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15 pages, 11756 KiB

Open AccessArticle

Identification of a Rye Spring Mutant Derived from a Winter Rye Variety by High-Altitude Environment Screening Using RNA Sequencing Technology

by Yangying Wang, Yixuan Liu, Chengqun Yu, Shizhan Chen, Yankun Li, Lina Wei, Junxi Wu and Jianping Yang

Genes 2024, 15(5), 572; https://doi.org/10.3390/genes15050572 - 29 Apr 2024

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Abstract

Wintergrazer-70 and Ganyin No1 are high-yield forage varieties suitable for cultivation in high-altitude areas of Tibet (4300 m above sea level). Ganyin No1 was developed from Wintergrazer-70, with the latter serving as its parent variety. Ganyin No1 was identified as a spring [...] Read more.

Wintergrazer-70 and Ganyin No1 are high-yield forage varieties suitable for cultivation in high-altitude areas of Tibet (4300 m above sea level). Ganyin No1 was developed from Wintergrazer-70, with the latter serving as its parent variety. Ganyin No1 was identified as a spring variety, and subsequent RNA sequencing was conducted. RNA sequencing analysis identified 4 differentially expressed genes related to vernalization and 28 genes related to photoperiod regulation. The Sc7296g5-i1G3 gene is related to the flowering inhibition of rye, which may be related to the phenotypic difference in the Ganyin No1 variety in winter and spring. This finding provides valuable insights for future research on Ganyin No1, especially in addressing feed shortages in Tibet during winter and spring. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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16 pages, 16398 KiB

Open AccessArticle

An R2R3-MYB Transcriptional Factor LuMYB314 Associated with the Loss of Petal Pigmentation in Flax (Linum usitatissimum L.)

by Dongliang Guo, Haixia Jiang and Liqiong Xie

Genes 2024, 15(4), 511; https://doi.org/10.3390/genes15040511 - 18 Apr 2024

Viewed by 406

Abstract

The loss of anthocyanin pigments is one of the most common evolutionary transitions in petal color, yet the genetic basis for these changes in flax remains largely unknown. In this study, we used crossing studies, a bulk segregant analysis, genome-wide association studies, a [...] Read more.

The loss of anthocyanin pigments is one of the most common evolutionary transitions in petal color, yet the genetic basis for these changes in flax remains largely unknown. In this study, we used crossing studies, a bulk segregant analysis, genome-wide association studies, a phylogenetic analysis, and transgenic testing to identify genes responsible for the transition from blue to white petals in flax. This study found no correspondence between the petal color and seed color, refuting the conclusion that a locus controlling the seed coat color is associated with the petal color, as reported in previous studies. The locus controlling the petal color was mapped using a BSA-seq analysis based on the F₂ population. However, no significantly associated genomic regions were detected. Our genome-wide association study identified a highly significant QTL (BP4.1) on chromosome 4 associated with flax petal color in the natural population. The combination of a local Manhattan plot and an LD heat map identified LuMYB314, an R2R3-MYB transcription factor, as a potential gene responsible for the natural variations in petal color in flax. The overexpression of LuMYB314 in both Arabidopsis thaliana and Nicotiana tabacum resulted in anthocyanin deposition, indicating that LuMYB314 is a credible candidate gene for controlling the petal color in flax. Additionally, our study highlights the limitations of the BSA-seq method in low-linkage genomic regions, while also demonstrating the powerful detection capabilities of GWAS based on high-density genomic variation mapping. This study enhances our genetic insight into petal color variations and has potential breeding value for engineering LuMYB314 to develop colored petals, bast fibers, and seeds for multifunctional use in flax. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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18 pages, 4255 KiB

Open AccessArticle

Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family

by Ying Han, Yan-Lei Feng, Jie Wang, Shan-Shan Zhu, Xin-Jie Jin, Zhi-Qiang Wu and Yong-Hua Zhang

Genes 2024, 15(1), 98; https://doi.org/10.3390/genes15010098 - 15 Jan 2024

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Abstract

Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. chingii through [...] Read more.

Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. chingii through a de novo assembly strategy. We carried out comparative genomic analyses and found that, in comparison with the plastid genome (plastome) showing a high degree of structural conservation, the R. chingii mitogenome structure is relatively complex, showing an intricate ring structure with 16 connections, owing to five repetitive sequences. The R. chingii mitogenome was 783,161 bp with a GC content of 44.8% and contained 77 genes, comprising 47 protein-coding genes (CDS), 27 tRNA genes, and 3 rRNA genes. We counted 579 RNA editing events in 47 CDS and 12,828 codons in all CDSs of the R. chingii mitogenome. Furthermore, 24 unique sequence transfer fragments were found between the mitogenome and plastome, comprising 8 mitogenome CDS genes and 16 plastome CDS genes, corresponding to 2.39% of the R. chingii mitogenome. Mitogenomes had shorter but more collinear regions, evidenced by a comparison of the organelles of non-parasitic R. chingii, hemiparasitic Pedicularis chinensis, and holoparasitic Aeginetia indica in the Orobanchaceae family. Moreover, from non-parasitic to holoparasitic species, the genome size in the mitogenomes of Orobanchaceae species did not decrease gradually. Instead, the smallest mitogenome was found in the hemiparasitic species P. chinensis, with a size of 225,612 bp. The findings fill the gap in the mitogenome research of the medicinal plant R. chingii, promote the progress of the organelle genome research of the Orobanchaceae family, and provide clues for molecular breeding. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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16 pages, 9124 KiB

Open AccessArticle

Estimation of Genetic Diversity and Number of Unique Genotypes of Cassava Germplasm from Burkina Faso Using Microsatellite Markers

by Monique Soro, Serge Marie Felicien Wend-Pagnagdé Zida, Koussao Somé, Fidèle Tiendrébéogo, Daniel H. Otron, Justin S. Pita, James B. Néya and Daouda Koné

Genes 2024, 15(1), 73; https://doi.org/10.3390/genes15010073 - 05 Jan 2024

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Abstract

Genetic diversity is very important in crop improvement. This study was carried out to assess the genetic diversity and the number of unique multilocus genotypes (MLGs) in a cassava collection in Burkina Faso. To achieve this objective, 130 cassava accessions were genotyped using [...] Read more.

Genetic diversity is very important in crop improvement. This study was carried out to assess the genetic diversity and the number of unique multilocus genotypes (MLGs) in a cassava collection in Burkina Faso. To achieve this objective, 130 cassava accessions were genotyped using 32 simple sequence repeat (SSR) markers. The results revealed that among these markers, twelve (12) were highly informative, with polymorphic information content (PIC) values greater than 0.50; twelve (12) were moderately informative, with PIC values ranging between 0.25 and 0.50; and eight (8) were not very informative, with PIC values lower than 0.25. A moderate level of genetic diversity was found for the population, indicated by the average expected heterozygosity (0.45) and the observed heterozygosity (0.48). About 83.8% of unique multilocus genotypes were found in the cassava collection, indicating that SSR markers seem to be most appropriate for MLG identification. Population structure analysis based on hierarchical clustering identified two subpopulations and the Bayesian approach suggested five clusters. Additionally, discriminant analysis of principal components (DAPC) separated the cassava accessions into 13 subpopulations. A comparison of these results and those of a previous study using single nucleotide polymorphisms (SNP) suggests that each type of marker can be used to assess the genetic structure of cassava grown in Burkina Faso. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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21 pages, 7631 KiB

Open AccessArticle

Identification and Analysis of Candidate Genes Associated with Yield Structure Traits and Maize Yield Using Next-Generation Sequencing Technology

by Bartosz Nowak, Agnieszka Tomkowiak, Aleksandra Sobiech, Jan Bocianowski, Przemysław Łukasz Kowalczewski, Julia Spychała and Tomasz Jamruszka

Genes 2024, 15(1), 56; https://doi.org/10.3390/genes15010056 - 29 Dec 2023

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Abstract

The main challenge of agriculture in the 21st century is the continuous increase in food production. In addition to ensuring food security, the goal of modern agriculture is the continued development and production of plant-derived biomaterials. Conventional plant breeding methods do not allow [...] Read more.

