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Plugatar YV, Suprun II, Khokhlov SY, Stepanov IV, Al-Nakib EA. Comprehensive agrobiological assessment and analysis of genetic relationships of promising walnut varieties of the Nikitsky Botanical Gardens. Vavilovskii Zhurnal Genet Selektsii 2023; 27:454-462. [PMID: 37867608 PMCID: PMC10587009 DOI: 10.18699/vjgb-23-55] [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: 12/13/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 10/24/2023] Open
Abstract
Walnut is an important horticultural crop, the production of which ranks second among all nut crops. Despite the significant demand in the domestic market in Russia, the industrial production of walnut fruits in Russia is currently underdeveloped. At the same time, there is a need to update the assortment with new highly productive varieties adapted to local agro-climatic conditions and having high quality nuts that are competitive at the world level. An important issue for the successful implementation of breeding programs is a comprehensive study of the gene pool. In this regard, within the framework of the study, the task was to evaluate promising varieties from the collection of the walnut gene pool of the Nikitsky Botanical Gardens and analyze genetic relationships based on microsatellite genotyping. On the basis of the performed phenotypic assessment, the study sample, which included 31 varieties, was divided into several groups according to the main phenotypic traits, such as frost and drought resistance, the start of the growing season, the ripening period, the weight and type of flowering, the weight of the fruit, and the thickness of the endocarp. Varieties with economically valuable traits that can be recommended as promising as initial parental forms in breeding work for resistance to abiotic stress factors have been identified, as well as varieties with increased productivity and large fruit sizes. Based on the analysis of eight SSR markers (WGA001, WGA376, WGA069, WGA276, WGA009, WGA202, WGA089 and WGA054), an analysis of the level of genetic diversity was performed and genetic relationships were established in the studied sample of varieties. Six (for WGA089) to eleven (for WGA276) alleles per locus have been identified. A total of 70 alleles were identified for the eight DNA markers used, with an average value of 8.75. Analysis of SSR genotyping data using Bayesian analysis established the presence of two main groups of genotypes. Taking into account the fact that all the studied varieties are selections from local seed populations in different regions of the Crimean Peninsula, the revealed level of polymorphism may indirectly reflect the level of genetic diversity of the local walnut populations. Furthermore, the presence of two genetically distant groups indicates the presence of two independently formed pools of the autochthonous gene pool of the species Juglans regia L. on the Crimean Peninsula.
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Affiliation(s)
- Yu V Plugatar
- The Order of the Red Banner of Labour Nikitsky Botanical Gardens - National Scientific Center of the Russian Academy of Sciences, Yalta, Republic of Crimea, Russia
| | - I I Suprun
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making, the Functional Scientific Center of "Breeding and Nursery", Krasnodar, Russia
| | - S Yu Khokhlov
- The Order of the Red Banner of Labour Nikitsky Botanical Gardens - National Scientific Center of the Russian Academy of Sciences, Yalta, Republic of Crimea, Russia
| | - I V Stepanov
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making, the Functional Scientific Center of "Breeding and Nursery", Krasnodar, Russia
| | - E A Al-Nakib
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making, the Functional Scientific Center of "Breeding and Nursery", Krasnodar, Russia
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Shahi Shavvon R, Qi HL, Mafakheri M, Fan PZ, Wu HY, Bazdid Vahdati F, Al-Shmgani HS, Wang YH, Liu J. Unravelling the genetic diversity and population structure of common walnut in the Iranian Plateau. BMC PLANT BIOLOGY 2023; 23:201. [PMID: 37072719 PMCID: PMC10111805 DOI: 10.1186/s12870-023-04190-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Common walnut (Juglans regia L.) has a long cultivation history, given its highly valuable wood and rich nutritious nuts. The Iranian Plateau has been considered as one of the last glaciation refugia and a centre of origin and domestication for the common walnut. However, a prerequisite to conserve or utilize the genetic resources of J. regia in the plateau is a comprehensive evaluation of the genetic diversity that is conspicuously lacking. In this regard, we used 31 polymorphic simple sequence repeat (SSR) markers to delineate the genetic variation and population structure of 508 J. regia individuals among 27 populations from the Iranian Plateau. RESULTS The SSR markers expressed a high level of genetic diversity (HO = 0.438, and HE = 0.437). Genetic differentiation among the populations was moderate (FST = 0.124), and genetic variation within the populations (79%) significantly surpassed among populations (21%). The gene flow (Nm = 1.840) may have remarkably influenced the population genetic structure of J. regia, which can be attributed to anthropological activities and wind dispersal of pollen. The STRUCTURE analysis divided the 27 populations into two main clusters. Comparing the neighbor-joining and principal coordinate analysis dendrograms and the Bayesian STRUCTURE analysis revealed the general agreement between the population subdivisions and the genetic relationships among the populations. However, a few geographically close populations dispersed into different clusters. Further, the low genetic diversity of the Sulaymaniyah (SMR) population of Iraq necessitates urgent conservation by propagation and seedling management or tissue culture methods; additionally, we recommend the indispensable preservation of the Gonabad (RGR) and Arak (AKR) populations in Iran. CONCLUSIONS These results reflected consistent high geographical affinity of the accession across the plateau. Our findings suggest that gene flow is a driving factor influencing the genetic structure of J. regia populations, whereas ecological and geological variables did not act as strong barriers. Moreover, the data reported herein provide new insights into the population structure of J. regia germplasm, which will help conserve genetic resources for the future, hence improving walnut breeding programs' efficiency.
