Plant Breeding Techniques Research Articles

Modern Plant Breeding Techniques in Crop Improvement and Genetic Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence—A Critical Review

With the development of new technologies in recent years, researchers have made significant progress in crop breeding. Modern breeding differs from traditional breeding because of great changes in technical means and breeding concepts. Whereas traditional breeding initially focused on high yields, modern breeding focuses on breeding orientations based on different crops’ audiences or by-products. The process of modern breeding starts from the creation of material populations, which can be constructed by natural mutagenesis, chemical mutagenesis, physical mutagenesis transfer DNA (T-DNA), Tos17 (endogenous retrotransposon), etc. Then, gene function can be mined through QTL mapping, Bulked-segregant analysis (BSA), Genome-wide association studies (GWASs), RNA interference (RNAi), and gene editing. Then, at the transcriptional, post-transcriptional, and translational levels, the functions of genes are described in terms of post-translational aspects. This article mainly discusses the application of the above modern scientific and technological methods of breeding and the advantages and limitations of crop breeding and diversity. In particular, the development of gene editing technology has contributed to modern breeding research.

Revolutionizing plant breeding: a historical perspective from cross-pollination to gene editing

The history of plant breeding can be broadly divided into four eras: the Pre-Mendelian era (before 1900), the Mendelian era (1900-1920), the post-Mendelian era (1921-1950), and the Modern era (after 1950). Significant milestones include the release of the first hybrid maize varieties in 1961, the first sorghum hybrid (CSH-1) in 1964, the first bajra hybrid (HB-1) in 1965, and the first pigeon pea hybrid (ICPH-8) in 1991. Achieving a world with zero hunger requires a sustainable increase in food production and distribution and elimination of poverty. This goal demands scientific, logistical, and humanitarian approaches to ensure food security from farmers and breeders to policymakers and governments. Conventional breeding techniques alone are insufficient to meet the challenges posed by climate change, biotic and abiotic stress, and the growing global population projected to reach 10 billion by 2050. Novel plant breeding techniques, such as genome editing, speed breeding, and omics technology integration, offer precise, cost-effective, and less time-consuming solutions. These techniques enable the editing of agriculturally significant genes, promoting hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress. Genome editing technologies have evolved, with CRISPR/Cas9 and its variants, base editing (BE), and prime editing (PE) playing pivotal roles in generating transgene-free plants. These advancements have significant implications for crop improvement, meeting food and nutrition security, and catering to regional preferences. Syngenta's initiative to open rights to CRISPR-based technologies through the Shoots by Syngenta platform exemplifies the collaborative efforts needed to drive agricultural innovation and sustainability. The review discusses the current regulatory regimes governing genome-edited crops, prospects of new tools such as DNA-free editing systems and nanotechnology, and their applicability in crop improvement. A multidisciplinary approach involving political, social, economic, and scientific stakeholders is essential for the successful adoption of genome editing technologies, which will ultimately make agriculture a lucrative profession and attract youth to the field.

Preferentially expressed endosperm genes reveal unique activities in wheat endosperm during grain filling

BackgroundBread wheat (Triticum aestivum L.) endosperm contains starch and proteins, which determine the final yield, quality, and nutritional value of wheat grain. The preferentially expressed endosperm genes can precisely provide targets in the endosperm for improving wheat grain quality and nutrition using modern bioengineering technologies. However, the genes specifically expressed in developing endosperms remain largely unknown.ResultsIn this study, 315 preferentially expressed endosperm genes (PEEGs) in the spring wheat landrace, Chinese Spring, were screened using data obtained from an open bioinformatics database, which reveals a unique grain reserve deposition process and special signal transduction in a developing wheat endosperm. Furthermore, transcription and accumulation of storage proteins in the wheat cultivar, XC26 were evaluated. The results revealed that 315 PEEG plays a critical role in storage protein fragment deposition and is a potential candidate for modifying grain quality and nutrition.ConclusionThese results provide new insights into endosperm development and candidate genes and promoters for improving wheat grain quality through genetic engineering and plant breeding techniques.

New genomic techniques, old divides: Stakeholder attitudes towards new biotechnology regulation in the EU and UK.

