Genetic Research and Plant Breeding

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (1 July 2022) | Viewed by 71396

Special Issue Editors


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Guest Editor
Division of Horticultural Biotechnology, Hankyung National University, Anseong 17579, Republic of Korea
Interests: functional analysis of genes via CRISPR/Cas9; functional genomics; MABc (marker-assisted backcross); transcriptomics; plant biotechnology; molecular breeding in plants
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Special Issue Information

Dear Colleagues,

Over the last two decades, molecular biology has improved markedly in QTL and functional analysis, as well as gene identification and cloning in plant species. In parallel, innovation in molecular technologies has been exponential in the areas of genetics and genomics.

Functional genomics has become one of the most promising scientific areas in the characterization of gene (and protein) functions and interactions using vast genetics and various omics data. In addition, there are various advanced tools and methodologies that could also allow the effective and efficient validation of gene functions when used in lab settings such as transcriptome, metabolomics, overexpression, knock-out, RNAi and gene editing, and when applying advanced computational methodologies such as machine learning and deep learning.

This Special Issue welcomes original research articles and reviews that explore agronomic trait characterization, gene discovery, and function and expression control analysis, using both wet lab technologies and computational biology which could accelerate plant breeding programs.

Prof. Dr. Yong-Gu Cho
Prof. Dr. Kwon-Kyoo Kang
Guest Editors

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Keywords

  • Transcriptomics
  • Metabolomics
  • Function of genes
  • Transcription factors
  • Plant gene regulation
  • Gene silencing and miRNAs
  • Molecular genetics
  • Molecular marker
  • Genetic mapping
  • Marker-assisted selection
  • Genomic selection
  • Genetic engineering
  • Molecular design breeding
  • Plant breeding

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Published Papers (26 papers)

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Editorial

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7 pages, 212 KiB  
Editorial
Genetic Research and Plant Breeding
by Kwon-Kyoo Kang and Yong-Gu Cho
Genes 2023, 14(1), 51; https://doi.org/10.3390/genes14010051 - 23 Dec 2022
Cited by 1 | Viewed by 2040
Abstract
In the past 20 years, plant genetics and breeding research using molecular biology has been greatly improved via the functional analysis of genes, species identification and transformation techniques [...] Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)

