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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 48317

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Prof. Dr. Igor G. Loskutov

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Department of Genetic Resources of Oat, Barley, Rye, N. I. Vavilov Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
Interests: Avena genetic resources; taxonomy and phylogeny of genus Avena; genetics; breeding; agronomy; plant industry; agrobiotechnology of cereals; biotic and abiotic resistance; grain quality of cereals
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Dear Colleagues,

Cereals are the main food and feed crops on our planet: wheat, rice, and corn occupy three-quarters of the total acreage. The vast majority of plant breeders and plant geneticists in the world are engaged in cereals breeding. The breeding methods are chosen on the basis of the biology of the crop (self-pollinating or cross-pollinating), the level of development of genetic research for a particular crop, and the country where the breeding is carried out. The history of crop breeding is long, beginning at the dawn of human civilization with the agricultural revolution and the creation of primitive landraces, continuing with the discovery of the genetic laws of G. Mendel and the creation of the first primitive (obsolete) breeding varieties of plants at the beginning of the twentieth century, and then further progressing with the development of genetics heterotic hybrids and physical and chemical crop mutants. The successes of biotechnology have allowed expanding the breeding possibilities to obtain interspecies and intergenus hybrids, and now the development of molecular biology and genomics has completely overcome the barriers limiting the breeding of any living organisms, while methods for genome editing of agricultural crops are still being improved to achieve higher levels of accuracy. All of the above methods require source material, i.e., the genetic materials of cereals and their wild relatives, maintained ex situ in gene banks that are repositories of valuable alleles for improving varieties and hybrids of crops using genome editing tools. Studies aimed at the finding genes and quantitative traits loci (QTL) that affect the main breeding traits and at identifying the desired allelic variants, as well as reviews summarizing these data are within the scope of this Special Issue. In addition, new data from traditional agronomic breeding methods, as well as data from traditional and new breeding strategies related to biotic and abiotic resistance, the quality of grain production and green mass, and the complex adaptability of plants on Earth in the context of climate change are of great interest.

Prof. Igor G. Loskutov
Guest Editor

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Keywords

Agrobiotechnology
biotic and abiotic resistance
breeding
cultivar
genetic resources
genome editing
germplasm
grain and green mass quality
landraces
QTL
site-directed mutagenesis

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Published Papers (10 papers)

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Editorial

Jump to: Research, Review

4 pages, 173 KiB

Open AccessEditorial

Advances in Cereal Crops Breeding

by Igor G. Loskutov

Plants 2021, 10(8), 1705; https://doi.org/10.3390/plants10081705 - 19 Aug 2021

Cited by 6 | Viewed by 2703

Abstract

Cereals are the main food and feed crops on our planet, with wheat, rice, and maize occupying three-quarters of the total acreage [...] Full article

(This article belongs to the Special Issue Advances in Cereal Crops Breeding)

Research

Jump to: Editorial, Review

20 pages, 2219 KiB

Open AccessArticle

Morphological Analysis, Protein Profiling and Expression Analysis of Auxin Homeostasis Genes of Roots of Two Contrasting Cultivars of Rice Provide Inputs on Mechanisms Involved in Rice Adaptation towards Salinity Stress

by Shivani Saini, Navdeep Kaur, Deeksha Marothia, Baldev Singh, Varinder Singh, Pascal Gantet and Pratap Kumar Pati

