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

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 415
Author(s):  
Hilde Nybom ◽  
Gunārs Lācis
Keyword(s):  
Genetic Resources ◽  
Dna Markers ◽  
Plant Material ◽  
Large Scale ◽  
Plant Genetic Resources ◽  
Large Sets ◽  
International Projects ◽  
Pros And Cons ◽  
Commercially Important ◽  
Generation Sequencing

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.

scholarly journals Ethylene and expansin biosynthesis related genes polymorphism in local apple (Malus domestica Borkh.) cultivars from VIR Collection of plant genetic resources

2018 ◽  
Vol 22 (6) ◽  
pp. 660-666 ◽  
Author(s):  
I. N. Shamshin ◽  
A. V. Shlyavas ◽  
A. A. Trifonova ◽  
K. V. Boris ◽  
A. M. Kudryavtsev
Keyword(s):  
Genetic Resources ◽  
Large Scale ◽  
Plant Genetic Resources ◽  
Prolonged Storage ◽  
Fruit Softening ◽  
Fruit Storage ◽  
Local Cultivars ◽  
Allelic Configuration ◽  
Apple Cultivars ◽  
Apple Production

At Pushkin and Pavlovsk Laboratories of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) a diverse collec tion of local apple cultivars is maintained. Some of the cultivars are widely used in breeding programs for their ecological plasticity, increased adaptation to abiotic stress and disease resistance, still there have been no large-scale studies of these local cultivars for fruit storage ability. Fruit softening during storage is an important problem for apple production. Retention of desirable firmness after prolonged storage is one of the key requirements for new apple cultivars. Expansin and ethy lene biosynthesis related genes are known to be involved in control of fruit softening in apple, and gene specific molecular markers have been reported. In this study the polymorphism and allelic configuration of ethylene and expansin biosynthesis related genes Md-ACS1, Md-ACO1 and Md-Exp7 involved in control of fruit softening in 87 local apple cultivars from VIR Collection of Plant Genetic Resources were analyzed. PCR markers Md-ACS1, Md-ACO1 and SSR-marker Md-Exp7 were used in the study. The allele frequencies in the collection generally coincided with the data from previous studies. Md-ACS1 allele 2 associated with reduced ethylene production was found only in three local cultivars, while all the studied local cultivars were heterozygous for the Md-ACO1 locus, as well as most modern Russian apple cultivars. Half of the studied local cultivars were heterozygous for Md-Exp7 (198 : 202). Thirteen local cultivars with rare Md-Exp7 alleles (206, 210 and 212) were detected. No association was found between the Md-Exp7 genotype and the cultivars’ maturation time. The obtained results can be used for additional evaluation of the cultivars’ potential for breeding.

Broadening the genetic base of sesame (Sesamum indicum L.) through germplasm enhancement

2004 ◽  
Vol 2 (3) ◽  
pp. 143-151 ◽  
Author(s):  
I.S. Bisht ◽  
K.V. Bhat ◽  
S. Lakhanpaul ◽  
B.K. Biswas ◽  
M. Pandiyan ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Large Scale ◽  
Plant Genetic Resources ◽  
Sesamum Indicum ◽  
Genetic Enhancement ◽  
National Bureau ◽  
Oil Crops ◽  
Rich Diversity ◽  
Ancient Times ◽  
Realized Genetic Gains

Sesame (Sesamum indicum L.) is one of the world's oldest oil crops and has been cultivated in Asia from ancient times. India has a rich diversity of this crop and a landrace collection is maintained at the National Genebank at the National Bureau of Plant Genetic Resources (NBPGR). The breeding potential of this germplasm has been hardly exploited to date. The major hindrance for the utilization of these resources is the transfer of diversity into a form that can be easily used by breeders and farmers. As part of a core collection strategy, a selection was made of 24 of the most diverse and unadapted parental lines, including one accession of the wild species S. mulayanum, and these were intercrossed in various combinations to maximize genetic diversity and to develop locally adapted pools of genetic resources. A weak and decentralized selection regime was maintained at four selected target sites on the progeny of 103 crosses. The range of variation in the selected F4 progenies was assessed, and promising types with desired plant characteristics and high seed yield were selected. Realized genetic gains, especially for yield-related traits, were also assessed. Only a limited fraction of the existing diversity held in the genebank was used in the present study and there is much more diversity available for large-scale genetic enhancement of sesame in the future.

