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Agronomy
Special Issues
Improvement of Crops: Current Status and Future Prospects
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Improvement of Crops: Current Status and Future Prospects

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (15 February 2022) | Viewed by 25300

Special Issue Editors

Dr. Margarita A. Vishnyakova

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

E-Mail Website
Co-Guest Editor
Department of Plant and Soil Science and Gund Institute for the Environment, University of Vermont, Burlington, VT 05405, USA
Interests: crop domestication; abiotic stress tolerance; legumes; forage crops
Special Issues, Collections and Topics in MDPI journals
Dr. Maria G. Samsonova

E-Mail Website
Co-Guest Editor
1. Institute of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
2. Mathematical Biology and Bioinformatics Lab, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
Interests: DNA methylation; histone modifications; RNA modifications and noncoding RNAs; gene regulation; data integration
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The genetic improvement of crops is a continuous endeavor. At present, a wide range of approaches are used to accelerate the breeding process, make the development of new genotypes more precise, and to broaden the genetic diversity of cultivated species. Thus, the methods of conventional breeding are combined with marker-assisted and genomic selection approaches, double haploid production, genetic engineering, genome editing, phenomics, as well as cell and chromosomal engineering techniques. The modern methods of genetics, genomics, biotechnology, and bioinformatics have contributed to advances in pre-breeding and the development of next-generation breeding. Future improvement of breeding process could be related with precise genotype modelling based on the analysis of big omics (genomics, phenomics, etc.) data with relation to climate and environmental characteristics. The key role in crop improvement belongs to appropriate germplasm. The genetic diversity of cultivated species and the application of the genetic potential of wild relatives is a basis for sustainable and environmentally friendly agriculture. In this Special Issue, we welcome original research and review articles on all related topics. The Guest Editors encourage applications which assess the benefits of technologies that contribute to the agronomic and economic performance of next-generation crops.

Dr. Margarita A. Vishnyakova
Dr. Eric J. Bishop von Wettberg
Dr. Maria Samsonova
Guest Editors

Manuscript Submission Information

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Keywords

  • breeding
  • molecular markers
  • genes
  • QTL
  • genetics
  • genetic and genomic resources
  • variation
  • desirable traits
  • next-generation crops
  • pre-breeding
  • gene editing

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Published Papers (7 papers)

