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Li X, Wang X, Zhang D, Huang J, Shi W, Wang J. Historical spread routes of wild walnuts in Central Asia shaped by man-made and nature. FRONTIERS IN PLANT SCIENCE 2024; 15:1394409. [PMID: 38903444 PMCID: PMC11187337 DOI: 10.3389/fpls.2024.1394409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/17/2024] [Indexed: 06/22/2024]
Abstract
Walnuts have substantial economic value and are of significant interest being a wild-cultivated species. The study has re-sequenced the entire genome of the wild walnut, aligning it with the walnut reference genome, to identify 2,021,717 single nucleotide polymorphisms (SNPs). These were used to examine the genetics of 130 wild walnut samples collected from three countries. Utilizing structural and principal component analysis, the walnut samples from Central Asia were classified into four populations: Ili ah in Xinjiang (I), Dushanbe region in Tajikistan (II), Sary-Chelek, Arslanbob in Kara-Alma regions of Kyrgyzstan (III), and Kok-Tundy region of Kyrgyzstan (IV). The 4 groups showed large differences in nucleotide diversity, population differentiation, and linkage disequilibrium decay, as well as gene flow among them. The present geographic distribution of these populations does not align with the genetic distribution pattern as the populations of Central Asian wild walnuts have experienced similar population dynamics in the past, i.e., the highest effective population size at ca. 6 Ma, two sharp population declines at 6 and 0.2 Ma, and convergence at ca. 0.2 Ma. The genetic distribution patterns are better explained by human activity, notably through archaeological findings of walnut use and the influence of the Silk Road, rather than by current geographic distributions.
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Affiliation(s)
- Xuerong Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
| | - Xiyong Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanic Garden, Chinese Academy of Sciences, Turpan, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
- Turpan Eremophytes Botanic Garden, Chinese Academy of Sciences, Turpan, China
| | - Junhua Huang
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Turpan Eremophytes Botanic Garden, Chinese Academy of Sciences, Turpan, China
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Han L, Luo X, Zhao Y, Li N, Xu Y, Ma K. A haplotype-resolved genome provides insight into allele-specific expression in wild walnut (Juglans regia L.). Sci Data 2024; 11:278. [PMID: 38459062 PMCID: PMC10923786 DOI: 10.1038/s41597-024-03096-4] [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: 10/11/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
Wild germplasm resources are crucial for gene mining and molecular breeding because of their special trait performance. Haplotype-resolved genome is an ideal solution for fully understanding the biology of subgenomes in highly heterozygous species. Here, we surveyed the genome of a wild walnut tree from Gongliu County, Xinjiang, China, and generated a haplotype-resolved reference genome of 562.99 Mb (contig N50 = 34.10 Mb) for one haplotype (hap1) and 561.07 Mb (contig N50 = 33.91 Mb) for another haplotype (hap2) using PacBio high-fidelity (HiFi) reads and Hi-C technology. Approximately 527.20 Mb (93.64%) of hap1 and 526.40 Mb (93.82%) of hap2 were assigned to 16 pseudochromosomes. A total of 41039 and 39744 protein-coding gene models were predicted for hap1 and hap2, respectively. Moreover, 123 structural variations (SVs) were identified between the two haplotype genomes. Allele-specific expression genes (ASEGs) that respond to cold stress were ultimately identified. These datasets can be used to study subgenome evolution, for functional elite gene mining and to discover the transcriptional basis of specific traits related to environmental adaptation in wild walnut.
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Affiliation(s)
- Liqun Han
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Xiang Luo
- College of Agriculture, Henan University, Zhengzhou, China
| | - Yu Zhao
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China
| | - Yuhui Xu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China.
| | - Kai Ma
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China.
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Zhou H, Ma J, Liu H, Zhao P. Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions. Int J Mol Sci 2023; 25:25. [PMID: 38203199 PMCID: PMC10778614 DOI: 10.3390/ijms25010025] [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: 11/13/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Cold stress impacts woody tree growth and perennial production, especially when the temperature rapidly changes in late spring. To address this issue, we conducted the genome-wide identification of two important transcription factors (TFs), CBF (C-repeat binding factors) and ICE (inducers of CBF expression), in three walnut (Juglans) genomes. Although the CBF and ICE gene families have been identified in many crops, very little systematic analysis of these genes has been carried out in J. regia and J. sigillata. In this study, we identified a total of 16 CBF and 12 ICE genes in three Juglans genomes using bioinformatics analysis. Both CBF and ICE had conserved domains, motifs, and gene structures, which suggests that these two TFs were evolutionarily conserved. Most ICE genes are located at both ends of the chromosomes. The promoter cis-regulatory elements of CBF and ICE genes are largely involved in light and phytohormone responses. Based on 36 RNA sequencing of leaves from four walnut cultivars ('Zijing', 'Lvling', 'Hongren', and 'Liao1') under three temperature conditions (8 °C, 22 °C, and 5 °C) conditions in late spring, we found that the ICE genes were expressed more highly than CBFs. Both CBF and ICE proteins interacted with cold-related proteins, and many putative miRNAs had interactions with these two TFs. These results determined that CBF1 and ICE1 play important roles in the tolerance of walnut leaves to rapid temperature changes. Our results provide a useful resource on the function of the CBF and ICE genes related to cold tolerance in walnuts.