Plants 2021, 10(8), 1544; https://doi.org/10.3390/plants10081544 - 28 Jul 2021

Cited by 15 | Viewed by 4339

Abstract

Plants remodel their root architecture in response to a salinity stress stimulus. This process is regulated by an array of factors including phytohormones, particularly auxin. In the present study, in order to better understand the mechanisms involved in salinity stress adaptation in rice, we compared two contrasting rice cultivars—Luna Suvarna, a salt tolerant, and IR64, a salt sensitive cultivar. Phenotypic investigations suggested that Luna Suvarna in comparison with IR64 presented stress adaptive root traits which correlated with a higher accumulation of auxin in its roots. The expression level investigation of auxin signaling pathway genes revealed an increase in several auxin homeostasis genes transcript levels in Luna Suvarna compared with IR64 under salinity stress. Furthermore, protein profiling showed 18 proteins that were differentially regulated between the roots of two cultivars, and some of them were salinity stress responsive proteins found exclusively in the proteome of Luna Suvarna roots, revealing the critical role of these proteins in imparting salinity stress tolerance. This included proteins related to the salt overly sensitive pathway, root growth, the reactive oxygen species scavenging system, and abscisic acid activation. Taken together, our results highlight that Luna Suvarna involves a combination of morphological and molecular traits of the root system that could prime the plant to better tolerate salinity stress. Full article

(This article belongs to the Special Issue Advances in Cereal Crops Breeding)

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24 pages, 2141 KiB

Open AccessFeature PaperArticle

Genome-Wide Association Mapping of Salinity Tolerance at the Seedling Stage in a Panel of Vietnamese Landraces Reveals New Valuable QTLs for Salinity Stress Tolerance Breeding in Rice

by Thao Duc Le, Floran Gathignol, Huong Thi Vu, Khanh Le Nguyen, Linh Hien Tran, Hien Thi Thu Vu, Tu Xuan Dinh, Françoise Lazennec, Xuan Hoi Pham, Anne-Aliénor Véry, Pascal Gantet and Giang Thi Hoang

Plants 2021, 10(6), 1088; https://doi.org/10.3390/plants10061088 - 28 May 2021

Cited by 23 | Viewed by 5193

Abstract

Rice tolerance to salinity stress involves diverse and complementary mechanisms, such as the regulation of genome expression, activation of specific ion-transport systems to manage excess sodium at the cell or plant level, and anatomical changes that avoid sodium penetration into the inner tissues of the plant. These complementary mechanisms can act synergistically to improve salinity tolerance in the plant, which is then interesting in breeding programs to pyramidize complementary QTLs (quantitative trait loci), to improve salinity stress tolerance of the plant at different developmental stages and in different environments. This approach presupposes the identification of salinity tolerance QTLs associated with different mechanisms involved in salinity tolerance, which requires the greatest possible genetic diversity to be explored. To contribute to this goal, we screened an original panel of 179 Vietnamese rice landraces genotyped with 21,623 SNP markers for salinity stress tolerance under 100 mM NaCl treatment, at the seedling stage, with the aim of identifying new QTLs involved in the salinity stress tolerance via a genome-wide association study (GWAS). Nine salinity tolerance-related traits, including the salt injury score, chlorophyll and water content, and K⁺ and Na⁺ contents were measured in leaves. GWAS analysis allowed the identification of 26 QTLs. Interestingly, ten of them were associated with several different traits, which indicates that these QTLs act pleiotropically to control the different levels of plant responses to salinity stress. Twenty-one identified QTLs colocalized with known QTLs. Several genes within these QTLs have functions related to salinity stress tolerance and are mainly involved in gene regulation, signal transduction or hormone signaling. Our study provides promising QTLs for breeding programs to enhance salinity tolerance and identifies candidate genes that should be further functionally studied to better understand salinity tolerance mechanisms in rice. Full article

(This article belongs to the Special Issue Advances in Cereal Crops Breeding)

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18 pages, 3608 KiB

Open AccessArticle

QMrl-7B Enhances Root System, Biomass, Nitrogen Accumulation and Yield in Bread Wheat

by Jiajia Liu, Qi Zhang, Deyuan Meng, Xiaoli Ren, Hanwen Li, Zhenqi Su, Na Zhang, Liya Zhi, Jun Ji, Junming Li, Fa Cui and Liqiang Song