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Research

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18 pages, 6592 KiB  
Article
Genome-Wide Identification of Long Non-Coding RNAs in Pearl Millet (Pennisetum glaucum (L.)) Genotype Subjected to Drought Stress
by Baibhav Kumar, Animesh Kumar, Sarika Jaiswal, Mir Asif Iquebal, Ulavappa B. Angadi, Rukam S. Tomar, Anil Rai and Dinesh Kumar
Agronomy 2022, 12(8), 1976; https://doi.org/10.3390/agronomy12081976 - 22 Aug 2022
Cited by 2 | Viewed by 2544
Abstract
Pearl millet (Pennisetum glaucum L.) is affected by drought stress, affecting crop productivity and survival. Long non-coding RNAs (lncRNAs) are reported to play a vital role in the response to drought stress. LncRNAs represent a major part of non-protein coding RNAs and [...] Read more.
Pearl millet (Pennisetum glaucum L.) is affected by drought stress, affecting crop productivity and survival. Long non-coding RNAs (lncRNAs) are reported to play a vital role in the response to drought stress. LncRNAs represent a major part of non-protein coding RNAs and are present prevalently. These are involved in various biological processes, which may functionally act as RNA rather than getting transcribed as protein. We targeted genome-wide identification of lncRNAs in pearl millet from root and leaf tissues subjected to drought stress. A total of 879 lncRNAs were identified, out of which 209 (leaf control, root control), 198 (leaf treated, root treated), 115 (leaf control, leaf treated) and 194 (root control, root treated) were differentially expressed. Two lncRNAs were found as potential target mimics of three miRNAs from the miRBase database. Gene ontology study revealed that drought-responsive lncRNAs are involved in biological processes like ‘metabolic process’ and ‘cellular process’, molecular functions like ‘binding’ and ‘catalytic activities’ and cellular components like ‘cell’, ‘cell part’ and ‘membrane part’. LncRNA-miRNA-mRNA network shows that it plays a vital role in the stress-responsive mechanism through their activities in hormone signal transduction, response to stress, response to auxin and transcription factor activity. Only four lncRNAs were found to get a match with the lncRNAs present in the plant lncRNA database CANTATAdb, which shows its poorly conserved nature among species. This information has been cataloged in the pearl millet drought-responsive long non-coding RNA database (PMDlncRDB). The discovered lncRNAs can be used in the improvement of important traits, as well as CISPR-Cas technology, in the editing of ncRNAs in plants for trait improvement. Such a study will increase our understanding of the expression behavior of lncRNAs, as well as its underlying mechanisms under drought stress in pearl millet. Full article
(This article belongs to the Special Issue Improvement of Crops: Current Status and Future Prospects)
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15 pages, 3142 KiB  
Article
Genome-Wide In Silico Analysis and Expression Profiling of Phosphoenolpyruvate Carboxylase Genes in Loquat, Apple, Peach, Strawberry and Pear
by Cao Zhi, Muhammad Moaaz Ali, Shariq Mahmood Alam, Shaista Gull, Sajid Ali, Ahmed F. Yousef, Mohamed A. A. Ahmed, Songfeng Ma and Faxing Chen
Agronomy 2022, 12(1), 25; https://doi.org/10.3390/agronomy12010025 - 23 Dec 2021
Cited by 8 | Viewed by 3030
Abstract
Phosphoenolpyruvate carboxylase (PEPC) genes have multiple potential roles in plant metabolism such as regulation and accumulation of organic acids in fruits, movement of guard cells and stress tolerance, etc. However, the systematic identification and characterization of PEPC genes in [...] Read more.
Phosphoenolpyruvate carboxylase (PEPC) genes have multiple potential roles in plant metabolism such as regulation and accumulation of organic acids in fruits, movement of guard cells and stress tolerance, etc. However, the systematic identification and characterization of PEPC genes in Rosaceae species i.e., loquat, apple, peach, strawberry, and pear are yet to be performed. In present study, 27 putative PEPC genes (loquat 4, apple 6, peach 3, strawberry 9, and pear 5) were identified. To further investigate the role of those PEPC genes, comprehensive bioinformatics and expression analysis were performed. In bioinformatic analysis, the physiochemical properties, conserved domains, gene structure, conserved motif, phylogenetic and syntenic analysis of PEPC genes were performed. The result revealed that the PEPcase superfamily domain was conserved in all examined PEPC proteins. Most of the PEPC proteins were predicted to be localized in cytonuclear. Genomic structural and motif analysis showed that the exon and motif number of each PEPC gene ranged dramatically, from 8 to 20, and 7 to 10, respectively. Syntenic analysis indicated that the segmental or whole-genome duplication played a vital role in extension of PEPC gene family in Rosacea species. The Ka and Ks values of duplicated genes depicted that PEPC genes have undergone a strong purifying selection. Furthermore, the expression analysis of PEPC genes in root, mature leaf, stem, full-bloom flower, and ripened fruit of loquat, apple, peach, strawberry, and pear was performed. Some genes were differentially expressed in aforementioned plant tissues, signifying their role in plant metabolism. This study provides the first genome-wide identification, characterization, and expression profiling of PEPC gene family in Rosaceae species, and provides the foundation for further functional analysis. Full article
(This article belongs to the Special Issue Improvement of Crops: Current Status and Future Prospects)
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16 pages, 885 KiB  
Article
Modeling of Flowering Time in Vigna radiata with Approximate Bayesian Computation
by Andrey Ageev, Cheng-Ruei Lee, Chau-Ti Ting, Roland Schafleitner, Eric Bishop-von Wettberg, Sergey V. Nuzhdin, Maria Samsonova and Konstantin Kozlov
Agronomy 2021, 11(11), 2317; https://doi.org/10.3390/agronomy11112317 - 16 Nov 2021
Cited by 3 | Viewed by 2347
Abstract
Flowering time is an important target for breeders in developing new varieties adapted to changing conditions. A new approach is proposed that uses Approximate Bayesian Computation with Differential Evolution to construct a pool of models for flowering time. The functions for daily progression [...] Read more.
Flowering time is an important target for breeders in developing new varieties adapted to changing conditions. A new approach is proposed that uses Approximate Bayesian Computation with Differential Evolution to construct a pool of models for flowering time. The functions for daily progression of the plant from planting to flowering are obtained in analytic form and depend on daily values of climatic factors and genetic information. The resulting pool of models demonstrated high accuracy on the dataset. Day length, solar radiation and temperature had a large impact on the model accuracy, while the impact of precipitation was comparatively small and the impact of maximal temperature has the maximal variation. The model pool was used to investigate the behavior of accessions from the dataset in case of temperature increase by 0.05–6.00°. The time to flowering changed differently for different accessions. The Pearson correlation coefficient between the SNP value and the change in time to flowering revealed weak but significant association of SNP7 with behavior of the accessions in warming climate conditions. The same SNP was found to have a considerable influence on model prediction with a permutation test. Our approach can help breeding programs harness genotypic and phenotypic diversity to more effectively produce varieties with a desired flowering time. Full article
(This article belongs to the Special Issue Improvement of Crops: Current Status and Future Prospects)
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15 pages, 2014 KiB  
Article
Combination Breeding and Marker-Assisted Selection to Develop Late Blight Resistant Potato Cultivars
by Mariya P. Beketova, Nadezhda A. Chalaya, Nadezhda M. Zoteyeva, Alena A. Gurina, Mariya A. Kuznetsova, Miles Armstrong, Ingo Hein, Polina E. Drobyazina, Emil E. Khavkin and Elena V. Rogozina
Agronomy 2021, 11(11), 2192; https://doi.org/10.3390/agronomy11112192 - 29 Oct 2021
Cited by 4 | Viewed by 2699
Abstract
(1) Background: Although resistance to pathogens and pests has been researched in many potato cultivars and breeding lines with DNA markers, there is scarce evidence as to the efficiency of the marker-assisted selection (MAS) for these traits when applied at the early stages [...] Read more.
(1) Background: Although resistance to pathogens and pests has been researched in many potato cultivars and breeding lines with DNA markers, there is scarce evidence as to the efficiency of the marker-assisted selection (MAS) for these traits when applied at the early stages of breeding. A goal of this study was to estimate the potential of affordable DNA markers to track resistance genes that are effective against the pathogen Phytophthora infestans (Rpi genes), as a practical breeding tool on a progeny of 68 clones derived from a cross between the cultivar Sudarynya and the hybrid 13/11-09. (2) Methods: this population was studied for four years to elucidate the distribution of late blight (LB) resistance and other agronomical desirable or simple to phenotype traits such as tuber and flower pigmentation, yield capacity and structure. LB resistance was phenotypically evaluated following natural and artificial infection and the presence/absence of nine Rpi genes was assessed with 11 sequence-characterized amplified region (SCAR) markers. To validate this analysis, the profile of Rpi genes in the 13/11-09 parent was established using diagnostic resistance gene enrichment sequencing (dRenSeq) as a gold standard. (3) Results: at the early stages of a breeding program, when screening the segregation of F1 offspring, MAS can halve the workload and selected SCAR markers for Rpi genes provide useful tools. Full article
(This article belongs to the Special Issue Improvement of Crops: Current Status and Future Prospects)
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Review