Research

Jump to: Editorial, Review

20 pages, 2705 KiB  
Article
Identifying the Genetic Basis of Mineral Elements in Rice Grain Using Genome-Wide Association Mapping
by A. S. M. Faridul Islam, Wardah Mustahsan, Rodante Tabien, Joseph M. Awika, Endang M. Septiningsih and Michael J. Thomson
Genes 2022, 13(12), 2330; https://doi.org/10.3390/genes13122330 - 10 Dec 2022
Cited by 6 | Viewed by 1447
Abstract
Mineral malnutrition is a major problem in many rice-consuming countries. It is essential to know the genetic mechanisms of accumulation of mineral elements in the rice grain to provide future solutions for this issue. This study was conducted to identify the genetic basis [...] Read more.
Mineral malnutrition is a major problem in many rice-consuming countries. It is essential to know the genetic mechanisms of accumulation of mineral elements in the rice grain to provide future solutions for this issue. This study was conducted to identify the genetic basis of six mineral elements (Cu, Fe, K, Mg, Mn, and Zn) by using three models for single-locus and six models for multi-locus analysis of a genome-wide association study (GWAS) using 174 diverse rice accessions and 6565 SNP markers. To declare a SNP as significant, −log10(P) ≥ 3.0 and 15% FDR significance cut-off values were used for single-locus models, while LOD ≥ 3.0 was used for multi-locus models. Using these criteria, 147 SNPs were detected by one or two GWAS methods at −log10(P) ≥ 3.0, 48 of which met the 15% FDR significance cut-off value. Single-locus models outperformed multi-locus models before applying multi-test correction, but once applied, multi-locus models performed better. While 14 (~29%) of the identified quantitative trait loci (QTLs) after multiple test correction co-located with previously reported genes/QTLs and marker associations, another 34 trait-associated SNPs were novel. After mining genes within 250 kb of the 48 significant SNP loci, in silico and gene enrichment analyses were conducted to predict their potential functions. These shortlisted genes with their functions could guide future experimental validation, helping us to understand the complex molecular mechanisms controlling rice grain mineral elements. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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17 pages, 4406 KiB  
Article
Development of SNP Markers from GWAS for Selecting Seed Coat and Aleurone Layers in Brown Rice (Oryza sativa L.)
by Me-Sun Kim, Seo-Rin Ko, Van Trang Le, Moo-Gun Jee, Yu Jin Jung, Kwon-Kyoo Kang and Yong-Gu Cho
Genes 2022, 13(10), 1805; https://doi.org/10.3390/genes13101805 - 6 Oct 2022
Cited by 6 | Viewed by 2032
Abstract
Ninety-five percent of the general nutrients in rice are concentrated in the rice bran and germ, and many nutrients such as vitamins, minerals, dietary fiber, and essential fatty acids, as well as antioxidants such as tocopherol, are lost during milling. In this study, [...] Read more.
Ninety-five percent of the general nutrients in rice are concentrated in the rice bran and germ, and many nutrients such as vitamins, minerals, dietary fiber, and essential fatty acids, as well as antioxidants such as tocopherol, are lost during milling. In this study, we investigated the thickness of seed coat and aleurone layers using a 294 rice core collection, and found candidate genes related to thickness of seed coat and aleurone layers, by performing a genome wide association study (GWAS) analysis using whole genome resequencing data. Two primer pairs that can be used as high-resolution melting (HRM) markers were developed. As a result of genotyping BC2F2 individuals derived from a cross between “Samgwang” and “Seolgaeng”, and using corresponding HRM markers, it was possible to finally develop HRM markers for selecting seed coat and aleurone layer thickness. This is expected to be used as basic data for the application of gene editing using CRISPR/Cas9 technology and for establishing a breeding strategy for high eating quality rice using molecular genetic technology. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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12 pages, 2588 KiB  
Article
Transcriptome Analysis Revealed Hormone Pathways and bZIP Genes Responsive to Decapitation in Sunflower
by Lili Dong, Yu Wu, Jianbin Zhang, Xinyi Deng and Tian Wang
Genes 2022, 13(10), 1737; https://doi.org/10.3390/genes13101737 - 27 Sep 2022
Cited by 4 | Viewed by 1788
Abstract
Decapitation is an essential agricultural practice and is a typical method for analyzing shoot branching. However, it is unclear exactly how decapitation controls branching. In this study, the decapitation of sunflower plants led to the development of lateral buds, accompanied by a decrease [...] Read more.
Decapitation is an essential agricultural practice and is a typical method for analyzing shoot branching. However, it is unclear exactly how decapitation controls branching. In this study, the decapitation of sunflower plants led to the development of lateral buds, accompanied by a decrease in indole-3-acetic acid (IAA) and abscisic acid (ABA) levels and an increase in cytokinin (CK) levels. Additionally, 82 members of the HabZIP family were discovered and categorized into 9 groups, using phylogenetic and conservative domain analysis. The intron/exon structure and motif compositions of HabZIP members were also investigated. Based on tissue-specific expression and expression analysis following decapitation derived from the transcriptome, several HabZIP members may be involved in controlling decapitation-induced bud outgrowth. Therefore, it is hypothesized that the dynamic variations in hormone levels, in conjunction with particular HabZIP genes, led to the development of axillary buds in sunflowers following decapitation. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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23 pages, 29821 KiB  
Article
Interspecific and Intraspecific Hybrid Rootstocks to Improve Horticultural Traits and Soil-Borne Disease Resistance in Tomato
by Mean Vanlay, Song Samnang, Hee-Jong Jung, Phillip Choe, Kwon Kyoo Kang and Ill-Sup Nou
Genes 2022, 13(8), 1468; https://doi.org/10.3390/genes13081468 - 17 Aug 2022
Cited by 7 | Viewed by 2315
Abstract
Tomato rootstocks are important to increase yield and control soil-borne pathogens, increasing vigor for a longer crop cycle and tolerance to biotic and abiotic stress. This study, conducted in the greenhouse of Sunchon National University during the period from 2019 to 2022, aimed [...] Read more.
Tomato rootstocks are important to increase yield and control soil-borne pathogens, increasing vigor for a longer crop cycle and tolerance to biotic and abiotic stress. This study, conducted in the greenhouse of Sunchon National University during the period from 2019 to 2022, aimed to identify local soil-borne-disease resistant interspecific and intraspecific tomato hybrid rootstocks. The 71 interspecific hybrids (S. lycopersicum × S. habrochaites) showed that the germination vigor (GV) was less than Maxifort, except for several combinations. The germination rate (GP) of cross-species hybrids showed a different pattern according to the hybrid combinations, of which three combinations showed less than 30%. The horticultural traits, such as GV and GP, of the intraspecies hybrid (S. l × S. l) combination were significantly improved compared to that of Maxifort. In 71 combinations (S. l × S. h) and 25 combinations (S. l × S. l), MAS was used to evaluate the resistance of eight genes related to soil-borne pathogens, four genes related to vector-mediated pathogens, and three genes related to air-borne pathogens. The results showed that the new hybrid combination had improved resistance over the commercial-stock Maxifort. Therefore, interspecies and intraspecies hybrid techniques for breeding commercial rootstocks can be utilized as a way to improve horticultural properties and resistance to soil-borne diseases in tomato. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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12 pages, 3406 KiB  
