Plants

Research

12 pages, 3724 KiB

Open AccessArticle

Authentication of Hippophae rhamnoides ssp. sinensis and ssp. mongolica Based on Single Nucleotide Polymorphism at Ribosomal DNA and Their Vitamin Content Analysis

by Xiangmin Piao, Padmanaban Mohanan, Gokulanathan Anandhapadmanaban, Jong Chan Ahn, Jin Kyu Park, Deok Chun Yang, Gi-young Kwak and Yingping Wang

Plants 2022, 11(14), 1843; https://doi.org/10.3390/plants11141843 - 14 Jul 2022

Cited by 2 | Viewed by 2085

Abstract

Hippophae rhamnoides widely known as sea buckthorn berries (SB) are rich in vitamins and phytonutrients. The subspecies ssp. sinensis and ssp. mongolica are highly valued for their medicinal properties and vitamin contents, hence domesticated widely across Eurasia and Southeast Asia. Due to the [...] Read more.

Hippophae rhamnoides widely known as sea buckthorn berries (SB) are rich in vitamins and phytonutrients. The subspecies ssp. sinensis and ssp. mongolica are highly valued for their medicinal properties and vitamin contents, hence domesticated widely across Eurasia and Southeast Asia. Due to the frequent usage of these two subspecies, accurate identification is required to prevent economically motivated adulteration. In this study, we report the single nucleotide polymorphism (SNP) based molecular markers to easily distinguish these two subspecies at 45S nrDNA region. From the determined 45S rDNA region, we designed two primers (5′ sinensis and 5′ mongolica) and developed a multiplex PCR profile. The developed primers effectively distinguished the sea buckthorn subspecies in commercial products as well. Along with the development of subspecies specific primers, we have profiled vitamin contents from H. rhamnoides ssp. sinensis and ssp. mongolica and found ascorbic acid and riboflavin contents were high in both ssp. sinensis and spp. mongolica, yet the content of folic acid was high only in ssp. mongolica. Thus, we provide species specific primers and vitamin profile as an effective authentication of H. rhamnoides. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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16 pages, 1587 KiB

Open AccessArticle

Characterization of the Spanish Pomegranate Germplasm Collection Maintained at the Agricultural Experiment Station of Elche to Identify Promising Breeding Materials

by Elena Zuriaga, Jitka Pintová, Julián Bartual and María Luisa Badenes

Plants 2022, 11(9), 1257; https://doi.org/10.3390/plants11091257 - 6 May 2022

Cited by 7 | Viewed by 2494

Abstract

Pomegranates were one of the first domesticated fruit crops, and their long history resulted in the development of local cultivars all over the world. Spain is one of the main producers and exporters of this crop in the Mediterranean Basin, but in order [...] Read more.

Pomegranates were one of the first domesticated fruit crops, and their long history resulted in the development of local cultivars all over the world. Spain is one of the main producers and exporters of this crop in the Mediterranean Basin, but in order to maintain the competitiveness of this crop, new varieties should be developed. For this purpose, the pomegranate germplasm collection hold at the Agricultural Experiment Station of Elche, a public institution dependent on the Valencian regional government, is an interesting tool. However, the detailed characterization of any germplasm collection is a fundamental requirement to be able to make the most of these resources, allowing to identify putative promising accessions and to optimize the design of the future crosses. In this work, the genetic diversity of 94 accessions of this collection was analyzed using 19 microsatellite markers. As a result, 85 different genotypes were identified. These genetic profiles could be useful for varietal identification. Despite this genetic diversity, no clear substructure was observed, except for the ornamental accessions, that could be related to the vegetative propagation of the species. Additionally, the morphological characterization of this collection has made it possible to identify some materials that may be of interest as a source of traits for breeding. Results presented here pave the way for further genetic analyses, allowing the selection of parents to obtain segregating populations, as well as their descendants by the use of molecular assisted selection. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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20 pages, 3736 KiB

Open AccessArticle

Evaluation of Genetic Diversity Based on Microsatellites and Phytochemical Markers of Core Collection of Cymbopogon winterianus Jowitt Germplasm

by Sunita Munda, Raktim Jyoti Saikia, Twahira Begum, Sangeeta Bhandari, Ankita Gogoi, Neelav Sarma, Raghu Tamang and Mohan Lal

Plants 2022, 11(4), 528; https://doi.org/10.3390/plants11040528 - 16 Feb 2022

Cited by 16 | Viewed by 3327

Abstract

Cymbopogon winterianus Jowitt is an industrially important crop due to its value in the aromatic, perfumery and pharmaceutical industries. In this study, 72 accessions of C. winterianus were selected for molecular diversity analysis using SSR markers. It revealed a total of 65 polymorphic [...] Read more.