Plants 2021, 10(4), 764; https://doi.org/10.3390/plants10040764 - 13 Apr 2021

Cited by 11 | Viewed by 2561

Abstract

Genetic improvement of root systems is an efficient approach to improve yield potential and nitrogen use efficiency (NUE) of crops. QMrl-7B was a major stable quantitative trait locus (QTL) controlling the maximum root length in wheat (Triticum aestivum L). Two types of near isogenic lines (A-NILs with superior and B-NILs with inferior alleles) were used to specify the effects of QMrl-7B on root, grain output and nitrogen-related traits under both low nitrogen (LN) and high nitrogen (HN) environments. Trials in two consecutive growing seasons showed that the root traits, including root length (RL), root area (RA) and root dry weight (RDW), of the A-NILs were higher than those of the B-NILs at seedling stage (SS) before winter, jointing stage (JS), 10 days post anthesis (PA10) and maturity (MS), respectively. Under the LN environment, in particular, all the root traits showed significant differences between the two types of NILs (p < 0.05). In contrast, there were no critical differences in aerial biomass and aerial N accumulation (ANA) between the two types of NILs at SS and JS stages. At PA10 stage, the aerial biomass and ANA of the A-NILs were significantly higher than those of the B-NILs under both LN and HN environments (p < 0.05). At MS stage, the A-NILs also exhibited significantly higher thousand-grain weight (TGW), plot grain yield, harvest index (HI), grain N accumulation (GNA), nitrogen harvest index (NHI) and nitrogen partial factor productivity (NPFP) than the B-NILs under the corresponding environments (p < 0.05). In summary, the QMrl-7B A-NILs manifested larger root systems compared to the B-NILs which is favorable to N uptake and accumulation, and eventually enhanced grain production. This research provides valuable information for genetic improvement of root traits and breeding elite wheat varieties with high yield potential and NPFP. Full article

(This article belongs to the Special Issue Advances in Cereal Crops Breeding)

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22 pages, 3039 KiB

Open AccessArticle

Factors Influencing Genomic Prediction Accuracies of Tropical Maize Resistance to Fall Armyworm and Weevils

by Arfang Badji, Lewis Machida, Daniel Bomet Kwemoi, Frank Kumi, Dennis Okii, Natasha Mwila, Symphorien Agbahoungba, Angele Ibanda, Astere Bararyenya, Selma Ndapewa Nghituwamhata, Thomas Odong, Peter Wasswa, Michael Otim, Mildred Ochwo-Ssemakula, Herbert Talwana, Godfrey Asea, Samuel Kyamanywa and Patrick Rubaihayo

Plants 2021, 10(1), 29; https://doi.org/10.3390/plants10010029 - 24 Dec 2020

Cited by 9 | Viewed by 3467

Abstract

Genomic selection (GS) can accelerate variety improvement when training set (TS) size and its relationship with the breeding set (BS) are optimized for prediction accuracies (PAs) of genomic prediction (GP) models. Sixteen GP algorithms were run on phenotypic best linear unbiased predictors (BLUPs) and estimators (BLUEs) of resistance to both fall armyworm (FAW) and maize weevil (MW) in a tropical maize panel. For MW resistance, 37% of the panel was the TS, and the BS was the remainder, whilst for FAW, random-based training sets (RBTS) and pedigree-based training sets (PBTSs) were designed. PAs achieved with BLUPs varied from 0.66 to 0.82 for MW-resistance traits, and for FAW resistance, 0.694 to 0.714 for RBTS of 37%, and 0.843 to 0.844 for RBTS of 85%, and these were at least two-fold those from BLUEs. For PBTS, FAW resistance PAs were generally higher than those for RBTS, except for one dataset. GP models generally showed similar PAs across individual traits whilst the TS designation was determinant, since a positive correlation (R = 0.92***) between TS size and PAs was observed for RBTS, and for the PBTS, it was negative (R = 0.44**). This study pioneered the use of GS for maize resistance to insect pests in sub-Saharan Africa. Full article

(This article belongs to the Special Issue Advances in Cereal Crops Breeding)

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19 pages, 1275 KiB

Open AccessArticle

Genetic Diversity of Selected Rice Genotypes under Water Stress Conditions

by Mahmoud M. Gaballah, Azza M. Metwally, Milan Skalicky, Mohamed M. Hassan, Marian Brestic, Ayman EL Sabagh and Aysam M. Fayed

