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Selected Articles from the 6th International Scientific Conference “Plant Genetics,...
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Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021)

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 (31 October 2021) | Viewed by 41627

Special Issue Editors

Dr. Irina N. Leonova

E-Mail Website
Guest Editor
Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
Interests: cereals; alien introgressions; resistance genes; fungal diseases; marker-assisted selection; genome-wide association studies
Special Issues, Collections and Topics in MDPI journals
Dr. Yuri Shavrukov

E-Mail Website
Guest Editor
Adjunct Professor, College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA 5042, Australia
Interests: plant biology; genetics; molecular markers; gene study and genetic analysis; genetic transformation and gene editing; tolerance to abiotic stresses; application of molecular markers; molecular plant breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

On behalf of the Organizing Committee, we are pleased to announce this call for papers for a Special Issue consisting of papers selected from the 6th International Scientific Conference “PlantGen2021”, which will be held on 14–18 June 2021 at the Federal Research Center Institute of Cytology and Genetics SB RAS in Novosibirsk, Russia (https://conf.icgbio.ru/plantgen2021/en/). The Conference will present the results of the latest original research related to the topics: 1) genetics of development and stress tolerance; 2) evolutionary and functional genomics; 3) plant biotechnology in the post-genome era; 4) bioinformatics, plant systems biology and digital phenotyping; 5) industrial biotechnology.

Dr. Irina N. Leonova
Dr. Yuri Shavrukov
Guest Editors

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 plant breeding
  • gene editing in plants
  • gene mapping in plants
  • genome-wide association study
  • marker-assisted selection
  • next-generation sequencing
  • resistance of crop plants to biotic and abiotic stresses
  • biodiversity of plants
  • plant genetic resources for breeding
  • transcriptome analysis in crop plants
  • gene expression in plants
  • computer modeling
  • plant genomic databases
  • gene networks in plants

Published Papers (16 papers)

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Research

40 pages, 36344 KiB  
Article
Features of Chromosome Introgression from Gossypium barbadense L. into G. hirsutum L. during the Development of Alien Substitution Lines
by Marina Feliksovna Sanamyan, Shukhrat Umarovich Bobohujayev, Sharoffidin Sayfiddinovich Abdukarimov, Abdusalom Khasanboyevich Makamov and Olga Gennadevna Silkova
Plants 2022, 11(4), 542; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11040542 - 18 Feb 2022
Cited by 5 | Viewed by 2692
Abstract
The creation of G. barbadense L./G. hirsutum L. chromosome-substitution lines is an important method to transfer agronomically valuable traits from G. barbadense into G. hirsutum. In this study, 30 monosomic lines of G. hirsutum from the Cytogenetic Collection of Uzbekistan, created [...] Read more.
The creation of G. barbadense L./G. hirsutum L. chromosome-substitution lines is an important method to transfer agronomically valuable traits from G. barbadense into G. hirsutum. In this study, 30 monosomic lines of G. hirsutum from the Cytogenetic Collection of Uzbekistan, created in the genotypic background of line L-458, were used in crosses with the G. barbadense line Pima 3-79 to create substitution lines. In the course of this work, new monosomic lines were identified for chromosome 12 and monotelodisome 6 of the Atsubgenome and for chromosomes 17, 21, and 22 of the Dtsubgenome using chromosome-specific SSR markers and a well-defined tester set of cotton translocation lines (USA). Compared to those in the F1 hybrids, a strong decrease in the crossing and setting rates was found in the BC1F1 backcross lines, with the substitution of chromosomes 2, 4, 6, 7, and 12 of the Atsubgenome and 17, 18, 21, and 22 of the Dtsubgenome. The F1 and BC1F1 offspring from interspecific crosses differed in their transmission of univalents. Despite the regular pairing of chromosomes and the high meiotic index, interspecific aneuploid hybrids were characterized by a decrease in pollen fertility, which may indicate hidden structural variability in these genomes that did not affect meiotic division. The identification of chromosomes using chromosome-specific SSR markers in the early stages of plant development has greatly accelerated the detection of monosomic plants. The analysis of morphobiological traits revealed that monosomic F1 hybrids were more similar to the donor line, while BC1F1 hybrids were more similar to the recurrent parent but also showed previously undetected traits. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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13 pages, 1964 KiB  
Article
Identification of QTLs for Grain Protein Content in Russian Spring Wheat Varieties
by Irina N. Leonova, Antonina A. Kiseleva, Alina A. Berezhnaya, Anatoly I. Stasyuk, Ivan E. Likhenko and Elena A. Salina
Plants 2022, 11(3), 437; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11030437 - 05 Feb 2022
Cited by 9 | Viewed by 1935
Abstract
Most modern breeding programs aim to develop wheat (T. aestivum L.) varieties with a high grain protein content (GPC) due to its greater milling and cooking quality, and improved grain price. Here, we used a genome-wide association study (GWAS) to map single [...] Read more.