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Affiliation(s)
- Huijuan Zhou
- Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi’an 710061, China;
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.M.); (H.L.)
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.M.); (H.L.)
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.M.); (H.L.)
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Manthos I, Sotiropoulos T, Karapetsi L, Ganopoulos I, Pratsinakis ED, Maloupa E, Madesis P. Molecular Characterization of Local Walnut ( Juglans regia) Genotypes in the North-East Parnon Mountain Region of Greece. Int J Mol Sci 2023; 24:17230. [PMID: 38139058 PMCID: PMC10743642 DOI: 10.3390/ijms242417230] [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: 10/31/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Walnut is one of the most important nuts regarding their production and consumption. The available but uncharacterized genetic resources of walnut are important for the development and breeding of local varieties. Greece holds an important number of genetically uncharacterized walnut landraces, especially within the area of Parnon, which is considered to play a significant role as an in situ gene bank, due to its unique location traits. However, the genetic characterization and further use of these resources has been insufficient, due to the absence of genetic studies. In this study, we implemented SSR molecular markers, both to genetically characterize the walnut tree genetic diversity of the Parnon area and to identify its unique genetic structure, which will form the starting material for subsequent breeding programs. Overall, high levels of genetic variation were found among the individual walnut accessions that were collected in the Parnon mountain region.
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Affiliation(s)
- Ioannis Manthos
- Department of Nut Trees, Institute of Plant Breeding & Genetic Resources, Hellenic Agricultural Organization (ELGO)-DIMITRA, Neo Krikello, 35100 Lamia, Greece;
| | - Thomas Sotiropoulos
- Department of Deciduous Fruit Trees, Institute of Plant Breeding & Genetic Resources, Hellenic Agricultural Organization (ELGO)-DIMITRA, 59200 Naousa, Greece;
| | - Lefkothea Karapetsi
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece;
- Institute of Applied Biosciences, Centre for Research & Technology-Hellas, 57001 Thessaloniki, Greece;
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, 57001 Thessaloniki, Greece; (I.G.); (E.M.)
| | - Emmanouil D. Pratsinakis
- Institute of Applied Biosciences, Centre for Research & Technology-Hellas, 57001 Thessaloniki, Greece;
| | - Eleni Maloupa
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, 57001 Thessaloniki, Greece; (I.G.); (E.M.)
| | - Panagiotis Madesis
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece;
- Institute of Applied Biosciences, Centre for Research & Technology-Hellas, 57001 Thessaloniki, Greece;
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Li M, Ou M, He X, Ye H, Ma J, Liu H, Yang H, Zhao P. DNA methylation role in subgenome expression dominance of Juglans regia and its wild relative J. mandshurica. PLANT PHYSIOLOGY 2023; 193:1313-1329. [PMID: 37403190 DOI: 10.1093/plphys/kiad394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023]
Abstract
Subgenome expression dominance plays a crucial role in the environmental adaptation of polyploids. However, the epigenetic molecular mechanism underlying this process has not been thoroughly investigated, particularly in perennial woody plants. Persian walnut (Juglans regia) and its wild relative, Manchurian walnut (Juglans mandshurica), are woody plants of great economic importance and are both paleopolyploids that have undergone whole-genome duplication events. In this study, we explored the characteristics of subgenome expression dominance in these 2 Juglans species and examined its epigenetic basis. We divided their genomes into dominant subgenome (DS) and submissive subgenome (SS) and found that the DS-specific genes might play critical roles in biotic stress response or pathogen defense. We comprehensively elucidated the characteristics of biased gene expression, asymmetric DNA methylation, transposable elements (TEs), and alternative splicing (AS) events of homoeologous gene pairs between subgenomes. The results showed that biased expression genes (BEGs) in 2 Juglans species were mainly related to external stimuli response, while non-BEGs were related to complexes that might be involved in signal transduction. DS genes had higher expression and more AS events while having less DNA methylation and TEs than homoeologous genes from the SS in the 2 Juglans species. Further studies showed that DNA methylation might contribute to the biased expression of gene pairs by modifying LTR/TIR/nonTIR TEs and improving the AS efficiency of corresponding precursor mRNAs in a particular context. Our study contributes to understanding the epigenetic basis of subgenome expression dominance and the environmental adaptation of perennial woody plants.