Plants 2021, 10(1), 27; https://doi.org/10.3390/plants10010027 - 24 Dec 2020

Cited by 32 | Viewed by 5218

Abstract

Drought is the most challenging abiotic stress for rice production in the world. Thus, developing new rice genotype tolerance to water scarcity is one of the best strategies to achieve and maximize high yield potential with water savings. The study aims to characterize 16 rice genotypes for grain and agronomic parameters under normal and drought stress conditions, and genetic differentiation, by determining specific DNA markers related to drought tolerance using Simple Sequence Repeats (SSR) markers and grouping cultivars, establishing their genetic relationship for different traits. The experiment was conducted under irrigated (normal) and water stress conditions. Mean squares due to genotype × environment interactions were highly significant for major traits. For the number of panicles/plants, the genotypes Giza179, IET1444, Hybrid1, and Hybrid2 showed the maximum mean values. The required sterility percentage values were produced by genotypes IET1444, Giza178, Hybrid2, and Giza179, while, Sakha101, Giza179, Hybrid1, and Hybrid2 achieved the highest values of grain yield/plant. The genotypes Giza178, Giza179, Hybrid1, and Hybrid2, produced maximum values for water use efficiency. The effective number of alleles per locus ranged from 1.20 alleles to 3.0 alleles with an average of 1.28 alleles, and the He values for all SSR markers used varied from 0.94 to 1.00 with an average of 0.98. The polymorphic information content (PIC) values for the SSR were varied from 0.83 to 0.99, with an average of 0.95 along with a highly significant correlation between PIC values and the number of amplified alleles detected per locus. The highest similarity coefficient between Giza181 and Giza182 (Indica type) was observed and are susceptible to drought stress. High similarity percentage between the genotypes (japonica type; Sakha104 with Sakha102 and Sakha106 (0.45), Sakha101 with Sakha102 and Sakha106 (0.40), Sakha105 with Hybrid1 (0.40), Hybrid1 with Giza178 (0.40) and GZ1368-S-5-4 with Giza181 (0.40)) was also observed, which are also susceptible to drought stress. All genotypes are grouped into two major clusters in the dendrogram at 66% similarity based on Jaccard’s similarity index. The first cluster (A) was divided into two minor groups A1 and A2, in which A1 had two groups A1-1 and A1-2, containing drought-tolerant genotypes like IET1444, GZ1386-S-5-4 and Hybrid1. On the other hand, the A1-2 cluster divided into A1-2-1 containing Hybrid2 genotype and A1-2-2 containing Giza179 and Giza178 at coefficient 0.91, showing moderate tolerance to drought stress. The genotypes GZ1368-S-5-4, IET1444, Giza 178, and Giza179, could be included as appropriate materials for developing a drought-tolerant variety breeding program. Genetic diversity to grow new rice cultivars that combine drought tolerance with high grain yields is essential to maintaining food security. Full article

(This article belongs to the Special Issue Advances in Cereal Crops Breeding)

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20 pages, 2025 KiB

Open AccessArticle

Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development

by Ilya Kirov, Maxim Dudnikov, Pavel Merkulov, Andrey Shingaliev, Murad Omarov, Elizaveta Kolganova, Alexandra Sigaeva, Gennady Karlov and Alexander Soloviev