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Affiliation(s)
| | - Hai-Ling Qi
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Mohammad Mafakheri
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - Pen-Zheng Fan
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Yu Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Hanady S Al-Shmgani
- Department of Biology, College of Education for Pure Sciences (Ibn Al-Haitham), University of Baghdad, Baghdad, Iraq
| | - Yue-Hua Wang
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Zhang Q, Zhang X, Yang Y, Xu L, Feng J, Wang J, Tang Y, Pei X, Zhao X. Genetic Diversity of Juglans mandshurica Populations in Northeast China Based on SSR Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:931578. [PMID: 35845684 PMCID: PMC9280368 DOI: 10.3389/fpls.2022.931578] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/03/2022] [Indexed: 05/25/2023]
Abstract
Juglans mandshurica is a native tree species in Northeast China. Due to habitat destruction and human disturbance, its population size has sharply decreased. Currently, information on molecular markers of J. mandshurica is limited and cannot meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of J. mandshurica. Based on transcriptomic data from three tissues (leaves, bark, and fruit pericarp), we developed expressed sequence tag-simple sequence repeats (EST-SSRs) for J. mandshurica, and 15 polymorphic EST-SSR primers were initially selected. The average number of alleles (Na), expected heterozygosity (He), and the polymorphic information content (PIC) at different loci were 18.27, 0.670, and 0.797, respectively. Population genetic diversity analysis revealed that the average Na, He, and Shannon information indices (I) for 15 J. mandshurica populations were 6.993, 0.670, and 1.455, respectively. Among them, population Hunchun exhibited the highest genetic diversity (Na = 7.933, He = 0.723, and I = 1.617), while population Heihe exhibited the lowest genetic diversity (Na = 4.200, He = 0.605, and I = 1.158). STRUCTURE analysis, neighbor-joining method cluster analysis, and principal coordinate analysis showed that the 343 individuals of J. mandshurica from 15 populations were clustered into three categories. Category 1 (green) had 147 individuals from eight populations in Qingyuan, Caohekou, Jian, Ningan, Yongji, Baishishan, Helong, and Maoershan; category 2 (blue) had 81 individuals from three populations in Hulin, Boli, and Sanchazi; and category 3 (red) had 115 individuals from four populations in Heihe, Hunchun, Fangzheng, and Liangshui. Analysis of molecular variance (AMOVA) showed that genetic variations among and within individuals accounted for 16.22% and 21.10% of the total genetic variation, respectively, indicating that genetic variations within populations were greater than genetic variations among populations. The average genetic differentiation coefficient (Fst) and gene flow (Nm) between different populations were 0.109 and 4.063, respectively, implying moderate levels of genetic differentiation and gene flow. Based on the genetic diversity characteristics of different populations, we proposed various genetic conservation strategies for J. mandshurica.
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Affiliation(s)
- Qinhui Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Xinxin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Yuchun Yang
- Jilin Provincial Academy of Forestry Sciences, Changchun, China
| | - Lianfeng Xu
- Qiqihar Branch of Heilongjiang Academy of Forestry, Qiqihar, China
| | - Jian Feng
- Liaoning Academy of Forest Science, Shenyang, China
| | - Jingyuan Wang
- Linjiang Forestry Bureau of Jilin Province, Lijiang, China
| | - Yongsheng Tang
- Linjiang Forestry Bureau of Jilin Province, Lijiang, China
| | - Xiaona Pei
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
| | - Xiyang Zhao
- College of Forestry and Grassland, Jilin Agricultural University, Changchun, China
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Mahmoodi R, Dadpour MR, Hassani D, Zeinalabedini M, Vendramin E, Leslie CA. Composite core set construction and diversity analysis of Iranian walnut germplasm using molecular markers and phenotypic traits. PLoS One 2021; 16:e0248623. [PMID: 33725012 PMCID: PMC7963058 DOI: 10.1371/journal.pone.0248623] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 03/02/2021] [Indexed: 11/29/2022] Open
Abstract
Iran is a center of origin and diversity for walnuts (Juglans regia L.) with very good potential for breeding purposes. The rich germplasm available, creates an opportunity for study and selection of the diverse walnut genotypes. In this study, the population structure of 104 Persian walnut accessions was assessed using AFLP markers in combination with phenotypic variability of 17 and 18 qualitative and quantitative traits respetively. The primers E-TG/M-CAG, with high values of number of polymorphic bands, polymorphic information content, marker index and Shannon’s diversity index, were the most effective in detecting genetic variation within the walnut germplasm. Multivariate analysis of variance indicated 93.98% of the genetic variability was between individuals, while 6.32% of variation was among populations. A relatively new technique, an advanced maximization strategy with a heuristic approach, was deployed to develop the core collection. Initially, three independent core collections (CC1–CC3) were created using phenotypic data and molecular markers. The three core collections (CC1–CC3) were then merged to generate a composite core collection (CC4). The mean difference percentage, variance difference percentage, variable rate of coefficient of variance percentage, coincidence rate of range percentage, Shannon’s diversity index, and Nei’s gene diversity were employed for comparative analysis. The CC4 with 46 accessions represented the complete range of phenotypic and genetic variability. This study is the first report describing development of a core collection in walnut using molecular marker data in combination with phenotypic values. The construction of core collection could facilitate the work for identification of genetic determinants of trait variability and aid effective utilization of diversity caused by outcrossing, in walnut breeding programs.
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Affiliation(s)
- Razieh Mahmoodi
- Department of Horticulture Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
- Temperate Fruits Research Center, Horticultural Science Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Dadpour
- Department of Horticulture Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
- * E-mail: (DH); (MRD)
| | - Darab Hassani
- Temperate Fruits Research Center, Horticultural Science Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
- * E-mail: (DH); (MRD)
| | - Mehrshad Zeinalabedini
- Systems Biology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Elisa Vendramin
- Centro di Ricerca per l’Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Roma, Italy
| | - Charles A. Leslie
- Department of Plant Sciences, University of California, Davis, CA, United States of America
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