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Affiliation(s)
- Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Mengwei Ou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xiaozhou He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Huijuan Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
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Itoo H, Shah RA, Qurat S, Jeelani A, Khursheed S, Bhat ZA, Mir MA, Rather GH, Zargar SM, Shah MD, Padder BA. Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut ( Juglans regia L.). 3 Biotech 2023; 13:136. [PMID: 37124992 PMCID: PMC10130282 DOI: 10.1007/s13205-023-03563-6] [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: 09/20/2022] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for 88.40% (175,075) of total SSRs. The SSR frequency was 377.312 SSR/Mb and it showed a decreasing trend from dinucleotide to octanucleotide motifs. We identified 20 highly polymorphic SSR markers and used them to genotype 72 walnut accessions. Over all, we obtained 118 alleles that ranged from 2 to 12 with an average value of 5.9. The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. Scientific communities may use this repository for walnut improvement such as QTL mapping, genetic studies, linkage map construction, and marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03563-6.
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Affiliation(s)
- H. Itoo
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Rafiq Ahmad Shah
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - S. Qurat
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - Afnan Jeelani
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - Sheikh Khursheed
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Zahoor A. Bhat
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - M. A. Mir
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - G. H. Rather
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - M. D. Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025 Srinagar, J&K India
| | - Bilal A. Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025 Srinagar, J&K India
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Huang L, Feng G, Li D, Shang W, Zhang L, Yan R, Jiang Y, Li S. Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.996617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionContinued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.MethodsTo explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.ResultsThe results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.DiscussionOur results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.
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Jiang X, Fang Z, Lai J, Wu Q, Wu J, Gong B, Wang Y. Genetic Diversity and Population Structure of Chinese Chestnut ( Castanea mollissima Blume) Cultivars Revealed by GBS Resequencing. PLANTS (BASEL, SWITZERLAND) 2022; 11:3524. [PMID: 36559637 PMCID: PMC9781913 DOI: 10.3390/plants11243524] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Chinese chestnut (Castanea mollissima Bl.) is one of the earliest domesticated and cultivated fruit trees, and it is widely distributed in China. Because of the high quality of its nuts and its high resistance to abiotic and biotic stresses, Chinese chestnut could be used to improve edible chestnut varieties worldwide. However, the unclear domestication history and highly complex genetic background of Chinese chestnut have prevented the efficiency of breeding efforts. To explore the genetic diversity and structure of Chinese chestnut populations and generate new insights that could aid chestnut breeding, heterozygosity statistics, molecular variance analysis, ADMIXTURE analysis, principal component analysis, and phylogenetic analysis were conducted to analyze single nucleotide polymorphism data from 185 Chinese chestnut landraces from five geographical regions in China via genotyping by sequencing. Results showed that the genetic diversity level of the five populations from different regions was relatively high, with an observed heterozygosity of 0.2796-0.3427. The genetic diversity level of the population in the mid-western regions was the highest, while the population north of the Yellow River was the lowest. Molecular variance analysis showed that the variation among different populations was only 2.07%, while the intra-group variation reached 97.93%. The Chinese chestnut samples could be divided into two groups: a northern and southern population, separated by the Yellow River; however, some samples from the southern population were genetically closer to samples from the northern population. We speculate that this might be related to the migration of humans during the Han dynasty due to the frequent wars that took place during this period, which might have led to the introduction of chestnut to southern regions. Some samples from Shandong Province and Beijing City were outliers that did not cluster with their respective groups, and this might be caused by the special geographical, political, and economic significance of these two regions. The findings of our study showed the complex genetic relationships among Chinese chestnut landraces and the high genetic diversity of these resources.