Cymbopogon winterianus Jowitt is an industrially important crop due to its value in the aromatic, perfumery and pharmaceutical industries. In this study, 72 accessions of C. winterianus were selected for molecular diversity analysis using SSR markers. It revealed a total of 65 polymorphic alleles showing an average of 68.10% polymorphism. The best SSR primer with competency in discriminating the germplasm was 3CM0506 with PIC (0.69), MI (0.69) and Rp (3.12). Genetic variation was studied between Assam, Manipur, Meghalaya and Arunachal Pradesh populations. A dendrogram based on the Neighbour-Joining Method showed clustering of germplasm on the collection site. A total of six relevant genetic populations were identified through a structure harvester software analysis. Moreover, a dendrogram based on similarity, complete linkage and Euclidean distance was also elucidated differentiating the genotypes with respect to the major phytochemical constituents of the essential oil. GC-FID and GC-MS analyses of the essential oil of the 72 germplasms revealed citronellal content from 2.58–51.45%, citronellol from 0.00–26.39% and geraniol from 0.00–41.15%. This is the first molecular diversity report with 72 accessions of C. winterianus collected from the NE region using 28 SSR primers as well as their diversity based on phytochemical markers. This diversity computation will help with acquisition of the knowledge and relationship among each individual accession leading to the development of improved and essential oil component-rich cultivars. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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17 pages, 1023 KiB

Open AccessArticle

As It Stands: The Palouse Wild Cider Apple Breeding Program

by Tymon James, Alexandra Johnson, Alexander Schaller, Stijn Vanderzande, Feixiong Luo, Paul Sandefur, Sushan Ru and Cameron Peace

Plants 2022, 11(4), 517; https://doi.org/10.3390/plants11040517 - 14 Feb 2022

Cited by 3 | Viewed by 2922

Abstract

Providing hands-on education for the next generation of plant breeders would help maximize effectiveness of future breeding efforts. Such education should include training in introgression of crop wild relative alleles, which can increase genetic diversity while providing cultivar attributes that meet industry and [...] Read more.

Providing hands-on education for the next generation of plant breeders would help maximize effectiveness of future breeding efforts. Such education should include training in introgression of crop wild relative alleles, which can increase genetic diversity while providing cultivar attributes that meet industry and consumer demands in a crop such as cider apple. Incorporation of DNA information in breeding decisions has become more common and is another skill future plant breeders need. The Palouse Wild Cider apple breeding program (PWCabp) was established at Washington State University in early 2014 as a student-run experiential learning opportunity. The objectives of this study were to describe the PWCabp’s approaches, outcomes, and student involvement to date that has relied on a systematic operational structure, utilization of wild relatives, and incorporation of DNA information. Students chose the crop (cider apple) and initial target market and stakeholders (backyard growers and hobbyists of the Palouse region). Twelve target attributes were defined including high phenolics and red flesh. Phase one and two field trials were established. Two promising high-bitterness selections were identified and propagated. By running the PWCabp, more than 20 undergraduate and graduate students gained experience in the decisions and operations of a fruit breeding program. PWCabp activities have produced desirable new germplasm via utilization of highly diverse Malus germplasm and trained new plant breeding professionals via experiential learning. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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17 pages, 2853 KiB