Most modern breeding programs aim to develop wheat (T. aestivum L.) varieties with a high grain protein content (GPC) due to its greater milling and cooking quality, and improved grain price. Here, we used a genome-wide association study (GWAS) to map single nucleotide polymorphisms (SNPs) associated with GPC in 93 spring bread wheat varieties developed by eight Russian Breeding Centers. The varieties were evaluated for GPC, grain weight per spike (GWS), and thousand-kernel weight (TKW) at six environments, and genotyped with 9351 polymorphic SNPs and two SNPs associated with the NAM-A1 gene. GPC varied from 9.8 to 20.0%, depending on the genotype and environment. Nearly 52% of the genotypes had a GPC > 14.5%, which is the threshold value for entry into high-class wheat varieties. Broad-sense heritability for GPC was moderate (0.42), which is due to the significant effect of environment and genotype × environment interactions. GWAS performed on mean GPC evaluated across six environments identified eleven significant marker-trait associations, of which nine were physically mapped on chromosome 6A. Screening of wheat varieties for allelic variants of the NAM-A1 gene indicated that 60% of the varieties contained the NAM-A1c allele, followed by 33% for NAM-A1d, and 5% for NAM-A1a alleles. Varieties with the NAM-A1d allele showed significantly (p < 0.01) smaller GPC than those with NAM-A1c and NAM-A1a. However, no significant differences between NAM-A1 alleles were observed for both GWS and TKW. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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14 pages, 769 KiB  
Article
Identification of Quantitative Trait Loci for Leaf Rust and Stem Rust Seedling Resistance in Bread Wheat Using a Genome-Wide Association Study
by Alibek Zatybekov, Yuliya Genievskaya, Aralbek Rsaliyev, Akerke Maulenbay, Gulbahar Yskakova, Timur Savin, Yerlan Turuspekov and Saule Abugalieva
Plants 2022, 11(1), 74; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11010074 - 27 Dec 2021
Cited by 5 | Viewed by 2862
Abstract
In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high [...] Read more.
In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high productivity and LR and SR disease resistance, including using marker-assisted selection, is becoming an important priority in local breeding projects. Therefore, the search for key genetic factors controlling resistance in all plant stages, including the seedling stage, is of great significance. In this work, we applied a genome-wide association study (GWAS) approach using 212 local bread wheat accessions that were phenotyped for resistance to specific races of Puccinia triticina Eriks. (Pt) and Puccinia graminis f. sp. tritici (Pgt) at the seedling stages. The collection was genotyped using a 20 K Illumina iSelect SNP assay, and 11,150 polymorphic SNP markers were selected for the association mapping. Using a mixed linear model, we identified 11 quantitative trait loci (QTLs) for five out of six specific races of Pt and Pgt. The comparison of the results from this GWAS with those from previously published work showed that nine out of eleven QTLs for LR and SR resistance had been previously reported in a GWAS study at the adult plant stages of wheat growth. Therefore, it was assumed that these nine common identified QTLs were effective for all-stage resistance to LR and SR, and the two other QTLs appear to be novel QTLs. In addition, five out of these nine QTLs that had been identified earlier were found to be associated with yield components, suggesting that they may directly influence the field performance of bread wheat. The identified QTLs, including novel QTLs found in this study, may play an essential role in the breeding process for improving wheat resistance to LR and SR. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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12 pages, 4163 KiB  
Article
Genetic Features of Triticale–Wheat Hybrids with Vaviloid-Type Spike Branching
by Irina G. Adonina, Andrey B. Shcherban, Maremyana V. Zorina, Sabina P. Mehdiyeva, Ekaterina M. Timonova and Elena A. Salina
Plants 2022, 11(1), 58; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11010058 - 25 Dec 2021
Cited by 3 | Viewed by 2397
Abstract
Vaviloid spike branching, also called sham ramification, is a typical trait of Triticum vavilovii Jakubz. and is characterized by a lengthening of the spikelet axis. In this article, we present the results of a study of three triticale–wheat hybrid lines with differences in [...] Read more.
