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Plant Genomics and Epigenomics in Breeding for Yield, Quality, and Sustainability

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

Deadline for manuscript submissions: closed (10 September 2022) | Viewed by 19168

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Special Issue Editor

Dr. Aphrodite Tsaballa

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Guest Editor

Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization–Demeter, Thermi, GR57001 Thessaloniki, Greece
Interests: plant breeding; genetics; genomics; epigenomics; fruit quality; vegetable grafting; transcriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant genomics is a continuously evolving and expanding area of plant science research. Assisted by advanced new technologies, DNA sequencing, and characterization of plant genomes have never been more complete. Moreover, epigenomics covers an exciting research field revolving around epigenetic changes, such as DNA methylation and small RNAs, across plant genomes. All this new knowledge is extremely valuable for modern plant breeding in dissecting complex plant characters related to yield, quality, and eventually adaptation, thus facilitating breeders’ work and efficiency. Integration of genomic information in modern breeding programs will aid the development of new cultivars that fit in sustainable agriculture. This Special Issue aims to collect original papers, reviews, and short communications that report novel findings related to the discovery, exploration, characterization, and utilization of genomics and epigenomics resources in crop breeding projects. Our goal is to collect the most recent advances in this field and compile a valuable collection of papers.

Dr. Aphrodite Tsaballa
Guest Editor

Twitter : @tsaballa

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Keywords

genomics
epigenomics
plant breeding
DNA methylation
small RNAs
transcriptomics
adaptation

Published Papers (6 papers)

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Research

Jump to: Review

24 pages, 1122 KiB

Open AccessArticle

Development of New Iso-Cytoplasmic Rice-Restorer Lines and New Rice Hybrids with Superior Grain Yield and Grain Quality Characteristics by Utilizing Restorers’ Fertility Genes

by Mamdouh M. A. Awad-Allah, Kotb A. Attia, Ahmad Alsayed Omar, Eldessoky S. Dessoky, Fahad Mohammed Alzuaibr, Mohammed Ali Alshehri, Mohamed A. Abdein and Azza H. Mohamed

Genes 2022, 13(5), 808; https://doi.org/10.3390/genes13050808 - 01 May 2022

Cited by 3 | Viewed by 1392

Abstract

This research was carried out at the Experimental Farm of Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the 2018–2020 rice-growing seasons to develop and evaluate four iso-cytoplasmic rice-restorer lines: NRL79, NRL80, NRL81, and NRL82, as well as Giza 178, with ten new hybrids in order to estimate genotypic coefficient, phenotypic coefficient, heritability in a broad sense, and advantage over Giza 178 as a check variety (control) of new restorer lines. This study also estimated combining ability, gene action, better-parent heterosis (BP), mid-parents heterosis (MP), and standard heterosis (SH) over Egyptian Hybrid one (IR69A × Giza 178) as a check hybrid (control) for grain yield, agronomic traits, and some grain quality characters in restorer lines and hybrids. The percentage of advantage over commercial-variety Giza 178 (check) was significant, and highly significant among the newly developed restorer fertility lines for all the studied traits. This indicates that the selection is a highly effective factor in improving these traits. New restorer fertility lines showed highly significant positive values over commercial restorer for grain yield; the values ranged from 51% for NRL80 to 100.4% for NRL82, respectively. Meanwhile, in regard to the grain shape of paddy rice, three lines of the promising lines showed highly significant negative desirable values compared with Giza 178; the values ranged from −7.7% for the NRL80 to −15.2% for NRL79, respectively. Based on the superiority of the new lines, the new lines can be used as new restorer fertility lines to breed promising new hybrids and new inbred rice lines or varieties. From the results of the testcross experiment, the four promising lines were identified as effective restorer fertility lines for two cytoplasmic male sterile (CMS) lines. Moreover, the six rice hybrids showed values for SH heterosis of grain yield/plant of more than 15% over the check hybrid variety, with high values of 1000-grain weight and desirable grain shape; these hybrids were G46A × NRL81 (125.1%), G46A × NRL80 (66.9%), IR69A × NRL79 (47.2%), G46A × NRL79 (24.6%), IR69A × NRL81 (23.4%), and IR69A × NRL82 (16.2%). Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics in Breeding for Yield, Quality, and Sustainability)

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20 pages, 355 KiB

Open AccessEditor’s ChoiceArticle

Assessment of Genetic Variability and Bran Oil Characters of New Developed Restorer Lines of Rice (Oryza sativa L.)