Open AccessArticle

SSR-Based Analysis of Genetic Diversity and Structure of Sweet Cherry (Prunus avium L.) from 19 Countries in Europe

by Teresa Barreneche, María Cárcamo de la Concepción, Marine Blouin-Delmas, Matthew Ordidge, Hilde Nybom, Gunars Lacis, Daina Feldmane, Jiri Sedlak, Mekjell Meland, Hedi Kaldmäe, Kersti Kahu, Zsuzsanna Békefi, Sanda Stanivuković, Gordana Đurić, Monika Höfer, Martin Galik, Elisabeth Schüller, Andreas Spornberger, Sorina Sirbu, Pavlina Drogoudi, Ana Cristina Agulheiro-Santos, Ossama Kodad, Aleš Vokurka, Marc Lateur, Felicidad Fernández Fernández, Daniela Giovannini and José Quero-García Show full author list Hide full author list

Plants 2021, 10(10), 1983; https://doi.org/10.3390/plants10101983 - 23 Sep 2021

Cited by 22 | Viewed by 5000

Abstract

Sweet cherry (Prunus avium L.) is a temperate fruit species whose production might be highly impacted by climate change in the near future. Diversity of plant material could be an option to mitigate these climate risks by enabling producers to have new [...] Read more.

Sweet cherry (Prunus avium L.) is a temperate fruit species whose production might be highly impacted by climate change in the near future. Diversity of plant material could be an option to mitigate these climate risks by enabling producers to have new cultivars well adapted to new environmental conditions. In this study, subsets of sweet cherry collections of 19 European countries were genotyped using 14 SSR. The objectives of this study were (i) to assess genetic diversity parameters, (ii) to estimate the levels of population structure, and (iii) to identify germplasm redundancies. A total of 314 accessions, including landraces, early selections, and modern cultivars, were monitored, and 220 unique SSR genotypes were identified. All 14 loci were confirmed to be polymorphic, and a total of 137 alleles were detected with a mean of 9.8 alleles per locus. The average number of alleles (N = 9.8), PIC value (0.658), observed heterozygosity (H_o = 0.71), and expected heterozygosity (H_e = 0.70) were higher in this study compared to values reported so far. Four ancestral populations were detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA), and two of them (K1 and K4) could be attributed to the geographical origin of the accessions. A N-J tree grouped the 220 sweet cherry accessions within three main clusters and six subgroups. Accessions belonging to the four STRUCTURE populations roughly clustered together. Clustering confirmed known genealogical data for several accessions. The large genetic diversity of the collection was demonstrated, in particular within the landrace pool, justifying the efforts made over decades for their conservation. New sources of diversity will allow producers to face challenges, such as climate change and the need to develop more sustainable production systems. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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16 pages, 1281 KiB

Open AccessArticle

Potential Markers for Selecting Self-Eliminating Apple Genotypes

by Aurelijus Starkus, Birute Frercks, Dalia Gelvonauskiene, Ingrida Mazeikiene, Rytis Rugienius, Vidmantas Bendokas and Vidmantas Stanys

Plants 2021, 10(8), 1612; https://doi.org/10.3390/plants10081612 - 5 Aug 2021

Cited by 1 | Viewed by 2061

Abstract

The heavy blooming of apple trees results in the inefficient usage of energy and nutritional material, and additional expenditure on fruitlet thinning is required to maintain fruit quality. A possible solution for controlling the fruit load on trees is the development of new [...] Read more.

The heavy blooming of apple trees results in the inefficient usage of energy and nutritional material, and additional expenditure on fruitlet thinning is required to maintain fruit quality. A possible solution for controlling the fruit load on trees is the development of new cultivars that self-eliminate excess fruitlets, thus controlling yield. The aim of our study was to identify biological differences in apple cultivars in terms of blooming intensity and fruitlet load self-regulation. In total, 19 apple cultivars were studied in the years 2015–2017. The dynamics of fruitlet self-elimination, seed development in fruitlets and fruits, photosynthetic parameters, carbohydrates, and plant hormones were evaluated. We established that apple cultivars self-eliminating a small number of fruitlets need a lower number of well-developed seeds in fruit, and their number of leaves and area per fruit on a bearing branch are larger, compared to cultivars, self-eliminating large numbers of fruitlets. A higher carbohydrate amount in the leaves may be related to smaller fruitlet self-elimination. The amount of auxin and a high indole-3-acetic acid/zeatin ratio between leaves of cultivar groups with heavy blooming were higher than in cultivars with moderate blooming. A lower amount of abscisic acid was found in heavy-blooming cultivars during drought stress. All these parameters may be used as markers for the selection of different apple genotypes that self-eliminate fruitlets. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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18 pages, 471 KiB