The European Union and United Kingdom are in the process of establishing new regulation regarding the use of new genomic techniques in crop and animal breeding. As part of this process, consultations have been launched to understand the views of stakeholders towards the use of new genomic techniques in plant and animal breeding. The responsible research and innovation framework emphasises the importance of dialogue between technology developers and stakeholders, including the public, but what are the opinions of stakeholders towards the regulation of NGTs in Europe and do they view these consultations as opportunities to engage with technology governance? We conducted semi-structured interviews with experts from a range of agri-food stakeholder groups in the European Union and United Kingdom to understand current attitudes towards new biotechnology regulation, how they viewed the process of consultation in both places and what influence they felt they had in shaping regulations. We found that the discussion is similar in both EU and UK, with predictable and fixed opinions determined by attitudes towards the perceived risks associated with direct mutagenesis. Both UK and EU consultations were considered to have the same weaknesses and stakeholders discussed a desire for more dialogic forms of engagement. We highlight several options for new forms of involvement in biotechnology regulation by exploring relevant responsible research and innovation literature.

Seed vigour testing of Acacia mangium Willd. as a result of mutation

Plant breeding techniques are applied to increase the genetic variation of a plant. Induction of plant mutation using gamma irradiation is one of the methods that can be applied to improve the genetic diversity of plants. This study aims to analyze the vigour of mangium seeds treated by mutation. Mutation treatment was administered to M0 of mangium seed. This study used M2 mangium seeds and control mangium seeds (without mutation treatment). Several assays, such as growth, stress, and biochemical tests, were conducted to determine the mangium seed’s vigour. The growth test showed that M2 mangium seeds had higher germination values, germination height, dry weight, and vigour index than control mangium seeds. The stress test consisting of the Hiltner test, accelerated ageing test, and saturation test of the germination value of M2 mangium seeds wass higher than control mangium seeds. In the biochemical test, the electrical conductivity value of control mangium seeds was more significant than M2 mangium seeds. In general, M2 mangium seeds had higher vigour than control mangium seeds.

Generation of major glutelin-deficient (GluA, GluB, and GluC) semi-dwarf Koshihikari rice line.

We generated a new Koshihikari rice line with a drastically reduced content of glutelin proteins and higher lodging resistance by using new and conventional plant breeding techniques. Using CRISPR/Cas9-mediated genome editing, we generated mutant rice with drastically decreased contents of major glutelins. A Koshihikari rice mutant line, a123, lacking four glutelins (GluA1, GluA2, GluB4, and GluB5) was used as a host, and another five major glutelin genes (GluA3, GluB1a, GluB1b, GluB2, and GluC) were knocked out through two iterations of Agrobacterium-mediated transformation. Mutant seeds were deficient in the GluA family, GluB family, and GluC, and the line obtained was named GluABC KO. Glutelin content was much lower in GluABC KO than in the existing low-glutelin rice mutant LGC-1. A null segregant of GluABC KO was selected using new-generation sequencing and backcrossing, and the sd-1 allele for the semi-dwarf trait was introduced to increase lodging resistance.

CRISPR-Cas9 based molecular breeding in crop plants: a review.

Traditional crop breeding techniques are not quickly boosting yields to fulfill the expanding population needs. Long crop lifespans hinder the ability of plant breeding to develop superior crop varieties. Due to the arduous crossing, selecting, and challenging processes, it can take decades to establish new varieties with desired agronomic traits. Develop new plant varieties instantly to reduce hunger and improve food security. As a result of the adoption of conventional agricultural techniques, crop genetic diversity has decreased over time. Several traditional and molecular techniques, such as genetic selection, mutant breeding, somaclonal variation, genome-wide association studies, and others, have improved agronomic traits associated with agricultural plant productivity, quality, and resistance to biotic and abiotic stresses. In addition, modern genome editing approaches based on programmable nucleases, CRISPR, and Cas9 proteins have escorted an exciting new era of plant breeding. Plant breeders and scientists worldwide rely on cutting-edge techniques like quick breeding, genome editing tools, and high-throughput phenotyping to boost crop breeding output. This review compiles discoveries in numerous areas of crop breeding, such as using genome editing tools to accelerate the breeding process and create yearly crop generations with the desired features, to describe the shift from conventional to modern plant breeding techniques.

Growth, ultrastructural and physiological characteristics of Abelmoschus cytotypes under elevated ozone stress: a study on ploidy-specific responses.

