressive segregation on both sides. Analysis by the mixed major gene and polygene inheritance model was performed. It was found that glucose is controlled by one additive-dominant major gene and polygenes, malic acid is controlled by two additive-dominant major genes and polygenes, and oxalic acid and quinic acid are controlled by two additive-dominant-epistatic major genes and polygenes. The results of this study provide insights into the genetic predisposition and molecular mechanisms underlying the role of sugar acids in jujube fruit.
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Affiliation(s)
- Yang Zhi
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Zhang Chuanjiang
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Yang Xinfang
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Dong Mengyi
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Wang Zhenlei
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Yan Fenfen
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Wu Cuiyun
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
| | - Wang Jiurui
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, China
| | - Liu Mengjun
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
- Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, China
| | - Lin Minjuan
- The National and Local Joint Engineering Laboratory of High Efficiency and High Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, the Production Engineering Laboratory of Characteristic Fruit Trees in Southern Xinjiang of Xinjiang Production and Construction Corps, College of Plant Science of Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Basin Biological Resources Protection and Utilization, Xinjiang Production and Construction Corps, Alar, Xinjiang, China
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Sareen A, Sharma V, Gupta RC. Assessment of genetic diversity and population structure in wild Ziziphus species from northwest India using SSR marker technique. J Genet Eng Biotechnol 2023; 21:4. [PMID: 36637660 PMCID: PMC9839936 DOI: 10.1186/s43141-022-00458-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Ziziphus species particularly Ziziphus mauritiana and Ziziphus nummularia constitute an important part of genetic resources in India. They contribute economically as a fruit crop with lots of morphological and pomological variability. In current study, 48 accessions belonging to two wild Ziziphus species, i.e., Z. mauritiana and Z. nummularia, were characterized using SSR markers. In addition, external features were also examined using stereomicroscope. RESULTS Present investigation was done to explore the genetic structure of North Indian jujube. In total, 23 SSR markers detected 57 SSR alleles with an average of 2.47 alleles. Highest number of alleles (4) were detected by three primers, namely BFU1178, BFU479, and ZCMS14, while lowest number of alleles (2) were detected by fifteen primers. Highest Polymorphism Information Content (PIC) was 0.500 and shown by two primers, namely BFU528 and BFU1248, while lowest PIC (0.041) was observed in primers BFU286 with mean value of 0.443. Similarly, highest value of marker index (MI) was detected by primer BFU1178 i.e. 1.969, and lowest value of marker index was observed in primer BFU286 i.e. 0.021. Dendrogram generated using SSR markers data and principal component analysis showed two major groups of the analyzed germplasm with intermixing. STRUCTURE analysis also clustered all the accessions into two groups. We did not found correlation between geographic and genetic distances. CONCLUSIONS The preliminary results suggest that there is high level of gene pool mixing in these species which can be attributed to their cross-pollination habit. However, more such studies with large numbers of samples are required in future to gain concrete insights of the genetic structure in these species.
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Affiliation(s)
- Amit Sareen
- grid.412580.a0000 0001 2151 1270Department of Botany, Punjabi University Patiala, Patiala, Punjab India
| | - Vikas Sharma
- Department of Agriculture, Sant Baba Bhag Singh University Khiala, Jalandhar, 144030 India
| | - Raghbir Chand Gupta
- grid.412580.a0000 0001 2151 1270Department of Botany, Punjabi University Patiala, Patiala, Punjab India
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Kim M, Park JH, Gil J, Kim JS, Kim HT, Oh HK, Lee KH, Lee M, Lee J, Lee Y. The complete chloroplast genome of Ziziphus jujuba cv. Bokjo (Rhamnaceae). Mitochondrial DNA B Resour 2022; 7:1805-1806. [PMID: 36278122 PMCID: PMC9586629 DOI: 10.1080/23802359.2022.2131366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We have sequenced the Ziziphus jujuba cv. Bokjo chloroplast genome by de novo assembly using next-generation sequencing. The complete circular chloroplast genome consisted of 161,714 bp and contained four parts: a large single-copy (LSC) region of 89,323 bp, a small single-copy (SSC) region of 19,361 bp, and two inverted repeat regions (IRa and IRb) of 26,515 bp each. The genome annotation predicted a total of 110 genes, including 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis demonstrated the close taxonomic relationship between Z. jujuba cv. Bokjo and two other members of the Ziziphus genus, Z. spina-christi and Z. mauritiana. We found 135 polymorphic loci, 63 single nucleotide polymorphism (SNP) and 72 insertion-deletion (InDel), from the comparison of Z. jujuba cultivar Bokjo and Z. jujuba reference (NC_030299). The polymorphic loci could be used for the differentiation of Z. jujuba genetic resources and for breeding in the future.