by Mamdouh M. A. Awad-Allah, Azza H. Mohamed, Mohamed A. El-Bana, Samira A. F. El-Okkiah, Mohamed F. M. Abdelkader, Mohamed H. Mahmoud, Mohamed Z. El-Diasty, Manal M. Said, Sahar A. M. Shamseldin and Mohamed A. Abdein

Genes 2022, 13(3), 509; https://doi.org/10.3390/genes13030509 - 13 Mar 2022

Cited by 7 | Viewed by 2557

Abstract

Rice is one of the most important crops in Egypt. Due to the gap between the demand and the availability of the local edible oils, there is need to raise the nutritional value of rice and, therefore, to improve the nutritional value of the consumer. This research was carried out at the Experimental Farm of Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the 2019 and 2020 seasons. Five newly developed genotypes of rice, namely NRL 63, NRL 64, NRL 65, NRL 66, and Giza 178 as check variety (control), were used to evaluate the analytical characterization of raw rice bran and rice bran oil from rice bran, study the genetic variability and genetic advance for various quantitative and qualitative traits in rice as well as, rice bran oil. The genotypes were evaluated in a randomized complete block design (RCBD) with three replications. Analysis of variance revealed highly significant variations among the genotypes for all the studied characters. Data revealed that high estimates of the phenotypic coefficient of variance (PCV%) and genotypic coefficient of variance (GCV%) were observed for amylose content percentage, peroxide value (meq/kg oil), myristic C14:0, and arachidic C20:0, indicating that they all interacted with the environment to some extent. The line NRL66 and NRL64 showed the highest and high values of mean performance for grain yield (t/h), grain type (shape), amylose content percentage, crude protein, ether extract and ash of milled rice, crude protein, ether extract, ash, phosphorus, magnesium, manganese, zinc, and iron of stabilized rice bran oil. Genetic advance as a percentage of mean was high for most of the studied traits. It indicates that most likely, the heritability is due to additive gene effects, and selection may be effective. The percentage of advantage over the Giza 178 as the commercial variety was significant and highly significant among the genotypes for all the characters studied in the two years, indicating that the selection is effective in the genetic improvements for these traits. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics in Breeding for Yield, Quality, and Sustainability)

14 pages, 10181 KiB

Open AccessArticle

Epigenetic and Physiological Responses to Varying Root-Zone Temperatures in Greenhouse Rocket

by Aphrodite Tsaballa, Ilektra Sperdouli, Evangelia V. Avramidou, Ioannis Ganopoulos, Athanasios Koukounaras and Georgios K. Ntinas

Genes 2022, 13(2), 364; https://doi.org/10.3390/genes13020364 - 17 Feb 2022

Cited by 3 | Viewed by 1646

Abstract

Greenhouse production of baby leaf vegetables grown in hydroponic floating trays has become extremely popular in recent years. Rocket (Eruca sativa Mill.) can grow in temperatures varying between 10 and 20 °C; nevertheless, a root-zone temperature (RZT) range of 18–23 °C is considered optimal for high productivity, photosynthesis, and production of metabolites. Maintaining such temperatures in winter raises production costs and prevents sustainability. In this study, we tested the impact of lower RZT on plants’ status and recorded their responses while providing energy for heating using photovoltaic solar panels. We used three hydroponic tanks for cultivation; a non-heated (control) tank (12 °C) and two heated tanks; a solar panel-powered one (16 °C) and a public grid-powered one (22 °C). Methylation-sensitive amplified polymorphisms (MSAP) analysis of global methylation profiles and chlorophyll fluorescence analysis were employed to assess methylation and physiology levels of rocket leaves. We found that there is demethylation at 16 °C RZT in comparison to 22 °C RZT. Reduction of temperature at 12 °C did not reduce methylation levels further but rather increased them. Furthermore, at 16 °C, the effective quantum yield of photosystem II (PSII) photochemistry (ΦPSII) was significantly higher, with a higher PSII electron transport rate (ETR) and a significantly decreased non-regulated energy loss (ΦΝO), suggesting a better light energy use by rocket plants with higher photosynthetic performance. ΦPSII was significantly negatively correlated with DNA methylation levels. Our results show that at 16 °C RZT, where plants grow efficiently without being affected by the cold, DNA methylation and photosynthesis apparatus systems are altered. These findings corroborate previous results where hydroponic production of rocket at RZT of 16 °C is accompanied by sufficient yield showing that rocket can effectively grow in suboptimal yet sustainable root-zone temperatures. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics in Breeding for Yield, Quality, and Sustainability)

