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Li Z, Wang T, Yun L, Ren X, Wang Y, Shi F. Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea. Genes (Basel) 2023; 14:1970. [PMID: 37895319 PMCID: PMC10606050 DOI: 10.3390/genes14101970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of P. juncea and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon's information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (r2) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker-trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of P. juncea germplasm.
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Affiliation(s)
- Zhen Li
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
| | - Tian Wang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
| | - Lan Yun
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
- Key Laboratory of Grassland Resources Ministry of Education, Hohhot 010010, China
| | - Xiaomin Ren
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
| | - Yong Wang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
| | - Fengling Shi
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
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Sepúlveda‐Espinoza F, Bertin‐Benavides A, Hasbún R, Toro‐Núñez Ó, Varas‐Myrik A, Alarcón D, Guillemin M. The impact of Pleistocene glaciations and environmental gradients on the genetic structure of Embothrium coccineum. Ecol Evol 2022; 12:e9474. [PMID: 36381388 PMCID: PMC9646505 DOI: 10.1002/ece3.9474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/11/2022] Open
Abstract
The South American temperate forests were subjected to drastic topographic and climatic changes during the Pliocene-Pleistocene as a consequence of the Andean orogeny and glacial cycles. Such changes are common drivers of genetic structure and adaptation. Embothrium coccineum (Proteaceae) is an emblematic tree of the South American temperate forest (around 20°S of latitude) that has strongly been affected by topographic and climatic events. Previous studies have shown a marked genetic structure in this species, and distinct ecotypes have been described. Yet, little is known about their adaptive genetic responses. The main goal of this study was to investigate the effects of historical and contemporary landscape features affecting the genetic diversity and connectivity of E. coccineum throughout its current natural distribution. Using over 2000 single nucleotide polymorphisms (SNPs), we identified two genetic groups (a Northern and a Central-Southern group) that diverged around 2.8 million years ago. The level of genetic structure was higher among populations within the Northern genetic group than within the Central-Southern group. We propose that these differences in genetic structure may be due to differences in the assemblages of pollinators and in the evolutionary histories of the two genetic groups. Moreover, the data displayed a strong pattern of isolation by the environment in E. coccineum, suggesting that selection could have led to adaptive divergence among localities. We propose that in the Chilean temperate forest, the patterns of genetic variation in E. coccineum reflect both a Quaternary phylogenetic imprint and signatures of selection as a consequence of a strong environmental gradient.
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Affiliation(s)
- Francisco Sepúlveda‐Espinoza
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
- Facultad de Ciencias, Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Ariana Bertin‐Benavides
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
- ONG Conciencia SurConcepciónChile
- Laboratorio de Genómica Forestal, Centro de BiotecnologíaUniversidad de ConcepciónConcepciónChile
| | - Rodrigo Hasbún
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
| | - Óscar Toro‐Núñez
- Departamento de Botánica, Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
| | - Antonio Varas‐Myrik
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
| | - Diego Alarcón
- Departamento de Ciencias Ecológicas, Instituto de Ecología y BiodiversidadUniversidad de ChileÑuñoaChile
| | - Marie‐Laure Guillemin
- Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Facultad de CienciasUniversidad Austral de ChileValdiviaChile
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRSSorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de ChileRoscoffFrance
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL)ValdiviaChile
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Genetic diversity and population structure of Ottelia alismoides (Hydrocharitaceae), a vulnerable plant in agro-ecosystems of Japan. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Xiong Y, Xiong Y, Yu Q, Zhao J, Lei X, Dong Z, Yang J, Song S, Peng Y, Liu W, Bai S, Ma X. Genetic variability and structure of an important wild steppe grass Psathyrostachys juncea (Triticeae: Poaceae) germplasm collection from north and central Asia. PeerJ 2020; 8:e9033. [PMID: 32341905 PMCID: PMC7182019 DOI: 10.7717/peerj.9033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/31/2020] [Indexed: 11/20/2022] Open
Abstract
Russian wildrye, Psathyrostachys junceus (Fisch.) Nevski, is an important wild steppe perennial grass, which is characterized by longevity and short robust rhizomes. It also has highly resistance in grazing and abiotic stress. In this study, the genetic diversity of eleven P. juncea wild germplasms from north and central Asia was investigated using AFLP markers. The P. juncea populations were divided into three clades in both UPGMA dendrogram and PCoA clustering corresponding to the three genetic memberships in STRUCTURE analysis. The genetic specificity of Xinjiang (XJ) populations was revealed by the highest Ne (1.5411) and Hj (0.3553) and their dispersion shown in UPGMA. High inbreeding coefficient (Wright’s F statistics, f = 0.496, Fst = 0.128) was observed although a moderate degree of gene flow (Nm = 1.4736) existed, that may ascribe to habitat fragmentation or the low seedling recruitment, which ultimately resulted in decrease of population size and their genetic diversity. The key factors inducing moderate genetic differentiation detected in this study were isolation by distance (IBD), climatic variabilities and geographical barriers. All these results provide insights into the study of genetic status and germplasm collecting of Russian wildrye.