Article
Identification and Characterization of PTE-2, a Stowaway-like MITE Activated in Transgenic Chinese Cabbage Lines
by Young-Ji Jeon, Yun-Hee Shin, Su-Jeong Cheon and Young-Doo Park
Genes 2022, 13(7), 1222; https://doi.org/10.3390/genes13071222 - 8 Jul 2022
Cited by 2 | Viewed by 1662
Abstract
Transposable elements (TEs) are DNA fragments that can be replicated or transposed within a genome. TEs make up a high proportion of the plant genome and contribute to genetic diversity and evolution, affecting genome structure or gene activity. Miniature inverted-repeat transposable elements (MITEs) [...] Read more.
Transposable elements (TEs) are DNA fragments that can be replicated or transposed within a genome. TEs make up a high proportion of the plant genome and contribute to genetic diversity and evolution, affecting genome structure or gene activity. Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II DNA transposable elements. MITEs have specific sequences, target site duplications (TSDs), and terminal inverted repeats(TIRs), which are characteristics of the classification of MITE families. In this study, a Stowaway-like MITE, PTE-2, was activated in transgenic Chinese cabbage lines. PTE-2 was revealed by in silico analysis as the putative activated element in transgenic Chinese cabbage lines. To verify the in silico analysis data, MITE insertion polymorphism (MIP) PCR was conducted and PTE-2 was confirmed to be activated in transgenic Chinese cabbage lines. The activation tendency of the copy elements of PTE-2 at different loci was also analyzed and only one more element was activated in the transgenic Chinese cabbage lines. Analyzing the sequence of MIP PCR products, the TSD sequence and TIR motif of PTE-2 were identified and matched to the characteristics of the Stowaway-like MITE family. In addition, the flanking region of PTE-2 was modified when PTE-2 was activated. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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13 pages, 2412 KiB  
Article
Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice
by Chaewon Lee, Kyeong-Seong Cheon, Yunji Shin, Hyoja Oh, Young-Min Jeong, Hoon Jang, Yong-Chan Park, Kyung-Yun Kim, Hang-Chul Cho, Yong-Jae Won, Jeongho Baek, Young-Soon Cha, Song-Lim Kim, Kyung-Hwan Kim and Hyeonso Ji
Genes 2022, 13(5), 794; https://doi.org/10.3390/genes13050794 - 28 Apr 2022
Cited by 8 | Viewed by 2722
Abstract
The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, [...] Read more.
The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for japonica and 1339 SNPs informative for indica, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F8 recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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19 pages, 3672 KiB  
Article
Using Transcriptome Analysis to Explore Gray Mold Resistance-Related Genes in Onion (Alliumcepa L.)
by Hyun-Min Lee, Jee-Soo Park, So-Jeong Kim, Seung-Gyu Kim and Young-Doo Park
Genes 2022, 13(3), 542; https://doi.org/10.3390/genes13030542 - 18 Mar 2022
Cited by 6 | Viewed by 2554
Abstract
Gray mold disease caused by Botrytis in onions (Allium cepa L.) during growth and storage negatively affects their yield and quality. Exploring the genes related to gray mold resistance in onion and their application to the breeding of resistant onion lines will [...] Read more.
Gray mold disease caused by Botrytis in onions (Allium cepa L.) during growth and storage negatively affects their yield and quality. Exploring the genes related to gray mold resistance in onion and their application to the breeding of resistant onion lines will support effective and ecological control methods of the disease. Here, the genetic relationship of 54 onion lines based on random amplified polymorphic DNA (RAPD) and in vitro-cultured onion lines infected with gray mold were used for screening resistance and susceptibility traits. Two genetically related onion lines were selected, one with a resistant and one with a susceptible phenotype. In vitro gray mold infection was repeated with these two lines, and leaf samples were collected for gene expression studies in time series. Transcript sequences obtained by RNA sequencing were subjected to DEG analysis, variant analysis, and KEGG mapping. Among the KEGG pathways, ‘α-linoleic acid metabolism’ was selected because the comparison of the time series expression pattern of Jasmonate resistant 1 (JAR1), Coronatine-insensitive protein 1 (COI 1), and transcription factor MYC2 (MYC2) genes between the resistant and susceptible lines revealed its significant relationship with gray-mold-resistant phenotypes. Expression pattern and SNP of the selected genes were verified by quantitative real-time PCR and high-resolution melting (HRM) analysis, respectively. The results of this study will be useful for the development of molecular marker and finally breeding of gray-mold-resistant onions. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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16 pages, 4033 KiB  
Article
Marker-Assisted Backcrossing (MABc) to Improve Eating Quality with Thin Seed Coat and Aleurone Layer of Non-Glutinous Japonica Variety in Rice
by Me-Sun Kim, Ju-Kyung Yu, Seo-Rin Ko, Ki-Jo Kim, Hyeonso Ji, Kwon-Kyoo Kang and Yong-Gu Cho
Genes 2022, 13(2), 210; https://doi.org/10.3390/genes13020210 - 24 Jan 2022
Cited by 8 | Viewed by 3041
Abstract
Brown rice is composed of rice bran, pericarp, seed coat, and aleurone layers, and the rice bran layer contains a large number of substances useful for the human body, such as dietary fiber, α-tocopherol, α-tocotrienol, and vitamins. However, more than 90% of these [...] Read more.
Brown rice is composed of rice bran, pericarp, seed coat, and aleurone layers, and the rice bran layer contains a large number of substances useful for the human body, such as dietary fiber, α-tocopherol, α-tocotrienol, and vitamins. However, more than 90% of these substances are removed when polished, and white rice has the disadvantage of losing food-related ingredients, such as umami-related amino acids, when compared to the unpolished group. In this study, we tried to develop new breeding lines with a thinner seed coat and aleurone layer to provide high eating quality with softer chewing characteristics and processability in rice grain. We detected an SNP for foreground selection for the backcross population by comparing genome sequences between Samgwang and Seolgaeng and developed high eating quality brown rice breeding lines by applying marker-assisted backcrossing (MABC) breeding programs to backcross populations between Samgwang and Seolgaeng using KASP markers. SNP markers for foreground selection were identified to improve eating and processability through SNP mapping of Samgwang and Seolgaeng with SSIIa as a target gene in this study. Line selection according to genotype of KASP markers was successful in BC1F1 and BC2F1 generations, with the recurrent parent genome recovery ratio ranging from 91.22% to 98.65%. In BC2F1 seeds of the selected lines, thickness of the aleurone layer was found to range from 13.82 to 21.67 μm, which is much thinner than the 30.91 μm of the wild type, suggesting that selection by MABc could be used as an additional breeding material for the development of highly processed rice varieties. These lines will be useful to develop new brown rice varieties with softer chewing characteristics and processability in rice grain. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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14 pages, 5208 KiB  
Article
Overexpression of Orange Gene (OsOr-R115H) Enhances Heat Tolerance and Defense-Related Gene Expression in Rice (Oryza sativa L.)
by Yu Jin Jung, Ji Yun Go, Hyo Ju Lee, Jung Soon Park, Jin Young Kim, Ye Ji Lee, Mi-Jeong Ahn, Me-Sun Kim, Yong-Gu Cho, Sang-Soo Kwak, Ho Soo Kim and Kwon Kyoo Kang