Vaviloid spike branching, also called sham ramification, is a typical trait of Triticum vavilovii Jakubz. and is characterized by a lengthening of the spikelet axis. In this article, we present the results of a study of three triticale–wheat hybrid lines with differences in terms of the manifestation of the vaviloid spike branching. Lines were obtained by crossing triticale with hexaploid wheat, T. aestivum var. velutinum. The parental triticale is a hybrid of synthetic wheat (T. durum × Ae. tauschii var. meyrei) with rye, S. cereale ssp. segetale. Line 857 has a karyotype corresponding to hexaploid wheat and has a spike morphology closest to normal, whereas Lines 808/1 and 844/4 are characterized by the greatest manifestation of vaviloid spike branching. In Lines 808/1 and 844/4, we found the substitution 2RL(2DL). The karyotypes of the latter lines differ in that a pair of telocentric chromosomes 2DS is detected in Line 808/1, and these telocentrics are fused into one unpaired chromosome in Line 844/4. Using molecular genetic analysis, we found a deletion of the wheat domestication gene Q located on 5AL in the three studied hybrid lines. The deletion is local since an analysis of the adjacent gene B1 showed the presence of this gene. We assume that the manifestation of vaviloid spike branching in two lines (808/1 and 844/4) is associated with a disturbance in the joint action of genes Q and AP2L2-2D, which is another important gene that determines spike morphology and is located on 2DL. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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20 pages, 4292 KiB  
Article
Relationship between the Characteristics of Bread Wheat Grains, Storage Time and Germination
by Dmitry A. Afonnikov, Evgenii G. Komyshev, Vadim M. Efimov, Mikhail A. Genaev, Vasily S. Koval, Peter U. Gierke and Andreas Börner
Plants 2022, 11(1), 35; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11010035 - 23 Dec 2021
Cited by 3 | Viewed by 2978
Abstract
Seed storage is important to farmers, breeders and for germplasm preservation. During storage, seeds accumulate damage at the structural and metabolic level, which disrupt their function and reduce resistance to adverse external conditions. In this regard, issues related to seed aging prove to [...] Read more.
Seed storage is important to farmers, breeders and for germplasm preservation. During storage, seeds accumulate damage at the structural and metabolic level, which disrupt their function and reduce resistance to adverse external conditions. In this regard, issues related to seed aging prove to be relevant for maintaining the viability of genetic collections. We analyzed morphological characteristics of grains and their coat color for 44 recombinant inbred lines (RILs) of bread wheat grown in four different seasons, 2003, 2004, 2009 and 2014. Our investigations were performed in 2020. For 19 RILs from the same seasons germination was evaluated. Our results demonstrate that genotype significantly affects the variability of all seed traits, and the year of harvesting affects about 80% of them (including all the traits of shape and size). To identify the trend between changes in grain characteristics and harvesting year, we estimated correlation coefficients between them. No significant trend was detected for the grain shape/size traits, while 90% of the color traits demonstrated such a trend. The most significant negative correlations were found between the harvesting year and the traits of grain redness: the greater the storage time, the more intensive is red color component for the grains. At the same time, it was shown that grains of longer storage time (earlier harvesting year) have lighter coat. Analysis of linear correlations between germination of wheat seeds of different genotypes and harvesting years and their seed traits revealed a negative linear relationship between the red component of coat color and germination: the redder the grains, the lower their germination rate. The results obtained demonstrate manifestations of metabolic changes in the coat of grains associated with storage time and their relationship with a decrease of seed viability. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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16 pages, 2575 KiB  
Article
Evolution of 14-3-3 Proteins in Angiosperm Plants: Recurring Gene Duplication and Loss
by Yulia V. Mikhaylova, Roman K. Puzanskiy and Maria F. Shishova
Plants 2021, 10(12), 2724; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10122724 - 11 Dec 2021
Cited by 8 | Viewed by 2688
Abstract
14-3-3 proteins are key regulatory factors in plants and are involved in a broad range of physiological processes. We addressed the evolutionary history of 14-3-3s from 46 angiosperm species, including basal angiosperm Amborella and major lineage of monocotyledons and eudicotyledons. Orthologs of Arabidopsis [...] Read more.
