Topic Editors

School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
Nutrition Institute, Tržaška 40, SI-1000 Ljubljana, Slovenia
Dept. of Applied Biosciences, Kyungpook National Univeristy, Daegu 41599, Korea

Advanced Breeding Technology for Plants

Abstract submission deadline
closed (20 December 2022)
Manuscript submission deadline
closed (28 February 2023)
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43552

Topic Information

Dear Colleagues,

Food security is one of the major global challenges that we face; specifically, the requirement to feed a global population of 9.2 billion by 2050. Thus, crop production should increase by 70% due to the increase in world population and the effect of climate change (FAO, 2009). However, climate change can dramatically reduce agricultural productivity. Thus, the improvement of cultivars in limited resources may be required for resolving the food security issues in the world. With the advent of new biological technologies, next-generation sequencing, high-throughput phenomics and high-throughput genotyping can be available to use in crop breeding programs for accelerating the development of new or improved cultivars. Phenomics may predict complex traits such as abiotic stresses, and genomics can be an approach in gene discovery for interested traits and development of molecular markers. In addition, these high throughput technologies can be used for plant selection in breeding programs. This Topic aims to promote research on plant breeding with a new advanced selection methods by the utilization of marker-assisted selection, genomics, and phenomics, leading the improvement of crop yield, seed quality, and abiotic stresses in plants. In this Topic, we encourage all original research papers, or reviews on the development of cultivars and relationships between phenotype and genotype using a new plant science approach. This includes plant breeding, advanced selection methods, molecular markers, and genomic selection. Obviously, papers relating to genomics and phenomics are extremely welcome.

Dr. Jeong-Dong Lee
Prof. Dr. Ivan Kreft
Prof. Dr. Hyun Jo
Topic Editors

Keywords

  • plant
  • breeding
  • advanced selection method
  • phenomics for selection
  • molecular maker
  • genomic selection

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Agriculture
agriculture
3.6 4.9 2011 17.7 Days CHF 2600
Agronomy
agronomy
3.7 6.2 2011 15.8 Days CHF 2600
Crops
crops
- - 2021 30.5 Days CHF 1000
Horticulturae
horticulturae
3.1 3.5 2015 14.7 Days CHF 2200
Plants
plants
4.5 6.5 2012 15.3 Days CHF 2700

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Published Papers (20 papers)

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20 pages, 13230 KiB  
Article
Genome-Wide Identification and Characterization of WRKY Transcription Factors and Their Expression Profile in Loropetalum chinense var. rubrum
by Yang Liu, Yifan Zhang, Yang Liu, Ling Lin, Xingyao Xiong, Donglin Zhang, Sha Li, Xiaoying Yu and Yanlin Li
Plants 2023, 12(11), 2131; https://doi.org/10.3390/plants12112131 - 27 May 2023
Cited by 3 | Viewed by 1593
Abstract
The WRKY gene family plays important roles in plant growth and development, as well as in the responses to biotic and abiotic stresses. Loropetalum chinense var. rubrum has high ornamental and medicinal value. However, few WRKY genes have been reported in this plant, and [...] Read more.
The WRKY gene family plays important roles in plant growth and development, as well as in the responses to biotic and abiotic stresses. Loropetalum chinense var. rubrum has high ornamental and medicinal value. However, few WRKY genes have been reported in this plant, and their functions remain unknown. To explore the roles that the WRKY genes play in L. chinense var. rubrum, we identified and characterized 79 LcWRKYs through BLAST homology analysis and renamed them (as LcWRKY1–79) based on their distribution on the chromosomes of L. chinense var. rubrum. In this way, according to their structural characteristics and phylogenetic analysis, they were divided into three groups containing 16 (Group I), 52 (Group II), and 11 (Group III) WRKYs, respectively. LcWRKYs in the same group have similar motifs and gene structures; for instance, Motifs 1, 2, 3, 4, and 10 constitute the WRKY domain and zinc-finger structure. The LcWRKY promoter region contains light response elements (ACE, G-box), stress response elements (TC-rich repeats), hormone response elements (TATC-box, TCA-element), and MYB binding sites (MBS, MBSI). Synteny analysis of LcWRKYs allowed us to establish orthologous relationships among the WRKY gene families of Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum L., Vitis vinifera L., Oryza sativa L., and Zea mays L.; furthermore, analysis of the transcriptomes of mature leaves and flowers from different cultivars demonstrated the cultivar-specific LcWRKY gene expression. The expression levels of certain LcWRKY genes also presented responsive changes from young to mature leaves, based on an analysis of the transcriptome in leaves at different developmental stages. White light treatment led to a significant decrease in the expression of LcWRKY6, 18, 24, 34, 36, 44, 48, 61, 62, and 77 and a significant increase in the expression of LcWRKY41, blue light treatment led to a significant decrease in the expression of LcWRKY18, 34, 50, and 77 and a significant increase in the expression of LcWRKY36 and 48. These results enable a better understanding of LcWRKYs, facilitating the further exploration of their genetic functions and the molecular breeding of L. chinense var. rubrum. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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10 pages, 299 KiB  
Article
Combining a Mutant Allele of FAD2-1A with HD Improves the ω-6/ω-3 Ratio in Soybeans
by Hwayeop Kim, Hyun Jo and Jeong-Dong Lee
Agronomy 2023, 13(3), 913; https://doi.org/10.3390/agronomy13030913 - 19 Mar 2023
Cited by 1 | Viewed by 1402
Abstract
The intake of foods with unbalanced ω-6/ω-3 ratios causes various health problems. Commodity soybeans generally have a ω-6/ω-3 ratio of 6–7:1. The recommended ratio in terms of health benefits is <4:1. This study aimed to identify the appropriate combination of mutant alleles that [...] Read more.