Open AccessArticle

Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm

by Matthew Ordidge, Suzanne Litthauer, Edward Venison, Marine Blouin-Delmas, Felicidad Fernandez-Fernandez, Monika Höfer, Christina Kägi, Markus Kellerhals, Annalisa Marchese, Stephanie Mariette, Hilde Nybom and Daniela Giovannini

Plants 2021, 10(6), 1243; https://doi.org/10.3390/plants10061243 - 18 Jun 2021

Cited by 14 | Viewed by 5028

Abstract

The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been [...] Read more.

The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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15 pages, 1486 KiB

Open AccessArticle

Differences in Leaf Morphological Parameters of Pear (Pyrus communis L.) Based on Their Susceptibility to European Pear Rust Caused by Gymnosporangium sabinae (Dicks.) Oerst.

by Katrīna Kārkliņa, Gunārs Lācis and Baiba Lāce

Plants 2021, 10(5), 1024; https://doi.org/10.3390/plants10051024 - 20 May 2021

Cited by 3 | Viewed by 3303

Abstract

European pear rust is an important disease; however, the relationship between its causal pathogen Gymnosporangium sabinae (Dicks.) Oerst. and host Pyrus communis L. is poorly understood. In this study, disease severity was measured, and leaf samples were collected over three years, and their [...] Read more.

European pear rust is an important disease; however, the relationship between its causal pathogen Gymnosporangium sabinae (Dicks.) Oerst. and host Pyrus communis L. is poorly understood. In this study, disease severity was measured, and leaf samples were collected over three years, and their leaf water content; leaf area; leaf mass per area; and epidermis, mesophyll, and vascular tissue width and stomatal density were measured and compared between susceptible and resistant genotypes for each year. Most genotypes either showed consistent disease symptoms or showed no symptoms during the study in terms of their susceptibility. A correlation between disease severity and mesophyll tissue thickness, and stomatal density and differences between several morphological parameters were found depending on the genotype’s susceptibility. The study showed that the following pear morphological traits were stable between the years: water content, leaf mass per area, spongy mesophyll thickness, phloem thickness, and stomatal density. When selecting for breeding, we found that candidates for traits that discern susceptible genotypes from resistant were mesophyll layer width, stomatal density, epidermis width, and xylem tissue width. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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16 pages, 5427 KiB

Open AccessArticle

Detection of Reproducible Major Effect QTL for Petal Traits in Garden Roses

by Dietmar Schulz, Marcus Linde and Thomas Debener

Plants 2021, 10(5), 897; https://doi.org/10.3390/plants10050897 - 29 Apr 2021

Cited by 15 | Viewed by 3326

Abstract

The detection of QTL by association genetics depends on the genetic architecture of the trait under study, the size and structure of the investigated population and the availability of phenotypic and marker data of sufficient quality and quantity. In roses, we previously demonstrated [...] Read more.

The detection of QTL by association genetics depends on the genetic architecture of the trait under study, the size and structure of the investigated population and the availability of phenotypic and marker data of sufficient quality and quantity. In roses, we previously demonstrated that major QTL could already be detected in small association panels. In this study, we analyzed petal number, petal size and fragrance in a small panel of 95 mostly tetraploid garden rose genotypes. After genotyping the panel with the 68 K Axiom WagRhSNP chip we detected major QTL for all three traits. Each trait was significantly influenced by several genomic regions. Some of the QTL span genomic regions that comprise several candidate genes. Selected markers from some of these regions were converted into KASP markers and were validated in independent populations of up to 282 garden rose genotypes. These markers demonstrate the robustness of the detected effects independent of the set of genotypes analyzed. Furthermore, the markers can serve as tools for marker-assisted breeding in garden roses. Over an extended timeframe, they may be used as a starting point for the isolation of the genes underlying the QTL. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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13 pages, 621 KiB

Open AccessFeature PaperArticle

Pomological Characteristics and Ploidy Levels of Japanese Plum (Prunus salicina Lindl.) Cultivars Preserved in Poland

by Agnieszka Głowacka, Mirosław Sitarek, Elżbieta Rozpara and Małgorzata Podwyszyńska

Plants 2021, 10(5), 884; https://doi.org/10.3390/plants10050884 - 27 Apr 2021

Cited by 17 | Viewed by 3262

Abstract

Research on the resistance to frost, susceptibility to sharka, flowering biology, fruit setting, yield, and ploidy levels of 36 Japanese plum cultivars (mostly hybrids of Prunus salicina with Prunus cerasifera) were carried out in 2015–2020 at the Experimental Orchard located in Dąbrowice [...] Read more.