Tropospheric ozone (O3 ) is a significant abiotic stressor whose rising concentration negatively influences plant growth. Studies related to the differential response of Abelmoschus cytotypes to elevated O3 treatment are scarce and need further exploration to recognise the role of polyploidisation in stress tolerance. In this study, we analysed the changes in growth pattern, ultrastructure, physiology and foliar protein profile occurring under O3 stress in Abelmoschus moschatus (monoploid), Abelmoschus esculentus (diploid) and Abelmoschus caillei (triploid). Our findings showed that higher stomatal conductance in A. moschatus triggered higher O3 intake, causing damage to stomatal cells and photosynthetic pigments. Additionally, it caused a reduction in photosynthetic rates, leading to reduced plant growth, total biomass and economic yield. This O3 -induced toxicity was less in diploid and triploid cytotypes of Abelmoschus . Protein profiling by sodium dodecyl sulpate-polyacrylamide gel electrophoresis showed a significant decrease in the commonly found RuBisCO larger and smaller subunits. The decrease was more prominent in monoploid compared to diploid and triploid. This study provides crucial data for research that aim to enhance plant ability to withstand O3 induced oxidative stress. Our findings may help in developing a tolerant variety through plant breeding techniques, which will be economically more advantageous in reaching the objective of sustainable production at the high O3 levels projected under a climate change scenario.

NOOR-2019: A High-yielding and Marvelous Chickpea Kabuli Variety Developed in Punjab, Pakistan

The advancement of the latest crop varieties with advantageous characteristics is an ongoing process. Over time, a cultivated variety becomes vulnerable to several factors of biotic and abiotic plant stresses. This article discusses creating a novel and inventive chickpea Kabuli variety known as "Noor-2019." This variety was developed using conventional plant breeding techniques to enhance yield capacity, seed form, coloration, and resistance against various diseases. During Rabi 2002-03 period, two local genotypes, namely K-90399 and K-52582 were interbred to induce heredity diversity. After a selection of six generations, a remarkably consistent lineage of Chickpea Kabuli PCK-09012, later denoted as Noor-2019, with pedigree noted as C.15/15/15/105/98/80/12, originated from the F6 generation in 2008-09. Concurrently, this line of Chickpea Kabuli was evaluated for yield potential, disease reaction, and other agronomic studies from 2009 to 2019 at eight different Chickpea growing areas of Punjab. On an average scale, Noor-2019 surpassed the corresponding control groups with a notable margin, displaying a 102.74% increase in PYT and 53.72% improvement in AYT. This specific candidate line exhibited slightly elevated yields, with 0.8% more in MYT and 2.84% increase in CYT. Throughout the national testing phase, this particular variety exhibited its superiority, achieving a 33.26% higher yield during 2014-15 season and 3.61% increase in the subsequent year, compared to the benchmark variety Noor-2013. This remarkable performance culminated in the candidate variant "Noor-19" achieving an impressive yield potential of 1963 kg/ha in the (NUYTs) during 2014-15 period at the Gram Breeding Research Sub Station, Kallurkot. Noor-19 contains 23.19% crude protein and 4.06% crude fat content. Significantly, it achieves higher seed yields and possesses in-built resistance against Fusarium wilt, accompanied by moderate resistance to Ascochyta blight. Furthermore, it shows a commendable tolerance towards insect pests. Notably, the cultivation of this novel variety doesn't necessitate specialized production techniques; instead, it harmonizes seamlessly with existing agronomic methods. Its adaptability extends to irrigated and rain-fed chickpea-growing regions within the province of Punjab.

Heterosis in horticultural crop breeding: combining old theoretical bases with modern genomic views

Heterosis in plants has been among the challenging topics for plant scientists worldwide. The production of F1 hybrid varieties of seed-propagated horticultural species is one of the most successful applications of plant breeding techniques. The exploitation of the heterosis phenomenon promotes homogeneity and maximizes crop yields and is a way for breeders to legally control and protect their commercial products. In the past heterosis has been largely studied and explored in cereal crop systems, considering maize as a model for understanding the genetic bases of this phenomenon. To date, crossbreeding in horticultural vegetables has also rapidly progressed. F1 hybrid varieties are available for many horticultural crops, including both allogamous and autogamous species. Several genetic and nongenetic mechanisms have been applied to facilitate the large-scale production of F1 hybrid seeds in vegetable crops to prevent undesirable selfing. Although the development and commercialization of F1 hybrids is currently common in agriculture, this phenomenon is still being investigated at different levels. With the rapid accumulation of knowledge on plant genome structures and gene activities and the advancement of new genomics platforms and methodologies, significant progress has been achieved in recent years in the study of the genetic and molecular bases of heterosis. This paper provides a brief overview of current theoretical advances and practical predictions of the molecular mechanisms underlying heterosis in plants. The aim is to carefully summarize the fundamental mechanisms of heterosis in plants, focusing on horticultural plant breeding, to improve the existing knowledge in this research area. We describe the quantitative genetic model of phenotypic variation and combine evolutionary, phenotypic and molecular genetic views to explain the origin and manifestation of heterosis and its significance for breeding F1 hybrid varieties in horticultural crops. The principles of genomic prediction and its applications in genomic selection are then covered.

