Plants

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14 pages, 1478 KiB

Open AccessArticle

Investigation of Imidazolinone Herbicide Resistance Gene with KASP Markers for Japonica/Geng Rice Varieties in the Huanghuaihai Region of China

by Peng Liu, Wenjie Feng, Tao Wang, Huadong Zhang, Shuaige Mao, Hua Zhang, Wenchao Huang, Haifeng Liu, Shangzong Feng and Zhaohui Chu

Plants 2024, 13(8), 1097; https://doi.org/10.3390/plants13081097 - 14 Apr 2024

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Abstract

Rice is a staple food for more than half of the global population due to its food security and sustainable development. Weeds compete with crops for sunlight and indispensable nutrients, affecting the yield and quality of crops. Breeding herbicide-tolerant rice varieties paired with [...] Read more.

Rice is a staple food for more than half of the global population due to its food security and sustainable development. Weeds compete with crops for sunlight and indispensable nutrients, affecting the yield and quality of crops. Breeding herbicide-tolerant rice varieties paired with herbicide application is expected to help with weed control. In this study, 194 Japonica/Geng rice varieties or lines collected from the Huanghuaihai region of China were screened by Kompetitive Allele-Specific PCR (KASP) markers based on four mutation sites within OsALS1 (LOC_Os02g30630), which is the target of imidazolinone (IMI) herbicides. Only the OsALS1^627N haplotype was identified in 18 varieties, including the previously reported Jingeng818 (JG818), and its herbicide resistance was validated by treatment with three IMIs. To investigate the origin of the OsALS1^627N haplotype in the identified varieties, six codominant PCR-based markers tightly linked with OsALS1 were developed. PCR analysis revealed that the other 17 IMI-tolerant varieties were derived from JG818. We randomly selected three IMI-tolerant varieties for comparative whole-genome resequencing with known receptor parent varieties. Sequence alignment revealed that more loci from JG818 have been introduced into IMI-tolerant varieties. However, all three IMI-tolerant varieties carried clustered third type single nucleotide polymorphism (SNP) sites from unknown parents, indicating that these varieties were not directly derived from JG818, whereas those from different intermediate improved lines were crossed with JG818. Overall, we found that only OsALS1^627N from JG818 has been broadly introduced into the Huanghuaihai region of China. Additionally, the 17 identified IMI-tolerant varieties provide alternative opportunities for improving such varieties along with other good traits. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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31 pages, 5900 KiB

Open AccessArticle

Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives

by Yoko Hiraoka, Sergio Pietro Ferrante, Guohong Albert Wu, Claire T. Federici and Mikeal L. Roose

Plants 2024, 13(5), 691; https://doi.org/10.3390/plants13050691 - 29 Feb 2024

Viewed by 708

Abstract

Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We [...] Read more.

Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom^® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom^® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, “PolyHighResolution” (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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21 pages, 5536 KiB

Open AccessArticle

Physiological and Molecular Responses of Pyrus pyraster Seedlings to Salt Treatment Analyzed by miRNA and Cytochrome P450 Gene-Based Markers

by Viera Paganová, Marek Hus, Helena Lichtnerová, Jana Žiarovská, Dagmar Moravčíková, Matúš Kučka, Katarína Ražná and Aqsa Abbas

Plants 2024, 13(2), 261; https://doi.org/10.3390/plants13020261 - 16 Jan 2024

Viewed by 849

Abstract

Physiological and molecular marker-based changes were studied in the tissues of two-year-old Pyrus pyraster (L.) Burgsd. seedlings under salt treatment. For 60 days, 5 mL of 100 mM NaCl solution was applied to each plant per day to a cumulative volume of 300 [...] Read more.