The intake of foods with unbalanced ω-6/ω-3 ratios causes various health problems. Commodity soybeans generally have a ω-6/ω-3 ratio of 6–7:1. The recommended ratio in terms of health benefits is <4:1. This study aimed to identify the appropriate combination of mutant alleles that can reduce the ω-6/ω-3 ratio using three segregating soybean populations. F2 individuals from each population were genotyped for three different alleles of microsomal delta-12 fatty acid desaturase 2 enzyme (FAD2-1A) and an allele of homeodomain-like transcriptional regulator (HD) genes, and their five major fatty acids were assessed. F2 seeds carrying both fad2-1a and hd had slightly different ω-6/ω-3 ratios according to the different fad2-1a alleles. The fad2-1aDEL, fad2-1aS117N, and fad2-1aW293STOP alleles combined with a hd allele resulted in ω-6/ω-3 ratios with a range of 1.9–2.7:1, 2.7–3.9:1, and 2.6–3.6:1 in soybean seeds, respectively. This study revealed that the induction of mutations in FAD2-1ADEL and HD was the most efficient strategy to improve the ω-6/ω-3 ratio and elevate the ω-3 fatty acid concentrations in soybean seeds. These results provide useful information in soybean breeding programs to release a new soybean cultivar with a lower ω-6/ω-3 ratio and elevated ω-3 fatty acids, which can be a beneficial ingredient for soybean-based foods. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
17 pages, 3952 KiB  
Article
Specific Gibberellin 2-Oxidase 3 (SbGA2ox3) Mutants Promote Yield and Stress Tolerance in Sorghum bicolor
by Wenfeng Weng, Yong Tang, Ruiqi Xiong, Qing Bai, Anjing Gao, Xin Yao, Weijiao Wu, Chao Ma, Jianping Cheng and Jingjun Ruan
Agronomy 2023, 13(3), 908; https://doi.org/10.3390/agronomy13030908 - 18 Mar 2023
Cited by 2 | Viewed by 1603
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a raw material that can be used as food, feed, bioenergy, and wine; it is also a gramineous crop with drought, salt, waterlogging, and high temperature resistance. However, liquor-making sorghum faces the disadvantages of having a [...] Read more.
Sorghum (Sorghum bicolor (L.) Moench) is a raw material that can be used as food, feed, bioenergy, and wine; it is also a gramineous crop with drought, salt, waterlogging, and high temperature resistance. However, liquor-making sorghum faces the disadvantages of having a narrow genetic basis, poor resources, and few high-quality varieties. Ethyl methane sulfonate (EMS) is a common alkylating agent that can react with one or more bases to alkylate and cause changes in the molecular structure of DNA, thereby causing mutations. It has a minimum effect on organisms and the highest efficiency. The obtained mutant populations are of great significance for cultivating new plant varieties and enriching plant germplasm resources. Therefore, in this study, ‘Hongyingzi’ a liquor-making sorghum variety, was studied using seeds treated with 0.5% EMS and 415 M3 generation plants were obtained. (1) Investigation and statistical analysis of agronomic traits in mutant libraries showed that in the M3 generation, nine important phenotypic mutant lines were obtained, including plant type, leaf blade, spike, glume, growth period, fertility, plant height, and drought resistance. The variation frequency from high to low was as follows: glume color (75.42%) > spike type (54.70%) > spike shape (47.23%) > chaff coating degree (28%) > plant growth period (23.86%) > plant height (23.61%) > absorption degree (16.14%) > branchiness (10.84%) > leaf color (4.58%) > tillering (2.16%). (2) The PCR sequencing of SbGA2ox3 from 415 sorghum M3 plants revealed that the mutation frequency of SbGA2ox3 was 1/99.02 kb. Eight plants underwent mutations, but only one line experienced missense mutations of different amino acid types, changing Ser/Ala/Val/Leu/Gln/Ser/Pro/Ala to Asn/Thr/Gly/Val/Gln/Ala/Ser. The mutant line also had shorter plant height, reduced glume coating degree, and enhanced drought resistance. The constructions of the sorghum mutant library widened the sorghum germplasm library and provided a method for sorghum breeding with a molecular basis for the functional verification of related genes and the analysis of related regulatory networks. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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13 pages, 2638 KiB  
Article
Genetic Diversity of Korean Wild Soybean Core Collections and Genome-Wide Association Study for Days to Flowering
by Hyun Jo, Bo-Keun Ha, Soo-Kwon Park, Soon-Chun Jeong, Jeong-Dong Lee and Jung-Kyung Moon
Plants 2023, 12(6), 1305; https://doi.org/10.3390/plants12061305 - 14 Mar 2023
Cited by 1 | Viewed by 1508
Abstract
The utilization of wild soybean germplasms in breeding programs increases genetic diversity, and they contain the rare alleles of traits of interest. Understanding the genetic diversity of wild germplasms is essential for determining effective strategies that can improve the economic traits of soybeans. [...] Read more.