Genes 2021, 12(12), 1891; https://doi.org/10.3390/genes12121891 - 26 Nov 2021
Cited by 6 | Viewed by 2702
Abstract
In plants, the orange (Or) gene plays roles in regulating carotenoid biosynthesis and responses to environmental stress. The present study investigated whether the expression of rice Or (OsOr) gene could enhance rice tolerance to heat stress conditions. The OsOr [...] Read more.
In plants, the orange (Or) gene plays roles in regulating carotenoid biosynthesis and responses to environmental stress. The present study investigated whether the expression of rice Or (OsOr) gene could enhance rice tolerance to heat stress conditions. The OsOr gene was cloned and constructed with OsOr or OsOr-R115H (leading to Arg to His substitution at position 115 on the OsOr protein), and transformed into rice plants. The chlorophyll contents and proline contents of transgenic lines were significantly higher than those of non-transgenic (NT) plants under heat stress conditions. However, we found that the levels of electrolyte leakage and malondialdehyde in transgenic lines were significantly reduced compared to NT plants under heat stress conditions. In addition, the levels of expression of four genes related to reactive oxygen species (ROS) scavenging enzymes (OsAPX2, OsCATA, OsCATB, OsSOD-Cu/Zn) and five genes (OsLEA3, OsDREB2A, OsDREB1A, OsP5CS, SNAC1) responded to abiotic stress was showed significantly higher in the transgenic lines than NT plants under heat stress conditions. Therefore, OsOr-R115H could be exploited as a promising strategy for developing new rice cultivars with improved heat stress tolerance. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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20 pages, 6360 KiB  
Article
Genetic and Proteomic Basis of Sclerotinia Stem Rot Resistance in Indian Mustard [Brassica juncea (L.) Czern & Coss.]
by Manjeet Singh, Ram Avtar, Nita Lakra, Ekta Hooda, Vivek K. Singh, Mahavir Bishnoi, Nisha Kumari, Rakesh Punia, Neeraj Kumar and Raju Ram Choudhary
Genes 2021, 12(11), 1784; https://doi.org/10.3390/genes12111784 - 10 Nov 2021
Cited by 12 | Viewed by 3794
Abstract
Sclerotinia stem rot is one of the utmost important disease of mustard, causing considerable losses in seed yield and oil quality. The study of the genetic and proteomic basis of resistance to this disease is imperative for its effective utilization in developing resistant [...] Read more.
Sclerotinia stem rot is one of the utmost important disease of mustard, causing considerable losses in seed yield and oil quality. The study of the genetic and proteomic basis of resistance to this disease is imperative for its effective utilization in developing resistant cultivars. Therefore, the genetic pattern of Sclerotinia stem rot resistance in Indian mustard was studied using six generations (P1, P2, F1, F2, BC1P1, and BC1P2) developed from the crossing of one resistant (RH 1222-28) and two susceptible (EC 766300 and EC 766123) genotypes. Genetic analysis revealed that resistance was governed by duplicate epistasis. Comparative proteome analysis of resistant and susceptible genotypes indicated that peptidyl-prolyl cis-trans isomerase (A0A078IDN6 PPIase) showed high expression in resistant genotype at the early infection stage while its expression was delayed in susceptible genotypes. This study provides important insight to mustard breeders for designing effective breeding programs to develop resistant cultivars against this devastating disease. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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14 pages, 2315 KiB  
Article
Leaf Size Development Differences and Comparative Transcriptome Analyses of Two Poplar Genotypes
by Lei Zhang, Jiujun Du, Xiaolan Ge, Demei Cao and Jianjun Hu
Genes 2021, 12(11), 1775; https://doi.org/10.3390/genes12111775 - 9 Nov 2021
Cited by 15 | Viewed by 2499
Abstract
The plant leaf, the main organ of photosynthesis, is an important regulator of growth. To explore the difference between leaf size of Populusdeltoides ‘Danhong’ (Pd) and Populus simonii ‘Tongliao1’ (Ps), we investigated the leaf length, leaf width, leaf thickness, leaf area, [...] Read more.
The plant leaf, the main organ of photosynthesis, is an important regulator of growth. To explore the difference between leaf size of Populusdeltoides ‘Danhong’ (Pd) and Populus simonii ‘Tongliao1’ (Ps), we investigated the leaf length, leaf width, leaf thickness, leaf area, leaf mass per area (LMA), and cell size of leaves from two genotypes and profiled the transcriptome-wide gene expression patterns through RNA sequencing. Our results show that the leaf area of Pd was significantly larger than that of Ps, but the epidermal cell area was significantly smaller than that of Ps. The difference of leaf size was caused by cell numbers. Transcriptome analysis also revealed that genes related to chromosome replication and DNA repair were highly expressed in Pd, while genes such as the EXPANSIN (EXPA) family which promoted cell expansion were highly expressed in Ps. Further, we revealed that the growth-regulating factors (GRFs) played a key role in the difference of leaf size between two genotypes through regulation of cell proliferation. These data provide a valuable resource for understanding the leaf development of the Populus genus. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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15 pages, 1744 KiB  
Article
Genomic Variation in Korean japonica Rice Varieties
by Hyeonso Ji, Yunji Shin, Chaewon Lee, Hyoja Oh, In Sun Yoon, Jeongho Baek, Young-Soon Cha, Gang-Seob Lee, Song Lim Kim and Kyung-Hwan Kim
Genes 2021, 12(11), 1749; https://doi.org/10.3390/genes12111749 - 30 Oct 2021
Cited by 8 | Viewed by 2258
Abstract
Next-generation sequencing technologies have enabled the discovery of numerous sequence variations among closely related crop varieties. We analyzed genome resequencing data from 24 Korean temperate japonica rice varieties and discovered 954,233 sequence variations, including 791,121 single nucleotide polymorphisms (SNPs) and 163,112 insertions/deletions (InDels). [...] Read more.
Next-generation sequencing technologies have enabled the discovery of numerous sequence variations among closely related crop varieties. We analyzed genome resequencing data from 24 Korean temperate japonica rice varieties and discovered 954,233 sequence variations, including 791,121 single nucleotide polymorphisms (SNPs) and 163,112 insertions/deletions (InDels). On average, there was one variant per 391 base-pairs (bp), a variant density of 2.6 per 1 kbp. Of the InDels, 10,860 were longer than 20 bp, which enabled conversion to markers resolvable on an agarose gel. The effect of each variant on gene function was predicted using the SnpEff program. The variants were categorized into four groups according to their impact: high, moderate, low, and modifier. These groups contained 3524 (0.4%), 27,656 (2.9%), 24,875 (2.6%), and 898,178 (94.1%) variants, respectively. To test the accuracy of these data, eight InDels from a pre-harvest sprouting resistance QTL (qPHS11) target region, four highly polymorphic InDels, and four functional sequence variations in known agronomically important genes were selected and successfully developed into markers. These results will be useful to develop markers for marker-assisted selection, to select candidate genes in map-based cloning, and to produce efficient high-throughput genome-wide genotyping systems for Korean temperate japonica rice varieties. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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23 pages, 6775 KiB  
Article
Analysis of SI-Related BoGAPDH Family Genes and Response of BoGAPC to SI Signal in Brassica oleracea L.
by Qinqin Xie, Hecui Zhang, Dengke Hu, Qianying Liu, Tonghong Zuo, Yizhong Zhang, Yimei Liu, Siru Zhou and Liquan Zhu