Physicochemical properties, eating and cooking quality and genetic variability: a comparative analysis in selected rice varieties of South India

The physicochemical characteristics and digestibility properties of rice are greatly influenced by its genetic variability. In this study, we attempt to understand the overall quality of five traditional and popularly consumed rice varieties of Kerala. The major traits affecting the eating and cooking quality of rice such as amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) were determined and correlated with the expression of the starch-synthesis-related genes (SSRGs). The Wx is a major SSRG, which modulates the amylose content and the eating as well as cooking qualities of rice. The rice varieties including, Jaya, Matta and Rakthashali were found to have intermediate amylose content (Wxa allele) while Kuruva and Pokkali were found to have high Amylose Content (Wxa allele). The glycemic index (GI) of all varieties was found to be in the range of 51.0–58.6. Among the screened rice varieties, Pokkali was found to have the lowest glycemic index and digestibility with appreciable eating and cooking qualities. Pokkali rice, with its low GI (51.0), could be a recommended variety for diabetes management. Furthermore, the rice eating and cooking qualities, and plant breeding techniques coordinated by the expression of the starch synthesis-related gene (Wx), could be a novel approach to improve the valuable germplasm.Graphical

Unveiling the phytochemical variability of fatty acids in world marigold (Calendula officinalis L.) germplasm affected by genotype

Marigold is an annual herbaceous medicinal and aromatic plant, native to the Mediterranean region. Although marigold flowers have attracted considerable attention, the noteworthy characteristics of marigold seeds have often been overlooked. The industrial sector holds keen interest in marigold due to the presence of calendic acid in its seeds. Moreover, calendic acid exhibits promising anti-cancer properties, adding to the growing interest in the medicinal potential of this plant. In this study, a total of 31 marigold genotype seeds from fifteen different countries were used as experimental material. The observed seed oil content exhibited a range of values spanning from 6.00% to 20.33%, with a mean value of 11.59%. GC/MS analysis was conducted to evaluate the chemical variability associated with genotypic changes. Notably, the main fatty acids observed in the oil of these genotypes were α-calendic acid (ranging from 6.91% to 51.42%), linoleic acid (ranging from 30.50% to 48.25%), oleic acid (ranging from 8.26% to 22.50%), and palmitic acid (ranging from 3.86% to 9.28%). Particularly noteworthy is the emergence of genotypes PI 420376, PI 545694, PI 545701, PI 578109, PI 597588, PI 597591, and PI 597594, boasting calendic acid content exceeding 50%. Furthermore, the values of calendic acid exhibit significant variation across countries. The range extends from the United Kingdom, displaying one of the lower values, to Ontario, Canada, which represents countries with notably higher values. Consequently, there exists a necessity to enhance the proportion of calendic acid within marigold through strategic plant breeding techniques. This can be achieved through the selection and development of marigold cultivars with higher calendic acid contents.

Enhancing Crop Resilience through CRISPR/Cas9-Mediated Development of Disease-Resistant Cultivars

A major issue in agriculture is the protection of crops against diseases and pests. Plant breeding has been primarily responsible for the growth of disease-resistant cultivars. The use of gene editing techniques in plant breeding is essential for obtaining desired features. Clustered Regular Interspaced Palindromic Repeats (CRISPER)/Cas9 (CRISPR-related protein) is a new advancement in gene editing technology. It can be utilised in plant defence mechanisms against pathogen attack by recognising the bacterial immune system and destroying invasive pathogen genes. Advances in plant breeding through CRISPR/Cas9 integration have helped develop cultivars including hereditary resistance to bacterial and viral diseases. Future crop generations can acquire CRISPR/Cas9-mediated transgene resistance if the Cas9/sgRNA transgene has been isolated in the F1 generation. Cas9/sgRNA transgene separation makes CRISPR/Cas9 safe for use in plant breeding. Although CRISPR/Cas9 has proven to be a wonderful tool to revolutionize plant breeding and develop various disease resistant varieties, its effect on many plant physiological processes remains to be thoroughly investigated.

Establishment of protoplasts transient expression system in Pinellia ternata (Thunb.) Breit.

In this study, we established an efficient and rapid transient expression system in the protoplasts of Pinellia ternata (Thunb.) Breit. (P. ternata). The protoplasts of P. ternata were prepared from plant leaves as the source material by digesting them with the combination of 20g·l-1 cellulase and 15g·l-1 macerozyme for 6h. Based on the screening of PEG concentration, the conditions for PEG-mediated protoplast transformation were improved, and the highest transformation efficiency was found for 40% PEG 4000. Furthermore, we used the subcellular protein localization technique in P. ternata protoplasts to allow further validation of transient expression system. We present the method that can be applicable for studying both gene verification and expression in P. ternata protoplasts, thus allowing for engineering the improved varieties of P. ternata through molecular plant breeding techniques. This method can also be widely applicable for analyzing protein interactions, detecting promoter activity, for somatic cell fusion in plant breeding, as well as for other related studies.