14-3-3 proteins are key regulatory factors in plants and are involved in a broad range of physiological processes. We addressed the evolutionary history of 14-3-3s from 46 angiosperm species, including basal angiosperm Amborella and major lineage of monocotyledons and eudicotyledons. Orthologs of Arabidopsis isoforms were detected. There were several rounds of duplication events in the evolutionary history of the 14-3-3 protein family in plants. At least four subfamilies (iota, epsilon, kappa, and psi) formed as a result of ancient duplication in a common ancestor of angiosperm plants. Recent duplication events followed by gene loss in plant lineage, among others Brassicaceae, Fabaceae, and Poaceae, further shaped the high diversity of 14-3-3 isoforms in plants. Coexpression data showed that 14-3-3 proteins formed different functional groups in different species. In some species, evolutionarily related groups of 14-3-3 proteins had coexpressed together under certain physiological conditions, whereas in other species, closely related isoforms expressed in the opposite manner. A possible explanation is that gene duplication and loss is accompanied by functional plasticity of 14-3-3 proteins. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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15 pages, 1691 KiB  
Article
The Effect of Daminozide, Dark/Light Schedule and Copper Sulphate in Tissue Culture of Triticum timopheevii
by Dmitry Miroshnichenko, Anna Klementyeva and Sergey Dolgov
Plants 2021, 10(12), 2620; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10122620 - 29 Nov 2021
Cited by 5 | Viewed by 2963
Abstract
Triticum timopheevii Zhuk. is a tetraploid wheat that is utilized worldwide as a valuable breeding source for wheat improvement. Gene-based biotechnologies can contribute to this field; however, T. timopheevii exhibits recalcitrance and albinism in tissue cultures, making this species of little use for [...] Read more.
Triticum timopheevii Zhuk. is a tetraploid wheat that is utilized worldwide as a valuable breeding source for wheat improvement. Gene-based biotechnologies can contribute to this field; however, T. timopheevii exhibits recalcitrance and albinism in tissue cultures, making this species of little use for manipulation through genetic engineering and genome editing. This study tested various approaches to increasing in vitro somatic embryogenesis and plant regeneration, while reducing the portion of albinos in cultures derived from immature embryos (IEs) of T. timopheevii. They included (i) adjusting the balance between 2,4-D and daminozide in callus induction medium; (ii) cultivation using various darkness/illumination schedules; and (iii) inclusion of additional concentrations of copper ions in the tissue culture medium. We achieved a 2.5-fold increase in somatic embryogenesis (up to 80%) when 50 mg L−1 daminozide was included in the callus induction medium together with 3 mg L−1 2,4-D. It was found that the dark cultivation for 20–30 days was superior in terms of achieving maximum culture efficiency; moreover, switching to light in under 2 weeks from culture initiation significantly increased the number of albino plants, suppressed somatic embryogenesis, and decreased the regeneration of green plants. Media containing higher levels of copper ions did not have a positive effect on the regeneration of green plants; contrarily, the elevated concentrations caused albinism in plantlets. The results and relevant conclusions of the present study might be valuable for establishing an improved protocol for the regeneration of green plants in tissue cultures of T. timopheevii. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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13 pages, 1276 KiB  
Article
Genetic Diversity of Peach Cultivars from the Collection of the Nikita Botanical Garden Based on SSR Markers
by Aya A. Trifonova, Ksenia V. Boris, Natalia V. Mesyats, Valentina A. Tsiupka, Anatoly V. Smykov and Irina V. Mitrofanova
Plants 2021, 10(12), 2609; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10122609 - 28 Nov 2021
Cited by 6 | Viewed by 2076
Abstract
The Nikita Botanical Garden (NBG) has a unique Prunus L. collection (peach, apricot, plum, cherry) comprising more than 3000 accessions. NBG is also a breeding center for stone fruits, including peach (Prunus persica (L.) Batsch). In the present study a set of [...] Read more.