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Affiliation(s)
- Moonkyo Kim
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, Republic of Korea,Korea Polar Research Institute, Incheon, Republic of Korea
| | - Jin Hee Park
- Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Jinsu Gil
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jung Sung Kim
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyoung Tae Kim
- College of Ecology and Environmental Science, Kyungpook National University, Sangju, Republic of Korea
| | - Ha Kyung Oh
- Chungcheongbuk-do Agricultural Research & Extension Services, Cheongju, Republic of Korea
| | - Kyeong Hee Lee
- Chungcheongbuk-do Agricultural Research & Extension Services, Cheongju, Republic of Korea
| | - Minjee Lee
- Green Plant Institute, Yongin, Republic of Korea
| | - Jungho Lee
- Green Plant Institute, Yongin, Republic of Korea, Jungho Lee Green Plant Institute, Yongin16954, Republic of Korea
| | - Yi Lee
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, Republic of Korea,CONTACT Yi Lee Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju28644, Republic of Korea
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Uddin N, Muhammad N, Ali N, Nisar M, Liu M. Genomic constitution and relationships of Ziziphus species collected from Malakand Division, Pakistan. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1939-1953. [PMID: 36484032 PMCID: PMC9723090 DOI: 10.1007/s12298-022-01249-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 03/11/2022] [Accepted: 04/07/2022] [Indexed: 06/01/2023]
Abstract
Polyploidization has played a major role in plant evolution and can alter plant morphology, phenology, and ecology within only one or a few generations. Ziziphus species are economically as well as nutritionally important fruit-yielding trees. Identification of genotypes with unique traits or those with higher ploidy levels or a broader genetic base could lead to further improvements within the species. The current study has assessed the ploidy levels in the Ziziphus species (Ziziphus jujuba Mill. and Ziziphus nummularia (Burm. f. Wight & Arn) with phenotypic traits, flow cytometry, and chromosomal count as well as with SSRs markers. Morphological traits were inferred to be the most important drivers of trait variations among the investigated genotypes. The total sugar, total cAMPs, titratable acid, and chlorophyll (a, b, and total) were also significantly different in contrast with diploid plants, which showed that tetraploid Ziziphus had the potential to increase nutritional contents. Out of twenty (20), five (5) Z. jujuba genotypes (ZJL-9, ZJL-12, ZJL-17, ZJL-18, and ZJL-19) were found tetraploid 2n = 4x = 48, with genome size ranging from 965.9 to1238.8 Mb that was significantly higher than the tetraploid Z. jujuba Mill. variety Dongzao. Similarly, Z. nummularia ZNL-07 to ZNL-15 have found tetraploid 2n = 4x = 72 with genomic sizes ranging from 1152.2 to 1746.8 Mb respectively. Simple sequence repeats (SSRs) marker was applied to assess the genetic relationship within Ziziphus genotypes. To the best of our understanding, this is the first report on the identification of naturalized random tetraploids within the Pakistani Ziziphus species. This study provides important insights into the genomic architecture of Ziziphus species with implications for classification, conservation, and improvements of Ziziphus germplasm resources.
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Affiliation(s)
- Nisar Uddin
- Department of Botany, Hazara University Mansehra, Khyber Pakhtunkhwa, Pakistan
- Department of Pomology, College of Horticulture, Hebei Agricultural University, Baoding, 071001 Hebei China
- Department of Botany, University of Malakand, Chakdara, Khyber Pakhtunkhwa Pakistan
| | - Noor Muhammad
- Department of Pomology, College of Horticulture, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Niaz Ali
- Department of Botany, Hazara University Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Mohammad Nisar
- Department of Botany, University of Malakand, Chakdara, Khyber Pakhtunkhwa Pakistan
| | - Mengjun Liu
- Department of Pomology, College of Horticulture, Hebei Agricultural University, Baoding, 071001 Hebei China
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Mehmood S, Ud Din I, Ullah I, Mohamed HI, Basit A, Khan MN, Hussain Shah SS, Ur Rehman A. Agro-morphological and genetic diversity studies in Rice (Oryza sativa L.) germplasm using microsatellite markers. Mol Biol Rep 2021; 48:7179-7192. [PMID: 34554387 DOI: 10.1007/s11033-021-06710-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Knowledge of the genetic diversity and population structure of germplasm collections is an important foundation for crop improvement. Rice production across a broad range of rice-growing environments results in a diverse array of local rice varieties. Many rice varieties have been lost as a result of biodiversity loss and are now grown in Pakistan. METHODS AND RESULTS To protect the biodiversity of rice varieties, an experiment was carried out to check