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Affiliation(s)
- Yi Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanli Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiong Lei
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhixiao Dong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jian Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Sijia Song
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Peng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibet Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xi-ning, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xiao Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Wu WD, Liu WH, Sun M, Zhou JQ, Liu W, Zhang CL, Zhang XQ, Peng Y, Huang LK, Ma X. Genetic diversity and structure of Elymus tangutorum accessions from western China as unraveled by AFLP markers. Hereditas 2019; 156:8. [PMID: 30733654 PMCID: PMC6352457 DOI: 10.1186/s41065-019-0082-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/17/2019] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Understanding genetic diversity of wild plant germplasm and the relationships between ecogeographic and genetic characteristics may provide insights for better utilizing and conserving genetic resources. Elymus tangutorum (Nevski) Hand.-Mazz, a cool-season hexaploid perennial, is an important pasture bunchgrass species used for forages and grassland restoration in Qinghai-Tibet Plateau and northwest China. In this study, 27 E. tangutorum accessions from diverse origins of western China were evaluated using AFLP markers in an effort to delve into the genetic relationships among them. The effects of eco-environmental factors and geographical isolation on the genetic diversity and population structure were also elucidated. RESULTS On account of 554 polymorphic fragments amplified with 14 primer combinations, the mean values of some marker parameters including polymorphic information content, resolving power and marker index were 0.2504, 14.10 and 23.07, respectively, validating the high efficiency and reliability of the markers selected. Genetic dissimilarity index values among accessions ranged from 0.1024 to 0.7137 with a mean of 0.2773. STRUCTURE, UPGMA clustering and PCoA analyses showed that all accessions could be divided into the three main clusters; however, this results do not exactly coincide with geographic groups. We found medium differentiation (F ST = 0.162) between Qinghai-Tibet Plateau (QTP) and Xinjiang (XJC), and high differentiation (F ST = 0.188) among three Bayesian subgroups. A significant correlation (r = 0.312) between genetic and geographical distance was observed by Mantel test in the species level, while the weak correlation was detected between genetic and environmental distance for all accessions and most of geographical groups. In addition, a significant ecological influence of average annual precipitation on genetic distance was revealed in XJC group and the Bayesian subgroup A. CONCLUSION This study indicates that AFLP technique are a useful tool to measure genetic diversity in E. tangutorum, showing that geographical and environmental factors (especially precipitation) together, play a crucial role in genetic differentiation patterns. These findings underline the importance of local adaptation in shaping patterns of genetic variability and population structure in E. tangutorum germplasm collected in Western China.
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Affiliation(s)
- Wen-Dan Wu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Wen-Hui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, 81108 China
| | - Ming Sun
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Ji-Qiong Zhou
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Wei Liu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Cheng-Lin Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xing-Quan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yan Peng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Lin-Kai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
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Zhang C, Sun M, Zhang X, Chen S, Nie G, Peng Y, Huang L, Ma X. AFLP-based genetic diversity of wild orchardgrass germplasm collections from Central Asia and Western China, and the relation to environmental factors. PLoS One 2018; 13:e0195273. [PMID: 29641553 PMCID: PMC5894997 DOI: 10.1371/journal.pone.0195273] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/19/2018] [Indexed: 12/31/2022] Open
Abstract
Dactylis glomerata L. (orchardgrass) is an important perennial forage species in temperate areas of the world. It is usually used for silage, grazing and hay because of its high nutritional value and reproducibility. Central Asia, Xinjiang and Tibetan Plateau in China possess various special micro-environments that harbor many valuable resources, while different degrees of degradation of the grassland ecosystem occurred due to climatic changing and human activities. Investigating the genetic diversity of wild D. glomerat could provide basis for collection, protection, and utilization of some excellent germplasm resources. Totally 210 individuals from 14 populations—five from Xinjiang, two from Kangding (Tibetan Plateau), and seven from Central Asia were identified using AFLP technology. The average values of Nei’s genetic diversity (Hj) and Shannon information index (Ho) were 0.383 and 0.394 respectively. UPGMA tree, STRUCTURE analysis and principal coordinate analysis (PCoA) showed populations from same region clustered together. AMOVA revealed 35.10% of the genetic differentiation (Fst) occurred among populations. Gene flow (Nm) was limited among all populations. Genetic diversity of D. glomerata was high but limited under isolation-by-distance pattern, resulting in high genetic differentiation and low gene flow among populations. Adjacent regions also exhibited similar results because of the barriers of high mountains. The environmental factors, such as precipitation, elevation, latitude and longitude also had some impacts on genetic diversity and structure pattern of populations.
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Affiliation(s)
- Chenglin Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Ming Sun
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Shiyong Chen
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Gang Nie
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Yan Peng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
- * E-mail:
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