The main challenge of agriculture in the 21st century is the continuous increase in food production. In addition to ensuring food security, the goal of modern agriculture is the continued development and production of plant-derived biomaterials. Conventional plant breeding methods do not allow breeders to achieve satisfactory results in obtaining new varieties in a short time. Currently, advanced molecular biology tools play a significant role worldwide, markedly contributing to biological progress. The aim of this study was to identify new markers linked to candidate genes determining grain yield. Next-generation sequencing, gene association, and physical mapping were used to identify markers. An additional goal was to also optimize diagnostic procedures to identify molecular markers on reference materials. As a result of the conducted research, 19 SNP markers significantly associated with yield structure traits in maize were identified. Five of these markers (28629, 28625, 28640, 28649, and 29294) are located within genes that can be considered candidate genes associated with yield traits. For two markers (28639 and 29294), different amplification products were obtained on the electrophorograms. For marker 28629, a specific product of 189 bp was observed for genotypes 1, 4, and 10. For marker 29294, a specific product of 189 bp was observed for genotypes 1 and 10. Both markers can be used for the preliminary selection of well-yielding genotypes. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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14 pages, 3689 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the SBP-Box Gene Family in Loquat Fruit Development

by Haiyan Song, Ke Zhao, Guoliang Jiang, Shuxia Sun, Jing Li, Meiyan Tu, Lingli Wang, Hongjiang Xie and Dong Chen

Genes 2024, 15(1), 23; https://doi.org/10.3390/genes15010023 - 23 Dec 2023

Cited by 2 | Viewed by 872

Abstract

The loquat (Eriobotrya japonica L.) is a special evergreen tree, and its fruit is of high medical and health value as well as having stable market demand around the world. In recent years, research on the accumulation of nutrients in loquat fruit, [...] Read more.

The loquat (Eriobotrya japonica L.) is a special evergreen tree, and its fruit is of high medical and health value as well as having stable market demand around the world. In recent years, research on the accumulation of nutrients in loquat fruit, such as carotenoids, flavonoids, and terpenoids, has become a hotspot. The SBP-box gene family encodes transcription factors involved in plant growth and development. However, there has been no report on the SBP-box gene family in the loquat genome and their functions in carotenoid biosynthesis and fruit ripening. In this study, we identified 28 EjSBP genes in the loquat genome, which were unevenly distributed on 12 chromosomes. We also systematically investigated the phylogenetic relationship, collinearity, gene structure, conserved motifs, and cis-elements of EjSBP proteins. Most EjSBP genes showed high expression in the root, stem, leaf, and inflorescence, while only five EjSBP genes were highly expressed in the fruit. Gene expression analysis revealed eight differentially expressed EjSBP genes between yellow- and white-fleshed fruits, suggesting that the EjSBP genes play important roles in loquat fruit development at the breaker stage. Notably, EjSBP01 and EjSBP19 exhibited completely opposite expression patterns between white- and yellow-fleshed fruits during fruit development, and showed a close relationship with SlCnr involved in carotenoid biosynthesis and fruit ripening, indicating that these two genes may participate in the synthesis and accumulation of carotenoids in loquat fruit. In summary, this study provides comprehensive information about the SBP-box gene family in the loquat, and identified two EjSBP genes as candidates involved in carotenoid synthesis and accumulation during loquat fruit development. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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24 pages, 7596 KiB

Open AccessArticle

Genetic Diversity and Phylogenetic Analysis of Zygophyllum loczyi in Northwest China’s Deserts Based on the Resequencing of the Genome

by Mengmeng Wei, Jingdian Liu, Suoming Wang, Xiyong Wang, Haisuang Liu, Qing Ma, Jiancheng Wang and Wei Shi

Genes 2023, 14(12), 2152; https://doi.org/10.3390/genes14122152 - 28 Nov 2023

Viewed by 948

Abstract

In order to study the genetics of local adaptation in all main deserts of northwest China, whole genomes of 169 individuals were resequenced, which covers 20 populations of Zygophyllum loczyi (Zygophyllales: Zygophylaceae). We describe more than 15 million single nucleotide polymorphisms and numerous [...] Read more.