the genetic and morphological variations between 8 exotic and 7 local rice genotypes, using 5 different SSR markers, i.e., RM3, RM259, RM341, RM520, and RM11943. The analysis of morphological and quality traits of rice observed significant variation across genotypes. The results revealed that genotype Irri-Pak attained the highest plant height and primary branch plant-1, while genotype Mushkan produced a higher number of productive tillers and obtained a higher fertility factor (%). Similarly, the highest value for panicle length was observed for genotype Faker-e-Malakand, 1000-grains weight in genotype Calmochi, and maximum days to maturity was noticed in genotype Swati-2014. Moreover, the genotype Brio attained the highest value of stem diameter, while maximum seed length was noted in the genotype Sug Dasi. The highest number of primary branches plant-1 in genotype Ibge-I and secondary branches plant-1 in genotype Calmochi were noticed. A higher concentration of sodium and potassium was observed for the genotype Marte, while the genotype Muskan attained the maximum content of copper. Moreover, the highest concentration of iron in genotype Originario, zinc in genotype JP-5, and cadmium content were noticed in genotype Ibge. Similarly, the dendrogram analysis for quantitative parameters showed three clusters at 74.13% similarities. Whereas all the genotypes of European origin formed a separate cluster. A set of 5 simple sequence repeat primers, covering four chromosomes, amplified a total of 14 alleles and showed 100% polymorphism with an average PIC value ranging from 0.39 to 0.91. The UPGMA cluster analysis separated the 15 rice genotypes into 3 main groups based on 32.5% similarities and the highest genetic distance (45.1%) was observed between two genotypes (Fakher-e-malakand and Musa), having different geographical origins. There was no genetic distance between the genotypes Marte and Brio, irrespective of having the same origin. CONCLUSIONS The maximum genetic distances were noted for genotype, Fakhre-e-Malakand and Musa having a different origin, while the minimum genetic distance was shown by genotypes, Marte and Onice, from the same origin.
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Affiliation(s)
- Shiraz Mehmood
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Israr Ud Din
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan.
| | - Izhar Ullah
- Department of Horticulture, The University of Agriculture, Peshawar, Pakistan
| | - Heba I Mohamed
- Biological and Geological Sciences Department, Faculty of Education, Ain Shams University, Cairo, Egypt.
| | - Abdul Basit
- Department of Horticulture, The University of Agriculture, Peshawar, Pakistan
| | - Mudassar Nawaz Khan
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Syed Saad Hussain Shah
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Attiq Ur Rehman
- Horticulture Technologies Production System Unit, Natural Resources Institute (Luke), Toivonlinnantie 518, 21500, Piikkiö, Finland.,Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, 00790, Helsinki, Finland
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8
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Chiou CY, Shih HC, Tsai CC, Jin XL, Ko YZ, Mantiquilla JA, Weng IS, Chiang YC. The genetic relationships of Indian jujube ( Ziziphus mauritiana Lam.) cultivars using SSR markers. Heliyon 2020; 6:e05078. [PMID: 33072904 PMCID: PMC7549064 DOI: 10.1016/j.heliyon.2020.e05078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/16/2020] [Accepted: 09/23/2020] [Indexed: 11/25/2022] Open
Abstract
The genetic relationships among 24 Indian jujube cultivars (Ziziphus mauritiana Lam.) were evaluated by genotyping the microsatellite loci using simple sequence repeat (SSR) markers. The SSR loci were scored by fluorescent labelling and automated detection systems for the high-throughput capillary electrophoresis and high-resolution gel electrophoresis. Out of the 29 newly characterized SSR loci, 26 were considered as polymorphic with a total of 181 alleles obtained. The number of alleles ranged from 2–12, while the polymorphism information content ranged from 0.08–0.83, and the expected and observed heterozygosity were 0.04–0.83 and 0.04–0.82, respectively. The allele pattern of Indian jujube for all SSR loci confirmed its karyotype as tetraploid. Similarity coefficients and UPGMA dendrogram revealed that the Taiwanese cultivars consisted of a large ‘A’ clade, which is further divided into ‘A1’ and ‘A2’ groups, and the ‘B’ clade where both are rooted by the wild accession, ‘Chad native’. These four genetic clusters were supported by the results of PCoA and the assignment test. The excess of heterozygotes based on F-statistics was attributed to its mating system as outcrossing and self-incompatible, and the introgression of the presumed mutation-derived cultivars with genetic admixture. Based on this study, SSR markers offer valuable information on the genetic relationship of this tropical fruit tree which is basically in agreement with the genealogy of its breeding history.