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Affiliation(s)
- Xibing Jiang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhou Fang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Junsheng Lai
- Qingyuan Bureau of Natural Resources and Planning, Lishui 323800, China
| | - Qiang Wu
- Qingyuan Bureau of Natural Resources and Planning, Lishui 323800, China
| | - Jian Wu
- Qingyuan Bureau of Natural Resources and Planning, Lishui 323800, China
| | - Bangchu Gong
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yanpeng Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
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Luo X, Zhou H, Cao D, Yan F, Chen P, Wang J, Woeste K, Chen X, Fei Z, An H, Malvolti M, Ma K, Liu C, Ebrahimi A, Qiao C, Ye H, Li M, Lu Z, Xu J, Cao S, Zhao P. Domestication and selection footprints in Persian walnuts (Juglans regia). PLoS Genet 2022; 18:e1010513. [PMID: 36477175 PMCID: PMC9728896 DOI: 10.1371/journal.pgen.1010513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J. regia), 70 J. regia landraces, and 86 J. regia cultivars. The phylogenetic tree indicated that J. regia samples (section Dioscaryon) were monophyletic within Juglans. The core areas of genetic diversity of J. regia germplasm were southwestern China and southern Asia near the Qinghai-Tibet Plateau and the Himalayas, and the uplift of the Himalayas was speculated to be the main factor leading to the current population dynamics of Persian walnut. The pattern of genomic variation in terms of nucleotide diversity, linkage disequilibrium, single nucleotide polymorphisms, and insertions/deletions revealed the domestication and selection footprints in Persian walnut. Selective sweep analysis, GWAS, and expression analysis further identified two transcription factors, JrbHLH and JrMYB6, that influence the thickness of the nut diaphragm as loci under selection during domestication. Our results elucidate the domestication and selection footprints in Persian walnuts and provide a valuable resource for the genomics-assisted breeding of this important crop.
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Affiliation(s)
- Xiang Luo
- College of Agriculture, Henan University, Kaifeng, Henan, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Xi’an Botanical Garden of Shaanxi Province, Xi’an, China
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Da Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Pengpeng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Jiangtao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Xin Chen
- Shandong Institute of Pomology, National Germplasm Repository of Walnut and Chestnut, Tai’an, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, United States of America
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America
| | - Maria Malvolti
- Research Institute on Terrestrial Ecosystems, National Research Council, Porano, Terni, Italy
| | - Kai Ma
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chaobin Liu
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Chengkui Qiao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Zhenhua Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- * E-mail: (JX); (SC); (PZ)
| | - Shangying Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- * E-mail: (JX); (SC); (PZ)
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- * E-mail: (JX); (SC); (PZ)
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10
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Genome-Wide Identification and Expression Analysis of the CAD Gene Family in Walnut (Juglans regia L.). Biochem Genet 2022; 61:1065-1085. [DOI: 10.1007/s10528-022-10303-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022]
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11
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Wambulwa MC, Fan PZ, Milne R, Wu ZY, Luo YH, Wang YH, Wang H, Gao LM, Xiahou ZY, Jin YC, Ye LJ, Xu ZC, Yang ZC, Li DZ, Liu J. Genetic analysis of walnut cultivars from southwest China: Implications for germplasm improvement. PLANT DIVERSITY 2022; 44:530-541. [PMID: 36540707 PMCID: PMC9751080 DOI: 10.1016/j.pld.2021.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/26/2021] [Accepted: 08/18/2021] [Indexed: 05/19/2023]
Abstract
Walnuts are highly valued for their rich nutritional profile and wide medicinal applications. This demand has led to the intensification of breeding activities in major walnut production areas such as southwest China, in order to develop more superior cultivars. With the increasing number of cultivars, accurate identification becomes fundamental to selecting the right cultivar for grafting, industrial processing or development of new cultivars. To ensure proper identification of cultivars and understand the genetic structure of wild and cultivated material, we genotyped 362 cultivated and wild individuals of walnut trees from southwest China (with two additional populations from Xinjiang, plus three cultivars from Canada, France and Belgium) using 36 polymorphic microsatellite loci. We found relatively low indices of genetic diversity (H O = 0.570, H E = 0.404, N A = 2.345) as well as a high level of clonality (>85% of cultivars), indicating reliance on genetically narrow sources of parental material for breeding. Our STRUCTURE and PCoA analyses generally delineated the two species, though considerable levels of introgression were also evident. More significantly, we detected a distinct genetic group of cultivated Juglans sigillata, which mainly comprised individuals of the popular 'Yangbidapao' landrace. Finally, a core set of 18 SSR loci was selected, which was capable of identifying 32 cultivars. In a nutshell, our results call for more utilization of genetically disparate material, including wild walnut trees, as parental sources to breed for more cultivars. The data reported herein will significantly contribute towards the genetic improvement and conservation of the walnut germplasm in southwest China.