The utilization of wild soybean germplasms in breeding programs increases genetic diversity, and they contain the rare alleles of traits of interest. Understanding the genetic diversity of wild germplasms is essential for determining effective strategies that can improve the economic traits of soybeans. Undesirable traits make it challenging to cultivate wild soybeans. This study aimed to construct a core subset of 1467 wild soybean accessions of the total population and analyze their genetic diversity to understand their genetic variations. Genome-wild association studies were conducted to detect the genetic loci underlying the time to flowering for a core subset collection, and they revealed the allelic variation in E genes for predicting maturity using the available resequencing data of wild soybean. Based on principal component and cluster analyses, 408 wild soybean accessions in the core collection covered the total population and were explained by 3 clusters representing the collection regions, namely, Korea, China, and Japan. Most of the wild soybean collections in this study had the E1e2E3 genotype according to association mapping and a resequencing analysis. Korean wild soybean core collections can provide helpful genetic resources to identify new flowering and maturity genes near the E gene loci and genetic materials for developing new cultivars, facilitating the introgression of genes of interest from wild soybean. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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17 pages, 4319 KiB  
Article
Genome-Wide Association Study and Genomic Prediction on Plant Architecture Traits in Sweet Corn and Waxy Corn
by Dongdong Dang, Yuan Guan, Hongjian Zheng, Xuecai Zhang, Ao Zhang, Hui Wang, Yanye Ruan and Li Qin
Plants 2023, 12(2), 303; https://doi.org/10.3390/plants12020303 - 9 Jan 2023
Cited by 4 | Viewed by 2667
Abstract
Sweet corn and waxy corn has a better taste and higher accumulated nutritional value than regular maize, and is widely planted and popularly consumed throughout the world. Plant height (PH), ear height (EH), and tassel branch number (TBN) are key plant architecture traits, [...] Read more.
Sweet corn and waxy corn has a better taste and higher accumulated nutritional value than regular maize, and is widely planted and popularly consumed throughout the world. Plant height (PH), ear height (EH), and tassel branch number (TBN) are key plant architecture traits, which play an important role in improving grain yield in maize. In this study, a genome-wide association study (GWAS) and genomic prediction analysis were conducted on plant architecture traits of PH, EH, and TBN in a fresh edible maize population consisting of 190 sweet corn inbred lines and 287 waxy corn inbred lines. Phenotypic data from two locations showed high heritability for all three traits, with significant differences observed between sweet corn and waxy corn for both PH and EH. The differences between the three subgroups of sweet corn were not obvious for all three traits. Population structure and PCA analysis results divided the whole population into three subgroups, i.e., sweet corn, waxy corn, and the subgroup mixed with sweet and waxy corn. Analysis of GWAS was conducted with 278,592 SNPs obtained from resequencing data; 184, 45, and 68 significantly associated SNPs were detected for PH, EH, and TBN, respectively. The phenotypic variance explained (PVE) values of these significant SNPs ranged from 3.50% to 7.0%. The results of this study lay the foundation for further understanding the genetic basis of plant architecture traits in sweet corn and waxy corn. Genomic selection (GS) is a new approach for improving quantitative traits in large plant breeding populations that uses whole-genome molecular markers. The marker number and marker quality are essential for the application of GS in maize breeding. GWAS can choose the most related markers with the traits, so it can be used to improve the predictive accuracy of GS. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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20 pages, 851 KiB  
Review
Inter-Specific Hybridization in Cotton (Gossypium hirsutum) for Crop Improvement
by Muhammad Anwar, Muhammad Zafar Iqbal, Aamir Ali Abro, Shabana Memon, Liaquat Ali Bhutto, Shamim Ara Memon and Yan Peng
Agronomy 2022, 12(12), 3158; https://doi.org/10.3390/agronomy12123158 - 13 Dec 2022
Cited by 2 | Viewed by 3594
Abstract
Interspecific hybridization has contributed significantly to land diversity, species evolution, and crops’ domestication, including upland cotton, the cultivated form of Gossypium hirsutum. Being the world’s most important fiber crop species, Gossypium hirsutum belongs to the allotetraploid Gossypium consisting of six additional tetraploid [...] Read more.
Interspecific hybridization has contributed significantly to land diversity, species evolution, and crops’ domestication, including upland cotton, the cultivated form of Gossypium hirsutum. Being the world’s most important fiber crop species, Gossypium hirsutum belongs to the allotetraploid Gossypium consisting of six additional tetraploid species. The lint fiber evolved once in diploid parent A-genome species in the Gossypium’s history and passed on during hybridization of the A-genome with the D-genome and was maintained in subsequent evolution. The domestication history of G. hirsutum involved the collection and use of lint fibers by indigenous people for the purpose of making strings and other textile products; hence, spinnable lint fibers were likely to have evolved under domestication. Crossing with G. barbadense has resulted in the development of multiple genetic lines in contemporary upland cotton. However, in later-generation hybrids between G. hirsutum and other polyploid species, reproductive barriers such as reduced fertility, segregation distortion, and hybrid breakdown are frequently observed, complicating the task of introgressing new, stably inherited allelic variation from inter-specific hybridization. Recent efforts in molecular genetics research have provided insights into the location and effects of QTLs from wild species that are associated with traits important to cotton production. These and future research efforts will undoubtedly provide the tools that can be utilized by plant breeders to access novel genes from wild and domesticated allotetraploid Gossypium for upland cotton improvement. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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19 pages, 5104 KiB  
Article
Low-Density Reference Fingerprinting SNP Dataset of CIMMYT Maize Lines for Quality Control and Genetic Diversity Analyses
by Jingtao Qu, Alberto A. Chassaigne-Ricciulli, Fengling Fu, Haoqiang Yu, Kate Dreher, Sudha K. Nair, Manje Gowda, Yoseph Beyene, Dan Makumbi, Thanda Dhliwayo, Felix San Vicente, Michael Olsen, Boddupalli M. Prasanna, Wanchen Li and Xuecai Zhang
Plants 2022, 11(22), 3092; https://doi.org/10.3390/plants11223092 - 14 Nov 2022
Cited by 1 | Viewed by 1778
Abstract
CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that [...] Read more.
CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that can be used to perform quality control (QC) and genetic diversity analyses. The QC analysis identified 25 CMLs with purity, identity, or mislabeling issues. Further field observation, purification, and re-genotyping of these CMLs are required. The reference fingerprinting SNP dataset was developed for all of the currently released CMLs with 152 high-quality SNPs. The results of principal component analysis and average genetic distances between subgroups showed a clear genetic divergence between temperate and tropical maize, whereas the three tropical subgroups partially overlapped with one another. More than 99% of the pairs of CMLs had genetic distances greater than 0.30, showing their high genetic diversity, and most CMLs are distantly related. The heterotic patterns, estimated with the molecular markers, are consistent with those estimated using pedigree information in two major maize breeding programs at CIMMYT. These research findings are helpful for ensuring the regeneration and distribution of the true CMLs, via QC analysis, and for facilitating the effective utilization of the CMLs, globally. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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24 pages, 5096 KiB  
Article
Identification of SNPs and Candidate Genes Associated with Salt Stress in Two Korean Sorghum Cultivars and Understanding Selection Pressures in the Breeding Process
by Donghyun Jeon, Solji Lee, Sehyun Choi, Yuna Kang and Changsoo Kim
Agronomy 2022, 12(10), 2511; https://doi.org/10.3390/agronomy12102511 - 14 Oct 2022
Cited by 1 | Viewed by 1495
Abstract
One of the abiotic stresses, salt stress, has an impact on the production and development of crops around the world. Sorghum is a functional genomics model crop of C4 plants due to its small genome size, and it is suitable for providing a [...] Read more.
One of the abiotic stresses, salt stress, has an impact on the production and development of crops around the world. Sorghum is a functional genomics model crop of C4 plants due to its small genome size, and it is suitable for providing a clue to the mechanism associated with salt tolerance at the transcriptomic level. However, the mechanism of salt-related genes in sorghum has not been well described. RNA sequencing, using QuantSeq, was performed on two Korean cultivars, ‘Sodamchal’ and ‘Nampungchal’, which are known to have different intensities in response to salt stress, between a control and high-salinity treatment over a different time-course. In addition, physiological responses such as the proline, anthocyanin, chlorophyll, and reducing sugar contents were evaluated under the salt-stress treatment between these two sorghum cultivars. Moreover, differentially expressed genes (DEGs) between the Nampungchal and Sodamchal cultivars were identified in their leaves and roots, respectively. Moreover, the function of DEGs was confirmed through GO classification and KEGG pathway. We also analyzed the correlation between the selection pressure with DEGs by identifying Ka/Ks of DEGs. In the breeding process, the role of positive or negative selected genes was analyzed. Therefore, a new hypothesis on selection pressure was proposed from the breeding perspective of cultivars. A comparative analysis of the two sorghum cultivars provides candidate genes involved in the salt-stress response and may offer a better understanding of the salt-tolerance mechanism in sorghum. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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25 pages, 9253 KiB  
Article
Leaf Count Aided Novel Framework for Rice (Oryza sativa L.) Genotypes Discrimination in Phenomics: Leveraging Computer Vision and Deep Learning Applications
by Mukesh Kumar Vishal, Rohit Saluja, Devarshi Aggrawal, Biplab Banerjee, Dhandapani Raju, Sudhir Kumar, Viswanathan Chinnusamy, Rabi Narayan Sahoo and Jagarlapudi Adinarayana
Plants 2022, 11(19), 2663; https://doi.org/10.3390/plants11192663 - 10 Oct 2022
Cited by 2 | Viewed by 2157
Abstract
Drought is a detrimental factor to gaining higher yields in rice (Oryza sativa L.), especially amid the rising occurrence of drought across the globe. To combat this situation, it is essential to develop novel drought-resilient varieties. Therefore, screening of drought-adaptive genotypes is [...] Read more.
Drought is a detrimental factor to gaining higher yields in rice (Oryza sativa L.), especially amid the rising occurrence of drought across the globe. To combat this situation, it is essential to develop novel drought-resilient varieties. Therefore, screening of drought-adaptive genotypes is required with high precision and high throughput. In contemporary emerging science, high throughput plant phenotyping (HTPP) is a crucial technology that attempts to break the bottleneck of traditional phenotyping. In traditional phenotyping, screening significant genotypes is a tedious task and prone to human error while measuring various plant traits. In contrast, owing to the potential advantage of HTPP over traditional phenotyping, image-based traits, also known as i-traits, were used in our study to discriminate 110 genotypes grown for genome-wide association study experiments under controlled (well-watered), and drought-stress (limited water) conditions, under a phenomics experiment in a controlled environment with RGB images. Our proposed framework non-destructively estimated drought-adaptive plant traits from the images, such as the number of leaves, convex hull, plant–aspect ratio (plant spread), and similarly associated geometrical and morphological traits for analyzing and discriminating genotypes. The results showed that a single trait, the number of leaves, can also be used for discriminating genotypes. This critical drought-adaptive trait was associated with plant size, architecture, and biomass. In this work, the number of leaves and other characteristics were estimated non-destructively from top view images of the rice plant for each genotype. The estimation of the number of leaves for each rice plant was conducted with the deep learning model, YOLO (You Only Look Once). The leaves were counted by detecting corresponding visible leaf tips in the rice plant. The detection accuracy was 86–92% for dense to moderate spread large plants, and 98% for sparse spread small plants. With this framework, the susceptible genotypes (MTU1010, PUSA-1121 and similar genotypes) and drought-resistant genotypes (Heera, Anjali, Dular and similar genotypes) were grouped in the core set with a respective group of drought-susceptible and drought-tolerant genotypes based on the number of leaves, and the leaves’ emergence during the peak drought-stress period. Moreover, it was found that the number of leaves was significantly associated with other pertinent morphological, physiological and geometrical traits. Other geometrical traits were measured from the RGB images with the help of computer vision. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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15 pages, 3670 KiB  
Article
Improving Broad Spectrum Blast Resistance by Introduction of the Pita2 Gene: Encoding the NB-ARC Domain of Blast-Resistant Proteins into Upland Rice Breeding Programs
by Reny Herawati, Siti Herlinda, Dwi Wahyuni Ganefianti, Hendri Bustamam and Sipriyadi
Agronomy 2022, 12(10), 2373; https://doi.org/10.3390/agronomy12102373 - 30 Sep 2022
Cited by 1 | Viewed by 1829
Abstract
Blast disease is generally more important in upland rather than lowland rice cultivation, representing one of the biotic obstacles in the development of upland rice. The objective of this study was to detect broad-spectrum blast resistance gene Pita2 encoding the NB-ARC (nucleotide-binding adaptor [...] Read more.