Plants 2020, 9(12), 1794; https://doi.org/10.3390/plants9121794 - 17 Dec 2020

Cited by 17 | Viewed by 5970

Abstract

The intergenic space of plant genomes encodes many functionally important yet unexplored RNAs. The genomic loci encoding these RNAs are often considered “junk”, DNA as they are frequently associated with repeat-rich regions of the genome. The latter makes the annotations of these loci and the assembly of the corresponding transcripts using short RNAseq reads particularly challenging. Here, using long-read Nanopore direct RNA sequencing, we aimed to identify these “junk” RNA molecules, including long non-coding RNAs (lncRNAs) and transposon-derived transcripts expressed during early stages (10 days post anthesis) of seed development of triticale (AABBRR, 2n = 6x = 42), an interspecific hybrid between wheat and rye. Altogether, we found 796 lncRNAs and 20 LTR retrotransposon-related transcripts (RTE-RNAs) expressed at this stage, with most of them being previously unannotated and located in the intergenic as well as intronic regions. Sequence analysis of the lncRNAs provide evidence for the frequent exonization of Class I (retrotransposons) and class II (DNA transposons) transposon sequences and suggest direct influence of “junk” DNA on the structure and origin of lncRNAs. We show that the expression patterns of lncRNAs and RTE-related transcripts have high stage specificity. In turn, almost half of the lncRNAs located in Genomes A and B have the highest expression levels at 10–30 days post anthesis in wheat. Detailed analysis of the protein-coding potential of the RTE-RNAs showed that 75% of them carry open reading frames (ORFs) for a diverse set of GAG proteins, the main component of virus-like particles of LTR retrotransposons. We further experimentally demonstrated that some RTE-RNAs originate from autonomous LTR retrotransposons with ongoing transposition activity during early stages of triticale seed development. Overall, our results provide a framework for further exploration of the newly discovered lncRNAs and RTE-RNAs in functional and genome-wide association studies in triticale and wheat. Our study also demonstrates that Nanopore direct RNA sequencing is an indispensable tool for the elucidation of lncRNA and retrotransposon transcripts. Full article

(This article belongs to the Special Issue Advances in Cereal Crops Breeding)

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13 pages, 3333 KiB

Open AccessArticle

Rice Breeding in Russia Using Genetic Markers

by Elena Dubina, Pavel Kostylev, Margarita Ruban, Sergey Lesnyak, Elena Krasnova and Kirill Azarin

Plants 2020, 9(11), 1580; https://doi.org/10.3390/plants9111580 - 15 Nov 2020

Cited by 5 | Viewed by 2812

Abstract

The article concentrates on studying tolerance to soil salinization, water flooding, and blast in Russian and Asian rice varieties, as well as hybrids of the second and third generations from their crossing in order to obtain sustainable paddy crops based on domestic varieties using DNA markers. Samples IR 52713-2B-8-2B-1-2, IR 74099-3R-3-3, and NSIC Rc 106 were used as donors of the SalTol tolerance gene. Varieties with the Sub1A locus were used as donors of the flood resistance gene: Br-11, CR-1009, Inbara-3, TDK-1, and Khan Dan. The lines C101-A-51 (Pi-2), C101-Lac (Pi-1, Pi-33), IR-58 (Pi-ta), and Moroberekan (Pi-b) were used to transfer blast resistance genes. Hybridization of the stress-sensitive domestic varieties Novator, Flagman, Virazh, and Boyarin with donor lines of the genes of interest was carried out. As a result of the studies carried out using molecular marking based on PCR in combination with traditional breeding, early-maturing rice lines with genes for resistance to salinity (SalTol) and flooding (Sub1A), suitable for cultivation in southern Russia, were obtained. Introgression and pyramiding of the blast resistance genes Pi-1, Pi-2, Pi-33, Pi-ta, and Pi-b into the genotypes of domestic rice varieties were carried out. DNA marker analysis revealed disease-resistant rice samples carrying 5 target genes in a homozygous state. The created rice varieties that carry the genes for blast resistance (Pentagen, Magnate, Pirouette, Argamac, Kapitan, and Lenaris) were submitted for state variety testing. The introduction of such varieties into production will allow us to avoid epiphytotic development of the disease, preserving the biological productivity of rice and obtaining environmentally friendly agricultural products. Full article

(This article belongs to the Special Issue Advances in Cereal Crops Breeding)

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23 pages, 1326 KiB

Open AccessArticle

Genetic Diversity and Combining Ability of White Maize Inbred Lines under Different Plant Densities

by Mohamed M. Kamara, Medhat Rehan, Khaled M. Ibrahim, Abdullah S. Alsohim, Mohsen M. Elsharkawy, Ahmed M. S. Kheir, Emad M. Hafez and Mohamed A. El-Esawi

