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Genetics and Genomics of Crop Breeding and Improvement
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Genetics and Genomics of Crop Breeding and Improvement

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 September 2024) | Viewed by 9497

Special Issue Editor

Dr. Margarita A. Vishnyakova

E-Mail Website
Guest Editor
Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
Interests: plant genetic resources; breeding; wild relatives; germplasm collections; pre-breeding; genebanks; phenotyping; genotyping
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genetics is the theoretical foundation for plant breeding. The existing genotypic variability of traits and the expansion of their spectrum serve as a practical basis for breeding. Knowledge about the structural organization of genomes became attainable through the development of molecular genetics and genomics, which provided new breeding tools and outlined the prospects for breeding a new generation. With the advent of molecular genetic markers, genotypic variability began to be assessed at the DNA level. Genetic manipulations to improve desired traits in plants were also performed on DNA molecules. The development of molecular genetic markers for the analysis of genetic resources and the emergence of full-scale molecular genetic maps of molecular markers to identify loci-controling key agronomic traits marked the development of marker-assisted selection. Genomic breeding using information about the complete genomes of agricultural plants, reveals the relationship between variants of genomic loci and the degree of manifestation of economically significant traits. Next-generation sequencing (NGS) technologies make a huge array of genetic information available. The analysis of this information, with the help of bioinformatics, makes it possible to detect new genes and regulatory sequences. To date, a huge amount of genomic and transcriptomic data has been accumulated on the structural and functional organization of molecular genetic systems and processes controlling the formation of phenotypic characteristics of agricultural plants. This Special Issue makes it possible to group original research papers and reviews on genetic, molecular genetic, genomic and transcriptomic studies of important agronomic traits of agricultural plants, the search for target genes for improving signs of productivity, adaptability and quality and contributing to the acceleration of the breeding of new varieties that meet the requirements of the day.

Dr. Margarita A. Vishnyakova
Guest Editor

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Keywords

  • molecular breeding
  • MAS
  • genetic resources
  • transcriptomic
  • agronomic traits
  • target genes

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Published Papers (6 papers)