The Nikita Botanical Garden (NBG) has a unique Prunus L. collection (peach, apricot, plum, cherry) comprising more than 3000 accessions. NBG is also a breeding center for stone fruits, including peach (Prunus persica (L.) Batsch). In the present study a set of 85 peach cultivars bred in NBG, Europe, and North America was analyzed using 12 SSR markers to assess their genetic diversity and relatedness. The detected polymorphism level was comparable to the previous estimates of genetic variability in peach cultivars. The average number of alleles per locus was 5.67, PIC value averaged 0.49, expected, and observed heterozygosity averaged 0.52 and 0.31, respectively. Among the detected alleles, 19 (27.94%) were rare and 12 (17.65%) were unique. All studied accessions except two could be identified with the used marker set. Cluster analysis revealed some groups according to the cultivars’ pedigrees. No clear differentiation of the studied sample according to geographic origin or fruit characteristics of peach cultivars was revealed. The results provide valuable information for identification and rational management of the material preserved in the NBG peach collection. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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18 pages, 332 KiB  
Article
Identification of Stripe Rust Resistance Genes in Common Wheat Cultivars and Breeding Lines from Kazakhstan
by Alma Kokhmetova, Aralbek Rsaliyev, Angelina Malysheva, Makpal Atishova, Madina Kumarbayeva and Zhenis Keishilov
Plants 2021, 10(11), 2303; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10112303 - 26 Oct 2021
Cited by 20 | Viewed by 2782
Abstract
Stripe (yellow) rust, caused by Puccinia striiformis f.sp. tritici (Pst), is a fungal disease that presents one of the most serious threats to the wheat crops, causing severe yield losses worldwide, including Kazakhstan. The objectives of this study were to: (1) [...] Read more.
Stripe (yellow) rust, caused by Puccinia striiformis f.sp. tritici (Pst), is a fungal disease that presents one of the most serious threats to the wheat crops, causing severe yield losses worldwide, including Kazakhstan. The objectives of this study were to: (1) evaluate a winter wheat collection for stripe rust resistance during an adult plant growth stage, (2) identify the presence of selected Yr genes using linked molecular markers in wheat germplasm, (3) identify potentially useful resistant wheat genotypes among leading cultivars and advanced breeding lines. This study evaluated 70 winter wheat genotypes for stripe rust resistance. According to the field reactions, 42 entries (60%) had R or MR reactions including 27 breeding lines (38.6%) and 15 (21.4%) cultivars. Twenty-eight breeding lines/cultivars (40.0%) were susceptible in both years. According to the average coefficient of infection value (ACI) six genotypes were regarded as possessing high level of adult plant resistance. Cultivars/lines carrying Yr10 alone or in combination with other Yr resistance genes provided resistance to stripe rust. Eleven breeding lines showed <5% disease severity in both years. Linked marker analysis revealed the presence of several gene and gene complexes (Yr5, Yr10, Yr15, Yr17/Lr37/Sr38 and Yr18/Lr34). Among a collection of 70 winter wheat breeding lines and cultivars produced in Kazakhstan three stripe rust resistance genes (Yr10, Yr5 and Yr15) demonstrated high frequency occurrence (31.4%, 14.0% and 7.0%, respectively). The most abundant was gene Yr10 identified in 22 genotypes. It was followed by the Yr5 gene, which conferred resistance in 14 lines (20%) and Yr18 gene-11 lines (15.7%). Yr15 was identified in 7 genotypes. Yr17/Lr37/Sr38 gene complex was found in 2 entries. Among 70 evaluated germplasm sources, 42 disease resistant entries are potentially useful resistant wheat genotypes. These carriers of different Yr genes can be used directly in breeding programs to improve stripe rust resistance of winter wheat. Marker-assisted selection can be efficiently applied to develop wheat cultivars with effective gene combinations that would directly assist in developing durable resistance in Kazakhstan. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
12 pages, 2714 KiB  
Article
Targeting the B1 Gene and Analysis of Its Polymorphism Associated with Awned/Awnless Trait in Russian Germplasm Collections of Common Wheat
by Andrey B. Shcherban, Diana D. Kuvaeva, Olga P. Mitrofanova, Svetlana E. Khverenets, Alexander I. Pryanishnikov and Elena A. Salina
Plants 2021, 10(11), 2285; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10112285 - 25 Oct 2021
Cited by 2 | Viewed by 1496
Abstract
The presence of awns on the ear is associated with a number of important plant properties, such as drought resistance, quality of the grain mass during processing, etc. The main manifestations of this trait are controlled by the B1 gene, which has recently [...] Read more.
