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Plants
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Plant Molecular Breeding
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Plant Molecular Breeding

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 13565

Special Issue Editor

Dr. Oleg Sergeevich Alexandrov

E-Mail Website
Guest Editor
All-Russia Research Institute of Agriculture Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia
Interests: molecular markers; DNA repeats; DNA polymorphism; cytogenetics; genetics; genome editing; CRISPR/Cas9 technology; 5S rDNA; poplars; sex chromosomes

Special Issue Information

Dear Colleagues,

Currently, plant breeding is carried out worldwide. The use of molecular genetics techniques makes this process more efficient, and that of molecular markers saves time and allows the successful separation of unnecessary breeding material. Studies of biodiversity, sex determination in dioecious crops in the juvenile period, as well as selection of parental pairs for crossing are greatly simplified by molecular methods. The application of modern genomics makes it possible to achieve high-quality results.

This Special Issue is devoted to the application of molecular genetics and genomics methods at any stages of the plant breeding process. Articles on the development of new molecular and cytogenetic markers, the sequencing of the genomes of agriculturally important plants, the analysis of valuable genes and DNA repeats in relation to plant breeding are invited. The submitted articles should present significant experimental results and be of interest to a wide range of readers.

Dr. Oleg Sergeevich Alexandrov
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular genetics
  • molecular markers
  • cytogenetic markers
  • genome sequencing
  • genome editing
  • genes
  • DNA repeats

Published Papers (6 papers)