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14 pages, 2440 KiB  
Review
Usage of Morphological Mutations for Improvement of a Garden Pea (Pisum sativum): The Experience of Breeding in Russia
by Andrey Sinjushin, Elena Semenova and Margarita Vishnyakova
Agronomy 2022, 12(3), 544; https://doi.org/10.3390/agronomy12030544 - 22 Feb 2022
Cited by 8 | Viewed by 4277
Abstract
The improvement of pea as a crop over many decades has been employing the use of mutants. Several hundreds of different mutations are known in pea (Pisum sativum subsp. sativum), some of which are valuable for breeding. Breeding strategies may be [...] Read more.
The improvement of pea as a crop over many decades has been employing the use of mutants. Several hundreds of different mutations are known in pea (Pisum sativum subsp. sativum), some of which are valuable for breeding. Breeding strategies may be diverse in different countries depending on different obstacles. In Russia, numerous spontaneous and induced mutations have been implemented in breeding. To our knowledge some of these, are not used in pea breeding beyond Russia. This review describes the use of mutations in pea breeding in Russia. The paper provides examples of cultivars created on the basis of mutations affecting the development of seeds (def), inflorescence (det, deh), compound leaves (af, af unitac), and symbiotic nitrogen fixation (various alleles of Sym and Nod loci). Novel mutations which are potentially promising for breeding are currently being investigated. Together with numerous cultivars of dry and fodder pea carrying commonly known mutations, new ‘chameleon’ and ‘lupinoid’ morphotypes, both double mutants, are under study. A cultivar Triumph which increases the effectiveness of interactions with beneficial soil microbes, was bred in Russia for the first time in the history of legume breeding. Full article
(This article belongs to the Special Issue Improvement of Crops: Current Status and Future Prospects)
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Graphical abstract

