genetic pattern
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2021 ◽  
Author(s):  
Siran lu ◽  
Xiangyu Luo ◽  
Hongfang Wang ◽  
Rodolfo Gentili ◽  
Sandra Citterio ◽  
...  

Abstract Common ragweed (Ambrosia artemisiifolia L.) is an invasive alien species (IAS) that can cause severe allergies among urban residents. Understanding its invasion pathways is critical for designing effective control programs. However, studies on the invasion of common ragweed normally skip urban areas. Results from a few studies based on analyzing occurrence records contain high uncertainties. We attempted to address this knowledge gap through a case study in East China cities by combining the population genetic method with the occurrence records. We first collected leaf samples of 37 common ragweed populations from 15 cities. We then quantified the spatial genetic pattern of common ragweed populations by analyzing genomic and chloroplast DNA extracted from the leaf samples. Combined with the analysis of occurrence data and trade data, we discovered that multiple introductions have impacted the spatial genetic pattern of common ragweed populations in East China Cities. We inferred that the modern-day grain trade between the United States and China could be the primary invasion source while the bridgehead introduction passage through Japan played a minor role. Among the studied cities, Nanjing and Shenyang dispersed more gene flows than other cities. The two cities' central roles in transportation and grain importation might explain the observed pattern. Based on our findings, we suggest that invasive species control programs should consider the potential role of cities as landing points and dispersal hubs of common ragweed in invaded countries.


2021 ◽  
Vol 243 ◽  
pp. 106075
Author(s):  
Binwei Liu ◽  
Xi Zhang ◽  
Ziwei Wang ◽  
Weiyuan Li ◽  
Qi Zhang ◽  
...  

2021 ◽  
Vol 50 (2) ◽  
pp. 289-294
Author(s):  
Muhammad Sajjad Iqbal ◽  
Abdul Ghafoor

Study revealed a first report of proteomics variation in Nigella sativa L. based on analyzing 32 accessions through SDS-PAGE. Three prominent regions along eight subunits were identified. Intra specific variation was observed low whereas the sharpness of bands was high between first and second regions. It was noted that in second region there was no clear evidence of band formation in N. sativa. Prominent and sharp protein peptide bands were recorded in four accessions, namely PK-020561, PK-020609, PK-020620 and PK-020646. Further investigation of single seeds showed almost similar genetic pattern within the single accession. Five clusters were formed on the basis of Euclidean distance. Cluster-I & II contain 1, 1 accession each, likewise Cluster-III and C-IV contain 2, 2 accessions whereas Cluster-V was found diversified as consisted of 26 accessions. Two accessions PK-020878 and PK-020877 were recommended for polymorphism and crop improvement programs. Bangladesh J. Bot. 50(2): 289-294, 2021 (June)


2021 ◽  
Author(s):  
Phanchita Vejchasarn ◽  
Jeremy R. Shearman ◽  
Usawadee Chaiprom ◽  
Yotwarit Phansenee ◽  
Tatpong Tulyananda ◽  
...  

Abstract BackgroundThailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice varieties from all across Thailand were sequenced to identify SNP variants allowing for the population structure to be explored.ResultsThe result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on SNPs selected by QTL analysis also supported the inferred population structure.ConclusionThe population structure, which was inferred in this study, contains ve subpopulations such that each subpopulation has a unique ecological system, genetic pattern, as well as agronomic traits. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice.


2021 ◽  
Author(s):  
Phanchita Vejchasarn ◽  
Jeremy R. Shearman ◽  
Usawadee Chaiprom ◽  
Yotwarit Phansenee ◽  
Tatpong Tulyananda ◽  
...  

Background: Thailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice varieties from all across Thailand were sequenced to identify SNP variants allowing for the population-structure to be explored. Results: The result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on SNPs selected by QTL analysis also supported the inferred population structure. Conclusion: The population structure, which was inferred in this study, contains five populations s.t. each population has a unique ecological system, genetic pattern, as well as agronomic traits. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice.


2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaoping Lian ◽  
Shilai Zhang ◽  
Guangfu Huang ◽  
Liyu Huang ◽  
Jing Zhang ◽  
...  

Oryza longistaminata, a wild species of African origin, has been reported to exhibit self-incompatibility (SI). However, the genetic pattern of its SI remained unknown. In this study, we conducted self-pollination and reciprocal cross-pollination experiments to verify that O. longistaminata is a strictly self-incompatible species. The staining of pollen with aniline blue following self-pollination revealed that although pollen could germinate on the stigma, the pollen tube was unable to enter the style to complete pollination, thereby resulting in gametophytic self-incompatibility (GSI). LpSDUF247, a S-locus male determinant in the gametophytic SI system of perennial ryegrass, is predicted to encode a DUF247 protein. On the basic of chromosome alignment with LpSDUF247, we identified OlSS1 and OlSS2 as Self-Incompatibility Stamen candidate genes in O. longistaminata. Chromosome segment analysis revealed that the Self-Incompatibility Pistil candidate gene of O. longistaminata (OlSP) is a polymorphic gene located in a region flanking OlSS1. OlSS1 was expressed mainly in the stamens, whereas OlSS2 was expressed in both the stamens and pistils. OlSP was specifically highly expressed in the pistils, as revealed by RT-PCR and qRT-PCR analyses. Collectively, our observations indicate the occurrence of GSI in O. longistaminata and that this process is potentially controlled by OlSS1, OlSS2, and OlSP. These findings provide further insights into the genetic mechanisms underlying self-compatibility in plants.


Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1482
Author(s):  
David González-Serna ◽  
Gonzalo Villanueva-Martin ◽  
Marialbert Acosta-Herrera ◽  
Ana Márquez ◽  
Javier Martín

Immune-mediated diseases (IMDs) are complex pathologies that are strongly influenced by environmental and genetic factors. Associations between genetic loci and susceptibility to these diseases have been widely studied, and hundreds of risk variants have emerged during the last two decades, with researchers observing a shared genetic pattern among them. Nevertheless, the pathological mechanism behind these associations remains a challenge that has just started to be understood thanks to functional genomic approaches. Transcriptomics, regulatory elements, chromatin interactome, as well as the experimental characterization of genomic findings, constitute key elements in the emerging understandings of how genetics affects the etiopathogenesis of IMDs. In this review, we will focus on the latest advances in the field of functional genomics, centering our attention on systemic rheumatic IMDs.


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