Blast disease is generally more important in upland rather than lowland rice cultivation, representing one of the biotic obstacles in the development of upland rice. The objective of this study was to detect broad-spectrum blast resistance gene Pita2 encoding the NB-ARC (nucleotide-binding adaptor common in APAF-1, R proteins, and CED-4) domain of blast-resistant proteins in new upland rice lines from the breeding program for landrace rice varieties, with the goal of providing a novel source of blast-resistant germplasm for application in future upland rice breeding programs. In this study, we screened 19 inbred lines of landrace rice varieties challenged using local virulent isolates in greenhouse conditions and performed field evaluations to confirm blast resistance. Molecular analysis was conducted using six specific primers to detect broad-spectrum blast resistance, and sequence analysis was performed to detect the NB-ARC domain of blast-resistant proteins in the lines. Consistent results were observed between greenhouse screening and field evaluations, although there was variance in the level of resistance. The PCR assay showed that there were eight positive lines (G7, G8, G9, G11, G13, G14, G15, and G18) containing the Pita2 gene. Conserved domain analysis revealed that eight blast-resistant rice lines encode NB-ARC at sequence lengths ranging between 300 and 870 (450 bp). Using these sequences in BLASTX searching revealed 15 gene homologs of the eight rice lines, which were detected as Pita2 genes, with a similarity level of 81–99%. Further comprehensive studies should be performed to confirm the performance and resistance of candidate lines in field trials in various blast-endemic areas before being released as new upland rice varieties able to overcome the problem of blast disease in the field. In addition, the lines can also be used as a novel genetic resource in the blast-resistant upland rice breeding program on various rice cultivars. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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13 pages, 1965 KiB  
Article
Comparison of Hyperspectral Imagery and Physiological Characteristics of Bentazone-Tolerant and -Susceptible Soybean Cultivars
by Liakat Ali, Hyun Jo, Seung Min Choi, Yoonha Kim, Jong Tae Song and Jeong-Dong Lee
Agronomy 2022, 12(10), 2241; https://doi.org/10.3390/agronomy12102241 - 20 Sep 2022
Cited by 2 | Viewed by 1739
Abstract
Bentazone is a broadleaf post-emergence herbicide widely used for crop production that inhibits photosynthetic activity, resulting in phytotoxicity and injury in plants. Evaluating and identifying herbicide-tolerant genotypes is a critical step in plant breeding programs. In this study, we determined the reaction of [...] Read more.
Bentazone is a broadleaf post-emergence herbicide widely used for crop production that inhibits photosynthetic activity, resulting in phytotoxicity and injury in plants. Evaluating and identifying herbicide-tolerant genotypes is a critical step in plant breeding programs. In this study, we determined the reaction of 138 Korean soybean cultivars to bentazone using visual evaluation, and selected cultivars were further evaluated to determine the effects of bentazone on physiological parameters. For physiological parameters, we measured the normalized difference vegetation index (NDVI) from hyperspectral reflectance images. From 2 to 4 DAT, the NDVI for two sensitive cultivars was between 0.60 and 0.69, while the NDVI for tolerant cultivars was between 0.70 and 0.86. Photosynthesis rate (A), transpiration (E), stomatal conductance (gsw), and total conductance of CO2 (gtc) were measured using chlorophyll fluorescence. Visual score evaluation showed that moderate bentazone-tolerant cultivars were predominant among the Korean cultivars. For physiological measurements, differences in NDVI were detected between bentazone-tolerant and -sensitive cultivars 2 days after treatment (DAT). However, the A, E, gsw, and gtc levels dramatically decreased 1 DAT in the sensitive cultivars. This study provides insights into the tolerance and sensitivity of soybeans to bentazone. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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23 pages, 5155 KiB  
Article
Molecular, Histological and Histochemical Responses of Banana Cultivars Challenged with Fusarium oxysporum f. sp. cubense with Different Levels of Virulence
by Anelita de Jesus Rocha, Julianna Matos da Silva Soares, Fernanda dos Santos Nascimento, Adailson dos Santos Rocha, Vanusia Batista Oliveira de Amorim, Andresa Priscila de Souza Ramos, Cláudia Fortes Ferreira, Fernando Haddad and Edson Perito Amorim
Plants 2022, 11(18), 2339; https://doi.org/10.3390/plants11182339 - 7 Sep 2022
Cited by 3 | Viewed by 2479
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is the most limiting factor in the banana agribusiness worldwide. Therefore, studies regarding pathogen attack mechanisms, and especially host defense responses, in this pathosystem are of utmost importance for genetic breeding programs in [...] Read more.
Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is the most limiting factor in the banana agribusiness worldwide. Therefore, studies regarding pathogen attack mechanisms, and especially host defense responses, in this pathosystem are of utmost importance for genetic breeding programs in the development of Foc-resistant banana cultivars. In this study, analysis at the molecular, histological and histochemical levels of the Musa spp. x Foc interaction was performed. Three Foc isolates representative of race 1 (R1), subtropical race 4 (ST4) and isolate 229A, which is a putative ST4, were inoculated in two Prata-type cultivars (Prata-Anã and BRS Platina) and one cultivar of the Cavendish type (Grand Naine). Of seven genes related to plant–pathogen interactions, five were overexpressed in ‘BRS Platina’ 12 h after inoculation (HAI) with Foc R1 and ST4 but had reduced or negative expression after inoculation with Foc 229A, according to RT–qPCR analyses. While hyphae, mycelia and spores of the Foc 229A isolate grow towards the central cylinder of the Grand Naine and Prata-Anã cultivars, culminating in the occlusion of the xylem vessels, the BRS Platina cultivar responds with increased presence of cellulose, phenolic compounds and calcium oxalate crystals, reducing colonization within 30 days after inoculation (DAI). In general, these data indicate that the cultivar BRS Platina has potential for use in banana-breeding programs focused on resistance to Foc tropical race 4 (TR4) and in aggregating information on the virulence relationships of the Foc pathogen and the defense responses of banana plants after infection. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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12 pages, 1340 KiB  
Article
Novel Allele of FAD2-1A from an EMS-Induced Mutant Soybean Line (PE529) Produces Elevated Levels of Oleic Acid in Soybean Oil
by Hyun Jo, Changwan Woo, Nabachwa Norah, Jong Tae Song and Jeong-Dong Lee
Agronomy 2022, 12(9), 2115; https://doi.org/10.3390/agronomy12092115 - 6 Sep 2022
Cited by 3 | Viewed by 1783
Abstract
Soybean seed oils contain approximately 23% oleic acid, and elevated amounts of oleic acid help prevent cardiovascular diseases and improve the quality of the oil. Chemically, it helps maintain the oxidative stability of oil; hence, soybean breeders primarily seek to increase its concentration [...] Read more.
Soybean seed oils contain approximately 23% oleic acid, and elevated amounts of oleic acid help prevent cardiovascular diseases and improve the quality of the oil. Chemically, it helps maintain the oxidative stability of oil; hence, soybean breeders primarily seek to increase its concentration for improved oil quality. As soybean seeds with mutant alleles of FAD2-1A and FAD2-1B genes have been reported to produce approximately 80% of oleic acid, a mutant population was developed from an ethyl methanesulfonate (EMS)-induced soybean cultivar (Pungsannamul). From this, a new mutant allele of FAD2-1A was identified using mutant lines with elevated oleic acid levels and the pooled-DNA sequencing method. This study identified PE529 as the allele with >40% oleic acid carrying the novel allele of the FAD2-1A gene. The single nucleotide polymorphism (SNP) in PE529 also induced the conversion from tryptophan to a premature stop codon at position 293 in the amino acid sequence (W293STOP). The inheritance analysis showed that the elevated oleic acids in PE529 were attributed to the fad2-1a W293STOP allele. In this study, seeds capable of producing approximately 80.0% oleic acid were identified from F2 populations where fad2-1a W293STOP and fad2-1b alleles were segregated. Hence, soybeans with novel alleles are useful genetic resources to improve soybean oil quality in breeding programs. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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19 pages, 3507 KiB  
Article
Characterizations of MYB Transcription Factors in Camellia oleifera Reveal the Key Regulators Involved in Oil Biosynthesis
by Sijia Li, Hu Huang, Xianjin Ma, Zhikang Hu, Jiyuan Li and Hengfu Yin
Horticulturae 2022, 8(8), 742; https://doi.org/10.3390/horticulturae8080742 - 18 Aug 2022
Cited by 2 | Viewed by 1998
Abstract
MYB (myeloblastosis) transcription factors plays an important role in various physiological and biochemical processes in plants. However, little is known about the regulatory roles of MYB family genes underlying seed oil biosynthesis in Camellia oleifera. To identify potential regulators, we performed the [...] Read more.
MYB (myeloblastosis) transcription factors plays an important role in various physiological and biochemical processes in plants. However, little is known about the regulatory roles of MYB family genes underlying seed oil biosynthesis in Camellia oleifera. To identify potential regulators, we performed the genome-wide characterizations of the MYB family genes and their expression profiles in C. oleifera. A total of 186 CoMYB genes were identified, including 128 R2R3-type MYB genes that had conserved R2 and R3 domains. Phylogenetic analysis revealed the CoR2R3-MYBs formed 25 subgroups and possessed some highly conserved motifs outside the MYB DNA-binding domain. We investigated the promoter regions of CoR2R3-MYBs and revealed a series of cis-acting elements related to development, hormone response, and environmental stress response, suggesting a diversified regulatory mechanism of gene functions. In addition, we identified four tandem clusters containing eleven CoR2R3-MYBs, which indicated that tandem duplications played an important role in the expansion of the CoR2R3-MYB subfamily. Furthermore, we analyzed the global gene expression profiles at five stages during seed development and revealed seven CoR2R3-MYB genes that potentially regulated lipid metabolism and seed maturation in C. oleifera. These results provide new insights into understanding the function of the MYB genes and the genetic improvement of seed oil. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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14 pages, 1381 KiB  
Article
Genetic Dissection of Stem Branch Trait and Envisioning of Fixing Heterosis by Vegetative Reproduction in Oryza rufipogon
by Feijun Wang, Chengkai Lu, Jinpeng Wan, Jun Yang, Lei Liu, Feifei Zhang, Zihao Wu, Xiao Zhang, Guimei Chang, Diqiu Yu and Peng Xu
Agronomy 2022, 12(7), 1503; https://doi.org/10.3390/agronomy12071503 - 23 Jun 2022
Cited by 1 | Viewed by 2865
Abstract
The stem branch trait of the stolon enables the common wild rice to produce new individuals through vegetative reproduction habit. In order to understand the genetic mechanism of stem branch character, we developed introgression lines (ILs) with the irrigated rice variety Yundao1 (YD1, [...] Read more.