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Research

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27 pages, 6716 KiB  
Article
Comparative Metabolome and Transcriptome Analysis of Rapeseed (Brassica napus L.) Cotyledons in Response to Cold Stress
by Xinhong Liu, Tonghua Wang, Ying Ruan, Xiang Xie, Chengfang Tan, Yiming Guo, Bao Li, Liang Qu, Lichao Deng, Mei Li and Chunlin Liu
Plants 2024, 13(16), 2212; https://doi.org/10.3390/plants13162212 - 9 Aug 2024
Viewed by 997
Abstract
Cold stress affects the seed germination and early growth of winter rapeseed, leading to yield losses. We employed transmission electron microscopy, physiological analyses, metabolome profiling, and transcriptome sequencing to understand the effect of cold stress (0 °C, LW) on the cotyledons of cold-tolerant [...] Read more.
Cold stress affects the seed germination and early growth of winter rapeseed, leading to yield losses. We employed transmission electron microscopy, physiological analyses, metabolome profiling, and transcriptome sequencing to understand the effect of cold stress (0 °C, LW) on the cotyledons of cold-tolerant (GX74) and -sensitive (XY15) rapeseeds. The mesophyll cells in cold-treated XY15 were severely damaged compared to slightly damaged cells in GX74. The fructose, glucose, malondialdehyde, and proline contents increased after cold stress in both genotypes; however, GX74 had significantly higher content than XY15. The pyruvic acid content increased after cold stress in GX74, but decreased in XY15. Metabolome analysis detected 590 compounds, of which 32 and 74 were differentially accumulated in GX74 (CK vs. cold stress) and XY15 (CK vs. cold stressed). Arachidonic acid and magnoflorine were the most up-accumulated metabolites in GX74 subjected to cold stress compared to CK. There were 461 and 1481 differentially expressed genes (DEGs) specific to XY15 and GX74 rapeseeds, respectively. Generally, the commonly expressed genes had higher expressions in GX74 compared to XY15 in CK and cold stress conditions. The expression changes in DEGs related to photosynthesis-antenna proteins, chlorophyll biosynthesis, and sugar biosynthesis-related pathways were consistent with the fructose and glucose levels in cotyledons. Compared to XY15, GX74 showed upregulation of a higher number of genes/transcripts related to arachidonic acid, pyruvic acid, arginine and proline biosynthesis, cell wall changes, reactive oxygen species scavenging, cold-responsive pathways, and phytohormone-related pathways. Taken together, our results provide a detailed overview of the cold stress responses in rapeseed cotyledons. Full article
(This article belongs to the Special Issue Genetics and Genomics of Crop Breeding and Improvement)
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14 pages, 1611 KiB  
Article
Newly Developed Restorer Lines of Sorghum [Sorghum bicolor (L.) Moench] Resistant to Greenbug
by Evgeny E. Radchenko, Irina N. Anisimova, Maria K. Ryazanova, Ilya A. Kibkalo and Natalia V. Alpatieva
Plants 2024, 13(3), 425; https://doi.org/10.3390/plants13030425 - 31 Jan 2024
Viewed by 1609
Abstract
Eight lines of grain sorghum [Sorghum bicolor (L.) Moench], which can be used as a promising source material in heterotic hybrid breeding as pollen fertility restorers and donors of resistance to the greenbug (Schizaphis graminum Rondani), are characterized. The new restorer [...] Read more.
Eight lines of grain sorghum [Sorghum bicolor (L.) Moench], which can be used as a promising source material in heterotic hybrid breeding as pollen fertility restorers and donors of resistance to the greenbug (Schizaphis graminum Rondani), are characterized. The new restorer lines (R-lines) were developed by crossing the maternal sterile line Nizkorosloe 81s (CMS A1) with two lines selected from the grain sorghum collection accessions VIR-928 and VIR-929 as the paternal forms. The R-lines were genotyped using PCR markers, and also characterized by height, duration of the seedling–flowering period, and some of the technological properties of flour. With the use of microsatellite markers linked to the Rf genes and by hybridological analysis, it was shown that the new lines carry the dominant allele of the gene Rf2. The PCoA analysis demonstrated clear differences of each R-line from the parents. The genotypes of the new lines and their parental forms for the Rf2 locus were confirmed by applying three allele-specific codominant CAPS markers which detected SNPs in the candidate Rf2 gene. All new lines were highly fertile, as demonstrated by cytological analysis of acetocarmine-stained pollen preparations. A high resistance to the greenbug was demonstrated for each new R-line both in the laboratory and field conditions against a severe aphid infestation. Grain quality parameters such as protein content and dough rheological properties varied widely and were quite satisfactory in some R-lines. Characteristics common to all eight sorghum lines studied, such as the ability to restore pollen fertility in the F1 generation, good pollen quality, greenbug resistance, early ripening, spreading panicle, and low stature, allow us to recommend them for producing commercial F1 hybrids with satisfactory grain quality for both fodder and food purposes. Full article
(This article belongs to the Special Issue Genetics and Genomics of Crop Breeding and Improvement)
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14 pages, 2428 KiB  
Article
Determination of the Allelic Composition of the sdw1/denso (HvGA20ox2), uzu1 (HvBRI1) and ari-e (HvDep1) Genes in Spring Barley Accessions from the VIR Collection
by Kseniia A. Lukina, Igor V. Porotnikov, Olga Yu. Antonova and Olga N. Kovaleva
Plants 2024, 13(3), 376; https://doi.org/10.3390/plants13030376 - 27 Jan 2024
Cited by 3 | Viewed by 1257
Abstract
The lodging of barley significantly limits its potential yield, leads to the deterioration of grain quality, and complicates mechanized harvesting. More than 30 dwarfness and semi-dwarfness genes and loci are known for barley, and their involvement in breeding can solve the problem of [...] Read more.
