Dates and rates in grape’s plastomes: evolution in slow motion

Lorenzis

2021

IJMS

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Domestication is a process of selection driven by humans, transforming wild progenitors into domesticated crops. The grapevine (Vitis vinifera L.), besides being one of the most extensively cultivated fruit trees in the world, is also a fascinating subject for evolutionary studies. The domestication process started in the Near East and the varieties obtained were successively spread and cultivated in different areas. Whether the domestication occurred only once, or whether successive domestication events occurred independently, is a highly debated mystery. Moreover, introgression events, breeding and intense trade in the Mediterranean basin have followed, in the last thousands of years, obfuscating the genetic relationships. Although a succession of studies has been carried out to explore grapevine origin and different evolution models are proposed, an overview of the topic remains pending. We review here the findings obtained in the main phylogenetic and genomic studies proposed in the last two decades, to clarify the fundamental questions regarding where, when and how many times grapevine domestication took place. Finally, we argue that the realization of the pan-genome of grapes could be a useful resource to discover and track the changes which have occurred in the genomes and to improve our understanding about the domestication.

Section: Plastid Dna To Explore the Maternal Lineagesmentioning

confidence: 99%

Section: Plastid Dna To Explore the Maternal Lineagesmentioning

confidence: 99%

Section: Introgression Between Wild and Domesticated Grapevinementioning

confidence: 99%

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Back to the Origins: Background and Perspectives of Grapevine Domestication

Lorenzis

2021

IJMS

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“…The Internal Transcribed Spacers (ITS1 and ITS2), the nuclear gene for Granule Bound Starch Synthase ( GBSSI ) and the plastid rps16 – trnK spacer, were PCR‐amplified from 30 accessions of A. donax and two accessions of A. formosana . ITS1 and ITS2 are two rapidly evolving spacers widely used in phylogeographic studies and taxonomic reconstructions while the rps16–trnK plastid spacer has shown to be highly informative in other Angiosperms (Shaw, Lickey, Schilling, & Small, ; Zecca et al, ). DNA was extracted from dried leaves with the DNeasy Plant Mini kit (Qiagen) according to the manufacturer's instructions.…”

Section: Methodsmentioning

confidence: 99%

Multiple evolutionary lineages detected in giant reed (Arundo donax L.): Applied and evolutionary perspectives

Zecca

Tommasi

Annals of Applied Biology

2020

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Identification of independent evolutionary lineages is a modern challenge for biologists especially in crops with high potential. Molecular methods, usually used to explore intraspecific variation, also offer important information regarding how and when lineages have evolved and spread. Today, several tools to define the demarcation of lineages based on single or multi-locus data are available, permitting objective results to be obtained. We tested nuclear and plastid loci using five different approaches to delimit the major lineages and estimate the divergence times in giant reed (Arundo donax L.). It is an emerging energy crop, widespread in sub-tropical and temperate regions but particularly aggressive outside its native range. Our results support the presence of six lineages distributed from the Asian regions to the Mediterranean basin and indicate the western and southern edges of the Qinghai-Tibet Plateau as the putative area of origin and source of ancient and cryptic lineages. We suppose it could be an area that has fertile populations. These results should be considered in breeding programmes to produce new cultivars, especially because the absence of fertility for Mediterranean giant reed lineages reduces the opportunity of crop improvement. Moreover, the description of multiple lineages and identifying its putative ancestral area may be helpful to researchers working on invasiveness management, phytoremediation programmes and conservation biology.

“…Nuclear DNA markers have been widely applied to explain the genetic relationships between wild and cultivated grape lineages while the hypervariable regions within plastid intergenic spacers have been used to investigate the maternal lineages involved in the domestication process ( Arroyo-García et al., 2002 ; Grassi et al., 2002 ; Snoussi et al., 2004 ; Arroyo-Garcia et al., 2006 ; De Mattia et al., 2008 ; Cunha et al., 2009 ; Zecca et al., 2010 ; Karataş et al., 2014 ). Unfortunately, the low number of markers used and the low variability in grapevine plastid genomes greatly limited domestication studies ( Zecca et al., 2020 ). Today, next-generation sequencing technologies are an extraordinary opportunity to access a large amount of genomic information allowing the debate about the origin of the grapevine to be deepened.…”

mentioning

confidence: 99%

Editorial: Origins and Domestication of the Grape

Arroyo-García

2020

Front. Plant Sci.

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Editorial on the Research TopicOrigins and Domestication of the Grape Domestication is the most important genetic process of selection driven by humans that transformed wild forms into domesticated crops modifying morphological and genetic traits. The domesticated grapevine (Vitis vinifera L.) belongs together with about another 70 species to the Vitis genus (Wen et al., 2018) and being one of the oldest and extensively cultivated fruit crops is a fascinating subject for evolutionary studies. Archaeological data suggest that domestication of the grapevine began 6,000-8,000 years ago in the Transcaucasian region, between the Black Sea and Iran, from populations of V. vinifera subsp. sylvestris (Zohary and Hopf, 1993). Starting from the primary center of domestication, cultivated varieties were spread by humans through Southern Greece to the Mediterranean region. This pattern of domestication has been recently confirmed by molecular data (Myles et al., 2011;De Lorenzis et al., 2019) even if some authors have proposed local and circumscribed secondary domestication events in other areas (Rivera-Nunez and Walker, 1989