The stem branch trait of the stolon enables the common wild rice to produce new individuals through vegetative reproduction habit. In order to understand the genetic mechanism of stem branch character, we developed introgression lines (ILs) with the irrigated rice variety Yundao1 (YD1, Oryza sativa) as the recipient parent and Yuanjiang common wild rice (YJCWR, O. rufipogon) as the donor parent for subsequent identification of the relevant genes. An IL named IL-J85 was selected, which can originate new individuals from stem branches on stem nodes. Furthermore, the newly formed individuals can survive cutting to bear normally and produce the same yield per plant as IL-J85, which saved the growth time and production cost. Two QTLs (quantitative traits loci) related to the stem branch trait, qSBR1 and qSBR5, were first mapped on chromosomes 1 and 5. The near isogenic lines NIL-Y37 and NIL-D1 in the background of Yunjing 37 and Dianjingyou 1 were cultivated, showing the same characteristics as IL-J85. Our results provide new insights into the underlying genetic mechanism of the stem branch trait in the common wild rice and have the value of breeding utilization using vegetative reproduction to fix heterosis and breed new rice varieties with the cutting characteristic. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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19 pages, 1205 KiB  
Review
Root Breeding in the Post-Genomics Era: From Concept to Practice in Apple
by Zhou Zhou, Lei Zhang, Jing Shu, Mengyu Wang, Han Li, Huairui Shu, Xiaoyun Wang, Qinghua Sun and Shizhong Zhang
Plants 2022, 11(11), 1408; https://doi.org/10.3390/plants11111408 - 26 May 2022
Cited by 6 | Viewed by 1921
Abstract
The development of rootstocks with a high-quality dwarf-type root system is a popular research topic in the apple industry. However, the precise breeding of rootstocks is still challenging, mainly because the root system is buried deep underground, roots have a complex life cycle, [...] Read more.
The development of rootstocks with a high-quality dwarf-type root system is a popular research topic in the apple industry. However, the precise breeding of rootstocks is still challenging, mainly because the root system is buried deep underground, roots have a complex life cycle, and research on root architecture has progressed slowly. This paper describes ideas for the precise breeding and domestication of wild apple resources and the application of key genes. The primary goal of this research is to combine the existing rootstock resources with molecular breeding and summarize the methods of precision breeding. Here, we reviewed the existing rootstock germplasm, high-quality genome, and genetic resources available to explain how wild resources might be used in modern breeding. In particular, we proposed the ‘from genotype to phenotype’ theory and summarized the difficulties in future breeding processes. Lastly, the genetics governing root diversity and associated regulatory mechanisms were elaborated on to optimize the precise breeding of rootstocks. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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20 pages, 3439 KiB  
Article
New Method for Sugarcane (Saccharum spp.) Variety Resources Evaluation by Projection Pursuit Clustering Model
by Yong Zhao, Yuebin Zhang, Jun Zhao, Fenggang Zan, Peifang Zhao, Jun Deng, Caiwen Wu and Jiayong Liu
Agronomy 2022, 12(6), 1250; https://doi.org/10.3390/agronomy12061250 - 24 May 2022
Cited by 1 | Viewed by 1629
Abstract
In the breeding of new sugarcane varieties, the survey data do not always conform with a normal or linear distribution. To apply non-normal or non-linear data to evaluate new material requires a suitable evaluation model or method. The projection pursuit clustering (PPC) model [...] Read more.
In the breeding of new sugarcane varieties, the survey data do not always conform with a normal or linear distribution. To apply non-normal or non-linear data to evaluate new material requires a suitable evaluation model or method. The projection pursuit clustering (PPC) model is a statistical method that does not require making normal assumptions or other model assumptions on sample data, and is suitable to analyze high-dimensional, non-linear, and non-normal data. However, this model has been applied infrequently to crop variety evaluation. In this study, 103 varieties that have been bred over the last 70 years in China were planted, and their main industrial and agronomic traits were collected. Through the exploratory analysis of the data structure characteristics, the PPC model was used to evaluate these sugarcane varieties. The model provided good projection directions of agronomic and industrial traits, with accurate projection values. PPC models could evaluate sugarcane resources well, and the results were objective and reliable. Thus, the PPC model could be used as a new method for crop variety evaluation. At the same time, 51 excellent industrial and agronomic variety resources were screened for application in breeding. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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8 pages, 1588 KiB  
Communication
The Citrus Mutant Jedae-unshiu Induced by Gamma Irradiation Exhibits a Unique Fruit Shape and Increased Flavonoid Content
by Chang-Ho Eun and In-Jung Kim
Plants 2022, 11(10), 1337; https://doi.org/10.3390/plants11101337 - 18 May 2022
Cited by 5 | Viewed by 1855
Abstract
Satsuma mandarin (Citrus unshiu Marc. cv. Miyagawa-wase) is the most widely cultivated citrus variety in Korea. Although most varieties are imported from Japan, efforts have focused on developing new domestic varieties. We produced mutants by irradiating C. unshiu Marc. cv. Miyagawa-wase scions [...] Read more.
Satsuma mandarin (Citrus unshiu Marc. cv. Miyagawa-wase) is the most widely cultivated citrus variety in Korea. Although most varieties are imported from Japan, efforts have focused on developing new domestic varieties. We produced mutants by irradiating C. unshiu Marc. cv. Miyagawa-wase scions with gamma rays and grafting them onto C. unshiu Marc. cv. Miyagawa-wase branches. We compared the characteristics of these mutants with Miyagawa-wase fruit as a control. A mutant line named Jedae-unshiu with a unique fruit shape was selected for investigation in detail. The phenotype of Jedae-unshiu fruit demonstrated vertical troughs on the flavedo, smooth albedo without rough protruding fibers, and good adhesion between peel and flesh. In addition, Jedae-unshiu had thicker peels and higher fruit hardness than the control. Higher levels of hesperetin and narirutin, representative flavonoids, accumulated in the peel and flesh of Jedae-unshiu than those of the control. Cellular-level microscopic observations of the mature fruit peels demonstrated epidermal cell disruption in the control but not in Jedae-unshiu. Our results suggest that Jedae-unshiu has high possibility for development as a good storage variety containing large amounts of flavonoids, in addition to potential for ornamental value due to the unique shape of the fruit. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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14 pages, 293 KiB  
Article
Genotype-by-Environment Interaction for the Contents of Micro-Nutrients and Protein in the Green Pods of Cowpea (Vigna unguiculata L. Walp.)