The lodging of barley significantly limits its potential yield, leads to the deterioration of grain quality, and complicates mechanized harvesting. More than 30 dwarfness and semi-dwarfness genes and loci are known for barley, and their involvement in breeding can solve the problem of lodging. The most common dwarfing alleles are of the genes sdw1/denso (HvGA20ox2), uzu1 (HvBRI1), and ari-e (HvDep1). The aim of this study was the design of dCAPS markers for the sdw1.c and ari-e.GP alleles and the molecular screening of barley accessions from the VIR collection for identifying these and other dwarfing alleles commonly used in breeding. Two dCAPS markers have been developed to identify the sdw1.c allele of the HvGA20ox2 gene and ari-e.GP of HvDep1. These dCAPS markers and two known from the literature CAPS and dCAPS markers of the alleles sdw1.a/sdw1.e, sdw1.c, sdw1.d, and uzu1.a were used in the molecular screening of 32 height-contrasting barley accessions. This made it possible to identify the accessions with alleles sdw1.a/sdw1.e, sdw1.c, and sdw1.d of the HvGA20ox2 gene, as well as accessions with a combination of sdw1.c and uzu1.a alleles of the genes HvGA20ox2 and HvBRI1. A comparison of the results of genotyping and phenotyping showed that the presence of dwarfing alleles in all genotypes determines high or medium lodging resistance regardless of the influence of weather conditions. Twelve accessions were found to contain the new allele sdw1.ins of the HvGA20ox2 gene, which differs from the known allele sdw1.c by a larger size of PCR products. It is characterized by the Thalos_2 transposon insertion; the subsequent GTTA insertion, common with the sdw1.c allele; and by a single-nucleotide G→A substitution at the 165 position. Full article
(This article belongs to the Special Issue Genetics and Genomics of Crop Breeding and Improvement)
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16 pages, 4866 KiB  
Article
Involvement of Abscisic Acid in Transition of Pea (Pisum sativum L.) Seeds from Germination to Post-Germination Stages
by Galina Smolikova, Ekaterina Krylova, Ivan Petřík, Polina Vilis, Aleksander Vikhorev, Ksenia Strygina, Miroslav Strnad, Andrej Frolov, Elena Khlestkina and Sergei Medvedev
Plants 2024, 13(2), 206; https://doi.org/10.3390/plants13020206 - 11 Jan 2024
Viewed by 1654
Abstract
The transition from seed to seedling represents a critical developmental step in the life cycle of higher plants, dramatically affecting plant ontogenesis and stress tolerance. The release from dormancy to acquiring germination ability is defined by a balance of phytohormones, with the substantial [...] Read more.
The transition from seed to seedling represents a critical developmental step in the life cycle of higher plants, dramatically affecting plant ontogenesis and stress tolerance. The release from dormancy to acquiring germination ability is defined by a balance of phytohormones, with the substantial contribution of abscisic acid (ABA), which inhibits germination. We studied the embryonic axis of Pisum sativum L. before and after radicle protrusion. Our previous work compared RNA sequencing-based transcriptomics in the embryonic axis isolated before and after radicle protrusion. The current study aims to analyze ABA-dependent gene regulation during the transition of the embryonic axis from the germination to post-germination stages. First, we determined the levels of abscisates (ABA, phaseic acid, dihydrophaseic acid, and neo-phaseic acid) using ultra-high-performance liquid chromatography–tandem mass spectrometry. Second, we made a detailed annotation of ABA-associated genes using RNA sequencing-based transcriptome profiling. Finally, we analyzed the DNA methylation patterns in the promoters of the PsABI3, PsABI4, and PsABI5 genes. We showed that changes in the abscisate profile are characterized by the accumulation of ABA catabolites, and the ABA-related gene profile is accompanied by the upregulation of genes controlling seedling development and the downregulation of genes controlling water deprivation. The expression of ABI3, ABI4, and ABI5, which encode crucial transcription factors during late maturation, was downregulated by more than 20-fold, and their promoters exhibited high levels of methylation already at the late germination stage. Thus, although ABA remains important, other regulators seems to be involved in the transition from seed to seedling. Full article
(This article belongs to the Special Issue Genetics and Genomics of Crop Breeding and Improvement)
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17 pages, 1832 KiB  
Article
Genetic and Morpho-Physiological Differences among Transgenic and No-Transgenic Cotton Cultivars
by Li Liu, Dan Wang, Jinping Hua, Xianhui Kong, Xuwen Wang, Juan Wang, Aijun Si, Fuxiang Zhao, Wenhao Liu, Yu Yu and Zhiwen Chen
Plants 2023, 12(19), 3437; https://doi.org/10.3390/plants12193437 - 29 Sep 2023
Cited by 2 | Viewed by 1353
Abstract
Three carbon-chain extension genes associated with fatty acid synthesis in upland cotton (Gossypium hirsutum), namely GhKAR, GhHAD, and GhENR, play important roles in oil accumulation in cotton seeds. In the present study, these three genes were cloned and [...] Read more.
Three carbon-chain extension genes associated with fatty acid synthesis in upland cotton (Gossypium hirsutum), namely GhKAR, GhHAD, and GhENR, play important roles in oil accumulation in cotton seeds. In the present study, these three genes were cloned and characterized. The expression patterns of GhKAR, GhHAD, and GhENR in the high seed oil content cultivars 10H1014 and 10H1041 differed somewhat compared with those of 10H1007 and 2074B with low seed oil content at different stages of seed development. GhKAR showed all three cultivars showed higher transcript levels than that of 2074B at 10-, 40-, and 45-days post anthesis (DPA). The expression pattern of GhHAD showed a lower transcript level than that of 2074B at both 10 and 30 DPA but a higher transcript level than that of 2074B at 40 DPA. GhENR showed a lower transcript level than that of 2074B at both 15 and 30 DPA. The highest transcript levels of GhKAR and GhENR were detected at 15 DPA in 10H1007, 10H1014, and 10H1041 compared with 2074B. From 5 to 45 DPA cotton seed, the oil content accumulated continuously in the developing seed. Oil accumulation reached a peak between 40 DPA and 45 DPA and slightly decreased in mature seed. In addition, GhKAR and GhENR showed different expression patterns in fiber and ovule development processes, in which they showed high expression levels at 20 DPA during the fiber elongation stage, but their expression level peaked at 15 DPA during ovule development processes. These two genes showed the lowest expression levels at the late seed maturation stage, while GhHAD showed a peak of 10 DPA in fiber development. Compared to 2074B, the oil contents of GhKAR and GhENR overexpression lines increased 1.05~1.08 folds. These results indicated that GhHAD, GhENR, and GhKAR were involved in both seed oil synthesis and fiber elongation with dual biological functions in cotton. Full article
(This article belongs to the Special Issue Genetics and Genomics of Crop Breeding and Improvement)
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Review