Physiological and molecular marker-based changes were studied in the tissues of two-year-old Pyrus pyraster (L.) Burgsd. seedlings under salt treatment. For 60 days, 5 mL of 100 mM NaCl solution was applied to each plant per day to a cumulative volume of 300 mL in the substrate. In response to osmotic stress, the seedlings increased their water use efficiency (WUE) on day 20 of regular NaCl application and maintained a stable net photosynthetic rate (A_n) per unit area. Under conditions of increasing salinity, the young plants maintained a balanced water regime of the leaf tissues (Ψ_wl). The seedlings invested mass to their root growth (R/S), retained a substantial portion (72%) of Na⁺ ions in the roots, and protected their leaves against intoxication and damage. A significant decrease in the leaf gas exchange parameters (g_s, E, A_n) was manifested on day 60 of the experiment when the cumulative NaCl intake was 300 mL per plant. The variability in the reactions of the seedlings to salinity is related to the use of open-pollinated progeny (54 genotypes) in the experiment. Lus-miR168 showed tissue- and genotype-specific genome responses to the applied stress. Polymorphic miRNA-based loci were mostly detected in the root samples on the 20th and 35th days of the experiment. The cumulative effect of the salt treatment was reflected in the predominance of polymorphic loci in the leaves. We can confirm that miRNA-based markers represent a sensitive detection tool for plant stress response on an individual level. The screening and selection of the optimal type of miRNA for this type of research is crucial. The cytochrome P450-Based Analog (PBA) techniques were unable to detect polymorphism among the control and treated seedlings, except for the primer pair CYP2BF+R, where, in the roots of the stressed plant, insertions in the amplicons were obtained. The expression ratios of cytochrome P450 in the salt-stressed plants were higher in the roots in the case of 20/100 mL and in the leaves with higher doses. The observed physiological and molecular responses to salinity reflect the potential of P. pyraster seedlings in adaptation to osmotic and ionic stress. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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16 pages, 2640 KiB

Open AccessArticle

Genome Studies in Four Species of Calendula L. (Asteraceae) Using Satellite DNAs as Chromosome Markers

by Tatiana E. Samatadze, Olga Yu. Yurkevich, Firdaus M. Khazieva, Irina V. Basalaeva, Olga M. Savchenko, Svyatoslav A. Zoshchuk, Alexander I. Morozov, Alexandra V. Amosova and Olga V. Muravenko

Plants 2023, 12(23), 4056; https://doi.org/10.3390/plants12234056 - 02 Dec 2023

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Abstract

The taxonomically challenging genus Calendula L. (Asteraceae) includes lots of medicinal species characterized by their high morphological and karyological variability. For the first time, a repeatome analysis of a valuable medicinal plant Calendula officinalis L. was carried out using high-throughput genome DNA sequencing [...] Read more.

The taxonomically challenging genus Calendula L. (Asteraceae) includes lots of medicinal species characterized by their high morphological and karyological variability. For the first time, a repeatome analysis of a valuable medicinal plant Calendula officinalis L. was carried out using high-throughput genome DNA sequencing and RepeatExplorer/TAREAN pipelines. The FISH-based visualization of the 45S rDNA, 5S rDNA, and satellite DNAs of C. officinalis was performed on the chromosomes of C. officinalis, C. stellata Cav., C. tripterocarpa Rupr., and C. arvensis L. Three satellite DNAs were demonstrated to be new molecular chromosome markers to study the karyotype structure. Karyograms of the studied species were constructed, their ploidy status was specified, and their relationships were clarified. Our results showed that the C. officinalis karyotype differed from the karyotypes of the other three species, indicating its separate position in the Calendula phylogeny. However, the presence of common repeats revealed in the genomes of all the studied species could be related to their common origin. Our findings demonstrated that C. stellata contributed its genome to allotetraploid C. tripterocarpa, and C. arvensis is an allohexaploid hybrid between C. stellata and C. tripterocarpa. At the same time, further karyotype studies of various Calendula species are required to clarify the pathways of chromosomal reorganization that occurred during speciation. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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16 pages, 3450 KiB

Open AccessArticle

A Genome-Wide Association Study of Nigerien and Senegalese Sorghum Germplasm of Exserohilum turcicum, the Causal Agent of Leaf Blight

by Louis K. Prom, Jacob R. Botkin, Ezekiel J. S. Ahn, Mame Penda Sarr, Cyril Diatta, Coumba Fall and Clint W. Magill

Plants 2023, 12(23), 4010; https://doi.org/10.3390/plants12234010 - 29 Nov 2023

Viewed by 741

Abstract

In Senegal, sorghum ranks third after millet and maize among dryland cereal production and plays a critical role in the daily lives of millions of inhabitants. Yet, the crop’s productivity and profitability are hampered by biotic stresses, including Exserohilum turcicum, causing leaf [...] Read more.