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Affiliation(s)
- Moses C. Wambulwa
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Department of Life Sciences, South Eastern Kenya University, 170-90200, Kitui, Kenya
| | - Peng-Zhen Fan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yue-Hua Wang
- School of School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, Yunnan, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zuo-Ying Xiahou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ye-Chuan Jin
- School of School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, Yunnan, China
| | - Lin-Jiang Ye
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zu-Chang Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zhi-Chun Yang
- Yangbi Forestry and Grassland Administration, Dali, 672500, Yunnan, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Corresponding author. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, 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 Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Corresponding author. CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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12
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Huanel OR, Quesada-Calderón S, Ríos Molina C, Morales-González S, Saenz-Agudelo P, Nelson WA, Arakaki N, Mauger S, Faugeron S, Guillemin ML. Pre-domestication bottlenecks of the cultivated seaweed Gracilaria chilensis. Mol Ecol 2022; 31:5506-5523. [PMID: 36029170 DOI: 10.1111/mec.16672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 08/02/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022]
Abstract
Gracilaria chilensis is the main cultivated seaweed in Chile. The low genetic diversity observed in the Chilean populations has been associated with the over-exploitation of natural beds and/or the founder effect that occurred during post-glacial colonization from New Zealand. How these processes have affected its evolutionary trajectory before farming and incipient domestication is poorly understood. In this study, we used 2232 single nucleotide polymorphisms (SNPs) to assess how the species' evolutionary history in New Zealand (its region of origin), the founder effect linked to transoceanic dispersion and colonization of South America, and the recent over-exploitation of natural populations have influenced the genetic architecture of G. chilensis in Chile. The contrasting patterns of genetic diversity and structure observed between the two main islands in New Zealand attest to the important effects of Quaternary glacial cycles on G. chilensis. Approximate Bayesian Computation (ABC) analyses indicated that Chatham Island and South America were colonized independently near the end of the Last Glacial Maximum and emphasized the importance of coastal and oceanic currents during that period. Furthermore, ABC analyses inferred the existence of a recent and strong genetic bottleneck in Chile, matching the period of over-exploitation of the natural beds during the 1970s, followed by rapid demographic expansion linked to active clonal propagation used in farming. Recurrent genetic bottlenecks strongly eroded the genetic diversity of G. chilensis prior to its cultivation, raising important challenges for the management of genetic resources in this incipiently domesticated species.
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Affiliation(s)
- Oscar R Huanel
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France
| | - Suany Quesada-Calderón
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,AUSTRAL-omics, Vicerrectoría de Investigación, Desarrollo y Creación Artística, Universidad Austral de Chile, Valdivia, Chile
| | - Cristian Ríos Molina
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Sarai Morales-González
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pablo Saenz-Agudelo
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France.,Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID- Millennium Science Initiative Nucleus (NUTME), Las Cruces, Chile
| | - Wendy A Nelson
- National Institute of Water and Atmospheric Research, Wellington, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Natalia Arakaki
- Instituto del Mar del Perú, Banco de Germoplasma de Organismos Acuáticos, Chucuito, Callao, Peru
| | - Stéphane Mauger
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France
| | - Sylvain Faugeron
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France
| | - Marie-Laure Guillemin
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France.,Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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13
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Du S, Hu X, Yang X, Yu W, Wang Z. Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China. Ecol Evol 2022; 12:e9101. [PMID: 35898427 PMCID: PMC9309028 DOI: 10.1002/ece3.9101] [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] [Received: 02/07/2022] [Revised: 06/04/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single-copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F st = 0.197). Relatively low long-distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction-expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high-latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.
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Affiliation(s)
- Shuhui Du
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern China Shanxi Agricultural University Taigu Jinzhong China
| | - Xiaoyan Hu
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern China Shanxi Agricultural University Taigu Jinzhong China
| | - Xiuyun Yang
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern China Shanxi Agricultural University Taigu Jinzhong China
| | - Wendong Yu
- College of Horticulture and Plant Protection Yangzhou University Yangzhou China
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry Chinese Academy of Forestry Beijing China
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14
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Walnut (Juglans regia L.) oil chemical composition depending on variety, locality, extraction process and storage conditions: A comprehensive review. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104534] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Zhang WP, Cao L, Lin XR, Ding YM, Liang Y, Zhang DY, Pang EL, Renner SS, Bai WN. Dead-End Hybridization in Walnut Trees Revealed by Large-Scale Genomic Sequence Data. Mol Biol Evol 2022; 39:msab308. [PMID: 34687315 PMCID: PMC8760940 DOI: 10.1093/molbev/msab308] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Although hybridization plays a large role in speciation, some unknown fraction of hybrid individuals never reproduces, instead remaining as genetic dead-ends. We investigated a morphologically distinct and culturally important Chinese walnut, Juglans hopeiensis, suspected to have arisen from hybridization of Persian walnut (J. regia) with Asian butternuts (J. cathayensis, J. mandshurica, and hybrids between J. cathayensis and J. mandshurica). Based on 151 whole-genome sequences of the relevant taxa, we discovered that all J. hopeiensis individuals are first-generation hybrids, with the time for the onset of gene flow estimated as 370,000 years, implying both strong postzygotic barriers and the presence of J. regia in China by that time. Six inversion regions enriched for genes associated with pollen germination and pollen tube growth may be involved in the postzygotic barriers that prevent sexual reproduction in the hybrids. Despite its long-recurrent origination and distinct traits, J. hopeiensis does not appear on the way to speciation.