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24 pages, 442 KiB  
Review
Drought Stress Response in Guar (Cyamopsis tetragonoloba (L.) Taub): Physiological and Molecular Genetic Aspects
by Margarita A. Vishnyakova, Nadezhda Frolova and Andrej Frolov
Plants 2023, 12(23), 3955; https://doi.org/10.3390/plants12233955 - 24 Nov 2023
Cited by 2 | Viewed by 1707
Abstract
Drought has become one of the main factors of crop yield losses worldwide. This negatively affects the plant industry, decreasing crop yields, and it may result in resource deficits in different sectors of the world economy and its national branches. Guar (Cyamopsis [...] Read more.
Drought has become one of the main factors of crop yield losses worldwide. This negatively affects the plant industry, decreasing crop yields, and it may result in resource deficits in different sectors of the world economy and its national branches. Guar (Cyamopsis tetragonoloba (L.) Taub) represents one of the strategic crops, as its seeds are the source of guar gum, which is critically important in the modern oil industry. Although guar is generally known to be a drought-tolerant plant, it is known that soil dehydration negatively affects plant fitness and crop productivity. As guar genotypes are characterized by high variability in the manifestation of drought tolerance, screening genetic resources for this feature seems to be a promising strategy for accessing drought-resistant varieties. The discovery of drought-tolerant genotypes is mandatory to secure sustainable guar production. In this context, the identification of reliable chemical and molecular markers of drought tolerance (i.e., drought-responsive and/or drought-protective metabolites, proteins and transcripts) will provide the solid basis for marker-driven breeding of new tolerant varieties. Therefore, here we provide a comprehensive overview of the available literature data on guar drought stress response, its physiological and molecular genetic aspects, and considerations on the approaches to improve the quality of this crop. Full article
(This article belongs to the Special Issue Genetics and Genomics of Crop Breeding and Improvement)
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