The presence of awns on the ear is associated with a number of important plant properties, such as drought resistance, quality of the grain mass during processing, etc. The main manifestations of this trait are controlled by the B1 gene, which has recently been identified and encodes the C2H2 zinc finger transcription factor. Based on the previously identified SNPs in the promoter region of this gene, we constructed markers for dominant and recessive alleles which determine awnless and awned phenotypes, respectively. The markers were successful for use in targeting the respective alleles of the B1 gene in 176 varieties of common wheat, accessions of T. spelta L., as well as on F2/F3 hybrids from crosses between awned and awnless forms of T. aestivum. We first identified a new allele, b1mite, which has both an insert of a miniature Stowaway-like transposon, 261 bp in length, and 33 novel SNPs in the promoter region. Despite these changes, this allele had no effect on the awned phenotype. The possible mechanisms of the influence of the analyzed gene on phenotype are discussed. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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14 pages, 1081 KiB  
Article
Development of SNP Set for the Marker-Assisted Selection of Guar (Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly
by Elizaveta Grigoreva, Yury Barbitoff, Anton Changalidi, Dmitry Karzhaev, Vladimir Volkov, Veronika Shadrina, Elizaveta Safronycheva, Cécile Ben, Laurent Gentzbittel and Elena Potokina
Plants 2021, 10(10), 2063; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10102063 - 30 Sep 2021
Cited by 3 | Viewed by 2291
Abstract
Guar gum, a polysaccharide derived from guar seeds, is widely used in a variety of industrial applications, including oil and gas production. Although guar is mostly propagated in India, interest in guar as a new industrial legume crop is increasing worldwide, demanding the [...] Read more.
Guar gum, a polysaccharide derived from guar seeds, is widely used in a variety of industrial applications, including oil and gas production. Although guar is mostly propagated in India, interest in guar as a new industrial legume crop is increasing worldwide, demanding the development of effective tools for marker-assisted selection. In this paper, we report a wide-ranging set of 4907 common SNPs and 327 InDels generated from RADseq genotyping data of 166 guar plants of different geographical origin. A custom guar reference genome was assembled and used for variant calling. A consensus set of variants was built using three bioinformatic pipelines for short variant discovery. The developed molecular markers were used for genome-wide association study, resulting in the discovery of six markers linked to the variation of an important agronomic trait—percentage of pods matured to the harvest date under long light day conditions. One of the associated variants was found inside the putative transcript sequence homologous to an ABC transporter in Arabidopsis, which has been shown to play an important role in D-myo-inositol phosphates metabolism. Earlier, we suggested that genes involved in myo-inositol phosphate metabolism have significant impact on the early flowering of guar plants. Hence, we believe that the developed SNP set allows for the identification of confident molecular markers of important agrobiological traits. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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16 pages, 3875 KiB  
Article
Introgression of Bacterial Blight Resistance Genes in the Rice Cultivar Ciherang: Response against Xanthomonas oryzae pv. oryzae in the F6 Generation
by Priya Lal Biswas, Ujjal Kumar Nath, Sharmistha Ghosal, Gayatri Goswami, Md. Shalim Uddin, Omar M. Ali, Arafat Abdel Hamed Abdel Latef, Alison M. Laing, Yong-Ming Gao and Akbar Hossain
Plants 2021, 10(10), 2048; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10102048 - 29 Sep 2021
Cited by 4 | Viewed by 2137
Abstract
Bacterial blight (BB) is caused by Xanthomonas oryzae pv. oryzae and is one of the most important diseases in rice. It results in significantly reduced productivity throughout all rice-growing regions of the world. Four BB resistance genes have been reported; however, introgression of [...] Read more.