Genes 2021, 12(11), 1719; https://doi.org/10.3390/genes12111719 - 28 Oct 2021
Cited by 4 | Viewed by 1735
Abstract
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is not only involved in carbohydrate metabolism, but also plays an important role in stress resistance. However, it has not been reported in Brassica oleracea. In this study, we performed a genome-wide identification of BoGAPDH in B. oleracea [...] Read more.
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is not only involved in carbohydrate metabolism, but also plays an important role in stress resistance. However, it has not been reported in Brassica oleracea. In this study, we performed a genome-wide identification of BoGAPDH in B. oleracea and performed cloning and expression analysis of one of the differentially expressed genes, BoGAPC. A total of 16 members of the BoGAPDH family were identified in B. oleracea, which were conserved, distributed unevenly on chromosomes and had tandem repeat genes. Most of the genes were down-regulated during self-pollination, and the highest expression was found in stigmas and sepals. Different transcriptome data showed that BoGAPDH genes were differentially expressed under stress, which was consistent with the results of qRT-PCR. We cloned and analyzed the differentially expressed gene BoGAPC and found that it was in the down-regulated mode 1 h after self-pollination, and the expression was the highest in the stigma, which was consistent with the result of GUS staining. The promoter region of the gene not only has stress response elements and plant hormone response elements, but also has a variety of specific elements for regulating floral organ development. Subcellular localization indicates that the BoGAPC protein is located in the cytoplasm and belongs to the active protein in the cytoplasm. The results of prokaryotic expression showed that the size of the BoGAPC protein was about 37 kDa, which was consistent with the expected results, indicating that the protein was induced in prokaryotic cells. The results of yeast two-hybrid and GST pull-down showed that the SRK kinase domain interacted with the BoGAPC protein. The above results suggest that the BoGAPDH family of B. oleracea plays an important role in the process of plant stress resistance, and the BoGAPC gene may be involved in the process of self-incompatibility in B. oleracea, which may respond to SI by encoding proteins directly interacting with SRK. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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16 pages, 1610 KiB  
Article
Genotyping Analysis by RAD-Seq Reads Is Useful to Assess the Genetic Identity and Relationships of Breeding Lines in Lavender Species Aimed at Managing Plant Variety Protection
by Francesco Scariolo, Fabio Palumbo, Alessandro Vannozzi, Gio Batta Sacilotto, Marco Gazzola and Gianni Barcaccia
Genes 2021, 12(11), 1656; https://doi.org/10.3390/genes12111656 - 21 Oct 2021
Cited by 7 | Viewed by 2742
Abstract
Lavender species are widely distributed in their wild forms around the Mediterranean Basin and they are also cultivated worldwide as improved and registered clonal varieties. The economic interest of the species belonging to the Lavandula genus is determined by their use as ornamental [...] Read more.
Lavender species are widely distributed in their wild forms around the Mediterranean Basin and they are also cultivated worldwide as improved and registered clonal varieties. The economic interest of the species belonging to the Lavandula genus is determined by their use as ornamental plants and important source of essential oils that are destinated to the production of cosmetics, pharmaceuticals and foodstuffs. Because of the increasing number of cases of illegal commercialization of selected varieties, the protection of plant breeders’ rights has become of main relevance for the recognition of breeding companies’ royalties. With this aim, genomic tools based on molecular markers have been demonstrated to be very reliable and transferable among laboratories, and also much more informative than morphological descriptors. With the rising of the next-generation sequencing (NGS) technologies, several genotyping-by-sequencing approaches are now available. This study deals with a deep characterization of 15 varietal clones, belonging to two distinct Lavandula species, by means of restriction-site associated DNA sequencing (RAD-Seq). We demonstrated that this technology screens single nucleotide variants that enable to assess the genetic identity of individual accessions, to reconstruct genetic relationships among related breeding lines, to group them into genetically distinguishable main subclusters, and to assign their molecular lineages to distinct ancestors. Moreover, a number of polymorphic sites were identified within genes putatively involved in biosynthetic pathways related to both tissue pigmentation and terpene production, useful for breeding and/or protecting newly registered varieties. Overall, the results highlighted the presence of pure ancestries and interspecific hybrids for the analyzed Lavandula species, and demonstrated that RAD-Seq analysis is very informative and highly reliable for characterizing Lavandula clones and managing plant variety protection. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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15 pages, 5310 KiB  
Article
DNA Methylation Level Changes in Transgenic Chinese Cabbage (Brassica rapa ssp. pekinensis) Plants and Their Effects on Corresponding Gene Expression Patterns
by Jee-Soo Park, Yun-Hee Shin and Young-Doo Park
Genes 2021, 12(10), 1563; https://doi.org/10.3390/genes12101563 - 30 Sep 2021
Cited by 3 | Viewed by 2078
Abstract
Plant tissue culture is an in vitro technique used to manipulate cells, tissues, or organs, and plays an important role in genetic transformation. However, plants cultured in vitro often exhibit unintended genetic and epigenetic variations. Since it is important to secure the stability [...] Read more.
Plant tissue culture is an in vitro technique used to manipulate cells, tissues, or organs, and plays an important role in genetic transformation. However, plants cultured in vitro often exhibit unintended genetic and epigenetic variations. Since it is important to secure the stability of endogenous and exogenous gene expressions in transgenic plants, it is preferable to avoid the occurrence of such variations. In this study, we focused on epigenetic variations, exclusively on methylation level changes of DNA, in transgenic Chinese cabbage (Brassica rapa ssp. pekinensis) plants. To detect these methylation level changes of DNA, bisulfite sequencing was performed and the obtained sequences were compared with the ‘CT001’ reference genome. Differentially methylated regions (DMRs) of DNA between the non-transgenic and transgenic lines were detected by bisulfite sequencing, and ten DMRs located in exonic regions were identified. The regions with methylation variations that were inherited and consistently maintained in the next generation lines were selected and validated. We also analyzed the relationship between methylation status and expression levels of transformant-conserved DMR (TCD) genes by quantitative reverse transcription-PCR. These results suggested that the changes in methylation levels of these DMRs might have been related to the plant transformation process, affecting subsequent gene expression. Our findings can be used in fundamental research on methylation variations in transgenic plants and suggest that these variations affect the expression of the associated genes. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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15 pages, 2892 KiB  
Article
Weighted Gene Co-Expression Network Analysis Reveals Hub Genes Contributing to Fuzz Development in Gossypium arboreum