In Senegal, sorghum ranks third after millet and maize among dryland cereal production and plays a critical role in the daily lives of millions of inhabitants. Yet, the crop’s productivity and profitability are hampered by biotic stresses, including Exserohilum turcicum, causing leaf blight. A total of 101 sorghum accessions collected from Niger and Senegal, SC748-5 and BTx623, were evaluated in three different environments (Kaymor, Kolda, and Ndiaganiao) in Senegal for their reactions against the leaf blight pathogen. The results showed that 11 out of the 101 accessions evaluated exhibited 100% incidence, and the overall mean incidence was 88.4%. Accession N15 had the lowest incidence of 50%. The overall mean severity was 31.6%, while accessions N15, N43, N38, N46, N30, N28, and N23 from Niger recorded the lowest severity levels, ranging from 15.5% to 25.5%. Accession N15 exhibited both low leaf blight incidence and severity, indicating that it may possess genes for resistance to E. turcicum. Also, the accessions evaluated in this study were sequenced. A GWAS identified six novel single-nucleotide polymorphisms (SNPs) associated with an average leaf blight incidence rate. The candidate genes were found in chromosomes 2, 3, 5, 8, and 9. Except for SNP locus S05_48064154, all five SNPs associated with the leaf blight incidence rate were associated with the plant defense and stress responses. In conclusion, the candidate genes identified could offer additional options for enhancing plant resistance against E. turcicum through plant breeding or gene editing. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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13 pages, 3486 KiB

Open AccessArticle

Species Delimitation and Genetic Relationship of Castanopsis hainanensis and Castanopsis wenchangensis (Fagaceae)

by Xing Chen, Yi Feng, Shuang Chen, Kai Yang, Xiangying Wen and Ye Sun

Plants 2023, 12(20), 3544; https://doi.org/10.3390/plants12203544 - 12 Oct 2023

Cited by 1 | Viewed by 827

Abstract

Castanopsis is one of the most common genus of trees in subtropical evergreen broad-leaved forests and tropical monsoon rainforests in China. Castanopsis hainanensis and Castanopsis wenchangensis are endemic to Hainan Island, but they were once confused as the same species due to very [...] Read more.

Castanopsis is one of the most common genus of trees in subtropical evergreen broad-leaved forests and tropical monsoon rainforests in China. Castanopsis hainanensis and Castanopsis wenchangensis are endemic to Hainan Island, but they were once confused as the same species due to very similar morphologies. In this study, nuclear microsatellite markers and chloroplast genomes were used to delimit C. hainanensis and C. wenchangensis. The allelic variations of nuclear microsatellites revealed that C. hainanensis and C. wenchangensis were highly genetically differentiated with very limited gene admixture. Both showed higher genetic diversity within populations and lower genetic diversity among populations, and neither had further population genetic structure. Furthermore, C. wenchangensis and C. hainanensis had very different chloroplast genomes. The independent genetic units, very limited gene admixture, different distribution ranges, and distinct habitats all suggest that C. wenchangensis and C. hainanensis are independent species, thus they should be treated as distinct conservation units. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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15 pages, 4637 KiB

Open AccessArticle

Effects of Climatic Change on Phylogeography and Ecological Niche of the Endemic Herb Elymus breviaristatus on the Qinghai-Tibet Plateau

by Jin Li, Changbing Zhang, Tserang Donko Mipam, Qingping Zhou and Shiyong Chen

Plants 2023, 12(18), 3326; https://doi.org/10.3390/plants12183326 - 20 Sep 2023

Cited by 1 | Viewed by 844

Abstract

Past climatic and topographic variations have created strong biogeographic barriers for alpine species and are key drivers of the distribution of genetic variation and population dynamics of species on the Qinghai-Tibet Plateau (QTP). Therefore, to better conserve and use germplasm resources, it is [...] Read more.