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Affiliation(s)
- Wei-Ping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lei Cao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xin-Rui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ya-Mei Ding
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yu Liang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Er-Li Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO, USA
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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16
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Ji F, Ma Q, Zhang W, Liu J, Feng Y, Zhao P, Song X, Chen J, Zhang J, Wei X, Zhou Y, Chang Y, Zhang P, Huang X, Qiu J, Pei D. A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits. Genome Biol 2021; 22:300. [PMID: 34706738 PMCID: PMC8554829 DOI: 10.1186/s13059-021-02517-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored. RESULTS We report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese J. regia diverged from J. sigillata with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which JrFAD2 and JrANR are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively. CONCLUSIONS The largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.
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Affiliation(s)
- Feiyang Ji
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qingguo Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wenting Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yu Feng
- Systematic & Evolutionary Botany and Biodiversity group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Xiaobo Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Junpei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ye Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yingying Chang
- Engineering Laboratory of Biotechnology for Green Medicinal Plant of Henan Province, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs of Colleges and Universities in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Pu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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17
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Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut ( Juglans regia L.). Genes (Basel) 2021; 12:genes12091444. [PMID: 34573426 PMCID: PMC8466090 DOI: 10.3390/genes12091444] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/07/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
The transcription factor WRKY is widely distributed in the plant kingdom, playing a significant role in plant growth, development and response to stresses. Walnut is an economically important temperate tree species valued for both its edible nuts and high-quality wood, and its response to various stresses is an important factor that determines the quality of its fruit. However, in walnut trees themselves, information about the WRKY gene family remains scarce. In this paper, we perform a comprehensive study of the WRKY gene family in walnut. In total, we identified 103 WRKY genes in the common walnut that are clustered into 4 groups and distributed on 14 chromosomes. The conserved domains all contained a WRKY domain, and motif 2 was observed in most WRKYs, suggesting a high degree of conservation and similar functions within each subfamily. However, gene structure was significantly differentiated between different subfamilies. Synteny analysis indicates that there were 56 gene pairs in J. regia and A. thaliana, 76 in J. regia and J. mandshurica, 75 in J. regia and J. microcarpa, 76 in J. regia and P. trichocarpa, and 33 in J. regia and Q. robur, indicating that the WRKY gene family may come from a common ancestor. GO and KEGG enrichment analysis showed that the WRKY gene family was involved in resistance traits and the plant-pathogen interaction pathway. In anthracnose-resistant F26 fruits (AR) and anthracnose-susceptible F423 fruits (AS), transcriptome and qPCR analysis results showed that JrWRKY83, JrWRKY73 and JrWRKY74 were expressed significantly more highly in resistant cultivars, indicating that these three genes may be important contributors to stress resistance in walnut trees. Furthermore, we investigate how these three genes potentially target miRNAs and interact with proteins. JrWRKY73 was target by the miR156 family, including 12 miRNAs; this miRNA family targets WRKY genes to enhance plant defense. JrWRKY73 also interacted with the resistance gene AtMPK6, showing that it may play a crucial role in walnut defense.