by Xiaoxu Feng, Shang Liu, Hailiang Cheng, Dongyun Zuo, Youping Zhang, Qiaolian Wang, Limin Lv and Guoli Song
Genes 2021, 12(5), 753; https://doi.org/10.3390/genes12050753 - 17 May 2021
Cited by 7 | Viewed by 2358
Abstract
Fuzzless mutants are ideal materials to decipher the regulatory network and mechanism underlying fuzz initiation and formation. In this study, we utilized two Gossypium arboreum accessions differing in fuzz characteristics to explore expression pattern differences and discriminate genes involved in fuzz development using [...] Read more.
Fuzzless mutants are ideal materials to decipher the regulatory network and mechanism underlying fuzz initiation and formation. In this study, we utilized two Gossypium arboreum accessions differing in fuzz characteristics to explore expression pattern differences and discriminate genes involved in fuzz development using RNA sequencing. Gene ontology (GO) analysis was conducted and found that DEGs were mainly enriched in the regulation of transcription, metabolic processes and oxidation–reduction-related processes. Weighted gene co-expression network analysis discerned the MEmagenta module highly associated with a fuzz/fuzzless trait, which included a total of 50 hub genes differentially expressed between two materials. GaFZ, which negatively regulates trichome and fuzz formation, was found involved in MEmagenta cluster1. In addition, twenty-eight hub genes in MEmagenta cluster1 were significantly up-regulated and expressed in fuzzless mutant DPL972. It is noteworthy that Ga04G1219 and Ga04G1240, which, respectively, encode Fasciclin-like arabinogalactan protein 18(FLA18) and transport protein, showed remarkable differences of expression level and implied that they may be involved in protein glycosylation to regulate fuzz formation and development. This module and hub genes identified in this study will provide new insights on fiber and fuzz formation and be useful for the molecular design breeding of cotton genetic improvement. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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15 pages, 3615 KiB  
Article
Transcriptomic Analysis of Rice Plants Overexpressing PsGAPDH in Response to Salinity Stress
by Hyemin Lim, Hyunju Hwang, Taelim Kim, Soyoung Kim, Hoyong Chung, Daewoo Lee, Soorin Kim, Soochul Park, Woosuk Cho, Hyeonso Ji and Gangseob Lee
Genes 2021, 12(5), 641; https://doi.org/10.3390/genes12050641 - 25 Apr 2021
Cited by 9 | Viewed by 2814
Abstract
In plants, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a main enzyme in the glycolytic pathway. It plays an essential role in glycerolipid metabolism and response to various stresses. To examine the function of PsGAPDH (Pleurotus sajor-caju GAPDH) in response to abiotic stress, we generated [...] Read more.
In plants, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a main enzyme in the glycolytic pathway. It plays an essential role in glycerolipid metabolism and response to various stresses. To examine the function of PsGAPDH (Pleurotus sajor-caju GAPDH) in response to abiotic stress, we generated transgenic rice plants with single-copy/intergenic/homozygous overexpression PsGAPDH (PsGAPDH-OX) and investigated their responses to salinity stress. Seedling growth and germination rates of PsGAPDH-OX were significantly increased under salt stress conditions compared to those of the wild type. To elucidate the role of PsGAPDH-OX in salt stress tolerance of rice, an Illumina HiSeq 2000 platform was used to analyze transcriptome profiles of leaves under salt stress. Analysis results of sequencing data showed that 1124 transcripts were differentially expressed. Using the list of differentially expressed genes (DEGs), functional enrichment analyses of DEGs such as Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed. KEGG pathway enrichment analysis revealed that unigenes exhibiting differential expression were involved in starch and sucrose metabolism. Interestingly, trehalose-6-phosphate synthase (TPS) genes, of which expression was enhanced by abiotic stress, showed a significant difference in PsGAPDH-OX. Findings of this study suggest that PsGAPDH plays a role in the adaptation of rice plants to salt stress. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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16 pages, 3862 KiB  
Article
Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (Brassica rapa ssp. pekinensis) by Next-Generation Sequencing
by So-Jeong Kim, Jee-Soo Park, Yun-Hee Shin and Young-Doo Park
Genes 2021, 12(5), 621; https://doi.org/10.3390/genes12050621 - 22 Apr 2021
Cited by 10 | Viewed by 2339
Abstract
Transgenic plants are usually produced through tissue culture, which is an essential step in Agrobacterium-mediated plant transformation. However, genomic variations, termed somaclonal variations, have been detected in transgenic plants cultured in vitro. The occurrence of these variations should be as low as [...] Read more.
Transgenic plants are usually produced through tissue culture, which is an essential step in Agrobacterium-mediated plant transformation. However, genomic variations, termed somaclonal variations, have been detected in transgenic plants cultured in vitro. The occurrence of these variations should be as low as possible to secure the stability of transgenic crops. Determining the cause and mechanism of somaclonal variations in tissue culture-derived plants will help reduce the rate of variation and promote the stable expression of genes in transgenic plants. In order to determine the genetic variability in transgenic Chinese cabbage plants, we performed whole-genome resequencing and compared the sequencing data with the ‘CT001’ reference genome. The variation candidates that were expected to consistently occur in the transgenic lines were selected and validated. The single nucleotide polymorphism (SNP) and insertion and deletion (InDel) candidates were identified using the resequencing data and validated by reverse transcription (RT)-PCR analysis. The deduced amino acid sequences were used to determine whether the variations caused changes in the resulting polypeptide, and the annotations of the mutated genes were analyzed to predict the possible effects of the SNPs on gene function. In conclusion, we selected and validated the genetic variations identified in transgenic Chinese cabbage plants. Their genomes were expected to be affected by the process of Agrobacterium-mediated transformation. The findings of our study will provide a genetic basis for transgenic plant research. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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11 pages, 2682 KiB  
Article
Overexpression of a Pak Choi Gene, BcAS2, Causes Leaf Curvature in Arabidopsis thaliana
by Ye Lin, Hualan Hou, Yuhang Zhang and Xilin Hou
Genes 2021, 12(1), 102; https://doi.org/10.3390/genes12010102 - 15 Jan 2021
Cited by 8 | Viewed by 2609
Abstract
The LBD (Lateral Organ Boundaries Domain) family are a new group of plant-specific genes, which encode a class of transcription factors containing conserved Lateral Organization Boundary (LOB) domains, and play an important role in regulating the adaxial–abaxial polarity of plant leaves. In Arabidopsis [...] Read more.
The LBD (Lateral Organ Boundaries Domain) family are a new group of plant-specific genes, which encode a class of transcription factors containing conserved Lateral Organization Boundary (LOB) domains, and play an important role in regulating the adaxial–abaxial polarity of plant leaves. In Arabidopsis thaliana, ASYMMETRIC LEAVES 2 (AS2) has a typical LOB domain and is involved in determining the adaxial cell fate. In this study, we isolated the BcAS2 gene from the pak choi cultivar “NHCC001”, and analyzed its expression pattern. The results showed that the BcAS2 encoded a protein made up of 202 amino acid residues which were located in the nucleus and cytomembrane. The Yeast two-hybrid system (Y2H) assay indicated that BcAS2 interacts with BcAS1-1 and BcAS1-2 (the homologous genes of AS1 gene in pak choi). In the transgenic Arabidopsis thaliana that overexpressed BcAS2 gene, it presented an abnormal phenotype with a curly shape. Taken together, our findings not only validate the function of BcAS2 in leaf development in Arabidopsis thaliana, but also contribute in unravelling the molecular regulatory mechanism of BcAS2, which fulfills a special role by forming complexes with BcAS1-1/2 in the establishment of the adaxial–abaxial polarity of the lateral organs in pak choi. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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18 pages, 5749 KiB  
