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

I. N. Shamshin; A. V. Shlyavas; A. A. Trifonova; K. V. Boris; A. M. Kudryavtsev

doi:10.18699/vj18.408

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

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj18.408 ◽

2018 ◽

Vol 22 (6) ◽

pp. 660-666 ◽

Cited By ~ 1

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.

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

Plant Genetic Resources ◽

10.1079/pgr200445 ◽

2004 ◽

Vol 2 (3) ◽

pp. 143-151 ◽

Cited By ~ 7

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.

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Nomenclatural standards of apple cultivars bred at the Pavlovsk experiment station of VIR

VAVILOVIA ◽

10.30901/2658-3860-2021-1-3-24 ◽

2021 ◽

Vol 4 (1) ◽

pp. 3-24

Author(s):

L. V. Bagmet ◽

A. V. Shlyavas

Keyword(s):

Genetic Resources ◽

Plant Genetic Resources ◽

Experiment Station ◽

Apple Cultivars

In the framework of the program of creating nomenclatural standards of domestic cultivars initiated by the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), nomenclatural standards of apple cultivars bred at the Pavlovsk Experiment Station of VIR have been developed. The cultivars in question are ‘Kormay’, ‘Kordonovka’, ‘Kryukovskoye’, ‘Krasnoshchyokoye’, ‘Leningradskaya Zelyonka’, ‘Leningradskiy Sinap’, ‘Leningradskoye Zheltoye’, ‘Lyubimitsa Tarasenko’, ‘Novogodneye’, ‘Novoye Polosatoye’, ‘Pashkevicha Krasnoye’, and ‘Sigovskoye’.

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

PROCEEDINGS ON APPLIED BOTANY GENETICS AND BREEDING ◽

10.30901/2227-8834-2019-4-44-47 ◽

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.

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Reliable genomic strategies for species classification of plant genetic resources

BMC Bioinformatics ◽

10.1186/s12859-021-04018-6 ◽

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.

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

Plants ◽

10.3390/plants10020415 ◽

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.

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