In order to study the genetics of local adaptation in all main deserts of northwest China, whole genomes of 169 individuals were resequenced, which covers 20 populations of Zygophyllum loczyi (Zygophyllales: Zygophylaceae). We describe more than 15 million single nucleotide polymorphisms and numerous InDels. The expected heterozygosity and PIC values associated with local adaptation varied significantly across biogeographic regions. Variation in environmental factors contributes largely to the population genetic structure of Z. loczyi. Bayesian analysis performed with STRUCTURE defined four genetic clusters, while the results of principle component analysis were similar. Our results shows that the Qaidam Desert group appears to be diverging into two branches characterized by significant geographic separation and gene flow with two neighboring deserts. Geological data assume that it is possible that the Taklamakan Desert was the original distribution site, and Z. loczyi could have migrated later on and expanded within other desert areas. The above findings provide insights into the processes involved in biogeography, phylogeny, and differentiation within the northwest deserts of China. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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16 pages, 4269 KiB

Open AccessArticle

Genome-Wide Identification of AhMDHs and Analysis of Gene Expression under Manganese Toxicity Stress in Arachis hypogaea

by Ying Liu, Min Zhao, Jianning Shi, Shaoxia Yang and Yingbin Xue

Genes 2023, 14(12), 2109; https://doi.org/10.3390/genes14122109 - 21 Nov 2023

Cited by 1 | Viewed by 894

Abstract

Malate dehydrogenase (MDH) is one kind of oxidation–reduction enzyme that catalyzes the reversible conversion of oxaloacetic acid to malic acid. It has vital functions in plant development, photosynthesis, abiotic stress responses, and so on. However, there are no reports on the genome-wide identification [...] Read more.

Malate dehydrogenase (MDH) is one kind of oxidation–reduction enzyme that catalyzes the reversible conversion of oxaloacetic acid to malic acid. It has vital functions in plant development, photosynthesis, abiotic stress responses, and so on. However, there are no reports on the genome-wide identification and gene expression of the MDH gene family in Arachis hypogaea. In this study, the MDH gene family of A. hypogaea was comprehensively analyzed for the first time, and 15 AhMDH sequences were identified. According to the phylogenetic tree analysis, AhMDHs are mainly separated into three subfamilies with similar gene structures. Based on previously reported transcriptome sequencing results, the AhMDH expression quantity of roots and leaves exposed to manganese (Mn) toxicity were explored in A. hypogaea. Results revealed that many AhMDHs were upregulated when exposed to Mn toxicity, suggesting that those AhMDHs might play an important regulatory role in A. hypogaea’s response to Mn toxicity stress. This study lays foundations for the functional study of AhMDHs and further reveals the mechanism of the A. hypogaea signaling pathway responding to high Mn stress. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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10 pages, 1861 KiB

Open AccessBrief Report

A High-Quality Reference Genome Assembly of Prinsepia uniflora (Rosaceae)

by Lei Zhang, Chaopan Zhang, Yajing An, Qiang Zhu and Mingcheng Wang

Genes 2023, 14(11), 2035; https://doi.org/10.3390/genes14112035 - 02 Nov 2023

Viewed by 1291

Abstract

This study introduces a meticulously constructed genome assembly at the chromosome level for the Rosaceae family species Prinsepia uniflora, a traditional Chinese medicinal herb. The final assembly encompasses 1272.71 megabases (Mb) distributed across 16 pseudochromosomes, boasting contig and super-scaffold N50 values of [...] Read more.

This study introduces a meticulously constructed genome assembly at the chromosome level for the Rosaceae family species Prinsepia uniflora, a traditional Chinese medicinal herb. The final assembly encompasses 1272.71 megabases (Mb) distributed across 16 pseudochromosomes, boasting contig and super-scaffold N50 values of 2.77 and 79.32 Mb, respectively. Annotated within this genome is a substantial 875.99 Mb of repetitive sequences, with transposable elements occupying 777.28 Mb, constituting 61.07% of the entire genome. Our predictive efforts identified 49,261 protein-coding genes within the repeat-masked assembly, with 45,256 (91.87%) having functional annotations, 5127 (10.41%) demonstrating tandem duplication, and 2373 (4.82%) classified as transcription factor genes. Additionally, our investigation unveiled 3080 non-coding RNAs spanning 0.51 Mb of the genome sequences. According to our evolutionary study, P. uniflora underwent recent whole-genome duplication following its separation from Prunus salicina. The presented reference-level genome assembly and annotation for P. uniflora will significantly facilitate the in-depth exploration of genomic information pertaining to this species, offering substantial utility in comparative genomics and evolutionary analyses involving Rosaceae species. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants)

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