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Affiliation(s)
- Chu-Ying Chiou
- Kaohsiung District Agricultural Research and Extension Station, Pingtung 900, Taiwan
| | - Huei-Chuan Shih
- Department of Nursing, Meiho University, Pingtung 912, Taiwan
| | - Chi-Chu Tsai
- Kaohsiung District Agricultural Research and Extension Station, Pingtung 900, Taiwan.,National Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Xiao-Lei Jin
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Ya-Zhu Ko
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Junaldo A Mantiquilla
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan.,Department of Biological Sciences and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Mintal, Davao City 8022, Philippines
| | - I-Szu Weng
- Kaohsiung District Agricultural Research and Extension Station, Pingtung 900, Taiwan
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan.,Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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9
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Kumar C, Kumar R, Singh SK, Goswami AK, Nagaraja A, Paliwal R, Singh R. Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies. PLoS One 2020; 15:e0237538. [PMID: 32804981 PMCID: PMC7431106 DOI: 10.1371/journal.pone.0237538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
Dearth of genomic resources particularly, microsatellite markers in nutritionally and commercially important fruit crop, guava necessitate the development of the novel genomic SSR markers through the library enrichment techniques. Three types of 3' -biotinylated oligonucleotide probes [(CT)14, (GT)12, and (AAC)8] were used to develop microsatellite enriched libraries. A total of 153 transformed colonies were screened of which 111 positive colonies were subjected for Sanger sequencing. The clones having more than five motif repeats were selected for primer designing and a total of 38 novel genomic simple sequence repeats could be identified. The g-SSRs had the motif groups ranging from monomer to pentamer out of which dimer group occurred the most (89.47%). Out of 38 g-SSRs markers developed, 26 were found polymorphic, which showed substantial genetic diversity among the guava genotypes including wild species. The average number of alleles per locus, major allele frequency, gene diversity, expected heterozygosity and polymorphic information content of 26 SSRs were 3.46, 0.56, 0.53, 0.29 and 0.46, respectively. The rate of cross-species transferability of the developed g-SSR loci varied from 38.46 to 80.77% among the studied wild Psidium species. Generation of N-J tree based on 26 SSRs grouped the 40 guava genotypes into six clades with two out-groups, the wild guava species showed genetic distinctness from cultivated genotypes. Furthermore, population structure analysis grouped the guava genotypes into three genetic groups, which were partly supported by PCoA and N-J tree. Further, AMOVA and PCoA deciphered high genetic diversity among the present set of guava genotypes including wild species. Thus, the developed novel g-SSRs were found efficient and informative for diversity and population structure analyses of the guava genotypes. These developed novel g-SSR loci would add to the new genomic resource in guava, which may be utilized in genomic-assisted guava breeding.
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Affiliation(s)
- Chavlesh Kumar
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ramesh Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar Singh
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Amit Kumar Goswami
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - A. Nagaraja
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ritu Paliwal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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González-Robles A, Manzaneda AJ, Salido T, Valera F, García C, Fernández-Ocaña AM, Rey PJ. Spatial genetic structure of a keystone long-lived semiarid shrub: historical effects prevail but do not cancel the impact of recent severe habitat loss on genetic diversity. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01291-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Liu X, Ma Y, Wan Y, Li Z, Ma H. Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas. FRONTIERS IN PLANT SCIENCE 2020; 11:580812. [PMID: 33329643 PMCID: PMC7734338 DOI: 10.3389/fpls.2020.580812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/11/2020] [Indexed: 05/05/2023]
Abstract
Phyllanthus emblica L. is a well-known medicinal and edible plant species. Various medicinal compounds in the fruit make it an important medicinal and promising economic material. The plant is widely distributed in Southwestern and Southern China. However, due to massive deforestation and land reclamation as well as deterioration of its natural habitat in recent years, the wild resources of this species have been sharply reduced, and it is rare to see large-scale wild P. emblica forests so far. In order to effectively protect and rationally utilize this species, we investigated the genetic diversity, genetic structure, and population dynamics of 260 individuals from 10 populations of P. emblica sampled from the dry climate area in Yunnan and wet climate area in Guangxi using 20 polymorphic EST-SSR markers. We found high genetic diversity at the species level (He = 0.796) and within populations (He = 0.792), but low genetic differentiation among populations (F ST = 0.084). In addition, most genetic variation existed within populations (92.44%) compared with variation among the populations (7.56%). Meanwhile, the NJ tree, STRUCTURE, and hierarchical analysis suggested that the sampled individuals were clustered into two distinct genetic groups. In contrast, the genetic diversity of the dry climate group (He = 0.786, Na = 11.790, I = 1.962) was higher than that of the wet climate group (He = 0.673, Na = 9.060, I = 1.555), which might be attributed to the combined effects of altitude, precipitation, and geographic distance. Interestingly, only altitude and precipitation had significant pure effects on the genetic diversity, and the former was slightly stronger. In addition, DIYABC analysis suggested the effective population size of P. emblica might have contracted in the beginning of the Last Glacial Maximum. These genetic features provided vital information for the conservation and sustainable development of genetic resources of P. emblica, and they also provided new insights and guidelines for ecological restoration and economic development in dry-hot valleys of Yunnan and karst areas in Guangxi.
