scholarly journals The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Gabriele Magris ◽  
Irena Jurman ◽  
Alice Fornasiero ◽  
Eleonora Paparelli ◽  
Rachel Schwope ◽  
...  

AbstractIn order to elucidate the still controversial processes that originated European wine grapes from its wild progenitor, here we analyse 204 genomes of Vitis vinifera and show that all analyses support a single domestication event that occurred in Western Asia and was followed by numerous and pervasive introgressions from European wild populations. This admixture generated the so-called international wine grapes that have diffused from Alpine countries worldwide. Across Europe, marked differences in genomic diversity are observed in local varieties that are traditionally cultivated in different wine producing countries, with Italy and France showing the largest diversity. Three genomic regions of reduced genetic diversity are observed, presumably as a consequence of artificial selection. In the lowest diversity region, two candidate genes that gained berry–specific expression in domesticated varieties may contribute to the change in berry size and morphology that makes the fruit attractive for human consumption and adapted for winemaking.

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoting Xia ◽  
Shunjin Zhang ◽  
Huaju Zhang ◽  
Zijing Zhang ◽  
Ningbo Chen ◽  
...  

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.


PLoS ONE ◽  
2018 ◽  
Vol 13 (9) ◽  
pp. e0201374 ◽  
Author(s):  
Sha Xie ◽  
Yonghong Tang ◽  
Peng Wang ◽  
Changzheng Song ◽  
Bingbing Duan ◽  
...  

2018 ◽  
Vol 115 (47) ◽  
pp. E11081-E11090 ◽  
Author(s):  
Ryan A. York ◽  
Chinar Patil ◽  
Kawther Abdilleh ◽  
Zachary V. Johnson ◽  
Matthew A. Conte ◽  
...  

Many behaviors are associated with heritable genetic variation [Kendler and Greenspan (2006) Am J Psychiatry 163:1683–1694]. Genetic mapping has revealed genomic regions or, in a few cases, specific genes explaining part of this variation [Bendesky and Bargmann (2011) Nat Rev Gen 12:809–820]. However, the genetic basis of behavioral evolution remains unclear. Here we investigate the evolution of an innate extended phenotype, bower building, among cichlid fishes of Lake Malawi. Males build bowers of two types, pits or castles, to attract females for mating. We performed comparative genome-wide analyses of 20 bower-building species and found that these phenotypes have evolved multiple times with thousands of genetic variants strongly associated with this behavior, suggesting a polygenic architecture. Remarkably, F1 hybrids of a pit-digging and a castle-building species perform sequential construction of first a pit and then a castle bower. Analysis of brain gene expression in these hybrids showed that genes near behavior-associated variants display behavior-dependent allele-specific expression with preferential expression of the pit-digging species allele during pit digging and of the castle-building species allele during castle building. These genes are highly enriched for functions related to neurodevelopment and neural plasticity. Our results suggest that natural behaviors are associated with complex genetic architectures that alter behavior via cis-regulatory differences whose effects on gene expression are specific to the behavior itself.


2019 ◽  
pp. 299-301
Author(s):  
Mayhan Hedaitulla ◽  
Roman Kravchenko ◽  
Leonid Troshin

В статье дан обзор современного состояния и тенденциозного развития виноградарской отрасли Афганистана. Виноград выращивается практически в каждой части страны, от Кандагара до Такара и Фарьяба. Наиболее интенсивно виноград возделывают в провинциях Кабул, Парван, Каписа, Кандагар, Гильменд, Джавзян, Герат и Газни. Но в большинстве районов страны культура выращивается не для коммерческого использования, а для семейного потребления. В основном весь виноград Афганистана принадлежит к подвиду Vitis vinifera sativa D.C.. В стране в наличии большое разнообразие доступных сортов (более 100), но самыми распространёнными являются три местных сорта столового направления использования: Шиндохани, Кишмиш белый и Тайфи розовый. При этом сорта Шиндохани и Кишмиш белый еще используются для приготовления изюма. К другим распространенным сортам винограда относятся Хусайне, Аскери, Голадан, Спен Манга, Надери и Бедана Кишмиш сиах (черный без косточек). Также вводятся в производство такие новые коммерческие сорта как Thompson Seedless, Red Globe, Cardinal, Emperor, Fantasy, Crimson Seedless, Flame Seedless, Ruby, Ribier и Black Emerald. В экспорте Афганистана виноград занимает 4%. В Афганистане виноградная лоза в основном возделывается по местной традиционной системе - на земляных курганах с головчатой формировкой. Используется также система «земля-решетчатая». Производственная система виноградарства Афганистана, его культурные практики, сортимент и послеуборочный процесс все еще традиционны. Поэтому для достижения более высоких результатов необходимо ориентироваться на международные стандарты качества, импортировать и распространять новые технологии, координировать процесс между всеми производителями виноградной продукции, повышать их грамотность.The article provides an overview of modern condition and development trends of the viticulture industry in Afghanistan. Grapes are cultivated in almost every part of the country, from the south to Kandahar and to the north to Takar and Faryaba. The most intensive cultivation areas are the provinces Kabul, Parvan, Kapisa, Kandahar, Helmand, Javzyan, Herat and Ghazni. In most parts of the country, grapes are grown not for commercial use but for family consumption. Most of grape varieties in Afghanistan belong to Vitis vinifera sativa D.C. The country has a wide range of available varieties (more than 100), but the most common are three local varieties: ‘Shindokhani’, ‘Kishmishi bely’ and ‘Typhi rozovy’. These are table varieties. At the same time, ‘Shindokhani’ and ‘Kishmishi bely’ are also used for raisin production. Other common grape varieties are ‘Hussaini’, ‘Askari’, ‘Goladan’, ‘Spen Manga’, ‘Naderi’ and ‘Bedana Kishmishi siah’ (black seedless). New commercial varieties ‘Thompson Seedless’, ‘Red Globe’, ‘Cardinal’, ‘Emperor’, ‘Fantasy’, ‘Crimson Seedless’, ‘Flame Seedless’, ‘Ruby’, ‘Ribier’ and ‘Black Emerald’ are being introduced into cultivation, too. Grapes account for 4% of the country’s total exports. In Afghanistan, grapes are mainly cultivated according to the local traditional system on mounds of earth with head training. ‘Earth-lattice’ trellis is also used. In Afghanistan, grape production, cultural practices, assortment and post-harvest process are still traditional. Therefore, to achieve better results, it is necessary to focus on international quality standards, to import and disseminate new technologies, to coordinate the process with all producers of grape products, and to increase their professional skills.