Bacterial blight (BB) is caused by Xanthomonas oryzae pv. oryzae and is one of the most important diseases in rice. It results in significantly reduced productivity throughout all rice-growing regions of the world. Four BB resistance genes have been reported; however, introgression of a single gene into rice has not been able to sufficiently protect rice against BB infection. Pyramiding of effective BB resistance genes (i.e., Xa genes) into background varieties is a potential approach to controlling BB infection. In this study, combinations of four BB resistance genes, Xa4, xa5, xa13, and Xa21, were pyramided into populations. The populations were derived from crossing Ciherang (a widespread Indonesian rice variety) with IRBB60 (resistance to BB). Promising recombinants from the F6 generation were identified by scoring the phenotype against three virulent bacterial strains, C5, P6, and V, which cause widespread BB infection in most rice-growing countries. Pyramiding of genes for BB resistance in 265 recombinant introgressed lines (RILs) were confirmed through marker-assisted selection (MAS) of the F5 and F6 generations using gene-specific primers. Of these 265 RILs, 11, 34 and 45 lines had four, three, or two BB resistance genes, respectively. The RILs had pyramiding of two or three resistance genes, with the Xa4 resistance gene showing broad spectrum resistance against Xoo races with higher agronomic performance compared to their donor and recipients parents. The developed BB-resistant RILs have high yield potential to be further developed for cultivation or as sources of BB resistance donor material for varietal improvement in other rice lines. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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18 pages, 3671 KiB  
Article
Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data
by Shyryn Almerekova, Yuliya Genievskaya, Saule Abugalieva, Kazuhiro Sato and Yerlan Turuspekov
Plants 2021, 10(10), 2025; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10102025 - 27 Sep 2021
Cited by 10 | Viewed by 2397
Abstract
The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the [...] Read more.
The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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16 pages, 33604 KiB  
Article
Genetic Diversity of Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici in Yunnan, China
by Md. Ashraful Alam, Haoxing Li, Akbar Hossain and Mingju Li
Plants 2021, 10(8), 1735; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10081735 - 23 Aug 2021
Cited by 3 | Viewed by 3138
Abstract
The stripe rust of wheat is one of the devastating diseases in China, which is caused by fungus Puccinia striiformis f. sp. tritici (Pst). The Yunnan Province of China is located in the south-western part, and holds distinctive geographical and climate [...] Read more.
The stripe rust of wheat is one of the devastating diseases in China, which is caused by fungus Puccinia striiformis f. sp. tritici (Pst). The Yunnan Province of China is located in the south-western part, and holds distinctive geographical and climate features, while wheat growth and epidemics of stripe rust fungus are fully dissimilar to the major wheat-growing regions of China. It is important to discover its origin and migration to control the disease. In this study, 352 isolates were sampled from 11 spots of the Yunnan Province during the wheat growing season from 2004 to 2015 and analyzed with SNPs markers of housekeeping genes. Results revealed that 220 haplotypes were inferred from the concatenating sequences; among them, 5 haplotypes (viz., ‘H86′, ‘H18′, ‘H8′, ‘H15′ and ‘H23′) comprised over 24.5% of the population. The haplotype diversity, nucleotide diversity, mutation rate and recombination events were 0.992, 6.04 × 10−3, 4.46 × 10−3 and 18.0 respectively, which revealed the genetic diversity of Pst populations among all locations. Four grouping methods, such as UPGMA-tree, PCA, PLS-DA and STRUCTURE, were employed for the categorization of the Pst populations conferring to their races and topographical localities. All methods were found significant and mostly had co-linear relations with each other. The analysis of molecular variance (AMOVA) conferred total variation was 9.09%, and 86.20% of variation was within the populations. The current study also exposed a comparatively high genetic multiplicity within the population, while low genetic inconsistency among the populations. Furthermore, the molecular records on the gene pole (Nm = 18.45) established that the migration of the stripe rust pathogen occurred among all locations in Yunnan province. The ancestral haplotype was detected in Yuxi. Based on the trajectories of upper airflow and genetic diversity of Pst populations in different locations, it is suggested that the locations Dehong, Dali, Lincang and Baoshan are probably a major source of Pst in Yunnan. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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13 pages, 1699 KiB  
Article
The Effect of Chromosome Arm 1BS on the Fertility of Alloplasmic Recombinant Lines in Bread Wheat with the Hordeum vulgare Cytoplasm
by Nataliya V. Trubacheeva, Mikhail G. Divashuk, Anastasiya G. Chernook, Igor A. Belan, Ludmila P. Rosseeva and Lidiya A. Pershina
Plants 2021, 10(6), 1120; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10061120 - 31 May 2021
Cited by 2 | Viewed by 2096
Abstract
The genetic mechanisms of fertility restoration in alloplasmic bread wheat with the barley cytoplasm are poorly explored. The effect of the 1BS chromosome arm on the fertility of bread wheat with the H. vulgare cytoplasm was studied depending on the incompleteness/completeness of the [...] Read more.