scholarly journals Characterisation of Latvia Fruit Crop Genetic Resources by Application of Molecular Genetics Methods

2013 ◽  
Vol 67 (2) ◽  
pp. 84-93
Author(s):  
Gunārs Lācis
Keyword(s):  
Molecular Markers ◽  
Genetic Resources ◽  
Plant Material ◽  
Data Exchange ◽  
Plant Genetic Resources ◽  
Germplasm Collection ◽  
Functional Markers ◽  
Fruit Crops ◽  
State Institute ◽  
Fruit Crop

A large diversity of fruit crop accessions is maintained at the Latvia State Institute of Fruit- Growing, which consists of modern cultivars, landraces and selections from local breeding programmes, as well as germplasm that has resulted from scientific exchange and co-operation with other institutes. Presently, the germplasm collection comprises 2509 accessions of 17 fruit crops; 676 accessions are designated as national genetic resources. Conservation of germplasm itself has little value without characterisation and further utilisation of the stored plant material. To intensify these activities, DNA-based technologies have been implemented in the characterisation of germplasm. Two main groups of molecular markers have been utilised: non-specific markers and gene-specific (functional) markers, subsequently applicable for Marker Assisted Selection (MAS). Genotyping protocols based on SSR, RAPD and Methylation-sensitive amplification polymorphism (MSAP) markers have been developed for twelve fruit crops for use in plant material identification, True-to-Type verification and evaluation of genetic diversity and internal collection structure. In total, 790 accessions have been genotyped using any of the mentioned markers. These markers have been harmonised with the European cooperative programme for plant genetic resources working group (ECPGR WG) recommended sets to ensure international data exchange. Gene specific molecular markers have been applied to apple and pear (resistance to scab), strawberry (resistance to Gnomonia fragariae), sweet cherries and plums (self-incompatibility).

scholarly journals STUDYING GENETIC RESOURCES OF SPRING BREAD WHEAT IN THE ENVIRONMENTS OF NORTHERN KAZAKHSTAN

2020 ◽  
Vol 180 (4) ◽  
pp. 44-47
Author(s):  
A. T. Babkenov ◽  
S. A. Babkenova ◽  
E. K. Kairzhanov
Keyword(s):  
Genetic Resources ◽  
Protein Content ◽  
Bread Wheat ◽  
Large Scale ◽  
Plant Genetic Resources ◽  
Sodium Dodecyl ◽  
Scale Production ◽  
Spring Bread Wheat ◽  
Wheat Varieties ◽  
Northern Kazakhstan

Background. Spring bread wheat is the main export crop in Kazakhstan. Unfortunately, wheat varieties cultivated for large-scale production do not fully meet the requirements of agricultural producers. The world diversity of wheat genetic resources should be widely used in breeding programs in order to develop new wheat cultivars with stable yields and with resistance to adverse environmental factors.Materials and methods. One hundred collection accessions of spring bread wheat were studied in 2015–2017 at the A.I. Barayev Science and Production Center of Grain Farming, Ltd. Seeds were sown at an optimum time (May 20–25), using an SSFC-7 seeder. Harvesting was conducted with a Wintersteiger combine. The study of the collection material was carried out in accordance with the guidelines developed by the N.I. Vavilov Institute of Plant Genetic Resources (VIR). The protein content was measured in line with State Standard 10846-91. The method of sodium dodecyl sulfate (SDS) sedimentation, modified by V. M. Bebyakin and M. V. Buntina, was used to measure the level of sedimentation.Results and conclusion. During the three-year study of spring bread wheat accessions in Northern Kazakhstan, only the cultivars ‘Shortandinskaya 2012’ and ‘Astana 2’ exceeded the reference ‘Astana’ in yield. The accessions ‘BW 252’, ‘Neepawa’ (Canada), ‘MANITUOU LR 13’ (CIMMYT, Mexico) and ‘Novosibirskaya 29’ (Russia) ripened 1–2 days earlier than the reference, while their average yield for 3 years was almost on the same level with the reference. The cultivars ‘Astana’ (the reference, Kazakhstan), ‘WA007824 WA7824’ (USA), ‘Novosibirskaya 29’, ‘Novosibirskaya 15’ (Russia), ‘OPATA85 LR10’ and ‘LR27+LR31,LR34’ (CIMMYT, Mexico) were distinguished for grain quality due to their high protein content and the level of sedimentation.