Past climatic and topographic variations have created strong biogeographic barriers for alpine species and are key drivers of the distribution of genetic variation and population dynamics of species on the Qinghai-Tibet Plateau (QTP). Therefore, to better conserve and use germplasm resources, it is crucial to understand the distribution and differentiation of genetic variation within species. Elymus breviaristatus, an ecologically important rare grass species with strong resistance, is restricted to a limited area of the QTP. In this study, we investigated the phylogeography of E. breviaristatus using five chloroplast genes and spacer regions in natural populations distributed along the eastern QTP. We identified a total of 25 haplotypes among 216 individuals from 18 E. breviaristatus populations, which were further classified into four haplogroups based on geographical distribution and haplotype network analysis. Notably, we did not observe any signs of population expansion. High genetic diversity was exhibited at both species and population levels, with precipitation being the main limiting factor for population genetic diversity levels. Higher genetic diversity was exhibited by populations located near the Mekong–Salween Divide genetic barrier, suggesting that they may have served as a glacial refuge. The significant pattern of genetic differentiation by environmental isolation highlights the influence of heterogeneous environments on the genetic structure of E. breviaristatus populations. Additionally, the results of ecological niche models indicated that the geographic distribution of E. breviaristatus populations has decreased rapidly since the Last Glacial Maximum but is not threatened by future global warming. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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14 pages, 1039 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Juniperus seravschanica Kom. Collected in Central Asia

by Moldir Yermagambetova, Shyryn Almerekova, Orzimat Turginov, Ormon Sultangaziev, Saule Abugalieva and Yerlan Turuspekov

Plants 2023, 12(16), 2961; https://doi.org/10.3390/plants12162961 - 16 Aug 2023

Cited by 1 | Viewed by 923

Abstract

Juniperus seravschanica Kom. is a species that grows widely in the mountain ranges from Central Asia to Oman. It is an important tree for the formation of shrub–forest massifs in mountainous areas and for draining and fixing soils from middle to high altitudes. [...] Read more.

Juniperus seravschanica Kom. is a species that grows widely in the mountain ranges from Central Asia to Oman. It is an important tree for the formation of shrub–forest massifs in mountainous areas and for draining and fixing soils from middle to high altitudes. A comprehensive study of the species’ genetic diversity and population structure is a basic approach to understanding the current status of J. seravschanica resources for the development of future conservation strategies. Samples from 15 populations of J. seravschanica were collected from the mountain ranges of Uzbekistan, Kyrgyzstan, and Kazakhstan. The genetic diversity and population structure of 15 Central Asian populations of J. seravschanica were assessed using 11 polymorphic simple sequence repeat (SSR) markers. Genetic diversity parameters, including the number of alleles (na), the effective number of alleles (ne), Shannon’s information index (I), the percentage of polymorphic loci (PPL), Nei’s genetic diversity index (Nei), principal coordinate analysis (PCoA), etc., were evaluated. The analysis of 15 J. seravschanica populations based on 11 polymorphic SSRs detected 35 alleles. The average PIC value was 0.432, and the highest value (0.662) was found in the JT_40 marker. Nei’s genetic diversity index for the J. seravschanica populations was 0.450, ranging from 0.407 (population 14) to 0.566 (population 4). The analysis of molecular variance (AMOVA) showed that 90.3% of total genetic variation is distributed within the population. Using the alleles of all the populations, the gene flow (Nm) was found to be 4.654. Population structure analysis revealed poor clustering in the studied populations and confirmed our AMOVA results. The output of this work can be efficiently used for the maintenance of the species across the Central Asian region. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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18 pages, 2299 KiB

Open AccessArticle

Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean

by Zuzana Hromadová, Zdenka Gálová, Lucia Mikolášová, Želmíra Balážová, Martin Vivodík and Milan Chňapek

Plants 2023, 12(15), 2763; https://doi.org/10.3390/plants12152763 - 25 Jul 2023

Cited by 1 | Viewed by 1357

Abstract

Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers [...] Read more.

Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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20 pages, 2446 KiB

Open AccessArticle

Identification of the Efficacy of Ex Situ Conservation of Ammopiptanthus nanus Based on Its ETS-SSR Markers

by Jingdian Liu, Xiyong Wang, Ting Lu, Jiancheng Wang and Wei Shi

Plants 2023, 12(14), 2670; https://doi.org/10.3390/plants12142670 - 17 Jul 2023

Viewed by 945

Abstract

Ammopiptanthus possesses ancestral traits and, as a tertiary relict, is one of the surviving remnants of the ancient Mediterranean retreat and climate drought. It is also the only genus of super xerophytic, evergreen, broad-leaved shrubs. Ammopiptanthus nanus, one of the two species in [...] Read more.

Ammopiptanthus possesses ancestral traits and, as a tertiary relict, is one of the surviving remnants of the ancient Mediterranean retreat and climate drought. It is also the only genus of super xerophytic, evergreen, broad-leaved shrubs. Ammopiptanthus nanus, one of the two species in this genus, is predominantly found in extremely arid and frigid environments, and is increasingly threatened with extinction. Study of the species’ genetic diversity is thus beneficial for its survival and the efficacy of ex situ conservation efforts. Based on transcriptome data, 15 pairs of effective EST-SSR were screened to evaluate A. nanus genetic diversity. In all, 87 samples from three populations were evaluated, the results of which show that ex situ conservation in the Wuqia region needs to be supplemented. Conservation and breeding of individual A. nanus offspring should be strengthened in the future to ensure their progeny continue to exhibit high genetic diversity and variation. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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14 pages, 3907 KiB

Open AccessArticle

Assessment of Genetic Diversity and Genetic Structure of Saussurea medusa (Asteraceae), a “Sky Island” Plant in the Qinghai–Tibet Plateau, Using SRAP Markers

by Jun Wang, Wei Dai, Jie Chen, Kunhao Ye, Qianglong Lai and Dan Zhao

Plants 2023, 12(13), 2463; https://doi.org/10.3390/plants12132463 - 27 Jun 2023

Cited by 1 | Viewed by 1261

Abstract

Saussurea medusa Maxim. is a typical “sky island” species and one with the highest altitude distributions among flowering plants. The present study aimed at analyzing the genetic diversity and population structure of 300 S. medusa accessions collected from 20 populations in the Qilian [...] Read more.

Saussurea medusa Maxim. is a typical “sky island” species and one with the highest altitude distributions among flowering plants. The present study aimed at analyzing the genetic diversity and population structure of 300 S. medusa accessions collected from 20 populations in the Qilian Mountains in the northeastern Qinghai–Tibet Plateau (QTP), using sequence-related amplified polymorphism (SRAP) markers. A total of 14 SRAP primer combinations were employed to analyze genetic diversity and population structure across all accessions. Out of 511 amplified bands, 496 (97.06%) were polymorphic. The populations in the eastern Qilian Mountains had significantly higher genetic diversity than those in the central and western groups. Population structure analysis revealed greater genetic differentiation among populations with a Gst of 0.4926. UPGMA-based clustering classified the 300 S. medusa accessions into 3 major clusters, while the Bayesian STRUCTURE analysis categorized them into 2 groups. Correlation analyses showed that the genetic affinity of the populations was based on differences in geographical distance, moisture conditions, and photothermal conditions between the habitats. This study represents the first comprehensive genetic assessment of S. medusa and provides important genetic baseline data for the conservation of the species. Full article

(This article belongs to the Special Issue Evaluation of Genetic Diversity and Germplasm in Plants Using Molecular and DNA Markers)

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