Research on the resistance to frost, susceptibility to sharka, flowering biology, fruit setting, yield, and ploidy levels of 36 Japanese plum cultivars (mostly hybrids of Prunus salicina with Prunus cerasifera) were carried out in 2015–2020 at the Experimental Orchard located in Dąbrowice near Skierniewice. Relatively mild winters with sporadic temperature drops to nearly −21 °C in January of 2017 and 2018 caused slight damage to several cultivars of Japanese plum insufficiently resistant to frost. The trees of most cultivars remained healthy, with no signs of damage. ‘Barkhatnaya’ and ‘Tatyana’ cultivars turned out to be very susceptible to sharka. ‘Herkules’ trees were the most vigorous. ‘Barkhatnaja’, ‘Blue Gigant’, ‘Shater’, and ‘Tatyana’ trees were characterized by weak growth. The trees of Japanese plum started flowering early, usually in the first or second decade of April. Most of the cultivars belonged to early season cultivars, the fruits of which ripened in July. Based on the assessment of tree productivity, ‘Barkhatnaya’, ‘Inese’, ‘Shater’, ‘Tatyana’, and ‘Vanier’ are the best for growing in the climate of Central Europe. ‘Tsernushka’, ‘Chuk’, ‘Dofi Sandra’, ‘Early Golden’, ‘Ewierch Rannyj’, ‘Yevraziya’, ‘Gek’, ‘General’, ‘Kometa’, ‘Kometa Late’, ‘Maschenka’, and ‘Naidyona’ trees also yielded well. ‘Blue Gigant’, ‘Black Amber’, and ‘Herkules’ had the largest fruits, and ‘Chuk’ and ‘Inese’ cultivars produced the smallest fruits. Among the assessed Japanese plum cultivars, those with round fruit, dark skin with various shades of purple, yellow flesh, and A cytometric analysis showed that almost all cultivars are diploid, except for ‘Herkules’ (possibly pentaploid) and ‘Yevraziya’ (possibly hexaploid or aneuploid). Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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14 pages, 3193 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Potato Germplasm in RDA-Genebank: Utilization for Breeding and Conservation

by Kyung-Jun Lee, Raveendar Sebastin, Gyu-Taek Cho, Munsup Yoon, Gi-An Lee and Do-Yoon Hyun

Plants 2021, 10(4), 752; https://doi.org/10.3390/plants10040752 - 12 Apr 2021

Cited by 12 | Viewed by 3630

Abstract

Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries. It is of critical importance to understand the genetic diversity and population structure for effective collection, conservation, and utilization of potato germplasm. Thus, the objective of the [...] Read more.

Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries. It is of critical importance to understand the genetic diversity and population structure for effective collection, conservation, and utilization of potato germplasm. Thus, the objective of the present study was to investigate the genetic diversity and population structure of potato germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea to provide basic data for future preservation and breeding of potato genetic resources. A total of 24 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 482 potato accessions. A total of 257 alleles were detected, with an average of 10.71 alleles per locus. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual accessions within the population, while only 3% was distributed among populations. Results of genetic structure analysis based on STRUCTURE and discriminant analysis of principal components revealed that 482 potato accessions could be divided into two main subpopulations. Accessions of subpopulation 1 mainly belonged to cultivars and breeding lines. Accessions of subpopulations 2 basically corresponded to wild relatives of potatoes. Results of this study provide useful information for potato improvement and conservation programs, although further studies are needed for a more accurate evaluation of genetic diversity and phenotypic traits of potatoes. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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12 pages, 2460 KiB

Open AccessArticle

Greek Tulips: Worldwide Electronic Trade over the Internet, Global Ex Situ Conservation and Current Sustainable Exploitation Challenges

by Nikos Krigas, Christos Lykas, Ioannis Ipsilantis, Theodora Matsi, Stina Weststrand, Mats Havström and Georgios Tsoktouridis

Plants 2021, 10(3), 580; https://doi.org/10.3390/plants10030580 - 19 Mar 2021

Cited by 10 | Viewed by 4126

Abstract

From an ornamental viewpoint, tulips are famous clonally propagated crops. This research focuses on 15 wild-growing Greek tulip species including 11 range-restricted species, i.e., six Greek endemics and five Balkan or Aegean endemics and subendemics, among which seven are currently threatened with extinction [...] Read more.