scholarly journals THE CYTOLOGICAL AND CYTOGENETIC STUDY OF THE ALTERNATED FORMS OF ALFALFA

2021 ◽  
pp. 40-43
Author(s):  
R. Mamedova ◽  
A. Shahaeva ◽  
O. Bayramov ◽  
Sh. Alizade
Keyword(s):  
Genetic Resources ◽  
Mitotic Activity ◽  
Plant Material ◽  
Cytogenetic Study ◽  
Plant Genetic Resources ◽  
Colchicine Treatment ◽  
Mutagenic Effect ◽  
Practical Application ◽  
Breeding Programs ◽  
Division Spindle

Colchicine in experimental mutagenesis is used to induce polyploidy, since it, by destroying the division spindle, prevents chromosomes from separating. The importance of studying the mutagenic effect of colchicine on a plant cell is also determined by the practical application of colchicine in the enrichment of plant genetic resources of plants, the creation of cytogenetic collections and their use in breeding programs. In our experiments, we studied the effect of colchicine on alfalfa and the effect of its influence. Seeds of varieties ASKHI-1 and AzNIKHI-262 obtained as a result of treatment with different concentrations of colchicine (0.02% and 0.04%) were used as plant material. In some anaphases, chromosome delays were observed when diverging to the poles. No cells with a doubled set of chromosomes were found. According to the results of studying the stages of mitosis, it should be noted that ASKHI-1 variety is more sensitive to colchicine treatment than AzNIKhI-252, since the first variety showed significantly greater deviations from the control and another variety at the stage of mitotic activity.

Advancement of taxonomic searches in the European search catalogue for plant genetic resources

2019 ◽  
Vol 17 (6) ◽  
pp. 559-561
Author(s):  
Stefanie Kreide ◽  
Markus Oppermann ◽  
Stephan Weise
Keyword(s):  
Genetic Resources ◽  
Plant Material ◽  
Plant Genetic Resources ◽  
New Developments ◽  
Fuzzy Search ◽  
Search Terms ◽  
Plant Names ◽  
Erroneous Data ◽  
Selection Of

AbstractGenebanks play an important role in the conservation of global plant biodiversity. The European Search Catalogue for Plant Genetic Resources (EURISCO) was created as a central entry point to provide information on these collections. However, a major challenge lies in the heterogeneity of scientific plant names. This makes the selection of suitable plant material, e.g. for research or breeding purposes, significantly more difficult. For this reason, the taxonomic backbone of EURISCO has been completely revised. Search terms entered by users are now automatically checked against taxonomic reference repositories, allowing a variety of synonyms to be identified. In addition, a fuzzy search has been implemented, which makes the search function tolerant of erroneous data (e.g. caused by typing errors). Besides improvements of the search interface, more support will be given to EURISCO's data providers. The new developments provide a tool that makes it easier to identify problem cases within the data, such as accepted/non-accepted taxonomic names, and will successively improve the quality of taxonomic information in EURISCO.

scholarly journals Reliable genomic strategies for species classification of plant genetic resources

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Artur van Bemmelen van der Plaat ◽  
Rob van Treuren ◽  
Theo J. L. van Hintum
Keyword(s):  
Genetic Resources ◽  
Large Scale ◽  
Plant Genetic Resources ◽  
Crop Wild Relatives ◽  
Training Data ◽  
Misclassification Rate ◽  
Species Classification ◽  
Marker Selection ◽  
Nearest Neighbours