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Affiliation(s)
- Xiongfang Liu
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Youming Wan
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, China
| | - Zhenghong Li
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, China
| | - Hong Ma
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, China
- *Correspondence: Hong Ma,
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Miklavčič Višnjevec A, Baruca Arbeiter A, Hladnik M, Ota A, Skrt M, Butinar B, Nečemer M, Krapac M, Ban D, Bučar-Miklavčič M, Poklar Ulrih N, Bandelj D. An Integrated Characterization of Jujube ( Ziziphus jujuba Mill.) Grown in the North Adriatic Region. Food Technol Biotechnol 2019; 57:17-28. [PMID: 31316273 PMCID: PMC6600307 DOI: 10.17113/ftb.57.01.19.5910] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Jujube (Ziziphus jujuba Mill.) has favourable horticultural properties including adaptation to arid conditions, abiotic and biotic stresses, as well as positive impact on human health. The present study describes the characterization of genetic diversity of the germplasm of jujube from the Istrian peninsula, the determination of important chemical compounds, antioxidative properties in relation to antibacterial and antifungal activities of jujube fruit extracts, and the determination of nutritional properties of jujube fruit. The results of the genetic analysis showed that most of the samples from the Istrian peninsula belong to two recently introduced varieties, 'Li' and 'Lang', and the most widespread local variety 'Navadna žižola'. The local variety has smaller fruit than the ‘Li’ and ‘Lang’ varieties, with thick and fleshy mesocarp. Chemical analysis indicated that fruits of the local variety contained a valuable source of dietary fibre ((9.7±0.6) g/100 g) and were rich in minerals such as (in g/100 g dry mass): potassium (829±51), calcium (177±11) and phosphorus (129±19). Aqueous extracts showed slight antibacterial activity, while ethanol extracts had higher mass fractions of phenolic compounds (expressed as gallic acid equivalents (GAE), 5.8-8.7 mg/g) than the aqueous extracts, but did not show antimicrobial activity. Compounds other than phenolic compounds in jujube fruit may be more biologically active. Based on the results of these analyses, the local Istrian jujube variety is a promising candidate for cultivation potential.
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Affiliation(s)
- Ana Miklavčič Višnjevec
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Alenka Baruca Arbeiter
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Matjaž Hladnik
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Ajda Ota
- Department of Food Science and Technology, Biotechnical Faculty, Jamnikarjeva ulica 101, 1000 Ljubljana, Slovenia
| | - Mihaela Skrt
- Department of Food Science and Technology, Biotechnical Faculty, Jamnikarjeva ulica 101, 1000 Ljubljana, Slovenia
| | - Bojan Butinar
- Science and Research Centre Koper, Garibaldijeva 1, 6000 Koper, Slovenia
| | - Marijan Nečemer
- Department of Environmental Sciences, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Marin Krapac
- Institute of Agriculture and Tourism, Ul. Karla Huguesa 8, 52440 Poreč, Croatia
| | - Dean Ban
- Institute of Agriculture and Tourism, Ul. Karla Huguesa 8, 52440 Poreč, Croatia
| | | | - Nataša Poklar Ulrih
- Department of Food Science and Technology, Biotechnical Faculty, Jamnikarjeva ulica 101, 1000 Ljubljana, Slovenia
| | - Dunja Bandelj
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
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Yadav R, Lone SA, Gaikwad K, Singh NK, Padaria JC. Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight & Arn) under drought stress. Sci Rep 2018; 8:2406. [PMID: 29402924 PMCID: PMC5799245 DOI: 10.1038/s41598-018-20548-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/02/2018] [Indexed: 11/09/2022] Open
Abstract
Ziziphus nummularia (Burm.f.) Wight & Arn., a perennial shrub that thrives in the arid regions, is naturally tolerant to drought. However, there are limited studies on the genomics of drought tolerance in Ziziphus sp. In this study, RNA-sequencing of one month old seedlings treated with PEG 6000 was performed using Roche GS-FLX454 Titanium pyrosequencing. A total of 367,176 raw sequence reads were generated, and upon adapter trimming and quality filtration 351,872 reads were assembled de novo into 32,739 unigenes. Further characterization of the unigenes indicated that 73.25% had significant hits in the protein database. Kyoto encyclopedia of genes and genomes database (KEGG) identified 113 metabolic pathways from the obtained unigenes. A large number of drought-responsive genes were obtained and among them differential gene expression of 16 highly induced genes was validated by qRT-PCR analysis. To develop genic-markers, 3,425 simple sequence repeats (SSRs) were identified in 2,813 unigene sequences. The data generated shall serve as an important reservoir for the identification and characterization of drought stress responsive genes for development of drought tolerant crops.