From an ornamental viewpoint, tulips are famous clonally propagated crops. This research focuses on 15 wild-growing Greek tulip species including 11 range-restricted species, i.e., six Greek endemics and five Balkan or Aegean endemics and subendemics, among which seven are currently threatened with extinction (two Critically Endangered, three Endangered and two Vulnerable). An overview of the global electronic trade over the internet is presented herein for these valuable phytogenetic resources in an attempt to define the extent of their commercialization (25 nurseries in three countries, mainly bulb trade at various prices) with concomitant conservation implications. In the frame of the repatriation initiatives launched, their global ex situ conservation is overviewed according to the PlantSearch facility of the Botanic Gardens Conservation International (materials from 15 species stored in 41 botanic gardens of 14 countries). The results of this study on the Greek tulips showed that there are both well-established value chains and gaps in the market regarding the “botanical tulips”; revealed the compromised effectiveness of ex situ conservation for the majority of them; raised conservation concerns related to authorized access to these wild phytogenetic resources; and indicated that their future utilization should comply with the provision of national and international legislation. All these are envisaged and discussed within the framework of the newly launched research project TULIPS.GR which aims to be the pilot establishment of a national collection regarding all Greek tulips (currently holding 38 accessions of 13 species, including almost all of the threatened ones). The project’s scope is to enable the creation of a sustainable value chain for the Greek tulips with authorized collections, sustainable conservation schemes, production of DNA barcoded propagation material, species-specific propagation and cultivation protocols, mycorrhizal investigations, field studies, applying innovative precise soil/foliar fertigation, and investigation of the postharvest treatment of fresh cut flowers, promoting networking and synergies with producers and associations in Greece and abroad. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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12 pages, 2562 KiB

Open AccessArticle

A Bioinformatics Pipeline to Identify a Subset of SNPs for Genomics-Assisted Potato Breeding

by Catja Selga, Alexander Koc, Aakash Chawade and Rodomiro Ortiz

Plants 2021, 10(1), 30; https://doi.org/10.3390/plants10010030 - 24 Dec 2020

Cited by 15 | Viewed by 4205

Abstract

Modern potato breeding methods following a genomic-led approach provide means for shortening breeding cycles and increasing breeding efficiency across selection cycles. Acquiring genetic data for large breeding populations remains expensive. We present a pipeline to reduce the number of single nucleotide polymorphisms (SNPs) [...] Read more.

Modern potato breeding methods following a genomic-led approach provide means for shortening breeding cycles and increasing breeding efficiency across selection cycles. Acquiring genetic data for large breeding populations remains expensive. We present a pipeline to reduce the number of single nucleotide polymorphisms (SNPs) to lower the cost of genotyping. First, we reduced the number of individuals to be genotyped with a high-throughput method according to the multi-trait variation as defined by principal component analysis of phenotypic characteristics. Next, we reduced the number of SNPs by pruning for linkage disequilibrium. By adjusting the square of the correlation coefficient between two adjacent loci, we obtained reduced subsets of SNPs. We subsequently tested these SNP subsets by two methods; (1) a genome-wide association study (GWAS) for marker identification, and (2) genomic selection (GS) to predict genomic estimated breeding values. The results indicate that both GWAS and GS can be done without loss of information after SNP reduction. The pipeline allows for creating custom SNP subsets to cover all variation found in any particular breeding population. Low-throughput genotyping will reduce the genotyping cost associated with large populations, thereby making genomic breeding methods applicable to large potato breeding populations by reducing genotyping costs. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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Review

Jump to: Research, Other

30 pages, 451 KiB

Open AccessFeature PaperReview

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

by Hilde Nybom and Gunārs Lācis

Plants 2021, 10(2), 415; https://doi.org/10.3390/plants10020415 - 23 Feb 2021

Cited by 23 | Viewed by 5947

Abstract

Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic [...] Read more.

Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

18 pages, 2339 KiB

Open AccessReview

Genetic Improvement of Arundo donax L.: Opportunities and Challenges

by Tommaso Danelli, Marina Laura, Marco Savona, Michela Landoni, Fabrizio Adani and Roberto Pilu

Plants 2020, 9(11), 1584; https://doi.org/10.3390/plants9111584 - 16 Nov 2020

Cited by 15 | Viewed by 7016

Abstract

Arundo donax L., the giant reed—being a long-duration, low-cost, non-food energy crop able to grow in marginal lands—has emerged as a potential alternative to produce biomass for both energy production, with low carbon emissions, and industrial bioproducts. In recent years, pioneering efforts have [...] Read more.

Arundo donax L., the giant reed—being a long-duration, low-cost, non-food energy crop able to grow in marginal lands—has emerged as a potential alternative to produce biomass for both energy production, with low carbon emissions, and industrial bioproducts. In recent years, pioneering efforts have been made to genetically improve this very promising energy crop. This review analyses the recent advances and challenges encountered in using clonal selection, mutagenesis/somaclonal variation and transgenesis/genome editing. Attempts to improve crop yield, in vitro propagation efficiency, salt and heavy metal tolerance by clonal selection were carried out, although limited by the species’ low genetic diversity and availability of mutants. Mutagenesis and somaclonal variation have also been attempted on this species; however, since Arundo donax is polyploid, it is very difficult to induce and select promising mutations. In more recent years, genomics and transcriptomics data are becoming available in Arundo, closing the gap to make possible the genetic manipulation of this energy crop in the near future. The challenge will regard the functional characterization of the genes/sequences generated by genomic sequencing and transcriptomic analysis in a complex polyploid genome. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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Other

Jump to: Research, Review

12 pages, 1423 KiB

Open AccessPerspective

Contributions of Reduced Susceptibility Alleles in Breeding Apple Cultivars with Durable Resistance to Fire Blight

by Sarah A. Kostick, Soon Li Teh and Kate M. Evans

Plants 2021, 10(2), 409; https://doi.org/10.3390/plants10020409 - 22 Feb 2021

Cited by 7 | Viewed by 3475

Abstract

Breeding apple cultivars with durable genetic resistance is a potential long-term solution to fire blight, a devastating bacterial disease caused by Erwinia amylovora. However, phenotyping resistance/susceptibility to fire blight is challenging due to E. amylovora strain virulence, differential host × strain interactions, [...] Read more.

Breeding apple cultivars with durable genetic resistance is a potential long-term solution to fire blight, a devastating bacterial disease caused by Erwinia amylovora. However, phenotyping resistance/susceptibility to fire blight is challenging due to E. amylovora strain virulence, differential host × strain interactions, quantitative host resistance, environmental influences on disease, and impacts of tree vigor on susceptibility. Inheritance of resistance/susceptibility to fire blight is complex and phenotypic information alone is insufficient to guide breeding decisions targeting resistance. Several quantitative trait loci (QTLs) associated with resistance/susceptibility to fire blight have been detected throughout the apple genome. Most resistance alleles at fire blight QTLs have been identified in wild Malus germplasm with poor fruit quality, which limits their breeding utility. Several QTLs have been identified in populations derived from cultivars and reduced-susceptibility alleles have been characterized in multiple important breeding parents. Although resistance to fire blight is an attractive target for DNA-informed breeding, relatively few trait-predictive DNA tests for breeding relevant fire blight QTLs are available. Here we discuss (1) considerations and challenges associated with phenotyping resistance/susceptibility to fire blight; (2) sources of resistance that have been identified for use as parents; and (3) our perspective on short and long-term strategies to breed apple cultivars with durable resistance to fire blight with emphasis on the potential contributions of reduced susceptibility alleles to achieve this goal. Full article

(This article belongs to the Special Issue Plant Genetic Resources and Breeding of Clonally Propagated Crops)

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