The genetic mechanisms of fertility restoration in alloplasmic bread wheat with the barley cytoplasm are poorly explored. The effect of the 1BS chromosome arm on the fertility of bread wheat with the H. vulgare cytoplasm was studied depending on the incompleteness/completeness of the cytonuclear compatibility. (i) Three self-fertile (SF) lines and one partially fertile (PF) line with an incomplete cytonuclear compatibility and (ii) four self-fertile (SF) lines with a complete cytonuclear compatibility were studied. For the lines in group (i), the heteroplasmy (simultaneous presence of barley and wheat copies) of the 18S/5S mitochondrial (mt) repeat was revealed as well as the barley-type homoplasmy of chloroplast simple sequence repeats (cpSSRs). In the lines in group (ii), the 18S/5S mt repeat and cpSSRs were found in the wheat-type homoplasmic state. In all of the lines, the 1BS chromosome arm was substituted for the 1RS arm. The F1 plants of SF(i)-1BS × 1RS hybrids were fertile. The results of a segregation analysis in the F2 plants of SF(i)-1BS × 1RS showed that 1BS carries a single dominant fertility restorer gene (Rf) of bread wheat with the H. vulgare cytoplasm. All of the F1 plants of PF(i)-1BS × 1RS hybrids were sterile. A single dose of this restorer gene is not sufficient to restore fertility in this alloplasmic PF(i) line. All of the F1 and F2 plants of SF(ii)-1BS × 1RS hybrids were self-fertile. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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24 pages, 1256 KiB  
Article
Regions of Chromosome 2A of Bread Wheat (Triticum aestivum L.) Associated with Variation in Physiological and Agronomical Traits under Contrasting Water Regimes
by Tatyana A. Pshenichnikova, Svetlana V. Osipova, Olga G. Smirnova, Irina N. Leonova, Marina D. Permyakova, Alexey V. Permyakov, Elena G. Rudikovskaya, Dmitrii K. Konstantinov, Vasiliy V. Verkhoturov, Ulrike Lohwasser and Andreas Börner
Plants 2021, 10(5), 1023; https://0-doi-org.brum.beds.ac.uk/10.3390/plants10051023 - 20 May 2021
Cited by 7 | Viewed by 2593
Abstract
Understanding the genetic architecture of drought tolerance is of great importance for overcoming the negative impact of drought on wheat yield. Earlier, we discovered the critical role of chromosome 2A for the drought-tolerant status of wheat spring cultivar Saratovskaya 29. A set of [...] Read more.
Understanding the genetic architecture of drought tolerance is of great importance for overcoming the negative impact of drought on wheat yield. Earlier, we discovered the critical role of chromosome 2A for the drought-tolerant status of wheat spring cultivar Saratovskaya 29. A set of 92 single-chromosome recombinant double haploid (SCRDH) lines were obtained in the genetic background of Saratovskaya 29. The lines carry fragments of chromosome 2A from the drought-sensitive cultivar Yanetzkis Probat. The SCRDH lines were used to identify regions on chromosome 2A associated with the manifestation of physiological and agronomical traits under distinct water supply, and to identify candidate genes that may be associated with adaptive gene networks in wheat. Genotyping was done with Illumina Infinium 15k wheat array using 590 SNP markers with 146 markers being polymorphic. In four identified regions of chromosome 2A, 53 out of 58 QTLs associated with physiological and agronomic traits under contrasting water supply were mapped. Thirty-nine candidate genes were identified, of which 18 were transcription factors. The region 73.8–78.1 cM included the largest number of QTLs and candidate genes. The variation in SNPs associated with agronomical and physiological traits revealed among the SCRDH lines may provide useful information for drought related marker-assisted breeding. Full article
(This article belongs to the Special Issue Selected Articles from the 6th International Scientific Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology” (PlantGen2021))
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