Genetic divergence for adaptability and stability in sugarcane: Proposal for a more accurate evaluation.
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ABSTRACT:
SUBMITTER: Filho JAD
PROVIDER: S-EPMC8282048 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Sorghum mosaic virus (SrMV, the genus Potyvirus of the family Potyviridae) is a causal agent of common mosaic in sugarcane and poses a threat to the global sugar industry. In this study, a total of 901 sugarcane leaf samples with mosaic symptom were collected from eight provinces in China and were detected via RT-PCR using a primer pair specific to the SrMV coat protein (CP). These leaf samples included 839 samples from modern cultivars (Saccharum spp. hybrids) and 62 samples from chewing cane (S. officinarum). Among these, 632 out of 901 (70.1%) samples were tested positive for SrMV. The incidences of SrMV infection were 72.3% and 40.3% in modern cultivars and chewing cane, respectively. Phylogenetic analysis showed that all tested SrMV isolates were clustered into three clades consisting of six phylogenetic groups based on 306 CP sequences (this study = 265 and GenBank database = 41). A total of 10 SrMV isolates from South America (the United States and Argentina) along with 106 isolates from China were clustered in group D, while the remaining 190 SrMV isolates from Asia (China and Vietnam) were dispersed in five groups. The SrMV isolates in group F were limited to Yunnan province in China, and those in group A were spread over eight provinces. A significant genetic heterogeneity was elucidated in the nucleotide sequence identities of all SrMV CPs, ranging from 69.0% to 100%. A potential recombination event was postulated among SrMV isolates based on CP sequences. All tested SrMV CPs underwent dominant negative selection. Geographical isolation (South America vs. Asia) and host types (modern cultivars vs. chewing cane) are important factors promoting the genetic differentiation of SrMV populations. Overall, this study contributes to the global understanding of the genetic evolution of SrMV and provides a valuable resource for the epidemiology and management of the mosaic in sugarcane.
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Project description:BackgroundThe existing frameworks for the evaluation of genetic and genomic applications clearly address the technical and clinical value of a test, but are less concerned with the way genetic services are delivered and organized. We therefore aimed to develop a comprehensive new framework that includes an assessment of service delivery.MethodsA new framework was built on the evaluation dimensions identified through a systematic review of the existing frameworks and a Delphi survey of Italian experts in public health genomics.ResultsOur framework has four sections. The first two sections, respectively, guide the evidence collection process for the genetic test (analytic validity; clinical validity; clinical utility; personal utility) and its delivery models (organizational aspects; economic evaluation; ethical, legal and social implications; patient perspective). The third section guides the formulation of the research priorities to be addressed in future research. Finally, the fourth section suggests three criteria to summarize the collected evidence (net benefit, cost-effectiveness, feasibility).ConclusionWe have successfully developed an evaluation framework for the evaluation of genetic tests that includes an assessment of service delivery. It also introduces some neglected evaluation dimensions such as personal utility and patient perspective.
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