1997 ◽  
Vol 11 (3) ◽  
pp. 532-536 ◽  
Author(s):  
Muhammad A. Bhatti ◽  
Kassim Al-Khatib ◽  
Robert Parker

‘Lemberger’ wine grape response to fall application of selected herbicides applied at simulated drift rates was studied in 1992 and 1993. Chlorsulfuron, thifensulfuron, 2,4-D, glyphosate, bromoxynil, and 2,4-D plus glyphosate were applied at 1/100, 1/33, 1/10, and 1/3 of a selected maximum rate for use in wheat or fallow. All herbicides, except bromoxynil and thifensufluron, caused symptoms on grapevines at the highest rate during the spring following fall application. The most severe symptoms were caused by 2,4-D and 2,4-D plus glyphosate, whereas the least symptoms were caused by chlorsulfuron and glyphosate. The severity of symptoms increased and shoot growth, leaf area, internode length, and dry cane weight decreased as the rates of 2,4-D and 2,4-D plus glyphosate increased. Chlorsulfuron and glyphosate reduced the growth of grapevines only when applied at the highest rate during the fall. The data show that exposure of wine grapes to 2,4-D or 2,4-D plus glyphosate during the fall can adversely affect the growth of grapevines the following spring.


Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 628-633 ◽  
Author(s):  
J. E. Bowers ◽  
G. S. Dangl ◽  
R. Vignani ◽  
C. P. Meredith

Four new simple sequence repeat (SSR) loci (designated VVMD5, VVMD6, VVMD7, and VVMD8) were characterized in grape and analyzed by silver staining in 77 cultivars of Vitis vinifera. Amplification products ranged in size from 141 to 263 base pairs (bp). The number of alleles observed per locus ranged from 5 to 11 and the number of diploid genotypes per locus ranged from 13 to 27. At each locus at least 75% of the cultivars were heterozygous. Alleles differing in length by only 1 bp could be distinguished by silver staining, and size estimates were within 1 or 2 bp, depending on the locus, of those obtained by fluorescence detection at previously reported loci. Allele frequencies were generally similar in wine grapes and table grapes, with some exceptions. Some alleles were found only in one of the two groups of cultivars. All 77 cultivars were distinguished by the four loci with the exception of four wine grapes considered to be somatic variants of the same cultivar, 'Pinot noir', 'Pinot gris', 'Pinot blanc', and 'Meunier'; two table grapes that are known to be synonymous, 'Keshmesh' and 'Thompson Seedless'; and three table grapes, 'Dattier', 'Rhazaki Arhanon', and 'Markandi', the first two of which have been suggested to be synonymous. Although the high polymorphism at grape SSR loci suggests that very few loci would theoretically be needed to separate all cultivars, the economic and legal significance of grape variety identification requires the increased resolution that can be provided by a larger number of loci. The ease with which SSR markers and data can be shared internationally should encourage their broad use, which will in turn increase the power of these markers for both identification and genetic analysis of grape. Key words : grape, Vitis, microsatellite, simple sequence repeat, DNA typing, identification.


2017 ◽  
Vol 219 ◽  
pp. 346-356 ◽  
Author(s):  
Delia Elena Urcan ◽  
Simone Giacosa ◽  
Fabrizio Torchio ◽  
Susana Río Segade ◽  
Stefano Raimondi ◽  
...  

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