by Abe Shegro Gerrano, Zamalotshwa Goodness Thungo, Hussein Shimelis, Jacob Mashilo and Isack Mathew
Agriculture 2022, 12(4), 531; https://doi.org/10.3390/agriculture12040531 - 8 Apr 2022
Cited by 6 | Viewed by 2184
Abstract
Cowpea (Vigna unguiculata L. Walp.) is a drought-tolerant legume crop widely cultivated in arid and semi-arid regions of sub-Saharan Africa (SSA), including South Africa. The leaves, young and immature pods, and grains of cowpea are a vital source of plant-based proteins and [...] Read more.
Cowpea (Vigna unguiculata L. Walp.) is a drought-tolerant legume crop widely cultivated in arid and semi-arid regions of sub-Saharan Africa (SSA), including South Africa. The leaves, young and immature pods, and grains of cowpea are a vital source of plant-based proteins and essential nutrients for human wellbeing. The objective of this study was to determine the effect of genotype-by-environment interaction (GEI) on the contents of micro-nutrients and protein content of the green pods of cowpea to recommend superior genotypes for cultivation and breeding. Fifteen genetically diverse cowpea genotypes were evaluated across six test environments in South Africa, using a randomized complete block design replicated three times. Micro-nutrients such as iron (Fe), manganese (Mn), zinc (Zn), and total protein (TP) content were determined in the immature pods of cowpea. Data were subjected to additive main effects and multiplicative interaction (AMMI) analysis. Significant (p < 0.05) genotype (G) differences were detected for Fe, Mn, Zn and TP, suggesting the presence of genetic divergence for selection. Furthermore, a significant (p < 0.05) environment (E) effect was recorded for all studied nutrient, indicating the impact of the test environments on nutrient compositions. The GEI effect was significant for all the assessed nutrients, indicating that specific and broadly adapted genotypes could be identified. Based on best linear unbiased estimates (BLUEs) and best linear unbiased predictors (BLUPs) analyses, the following ranges of nutrient compositions were observed: Fe (83.70–109.03 and 69.77–134.16 mg/kg), Mn (20.60–33.83 and 18.75–36.83 mg/kg), Zn (33.79–40.53 and 28.81 mg/kg), and TP (22.37–24.54 and 21.44–25.25 mg/kg), respectively, across the tested environments. The AMMI test procedure (FR-test) identified the first interaction principal component axis (IPCA-1) to be a significant (p < 0.05) component of the GEI, explaining >91% of phenotypic variation in nutrient contents among the tested genotypes across environments. Cowpea genotypes Meterlong Bean and TVU-14196 were identified for their high Fe, Zn and Mn contents and recommended for cultivation in Mafikeng, Potchefstroom and Roodeplaat in South Africa. For TP, genotypes Meterlong Bean and Kisumu Mix had stable performance and are recommended for production at all the test environments. The identified genotypes are recommended for future cultivation and breeding to supplement micro-nutrients and protein and combat nutrient deficiencies and malnutrition in South Africa. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
12 pages, 270 KiB  
Article
Combining Ability of Drought-Tolerant Bread Wheat Genotypes for Agronomic and Physiological Traits
by Zamalotshwa Goodness Thungo, Hussein Shimelis and Jacob Mashilo
Agronomy 2022, 12(4), 862; https://doi.org/10.3390/agronomy12040862 - 31 Mar 2022
Cited by 1 | Viewed by 1873
Abstract
A combining-ability analysis is key to select desirable parents and progenies with enhanced response to selection under water-limited environments. The objective of this study was to determine combining ability for agronomic and physiological traits among distantly related drought-tolerant bread wheat (Triticum aestivum [...] Read more.
A combining-ability analysis is key to select desirable parents and progenies with enhanced response to selection under water-limited environments. The objective of this study was to determine combining ability for agronomic and physiological traits among distantly related drought-tolerant bread wheat (Triticum aestivum L.) genotypes under well-watered (WW) and terminal-drought (TD) conditions to determine their genetic merit for breeding. Ten heat- and drought-tolerant wheat genotypes were crossed in a half-diallel mating design to generate 45 F1s, which were evaluated under WW and TD moisture regimes in rainout shelter (RS) and greenhouse (GH) environments. The following agronomic traits were assessed: days to 50% maturity (DTM), plant height (PH), spike length (SL), number of productive tillers (TN), spikelets number per spike (SPS), number of grains per spike (GPS), grain yield (GY) and thousand-kernel weight (TKW); and physiological traits (stomatal conductance (SC) and chlorophyll content index (CCI)). Variances attributable to general combining ability (GCA) and specific combining ability (SCA) were significant (p < 0.05) for GY, DTM, PH, SL, SPS, GPS, TKW and CCI. The parental genotypes LM72, LM81 and LM95 with positive and significant GCA effects on GY were selected to make crosses to develop high-yielding wheat genotypes for water-limited environments. Crosses LM71 × LM02, LM71 × LM81, LM82 × LM02, LM82 × LM81, LM22 × LM100, LM22 × LM81 and LM95 × LM22 were selected with positive and significant SCA effects for GY. The selected parents and crosses are valuable genetic resources for breeding and genetic advancement. Full article
(This article belongs to the Topic Advanced Breeding Technology for Plants)
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