Article
Molecular Mechanism of Slow Vegetative Growth in Populus Tetraploid
by Congping Xu, Ying Zhang, Qiang Han and Xiangyang Kang
Genes 2020, 11(12), 1417; https://doi.org/10.3390/genes11121417 - 27 Nov 2020
Cited by 16 | Viewed by 2440
Abstract
Tetraploid plants often have altered rates of vegetative growth relative to their diploid progenitors. However, the molecular basis for altered growth rates remains a mystery. This study reports microRNA (miRNA) and gene expression differences in Populus tetraploids and counterpart diploids using RNA and [...] Read more.
Tetraploid plants often have altered rates of vegetative growth relative to their diploid progenitors. However, the molecular basis for altered growth rates remains a mystery. This study reports microRNA (miRNA) and gene expression differences in Populus tetraploids and counterpart diploids using RNA and miRNA sequencing. The results showed that there was no significant difference between young leaves in the expression of vegetative growth-related miRNAs. However, as leaves aged, the expression of auxin- and gibberellin-related miRNAs was significantly upregulated, while the expression of senescence-related miRNAs was significantly downregulated. The dose effect enhanced the negative regulation of the target genes with ARFs, GA20ox, GA3ox, and GAMYB being downregulated, and TCP and NAC being upregulated. As a result, the chloroplast degradation of tetraploid leaves was accelerated, the photosynthetic rate was decreased, and the synthesis and decomposition ability of carbohydrate was decreased. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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14 pages, 2516 KiB  
Article
Transcriptome Dynamics during Black and White Sesame (Sesamum indicum L.) Seed Development and Identification of Candidate Genes Associated with Black Pigmentation
by Linhai Wang, Senouwa Segla Koffi Dossou, Xin Wei, Yanxin Zhang, Donghua Li, Jingyin Yu and Xiurong Zhang
Genes 2020, 11(12), 1399; https://doi.org/10.3390/genes11121399 - 25 Nov 2020
Cited by 24 | Viewed by 3190
Abstract
Seed coat color is a crucial agronomic trait in sesame (Sesamum indicum L.) since it is strongly linked to seed oil, proteins, and lignans contents, and also influences consumer preferences. In East Asia, black sesame seed is used in the treatment [...] Read more.
Seed coat color is a crucial agronomic trait in sesame (Sesamum indicum L.) since it is strongly linked to seed oil, proteins, and lignans contents, and also influences consumer preferences. In East Asia, black sesame seed is used in the treatment and the prevention of various diseases. However, in sesame, little is known about the establishment of the seed coat color, and only one gene has been reported to control black pigmentation. This study provides an overview of developing seeds transcriptome of two varieties of sesame “Zhongfengzhi No.1” (white seed) and “Zhongzhi No.33” (black seed) and shed light on genes involving in black seed formation. Until eight days post-anthesis (DPA), both the seeds of the two varieties were white. The black sesame seed turned to yellow between 9 and 11 DPA and then black between 12 and 14 DPA. The black and white sesame showed similar trend-expressed genes with the numbers increased at the early stages of seed development. The differentially expressed genes (DEGs) number increased with seed development in the two sesame varieties. We examined the DEGs and uncovered that more were up-regulated at the early stages. The DEGs between the black and white sesame were mainly enriched in 37 metabolic pathways, among which the flavonoid biosynthesis and biosynthesis of secondary metabolites were dominants. Furthermore, we identified 20 candidate genes associated with pigment biosynthesis in black sesame seed, among which 10 were flavonoid biosynthesis and regulatory genes. These genes also include isochorismate and polyphenol oxidase genes. By comparing the phenotypes and genes expressions of the black and white sesame seed at different development stages, this work revealed the important role of 8–14 DPA in black pigment biosynthesis and accumulation. Moreover, it unfolded candidate genes associated with black pigmentation in sesame. These findings provide a vast transcriptome dataset and list of genes that will be targeted for functional studies related to the molecular mechanism involved in biosynthesis and regulation of seed coat color in sesame. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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18 pages, 4790 KiB  
Article
Genome-Wide Association Study of Root System Development at Seedling Stage in Rice
by Hongjia Zhang, Mar Lar San, Seong-Gyu Jang, Ja-Hong Lee, Na-Eun Kim, Ah-Rim Lee, So-Yeon Park, Fang-Yuan Cao, Joong-Hyoun Chin and Soon-Wook Kwon
Genes 2020, 11(12), 1395; https://doi.org/10.3390/genes11121395 - 25 Nov 2020
Cited by 12 | Viewed by 3828
Abstract
Root network structure plays a crucial role in growth and development processes in rice. Longer, more branched root structures help plants to assimilate water and nutrition from soil, support robust plant growth, and improve resilience to stresses such as disease. Understanding the molecular [...] Read more.
Root network structure plays a crucial role in growth and development processes in rice. Longer, more branched root structures help plants to assimilate water and nutrition from soil, support robust plant growth, and improve resilience to stresses such as disease. Understanding the molecular basis of root development through screening of root-related traits in rice germplasms is critical to future rice breeding programs. This study used a small germplasm collection of 137 rice varieties chosen from the Korean rice core set (KRICE_CORE) to identify loci linked to root development. Two million high-quality single nucleotide polymorphisms (SNPs) were used as the genotype, with maximum root length (MRL) and total root weight (TRW) in seedlings used as the phenotype. Genome-wide association study (GWAS) combined with Principal Components Analysis (PCA) and Kinship matrix analysis identified four quantitative trait loci (QTLs) on chromosomes 3, 6, and 8. Two QTLs were linked to MRL and two were related to TRW. Analysis of Linkage Disequilibrium (LD) decay identified a 230 kb exploratory range for detection of candidate root-related genes. Candidates were filtered using RNA-seq data, gene annotations, and quantitative real-time PCR (qRT-PCR), and five previously characterized genes related to root development were identified, as well as four novel candidate genes. Promoter analysis of candidate genes showed that LOC_Os03g08880 and LOC_Os06g13060 contained SNPs with the potential to impact gene expression in root-related promoter motifs. Haplotype analysis of candidate genes revealed diverse haplotypes that were significantly associated with phenotypic variation. Taken together, these results indicate that LOC_Os03g08880 and LOC_Os06g13060 are strong candidate genes for root development functions. The significant haplotypes identified in this study will be beneficial in future breeding programs for root improvement. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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Review