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18
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Yan F, Xi RM, She RX, Chen PP, Yan YJ, Yang G, Dang M, Yue M, Pei D, Woeste K, Zhao P. Improved de novo chromosome-level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode. Mol Ecol Resour 2021; 21:2063-2076. [PMID: 33817972 DOI: 10.1111/1755-0998.13394] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 03/15/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022]
Abstract
Manchurian walnut (Juglans mandshurica Maxim.) is a synonym of J. cathayensis, a diploid, vulnerable, temperate deciduous tree valued for its wood and nut. It is also valued as a rootstock for Juglans regia because of its reported tolerance of lesion nematode. Reference genomes are available for several Juglans species, our goal was to produce a de novo, chromosome-level assembly of the J. mandshurica genome. Here, we reported an improved assembly of J. mandshurica with a contig N50 size of 6.49 Mb and a scaffold N50 size of 36.1 Mb. The total genome size was 548 Mb encoding 29,032 protein coding genes which were annotated. The collinearity analysis showed that J. mandshurica and J. regia originated from a common ancestor, with both species undergoing two WGD events. A genomic comparison showed that J. mandshurica was missing 1657 genes found in J. regia, and J. mandshurica includes 2827 genes not found in of the J. regia genome. The J. mandshurica contained 1440 unique paralogues that were highly enriched for flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant-pathogen interaction. Four gene families related to disease resistance notable contraction (rapidly evolving; LEA, WAK, PPR, and PR) in J. mandshurica compared to eight species. JmaPR10 and JmaPR8 contained three orthologous gene pairs with J. regia that were highly expressed in root bark. JmaPR10 is a strong candidate gene for lesion nematodes resistance in J. mandshurica. The J. mandshurica genome should be a useful resource for study of the evolution, breeding, and genetic variation in walnuts (Juglans).
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Affiliation(s)
- Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Rui-Min Xi
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Rui-Xue She
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Peng-Peng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Yu-Jie Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Ge Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Meng Dang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Ming Yue
- Xi'an Botanical Garden of Shaanxi Province, Xi'an, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Keith Woeste
- Department of Forestry and Natural Resources, USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Purdue University, West Lafayette, IN, USA
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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19
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Comprehensive Analysis of the Components of Walnut Kernel (Juglans regia L.) in China. J FOOD QUALITY 2021. [DOI: 10.1155/2021/9302181] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The contents of main components in 45 walnut kernels from 5 walnut-planting provinces in China (Yunnan, Shaanxi, Shandong, Hebei, and Sichuan) were determined using colorimetry, high-performance liquid chromatography, and gas chromatography, including flavonoids, vitamin E, trace elements, fatty acids, and amino acids. The levels of flavonoids and vitamin E were higher in walnuts from Yunnan than in walnuts from the other four provinces. The levels of zinc and iron were relatively higher in walnuts from Shandong, and the calcium content in walnuts from Yunnan was much lower. No obvious difference was found in crude fat concentration for nuts from the five provinces, but differences were observed in the crude protein content. Oleic acid was the predominant unsaturated fatty acids in all walnut species; the monounsaturated fatty acid content was the highest in walnuts from Yunnan. The data obtained here provided insight into differences in walnuts resulting from different growing environments and germplasm genetic traits.
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20
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Soil Cover Improves Soil Quality in a Young Walnut Forest in the Sichuan Basin, China. FORESTS 2021. [DOI: 10.3390/f12020236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The soil quality index (SQI) is based on several key indicators and is used to assess soil quality. More than 250,000 ha of walnut saplings (Juglans regia L.) were planted in previous cropland areas in the Sichuan Basin, China, using a range of soil cover types that may affect soil quality with effects that are unclear. We investigated the effects of white film (WF), black film (BF), shade netting (SN), and maize straw (MS) soil cover types and an uncovered control type (CK) on soil chemical and biological indicators and the SQI in the 0–15 cm soil layer in a young walnut forest in the Sichuan Basin over a 27-month study period. The results showed that all soil cover types increased the soil organic matter (SOM), total potassium (TK), and available potassium (AK) concentrations (p < 0.05), whereas the total nitrogen (TN) and available nitrogen (AN) concentrations were greater only in soils covered by MS than in CK (p < 0.05). The available phosphorus concentrations were 64.1 and 193.2% greater in soils covered by BF and MS treatments, respectively, than in the CK (p < 0.05). The numbers of soil faunal groups (N) were 45.7, 36.4, 37.2, and 101.5% higher in WF, BF, SN, and MS, respectively, than in CK (p < 0.05); the individual numbers (S) were 92.3, 36.2, 100.8, and 154.5% greater in WF, BF, SN, and MS, respectively, than in CK (p < 0.05). The microbial biomass carbon (MBC) was 15.5, 32.3, 45.0, and 77.1% greater in WF, BF, SN, and MS than in CK, respectively (p < 0.05). Redundancy discriminant analysis revealed strong positive interactions between biological indicators (MBC, N, and S) and SOM, AN, and AK concentrations. SOM, TN, AK, S, and MBC were the minimum required variables for the effective assessment of the SQI. All four soil cover types led to an improved SQI (p < 0.05), and MS had the greatest effect on SOM, TN, AN, AP, N, S, MBC, and SQI (p < 0.05). In conclusion, all four soil cover types increased the SOM levels, TK, AK, and MBC concentrations, soil faunal diversity, and SQI. The MS treatment was the most cost-effective and efficient measure to improve soil fertility, ecological function, and overall soil quality in the studied walnut forest.