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Research

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17 pages, 2979 KiB  
Article
Development and Complex Application of Methods for the Identification of Mutations in the FAD3A and FAD3B Genes Resulting in the Reduced Content of Linolenic Acid in Flax Oil
by Liubov V. Povkhova, Elena N. Pushkova, Tatiana A. Rozhmina, Alexander A. Zhuchenko, Roman I. Frykin, Roman O. Novakovskiy, Ekaterina M. Dvorianinova, Aleksey A. Gryzunov, Elena V. Borkhert, Elizaveta A. Sigova, Gleb N. Vladimirov, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, George S. Krasnov, Alexey A. Dmitriev and Nataliya V. Melnikova
Plants 2023, 12(1), 95; https://doi.org/10.3390/plants12010095 - 24 Dec 2022
Cited by 5 | Viewed by 1632
Abstract
Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. [...] Read more.
Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. Inactivating mutations in the FAD3A and FAD3B genes lead to a decrease in the LIN content and an increase in the LIO content. For the identification of the three most common low-LIN mutations in flax varieties (G-to-A in exon 1 of FAD3A substituting tryptophan with a stop codon, C-to-T in exon 5 of FAD3A leading to arginine to a stop codon substitution, and C-to-T in exon 2 of FAD3B resulting in histidine to tyrosine substitution), three approaches were proposed: (1) targeted deep sequencing, (2) high resolution melting (HRM) analysis, (3) cleaved amplified polymorphic sequences (CAPS) markers. They were tested on more than a thousand flax samples of various types and showed promising results. The proposed approaches can be used in marker-assisted selection to choose parent pairs for crosses, separate heterogeneous varieties into biotypes, and select genotypes with desired homozygous alleles of the FAD3A and FAD3B genes at the early stages of breeding for the effective development of varieties with a particular LIN and LIO content, as well as in basic studies of the molecular mechanisms of fatty acid synthesis in flax seeds to select genotypes adequate to the tasks. Full article
(This article belongs to the Special Issue Plant Molecular Breeding)
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11 pages, 942 KiB  
Article
Development of Microsatellite Markers for Tanacetum cinerariifolium (Trevis.) Sch. Bip., a Plant with a Large and Highly Repetitive Genome
by Filip Varga, Zlatko Liber, Jernej Jakše, Ante Turudić, Zlatko Šatović, Ivan Radosavljević, Nina Jeran and Martina Grdiša
Plants 2022, 11(13), 1778; https://doi.org/10.3390/plants11131778 - 5 Jul 2022
Cited by 3 | Viewed by 1607
Abstract
Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevis.) Sch. Bip.) is an outcrossing plant species (2n = 18) endemic to the eastern Adriatic coast and source of the natural insecticide pyrethrin. Due to the high repeatability and large genome (1C-value = 9.58 pg) our previous [...] Read more.
Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevis.) Sch. Bip.) is an outcrossing plant species (2n = 18) endemic to the eastern Adriatic coast and source of the natural insecticide pyrethrin. Due to the high repeatability and large genome (1C-value = 9.58 pg) our previous attempts to develop microsatellite markers using the traditional method were unsuccessful. Now we have used Illumina paired-end whole genome sequencing and developed a specific procedure to obtain useful microsatellite markers. A total of 796,130,142 high-quality reads (approx. 12.5× coverage) were assembled into 6,909,675 contigs using two approaches (de novo assembly and joining of overlapped pair-end reads). A total of 31,380 contigs contained one or more microsatellite sequences, of which di-(59.7%) and trinucleotide (25.9%) repeats were the most abundant. Contigs containing microsatellites were filtered according to various criteria to achieve better yield of functional markers. After two rounds of testing, 17 microsatellite markers were developed and characterized in one natural population. Twelve loci were selected for preliminary genetic diversity analysis of three natural populations. Neighbor-joining tree, based on the proportion of shared alleles distances, grouped individuals into clusters according to population affiliation. The availability of codominant SSR markers will allow analysis of genetic diversity and structure of natural Dalmatian pyrethrum populations as well as identification of breeding lines and cultivars. Full article
(This article belongs to the Special Issue Plant Molecular Breeding)
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10 pages, 1437 KiB  
Article
Genomic Position and Markers Associated with the Hull-Less Seed Trait in Pumpkin
by Geoffrey Meru, Yuqing Fu, Swati Shrestha, Vincent Njung’e Michael, Marie Dorval and Riphine Mainviel
Plants 2022, 11(9), 1238; https://doi.org/10.3390/plants11091238 - 3 May 2022
Cited by 6 | Viewed by 2179
Abstract
Pumpkin (Cucurbita pepo) seeds are nutritious and valued as a source of vegetable oil, protein, healthy fatty acids, and minerals. Pumpkin seeds that are naturally devoid of the seedcoat (hull-less) are preferred by the industry as they eliminate the need for [...] Read more.
Pumpkin (Cucurbita pepo) seeds are nutritious and valued as a source of vegetable oil, protein, healthy fatty acids, and minerals. Pumpkin seeds that are naturally devoid of the seedcoat (hull-less) are preferred by the industry as they eliminate the need for de-hulling prior to use. A single recessive gene, designated as n or h, controls the hull-less seed trait in pumpkin. Visual selection for the trait is easy, however, it is resource intensive when applied to large breeding populations. High throughput genotyping assays can aid in the identification of suitable individuals in segregating populations through marker-assisted selection. In the current study, the QTL-seq approach was used to identify genetic loci, SNP markers and candidate genes associated with the hull-less trait in a segregating F2 population (n = 143) derived from a cross between Kakai (hull-less) × Table Gold Acorn (hulled). The segregation of the hull-less trait in the F2 population fit a 3:1 ratio (p < 0.05). QTL-seq analysis detected a single QTL on chromosome 12 (Qtlhull-less-C12) which was significantly associated with the hull-less trait in C. pepo. Twenty-eight SNPs were genotyped in the population, two among which (Ch12_3412046 and Ch12_3417142) were significantly associated (p < 0.05) with the hull-less trait in cultivars and accessions of diverse genetic background. Several candidate genes fall within the Qtlhull-less-C12 interval, among them is the No Apical meristem (NAC) domain-containing protein and a Fiber Protein fb11 gene involved in lignin accumulation and cell wall deposition across plant species, respectively. The findings of this study will facilitate the marker-assisted selection for the hull-less seed trait in pumpkin and further our understanding of the functional mechanisms underlying the trait across cucurbit crops. Full article