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Affiliation(s)
- Radha Yadav
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
| | - Showkat Ahmad Lone
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Kishor Gaikwad
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
| | - Nagendra Kumar Singh
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
| | - Jasdeep Chatrath Padaria
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India.
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Evaluation of efficiency of controlled pollination based parentage analysis in a Larix gmelinii var. principis-rupprechtii Mayr. seed orchard. PLoS One 2017; 12:e0176483. [PMID: 28448554 PMCID: PMC5407790 DOI: 10.1371/journal.pone.0176483] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/11/2017] [Indexed: 11/19/2022] Open
Abstract
Controlled pollination (CP) is an important tool for breeding programs to improve seed quality, as it rapidly generates desirable genotypes and maximizes genetic gains. However, few studies have evaluated the success rate of CP, especially in Larix gmelinii var. principis-rupprechtii Mayr. seed orchards. In this study, we estimated the rate of correct parentage in 257 CP progeny in an L. gmelinii var. principis-rupprechtii seed orchard from ten candidate parents using 13 microsatellites. The parentage exclusion probabilities of all combined loci in the single parent and parent pair tests were > 0.99, which was sufficient to distinguish the relatedness of the sampled individuals. Comparing the maximum likelihood-based parentage analysis results with breeding records revealed that the percentages of correctly identified maternal and paternal parents were 22.6% and 35.0% at 95% CL, respectively, suggestive of parent mislabeling and pollen contamination in the CP population. We conducted a pedigree reconstruction by identifying the expected parents and assigned maternity, paternity, and parent pairs to 176 (68.5%), 199 (77.4%), and 132 (51.4%) progeny, respectively. This study provides a reference for future selection of elite genotypes for commercial production. To increase the efficiency of CP, molecular markers should be used to correctly identify individuals in seed orchards before conducting CP.
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Chen W, Hou L, Zhang Z, Pang X, Li Y. Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection of Ziziphus jujuba Assessed with Genome-wide SNPs Developed by Genotyping-by-sequencing and SSR Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:575. [PMID: 28458680 PMCID: PMC5394126 DOI: 10.3389/fpls.2017.00575] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 03/30/2017] [Indexed: 05/24/2023]
Abstract
Chinese jujube (Ziziphus jujuba Mill) is an economically important fruit species native to China with high nutritious and medicinal value. Genotyping-by-sequencing was used to detect and genotype single nucleotide polymorphisms (SNPs) in a core collection of 150 Chinese jujube accessions and further to characterize their genetic diversity, population structure, and linkage disequilibrium (LD). A total of 4,680 high-quality SNPs were identified, of which 38 sets of tri-allelic SNPs were detected. The average polymorphism information content (PIC) values based on bi-allelic SNPs and tri-allelic SNPs were 0.27 and 0.38, respectively. STRUCTURE and principal coordinate analyses based on SNPs revealed that the 150 accessions could be clustered into two groups. However, neighbor-joining trees indicated the accessions should be grouped into three major clusters. Our data confirm that the resolving power for genetic diversity was similar for the SSRs and SNPs. In contrast, regarding population structure, the resolving power was higher for SSRs than for SNPs. The LD pattern in Chinese jujube was investigated for the first time. We observed a relatively rapid LD decay with a short range (∼10 kb) for all pseudo-chromosomes and for individual pseudo-chromosomes. Our findings provide important information for future genome-wide association analyses and marker-assisted selective breeding of Chinese jujube.
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Affiliation(s)
- Wu Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
| | - Lu Hou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
| | - Zhiyong Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
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16
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Xu C, Gao J, Du Z, Li D, Wang Z, Li Y, Pang X. Identifying the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers. Sci Rep 2016; 6:31503. [PMID: 27531220 PMCID: PMC4987672 DOI: 10.1038/srep31503] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/21/2016] [Indexed: 01/02/2023] Open
Abstract
Ziziphus is a genus of spiny shrubs and small trees in the Rhamnaceae family. This group has a controversial taxonomy, with more than 200 species described, including Chinese jujube (Ziziphus jujuba Mill. var. jujuba) and Indian jujube (Z. mauritiana), as well as several other important cultivated fruit crops. Using 24 SSR markers distributed across the Chinese jujube genome, 962 jujube accessions from the two largest germplasm repositories were genotyped with the aim of analyzing the genetic diversity and structure and constructing a core collection that retain high genetic diversity. A molecular profile comparison revealed 622 unique genotypes, among which 123 genotypes were genetically identical to at least one other accessions. STRUCTURE analysis and multivariate analyses (Cluster and PCoA) roughly divided the accessions into three major groups, with some admixture among groups. A simulated annealing algorithm and a heuristic algorithm were chosen to construct the core collection. A final core of 150 accessions was selected, comprising 15.6% of the analyzed accessions and retaining more than 99.5% of the total alleles detected. We found no significant differences in allele frequency distributions or in genetic diversity parameters between the chosen core accessions and the 622 genetically unique accessions. This work contributes to the understanding of Chinese jujube diversification and the protection of important germplasm resources.