25 pages, 740 KiB  
Review
Grapevine Gene Systems for Resistance to Gray Mold Botrytis cinerea and Powdery Mildew Erysiphe necator
by Jaroslava Fedorina, Nadezhda Tikhonova, Yulia Ukhatova, Roman Ivanov and Elena Khlestkina
Agronomy 2022, 12(2), 499; https://doi.org/10.3390/agronomy12020499 - 17 Feb 2022
Cited by 13 | Viewed by 5005
Abstract
Grapevine is one of the world’s most economically important fruit crops. It is known that Vitis vinifera is a host for a large number of pathogenic agents, which significantly reduce the yield and berry quality. This forces the agronomists to use a huge [...] Read more.
Grapevine is one of the world’s most economically important fruit crops. It is known that Vitis vinifera is a host for a large number of pathogenic agents, which significantly reduce the yield and berry quality. This forces the agronomists to use a huge amount of fungicides. Over the last few decades, alternative methods for solving this problem have been developed and continue to be developed. Such new technologies as marker-assisted selection, bioengineering of the rhizosphere, genetic engineering (transgenesis, cisgenesis and intragenesis) allow the production of pathogen-resistant cultivars. However, they are linked to a number of problems. One of the most promising methods is the creation of modified non-transgenic cultivars via CRISPR/Cas9-targeted mutagenesis. Therefore, researchers are actively looking for target genes associated with pathogen resistance and susceptibility. This review elucidates the main mechanisms of plant—pathogen interactions, the immune systems developed by plants, as well as the identified genes for resistance and susceptibility to the biotrophic pathogen Erysiphe necator and the necrotrophic pathogen Botrytis cinerea. Full article
(This article belongs to the Special Issue Improvement of Crops: Current Status and Future Prospects)
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Other

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10 pages, 926 KiB  
Opinion
Breeding Temperate Japonica Rice Varieties Adaptable to Tropical Regions: Progress and Prospects
by Myrish Pacleb, O-Young Jeong, Jeom-Sig Lee, Thelma Padolina, Rustum Braceros, Lenie Pautin, Gideon Torollo, Elbert E. Sana, Jesson Y. Del-Amen, Man-Kee Baek, Sumin Jo, Woong-Jo Hyun, Hyun-Su Park, Jong-Min Jeong, Ji-Youn Lee, Jun-Hyeon Cho, Jeong-Heui Lee, Sais-Beul Lee, Il-Ryong Choi, Sung-Ryul Kim, Jae-Sung Lee, Nese Sreenivasulu, Jong-Cheol Ko, Joum-Ho Lee, Byeong-Ju Kim, Ki-Young Kim and Dong-Soo Parkadd Show full author list remove Hide full author list
Agronomy 2021, 11(11), 2253; https://doi.org/10.3390/agronomy11112253 - 8 Nov 2021
Cited by 1 | Viewed by 4085
Abstract
Temperate japonica rice is mainly cultivated in temperate regions. Many temperate japonica varieties have a superior grain quality that is preferred in Northeast Asian countries such as Japan, Korea, and China. The changes in consumers’ preferences in Southeast Asia and Western countries has [...] Read more.
Temperate japonica rice is mainly cultivated in temperate regions. Many temperate japonica varieties have a superior grain quality that is preferred in Northeast Asian countries such as Japan, Korea, and China. The changes in consumers’ preferences in Southeast Asia and Western countries has contributed to increasing the demand for temperate japonica. Most temperate japonica varieties developed in temperate regions typically exhibit extra-early flowering under the short-day conditions in the tropics, which usually results in severely reduced yields. Since 1992, we have been developing temperate japonica varieties that can adapt to tropical environments to meet the increasing demand for temperate japonica rice, having released six varieties in the Philippines. Especially, the yield of one of the temperate japonica varieties, Japonica 7, was comparable to the yields of leading indica varieties in the Philippines. Here, we discuss the current breeding initiatives and future plans for the development of tropical-region-bred temperate japonica rice. Full article
(This article belongs to the Special Issue Improvement of Crops: Current Status and Future Prospects)
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