(This article belongs to the Special Issue Plant Molecular Breeding)
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14 pages, 1946 KiB  
Article
Response of Tomato (Solanum lycopersicum L.) Genotypes to Heat Stress Using Morphological and Expression Study
by Abdulhakim A. Aldubai, Abdullah A. Alsadon, Hussein H. Migdadi, Salem S. Alghamdi, Sulieman A. Al-Faifi and Muhammad Afzal
Plants 2022, 11(5), 615; https://doi.org/10.3390/plants11050615 - 24 Feb 2022
Cited by 12 | Viewed by 2584
Abstract
Due to unfavorable environmental conditions, heat stress is one of the significant production restrictions for the tomato (Solanum lycopersicum L.) crop. The tomato crop is considered an important vegetable crop globally and represents a model plant for fruit development research. The heat [...] Read more.
Due to unfavorable environmental conditions, heat stress is one of the significant production restrictions for the tomato (Solanum lycopersicum L.) crop. The tomato crop is considered an important vegetable crop globally and represents a model plant for fruit development research. The heat shock factor (HSF) gene family contains plant-specific transcription factors (TFs) that are highly conserved and play a key role in plant high-temperature stress responses. The current study was designed to determine the relative response of heat stress under three different temperatures in the field condition to determine its relative heat tolerance. Furthermore, the study also characterized heat shock genes in eight tomato genotypes under different temperature regimes. The expressions of each gene were quantified using qPCR. The descriptive statistics results suggested a high range of diversity among the studied variables growing under three different temperatures. The qPCR study revealed that the SlyHSF genes play an important role in plant heat tolerance pathways. The expression patterns of HSF genes in tomatoes have been described in various tissues were determined at high temperature stress. The genes, SlyHSFs-1, SlyHSFs-2, SlyHSFs-8, SlyHSFs-9 recorded upregulation expression relative to SlyHSFs-3, SlyHSFs-5, SlyHSFs-10, and SlyHSFs-11. The genotypes, Strain B, Marmande VF, Pearson’s early, and Al-Qatif-365 recorded the tolerant tomato genotypes under high-temperature stress conditions relative to other genotypes. The heat map analysis also confirmed the upregulation and downregulation of heat shock factor genes among the tomato genotypes. These genotypes will be introduced in the breeding program to improve tomato responses to heat stress. Full article
(This article belongs to the Special Issue Plant Molecular Breeding)
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11 pages, 1856 KiB  
Article
TaGRF3-2A Improves Some Agronomically Valuable Traits in Semi-Dwarf Spring Triticale
by Mikhail Divashuk, Anastasiya Chernook, Aleksandra Kroupina, Milena Vukovic, Gennady Karlov, Aleksey Ermolaev, Sergey Shirnin, Sergey Avdeev, Vladimir Igonin, Vladimir Pylnev and Pavel Kroupin
Plants 2021, 10(10), 2012; https://doi.org/10.3390/plants10102012 - 25 Sep 2021
Cited by 1 | Viewed by 1717
Abstract
The breeding improvement of triticale is tightly associated with the introgression of dwarfing genes, in particular, gibberellin (GA)-insensitive Ddw1 from rye. Despite the increase in harvest index and resistance to lodging, this gene adversely affects grain weight and size. Growth regulation factor ( [...] Read more.
The breeding improvement of triticale is tightly associated with the introgression of dwarfing genes, in particular, gibberellin (GA)-insensitive Ddw1 from rye. Despite the increase in harvest index and resistance to lodging, this gene adversely affects grain weight and size. Growth regulation factor (GRF) genes are plant-specific transcription factors that play an important role in plant growth, including GA-induced stem elongation. This study presents the results of a two-year field experiment to assess the effect of alleles of the TaGRF3-2A gene in interaction with DDW1 on economically valuable traits of spring triticale plants grown in the Non-Chernozem zone. Our results show that, depending on the allelic state, the TaGRF3-2A gene in semi-dwarf spring triticale plants influences the thousand grain weight and the grain weight of the main spike in spring triticale, which makes it possible to use it to compensate for the negative effects of the dwarfing allele Ddw1. The identified allelic variants of the TaGRF3-2A gene can be included in marker-assisted breeding for triticale to improve traits. Full article
(This article belongs to the Special Issue Plant Molecular Breeding)
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10 pages, 924 KiB  
Technical Note
The Development of New Species-Specific Molecular Markers Based on 5S rDNA in Elaeagnus L. Species
by Oleg S. Alexandrov and Gennady I. Karlov
Plants 2021, 10(12), 2713; https://doi.org/10.3390/plants10122713 - 10 Dec 2021
Cited by 3 | Viewed by 2311
Abstract
The Elaeagnus L. species are trees and bushes that mainly grow in temperate zones of Western Europe; Minor, Central, and Southeast Asia; the Far East; and North America. Some species are used as fruit or ornamental plants and have economic value. Problems with [...] Read more.
The Elaeagnus L. species are trees and bushes that mainly grow in temperate zones of Western Europe; Minor, Central, and Southeast Asia; the Far East; and North America. Some species are used as fruit or ornamental plants and have economic value. Problems with the identification of species in the Elaeagnus genus by molecular genetical methods arise in the study of populations, systematics, breeding, and other areas of plant science and practice. Recently, the polymorphism of 5S ribosomal DNA non-transcribed spacers (5S rDNA NTSs) in Elaeagnaceae Adans. has been described. The results were used in our study as a basis for development of new species-specific molecular markers for some members of the Elaeagnus genus. The author’s method was applied for finding regions that were potentially applicable for species-specific primer design. As a result, some species-specific molecular markers were developed for Elaeagnus angustifolia L., E. commutata Bernh., E. pungens Thunb., and E. multiflora Thunb. These markers were tested in a range of samples and showed the presence of amplified fragments in lanes of the marked species only. Samples of other species showed no amplifications. Thus, the developed markers may be useful for the species identification of the studied Elaeagnus plants in botanical, dendrological, and genetic research (especially in a leafless period of year), as well as in breeding and hybridization experiments. Full article
(This article belongs to the Special Issue Plant Molecular Breeding)
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