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Affiliation(s)
- Chaoqun Xu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing (100083), China
| | - Jiao Gao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing (100083), China
| | - Zengfeng Du
- National Foundation for Improved Cultivar of Chinese Jujube, Cangzhou Heibei, 061000, China
| | - Dengke Li
- Pomology Institute, Shanxi Academy of Agricultural Science, Taigu, Shanxi 030815, China
| | - Zhe Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing (100083), China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing (100083), China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing (100083), China
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17
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Fu PC, Zhang YZ, Ya HY, Gao QB. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.). PeerJ 2016; 4:e1735. [PMID: 26925343 PMCID: PMC4768703 DOI: 10.7717/peerj.1735] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 02/03/2016] [Indexed: 01/10/2023] Open
Abstract
Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1–6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+ T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop.
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Affiliation(s)
- Peng-Cheng Fu
- College of Life Science, Luoyang Normal University , Luoyang , China
| | - Yan-Zhao Zhang
- College of Life Science, Luoyang Normal University , Luoyang , China
| | - Hui-Yuan Ya
- College of Life Science, Luoyang Normal University , Luoyang , China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining , China
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Hao DC, Xiao PG. Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life. Evol Bioinform Online 2015; 11:197-212. [PMID: 26461812 PMCID: PMC4597484 DOI: 10.4137/ebo.s31326] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/24/2015] [Accepted: 08/31/2015] [Indexed: 02/07/2023] Open
Abstract
Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide. This review presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with the evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of the plant genotype and metabolic phenotype, interaction between medicinal plant genomes and their environment, the correlation between genomic diversity and metabolite diversity, and so on. Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.
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Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian, P. R. China
| | - Pei-Gen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, P. R. China
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Huang J, Yang X, Zhang C, Yin X, Liu S, Li X. Development of Chloroplast Microsatellite Markers and Analysis of Chloroplast Diversity in Chinese Jujube (Ziziphus jujuba Mill.) and Wild Jujube (Ziziphus acidojujuba Mill.). PLoS One 2015; 10:e0134519. [PMID: 26406601 PMCID: PMC4583483 DOI: 10.1371/journal.pone.0134519] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/09/2015] [Indexed: 12/31/2022] Open
Abstract
Ziziphus is an important genus within the family Rhamnaceae. This genus includes several important fruit tree species that are widely planted in China and India, such as the Chinese jujube (Ziziphus jujuba Mill.), the wild jujube (Z. acidojujuba), and the Indian jujube (Z. mauritiana). However, information about their domestication based on the chlorotype diversity of Chinese jujube population is lacking. In this study, chloroplast microsatellite (cpSSR) markers were developed and used to investigate the genetic relationships between and domestication of jujube cultivars and wild jujube populations. Primer sets flanking each of the 46 cpSSR loci in non-coding regions of the chloroplast genome sequence of Z. jujuba Mill. cv. 'Junzao' were designed. In total, 10 markers showed polymorphisms from 15 samples (9 jujube cultivars and 6 wild jujube individuals), of which 8 loci were due to variations in the number of mononucleotide (A/T) repeats and 2 were due to indels. Six cpSSR markers were used in further analyses of 81 additional samples (63 jujube cultivars, 17 wild jujube samples, and 1 Indian jujube). Using these cpSSR markers, the number of alleles per locus ranged from two to four. In general, the Shannon Index (I) for each cpSSR ranged from 0.159 to 0.1747, and the diversity indices (h) and uh were 0.061 to 0.435 and 0.062 to 0.439, respectively. Seven chlorotypes were found; the Indian jujube showed distinct chlorotypes, and both the Chinese and wild jujube had four chlorotypes and shared two chlorotypes. A dominant chlorotype (G) accounted for 53 of 72 jujube cultivars and 13 of 23 wild jujube individuals. All chlorotypes were highly localized along the Yellow River, from the mid- to the lower reaches, suggesting a wide origin of jujube. These cpSSR markers can be applied to population and evolution studies of Chinese jujube and wild jujube.