Plants 2020, 9(9), 1140; https://doi.org/10.3390/plants9091140 - 3 Sep 2020

Cited by 31 | Viewed by 4772

Abstract

Knowledge of combining ability and genetic diversity are important prerequisites for the development of outstanding hybrids that are tolerant to high plant density. This work was carried out to assess general combining ability (GCA) and specific combining ability (SCA), identify promising hybrids, estimate genetic diversity among the inbred lines and correlate genetic distance to hybrid performance and SCA across different plant densities. A total of 28 F₁ hybrids obtained by crossing eight adverse inbred lines (four local and four exotic) were evaluated under three plant densities 59,500 (D1), 71,400 (D2) and 83,300 (D3) plants ha⁻¹ using spilt plot design with three replications at two locations during 2018 season. Increasing plant density from D1 to D3 significantly decreased leaf angle (LANG), chlorophyll content (CHLC), all ear characteristics and grain yield per plant (GYPP). Contrarily, days to silking (DTS), anthesis–silking interval (ASI), plant height (PLHT), ear height (EHT), and grain yield per hectare (GYPH) were significantly increased. Both additive and non-additive gene actions were involved in the inheritance of all the evaluated traits, but additive gene action was predominant for most traits. Inbred lines L₁, L₂, and L₅ were the best general combiners for increasing grain yield and other desirable traits across research environments. Two hybrids L₂ × L₅ and L₂ × L₈ were found to be good specific combiners for ASI, LANG, GYPP and GYPH. Furthermore, these hybrids are ideal for further testing and promotion for commercialization under high plant density. Genetic distance (GD) among pairs of inbred lines ranged from 0.31 to 0.78, with an average of 0.61. Clustering based on molecular GD has effectively grouped the inbred lines according to their origin. No significant correlation was found between GD and both hybrid performance and SCA for grain yield and other traits and proved to be of no predictive value. Nevertheless, SCA could be used to predict the hybrid performance across all plant densities. Overall, this work presents useful information regarding the inheritance of maize grain yield and other important traits under high plant density. Full article

(This article belongs to the Special Issue Advances in Cereal Crops Breeding)

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Review

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18 pages, 385 KiB

Open AccessFeature PaperReview

Wheat, Barley, and Oat Breeding for Health Benefit Components in Grain

by Igor G. Loskutov and Elena K. Khlestkina

Plants 2021, 10(1), 86; https://doi.org/10.3390/plants10010086 - 3 Jan 2021

Cited by 78 | Viewed by 8593

Abstract

Cereal grains provide half of the calories consumed by humans. In addition, they contain important compounds beneficial for health. During the last years, a broad spectrum of new cereal grain-derived products for dietary purposes emerged on the global food market. Special breeding programs aimed at cultivars utilizable for these new products have been launched for both the main sources of staple foods (such as rice, wheat, and maize) and other cereal crops (oat, barley, sorghum, millet, etc.). The breeding paradigm has been switched from traditional grain quality indicators (for example, high breadmaking quality and protein content for common wheat or content of protein, lysine, and starch for barley and oat) to more specialized ones (high content of bioactive compounds, vitamins, dietary fibers, and oils, etc.). To enrich cereal grain with functional components while growing plants in contrast to the post-harvesting improvement of staple foods with natural and synthetic additives, the new breeding programs need a source of genes for the improvement of the content of health benefit components in grain. The current review aims to consider current trends and achievements in wheat, barley, and oat breeding for health-benefiting components. The sources of these valuable genes are plant genetic resources deposited in genebanks: landraces, rare crop species, or even wild relatives of cultivated plants. Traditional plant breeding approaches supplemented with marker-assisted selection and genetic editing, as well as high-throughput chemotyping techniques, are exploited to speed up the breeding for the desired genotуpes. Biochemical and genetic bases for the enrichment of the grain of modern cereal crop cultivars with micronutrients, oils, phenolics, and other compounds are discussed, and certain cases of contributions to special health-improving diets are summarized. Correlations between the content of certain bioactive compounds and the resistance to diseases or tolerance to certain abiotic stressors suggest that breeding programs aimed at raising the levels of health-benefiting components in cereal grain might at the same time match the task of developing cultivars adapted to unfavorable environmental conditions. Full article

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