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21
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Mao R, Wu L, Zhu N, Liu X, Hao Y, Liu R, Du Q, Li Y. Immunomodulatory effects of walnut (Juglans regia L.) oligopeptides on innate and adaptive immune responses in mice. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104068] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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22
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23
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Mu XY, Tong L, Sun M, Zhu YX, Wen J, Lin QW, Liu B. Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data. Mol Phylogenet Evol 2020; 147:106802. [DOI: 10.1016/j.ympev.2020.106802] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 11/25/2022]
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24
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Sun Y, Hou N, Woeste K, Zhang C, Yue M, Yuan X, Zhao P. Population genetic structure and adaptive differentiation of iron walnut Juglans regia subsp. sigillata in southwestern China. Ecol Evol 2019; 9:14154-14166. [PMID: 31938510 PMCID: PMC6953554 DOI: 10.1002/ece3.5850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 11/07/2022] Open
Abstract
Southwestern (SW) China is an area of active tectonism and erosion, yielding a dynamic, deeply eroded landscape that influences the genetic structure of the resident populations of plants and animals. Iron walnut (Juglans regia subsp. sigillata) is a deciduous tree species endemic to this region of China and cultivated there for its edible nuts. We sampled 36 iron walnut populations from locations throughout the species' range in SW China and genotyped a total of 765 individuals at five chloroplast DNA regions and 22 nuclear microsatellite loci. Species distribution models were produced to predict the evolution and historical biogeography of iron walnut and to estimate the impacts of climate oscillations and orographic environments on the species' demography. Our results indicated that J. regia subsp. sigillata had relatively low genetic diversity, high interpopulation genetic differentiation, and asymmetric interpopulation gene flow. Based on DIYABC analysis, we identified two lineages of J. sigillata in southwestern China. The lineages (subpopulations) diverge during the last glacial period (~1.34 Ma). Southwestern China was a glacial refuge during the last glacial period, but increasingly colder and arid climates might have fostered the fragmentation of J. regia subsp. sigillata within this refugium. Finally, we found that recent habitat fragmentation has led to a reduction in population connectivity and increased genetic differentiation by genetic drift in isolated populations. Our results support a conclusion that geological and climatic factors since the Miocene triggered the differentiation, evolutionary origin, and range shifts of J. sigillata in the studied region.
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Affiliation(s)
- Yi‐Wei Sun
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Na Hou
- Guizhou Academy of ForestryGuiyangChina
| | - Keith Woeste
- Department of Forestry and Natural ResourcesUSDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC)Purdue UniversityWest LafayetteINUSA
| | - Chuchu Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
- Xi'an Botanical Garden of Shaanxi ProvinceXi'anChina
| | - Xiao‐Ying Yuan
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
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25
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Gene Introgression among Closely Related Species in Sympatric Populations: A Case Study of Three Walnut (Juglans) Species. FORESTS 2019. [DOI: 10.3390/f10110965] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Gene introgression usually results from natural hybridization occurring among closely related species in sympatric populations. In this study, we discussed two rare and frequent gene flow phenomena between three species of Juglans plants and analyzed the possible causes for the difference. We collected 656 individuals from 40 populations of Persian walnut (Juglans regia L.), Chinese walnut (J. cathayensis Dode), and Iron walnut (J. sigillata Dode) that were genotyped at 17 expressed sequence tag simple sequence repeat (EST-SSR) loci to analyze the introgressions between J. regia and J. cathayensis, and J. regia and J. sigillata. Our study compared the spatial patterns of expected heterozygosity (HE), allelic richness (Rs), and private allele richness (PAR) so as to vividly infer the biogeographic history of related species of Juglans in the two regions. The results of the PCoA, UPGMA, and STRUCTURE analyses showed that all J. regia and J. sigillata populations clustered into one group, and the J. cathayensis populations clustered into the other group. The results of the historical gene flow analysis indicated that J. regia and J. sigillata have no genetic barriers, and the directional gene flow is mainly from J. regia to J. sigillata. For the three species of Juglans, all the above results indicated that gene flow was common among the same group of Juglans, and only rare and low-level gene flow appeared in distinct groups. Therefore, our study revealed multiple phenomena of gene flow and introgression among closely related species in sympatric populations, thereby providing a theoretical basis for the genetic evolution of the genus Juglans.
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