Jump to: Editorial, Research

13 pages, 769 KiB  
Review
Interspecific Hybridization of Transgenic Brassica napus and Brassica rapa—An Overview
by Soo-In Sohn, Senthil Kumar Thamilarasan, Subramani Pandian, Young-Ju Oh, Tae-Hun Ryu, Gang-Seob Lee and Eun-Kyoung Shin
Genes 2022, 13(8), 1442; https://doi.org/10.3390/genes13081442 - 13 Aug 2022
Cited by 11 | Viewed by 3243
Abstract
In nature, interspecific hybridization occurs frequently and can contribute to the production of new species or the introgression of beneficial adaptive features between species. It has great potential in agricultural systems to boost the process of targeted crop improvement. In the advent of [...] Read more.
In nature, interspecific hybridization occurs frequently and can contribute to the production of new species or the introgression of beneficial adaptive features between species. It has great potential in agricultural systems to boost the process of targeted crop improvement. In the advent of genetically modified (GM) crops, it has a disadvantage that it involves the transgene escaping to unintended plants, which could result in non-specific weedy crops. Several crop species in the Brassica genus have close kinship: canola (Brassica napus) is an ancestral hybrid of B. rapa and B. oleracea and mustard species such as B. juncea, B. carinata, and B. nigra share common genomes. Hence, intraspecific hybridization among the Brassica species is most common, especially between B. napus and B. rapa. In general, interspecific hybrids cause numerous genetic and phenotypic changes in the parental lines. Consequently, their fitness and reproductive ability are also highly varied. In this review, we discuss the interspecific hybridization and reciprocal hybridization studies of B. napus and B. rapa and their potential in the controlled environment. Further, we address the fate of transgenes (herbicide resistance) and their ability to transfer to their progenies or generations. This could help us to understand the environmental influence of interspecific hybrids and how to effectively manage their transgene escape in the future. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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24 pages, 1958 KiB  
Review
Metabolomics for Crop Breeding: General Considerations
by Dmitry Y. Litvinov, Gennady I. Karlov and Mikhail G. Divashuk
Genes 2021, 12(10), 1602; https://doi.org/10.3390/genes12101602 - 12 Oct 2021
Cited by 12 | Viewed by 3168
Abstract
The development of new, more productive varieties of agricultural crops is becoming an increasingly difficult task. Modern approaches for the identification of beneficial alleles and their use in elite cultivars, such as quantitative trait loci (QTL) mapping and marker-assisted selection (MAS), are effective [...] Read more.
The development of new, more productive varieties of agricultural crops is becoming an increasingly difficult task. Modern approaches for the identification of beneficial alleles and their use in elite cultivars, such as quantitative trait loci (QTL) mapping and marker-assisted selection (MAS), are effective but insufficient for keeping pace with the improvement of wheat or other crops. Metabolomics is a powerful but underutilized approach that can assist crop breeding. In this review, basic methodological information is summarized, and the current strategies of applications of metabolomics related to crop breeding are explored using recent examples. We briefly describe classes of plant metabolites, cellular localization of metabolic pathways, and the strengths and weaknesses of the main metabolomics technique. Among the commercialized genetically modified crops, about 50 with altered metabolic enzyme activities have been identified in the International Service for the Acquisition of Agri-biotech Applications (ISAAA) database. These plants are reviewed as encouraging examples of the application of knowledge of biochemical pathways. Based on the recent examples of metabolomic studies, we discuss the performance of metabolic markers, the integration of metabolic and genomic data in metabolic QTLs (mQTLs) and metabolic genome-wide association studies (mGWAS). The elucidation of metabolic pathways and involved genes will help in crop breeding and the introgression of alleles of wild relatives in a more targeted manner. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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12 pages, 674 KiB  
Review
Plant Variety Protection: Current Practices and Insights
by Ju-Kyung Yu and Yong-Suk Chung
Genes 2021, 12(8), 1127; https://doi.org/10.3390/genes12081127 - 25 Jul 2021
Cited by 17 | Viewed by 4644
Abstract
Breeders persistently supply farmers with the best varieties in order to exceed consumer demand through plant-breeding processes that are resource-intensive. In order to motivate continuous innovation in variety development, a system needs to provide incentives for plant breeders to develop superior varieties, for [...] Read more.
Breeders persistently supply farmers with the best varieties in order to exceed consumer demand through plant-breeding processes that are resource-intensive. In order to motivate continuous innovation in variety development, a system needs to provide incentives for plant breeders to develop superior varieties, for example, exclusive ownership to produce and market those varieties. The most common system is the acquisition of intellectual property protection through plant variety protection, also known as the breeder’s right. Most countries have adopted the system established by the International Union for the Protection of New Varieties of Plants (UPOV). To be granted plant variety protection, the variety should prove to be unique by meeting three requirements: distinctness, uniformity, and stability. This review summarizes (1) the plant variety protection via UPOV convention, (2) technical methods for distinctness, uniformity, and stability testing via phenotype, molecular markers, and sequencing as well as their challenges and potentiality, and (3) additional discussions in essentially derived variety, value for cultivation and use testing, and open source seed initiative. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding)
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