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14 pages, 23672 KiB

Open AccessArticle

Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses

by Lisha Shi, Huimin Shen, Jiawei Liu, Hongmin Hu, Hongyan Tan, Xiulian Yang, Lianggui Wang and Yuanzheng Yue

Genes 2022, 13(2), 314; https://doi.org/10.3390/genes13020314 - 08 Feb 2022

Cited by 2 | Viewed by 1508

Abstract

Cytosine-5 DNA methyltransferases (C5-MTases) and methyl-CpG-binding-domain (MBD) genes can be co-expressed. They directly control target gene expression by enhancing their DNA methylation levels in humans; however, the presence of this kind of cooperative relationship in plants has not been determined. A popular garden plant worldwide, petunia (Petunia hybrida) is also a model plant in molecular biology. In this study, 9 PhC5-MTase and 11 PhMBD proteins were identified in petunia, and they were categorized into four and six subgroups, respectively, on the basis of phylogenetic analyses. An expression correlation analysis was performed to explore the co-expression relationships between PhC5-MTases and PhMBDs using RNA-seq data, and 11 PhC5-MTase/PhMBD pairs preferentially expressed in anthers were identified as having the most significant correlations (Pearson’s correlation coefficients > 0.9). Remarkably, the stability levels of the PhC5-MTase and PhMBD pairs significantly decreased in different tissues and organs compared with that in anthers, and most of the selected PhC5-MTases and PhMBDs responded to the abiotic and hormonal stresses. However, highly correlated expression relationships between most pairs were not observed under different stress conditions, indicating that anther developmental processes are preferentially influenced by the co-expression of PhC5-MTases and PhMBDs. Interestingly, the nuclear localization genes PhDRM2 and PhMBD2 still had higher correlations under GA treatment conditions, implying that they play important roles in the GA-mediated development of petunia. Collectively, our study suggests a regulatory role for DNA methylation by C5-MTase and MBD genes in petunia anther maturation processes and multi-stress responses, and it provides a framework for the functional characterization of C5-MTases and MBDs in the future. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics in Breeding for Yield, Quality, and Sustainability)

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15 pages, 2260 KiB

Open AccessArticle

Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers

by Yheni Dwiningsih, Anuj Kumar, Julie Thomas, Charles Ruiz, Jawaher Alkahtani, Abdulrahman Al-hashimi and Andy Pereira

Genes 2021, 12(11), 1690; https://doi.org/10.3390/genes12111690 - 24 Oct 2021

Cited by 8 | Viewed by 2538

Abstract

Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of “Kaybonnet (KBNT lpa)” and “ZHE733” named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics in Breeding for Yield, Quality, and Sustainability)

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Review

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18 pages, 2426 KiB

Open AccessReview

Revisiting Plant Heterosis—From Field Scale to Molecules

by Attiq ur Rehman, Trang Dang, Shanzay Qamar, Amina Ilyas, Reemana Fatema, Madan Kafle, Zawar Hussain, Sara Masood, Shehyar Iqbal and Khurram Shahzad

Genes 2021, 12(11), 1688; https://doi.org/10.3390/genes12111688 - 24 Oct 2021

Cited by 13 | Viewed by 8028

Abstract

Heterosis refers to the increase in biomass, stature, fertility, and other characters that impart superior performance to the F1 progeny over genetically diverged parents. The manifestation of heterosis brought an economic revolution to the agricultural production and seed sector in the last few decades. Initially, the idea was exploited in cross-pollinated plants, but eventually acquired serious attention in self-pollinated crops as well. Regardless of harvesting the benefits of heterosis, a century-long discussion is continued to understand the underlying basis of this phenomenon. The massive increase in knowledge of various fields of science such as genetics, epigenetics, genomics, proteomics, and metabolomics persistently provide new insights to understand the reasons for the expression of hybrid vigor. In this review, we have gathered information ranging from classical genetic studies, field experiments to various high-throughput omics and computational modelling studies in order to understand the underlying basis of heterosis. The modern-day science has worked significantly to pull off our understanding of heterosis yet leaving open questions that requires further research and experimentation. Answering these questions would possibly equip today’s plant breeders with efficient tools and accurate choices to breed crops for a sustainable future. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics in Breeding for Yield, Quality, and Sustainability)

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