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Affiliation(s)
- Jian Huang
- Research Center for Jujube Engineering and Technology of State Forestry Administration, College of Forestry, Northwest A&F University, Yangling, China
- Key Laboratory of jujube for Shaanxi Province, College of Life Science, Yan’an University, Yan’an, China
| | - Xiaoting Yang
- Key Comprehensive Laboratory of Forest for Shaanxi Province, College of Forestry, Northwest A&F University, Yangling, China
| | - Chunmei Zhang
- Key Comprehensive Laboratory of Forest for Shaanxi Province, College of Forestry, Northwest A&F University, Yangling, China
| | - Xiao Yin
- Key Comprehensive Laboratory of Forest for Shaanxi Province, College of Forestry, Northwest A&F University, Yangling, China
| | - Shipeng Liu
- Key Laboratory of jujube for Shaanxi Province, College of Life Science, Yan’an University, Yan’an, China
| | - Xingang Li
- Research Center for Jujube Engineering and Technology of State Forestry Administration, College of Forestry, Northwest A&F University, Yangling, China
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Zhang Z, Gao J, Kong D, Wang A, Tang S, Li Y, Pang X. Assessing genetic diversity in Ziziphus jujuba ‘Jinsixiaozao’ using morphological and microsatellite (SSR) markers. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Xiao J, Zhao J, Liu M, Liu P, Dai L, Zhao Z. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability. PLoS One 2015; 10:e0127812. [PMID: 26000739 PMCID: PMC4441482 DOI: 10.1371/journal.pone.0127812] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 04/18/2015] [Indexed: 12/18/2022] Open
Abstract
Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization.
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Affiliation(s)
- Jing Xiao
- Research Center for Chinese Jujube, Agricultural University of Hebei, Baoding, 071000, China
| | - Jin Zhao
- College of Life Science, Agricultural University of Hebei, Baoding, 071000, China
| | - Mengjun Liu
- Research Center for Chinese Jujube, Agricultural University of Hebei, Baoding, 071000, China
| | - Ping Liu
- Research Center for Chinese Jujube, Agricultural University of Hebei, Baoding, 071000, China
| | - Li Dai
- Research Center for Chinese Jujube, Agricultural University of Hebei, Baoding, 071000, China
| | - Zhihui Zhao
- Research Center for Chinese Jujube, Agricultural University of Hebei, Baoding, 071000, China
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Genetic Diversity and Population Structure of Toona Ciliata Roem. Based on Sequence-Related Amplified Polymorphism (SRAP) Markers. FORESTS 2015. [DOI: 10.3390/f6041094] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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De novo assembly and characterization of the fruit transcriptome of Chinese jujube (Ziziphus jujuba Mill.) Using 454 pyrosequencing and the development of novel tri-nucleotide SSR markers. PLoS One 2014; 9:e106438. [PMID: 25184704 PMCID: PMC4153635 DOI: 10.1371/journal.pone.0106438] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/29/2014] [Indexed: 12/14/2022] Open
Abstract
Chinese jujube (Ziziphus jujuba Mill.) is an economically important deciduous tree that has high therapeutic value and health benefits. However, a lack of sequence data and molecular markers have constrained genetic and breeding studies for better fruit quality and other traits in Chinese jujube. In this study, two combined cDNA libraries of ‘Dongzao’ fruit representing the early and late stages of fruit development were constructed and sequenced on the 454 GS FLX Titanium platform. In total, 1,124,197 reads were generated and then de novo assembled into 97,479 unigenes. A total of 52,938 unigenes were homologous to genes in the NCBI non-redundant sequence database. A total of 33,123 unigenes were assigned to one or more Gene Ontology terms, and 16,693 unigenes were classified into 319 Kyoto Encyclopedia of Genes and Genomes pathways. The results showed that the Smirnoff-Wheeler pathway was the main pathway for the biosynthesis of ascorbic acid in Chinese jujube. The number of differentially expressed genes between the two stages of fruit development was 1,764, among which 974 and 790 genes were up-regulated and down-regulated, respectively. Furthermore, 9,893 sequences were identified containing SSRs. 93 primer pairs designed from the sequences with a tri-nucleotide repeat showed successful PCR amplification and could be validated in Chinese jujube accessions and Z. mauritiana Lam and Z. acidojujuba as well, of which 71 primer pairs were polymorphic. The obtained transcriptome provides a most comprehensive resource currently available for gene discovery and the development of functional markers in Z. jujuba. The newly developed microsatellite markers could be used in applications such as genetic linkage analysis and association studies, diversity analysis, and marker-assisted selection in Chinese jujube and related species.
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