Abstract Background To address the need for easy and reliable species classification in plant genetic resources collections, we assessed the potential of five classifiers (Random Forest, Neighbour-Joining, 1-Nearest Neighbour, a conservative variety of 3-Nearest Neighbours and Naive Bayes) We investigated the effects of the number of accessions per species and misclassification rate on classification success, and validated theirs generic value results with three complete datasets. Results We found the conservative variety of 3-Nearest Neighbours to be the most reliable classifier when varying species representation and misclassification rate. Through the analysis of the three complete datasets, this finding showed generic value. Additionally, we present various options for marker selection for classification taks such as these. Conclusions Large-scale genomic data are increasingly being produced for genetic resources collections. These data are useful to address species classification issues regarding crop wild relatives, and improve genebank documentation. Implementation of a classification method that can improve the quality of bad datasets without gold standard training data is considered an innovative and efficient method to improve gene bank documentation.

scholarly journals Nomenclatural standards, voucher specimens and genetic passports of potato cultivars created in the Siberian and Ural breeding centers

2020 ◽  
Author(s):  
N. A. Fomina ◽  
O. Yu. Antonova ◽  
I. G. Chukhina ◽  
D. A. Rybakov ◽  
A. D. Safonova ◽  
...  
Keyword(s):  
Dna Markers ◽  
Plant Material ◽  
Plant Genetic Resources ◽  
Potato Cultivars ◽  
Cultivated Plants ◽  
Research Centers ◽  
Joint Research ◽  
Experimental Field ◽  
Voucher Specimens ◽  
Research Institute

The present paper discusses methodological approaches to the creation of nomenclatural standards and genetic passports for Russian cultivars, currently being developed at the N.I. Vavilov Institute of Plant Genetic Resources (VIR) in collaboration with different breeding research centers. Plant material of potato cultivars bred in the Siberian Research Institute of Plant Cultivation and Breeding was collected by the cultivar creator A.D. Safonova in the experimental field of this institute and transferred to the VIR herbarium for preparation of their nomenclatural standards. Plant shoots and tubers of potato cultivars bred in other Siberian research centers in collaboration with the A.G. Lorkh All-Russian Research Institute of Potato Farming (VNIIKH) was collected by the representative of this institute in the experimental field of VNIIKH. As a result of joint research, nomenclatural standards were accomplished for 11 cultivars, namely ‘Аntonina’, ‘Zlatka’, ‘Lina’, ‘Lûbava’, ‘Nakra’, ‘Pamâti Rogačeva’, ‘Sarovskij’, ‘Safo’, ‘Solnečnyj’, ‘Tuleevskij’, ‘Ûna’** bred in five different Siberian breeding institutes including cultivars developed in collaboration with VNIIKH. Nomenclatural standards were prepared according to the ‘International Code of Nomenclature for Cultivated Plants’. DNA samples isolated from nomenclatural standards were used for preparation of genetic passports of these 11 cultivars. These genetic passports include information of the polymorphism of eight chromosome-specific microsatellites, data on the markers of 11 R-genes conferring resistance to various harmful organisms, as well as the information about cytoplasm types. Voucher specimens of additional three Siberian cultivars ‘Kemerovčanin’, ‘Kuznečanka’, ‘Tanaj’ and five Ural cultivars ‘Аlâska’, ‘Bravo’, ‘Irbitskij’, ‘Lûks’, ‘Terra’ from the Ural Research Institute for Agriculture were also registered in the VIR herbarium collection. For these eight cultivars, the genetic passports were not issued, but the results of SSR genotyping and molecular screening of voucher specimens performed with the same set of the DNA markers are presented in this report. A similar set of DNA markers was used for genotyping cultivar accessions from the in vitro and field collections of various institutes as well as cultivar specimens from eco-geographical tests performed within the framework of the Comprehensive Research Plan of the subprogram “Development of potato breeding and seed production in the Russian Federation”. The comparison of cultivar genetic passport data with genotyping results of specimens having the same name, but obtained from different sources made it possible to verify this plant material.

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