Epigenomics: a new tool for the generation of climate resilient grapevines

Climate change is expected to increase the occurrence of extreme environmental conditions. Viticulture, as agriculture in general, is highly dependent on climatic conditions, not only for yield but also for fruit quality, which is the most important factor affecting produce value at the farm-gate. This demands the development of novel plant breeding techniques that will lead to the accelerated production of more resilient grape varieties, as conventional breeding programs for perennials are often prolonged. Recent research has suggested that environmental conditions can activate a memory of stress that could result in a primed response to subsequent stress events. This is a process capable of increasing plant’s resilience to abiotic stimuli, allowing plants to better adapt to extreme environmental conditions. While the effect of priming has been observed in many plants, the underlying mechanisms are puzzling and seldom studied in perennial crops. A large body of research has been developed in the last decade linking response to stress, stress priming, and memory of stress with epigenetic mechanisms. This understanding of plant epigenetics has opened the door to the application of epigenetics to crop improvement, such as the use of epigenetic breeding for the generation of more resilient crops. Perennial crop agriculture in general, and viticulture in particular, would benefit from more in-depth knowledge on epigenetic memory of stress.

Genome editing in plants as a key technology in sustainable bioeconomy

According to the definition of OECD, bioeconomy refers to the set of economic activities relating to the innovation, development, production and use of biological products and processes. The aim of the bioeconomy is to provide more sustainable use of resources. In Europe, the concept of bioeconomy has become increasingly popular as many regions and nations have developed a national bioeconomy strategy or policies relevant to bioeconomy. However, it may not be enough to face challenges such as climate change, reduction of biodiversity, or ensuring food security. One of the solutions, especially in times of pandemic and Russia's war in Ukraine, is using new plant breeding techniques such as genome editing in agriculture. It requires radical changes in regulation and society's perception of plant breeding, especially in Europe. An important aspect is also involving the community in the bioeconomy, strengthening national and international collaboration, and providing educational tools for the public.

Evidence of scientific research on organic plant breeding: A bibliometric study

AbstractUse of varieties bred under organic conditions is essential in order to minimize the yield gap between organic and conventional agriculture. The aim of this study was to analyse research publications related to the topic ‘organic plant breeding’ from the Web of Science database using bibliometric science mapping and visualization tools. The number of analysed documents in the bibliographic dataset was 204 from the 53 sources. The overall trend in the organic plant breeding literature showed that the number of publications increased during the observed time‐span. We found that in total, 65 countries and 337 institutions are active in the field of organic plant breeding with a high degree of international collaboration. The top five countries according to the number of publications were the United States, Italy, Germany, France, and Canada, while the most active institutions were Wageningen University, Iowa State University, University of Alberta, University of Copenhagen, and University of Hohenheim. All keywords from the organic plant breeding research in the agronomy category were separated into seven clusters for different research topics. Although there is evident progress viewed through the increased trend in the number of publications, organic plant breeding needs further expansion and development. This is especially through the implementation of novel plant breeding techniques and methods aiming to improve traits that are highly specific to organic conditions.

Perceived Knowledge of Cassava Value Chain Actors on Varietal Preferences for Various End Uses

This study assessed end users’ perceptions about preferred traits for various end uses, constraints, and varietal preferences using Participatory Rural Appraisal (PRA). A purposive sampling procedure was used to identify value chain actors. A total of 360 questionnaires were administered to 120 producers, 72 processors, 72 consumers and 96 traders. The study revealed that, 89.2% of the respondents grow cassava only whilst 82.5% grow and process in the three study districts. Farmers commonly select cassava varieties with focus on high yield, root size, root taste, early maturity period and inner color. Mean rank of studied traits were significantly (p ≤ 0.0001) differed among cassava producers and processors. In Bo district, high root yield (1st), root size (2nd), dry matter content (3rd) and starch content (4th), were the most important traits. In Bombali district, high root yield (1st), root taste (2st), dry matter content (3rd) and poundability (4th) were the most desired. In Kenema district, high root yield (1st), root taste (2st), maturity period (3rd), and poundability (4th), were the most desired. The overall ranking based on producers’ selection criteria revealed that starch content, dry matter content, root size and ease of peeling as the top key traits considered for cassava processing. Results suggest that participatory variety selection and participatory plant breeding techniques should be explored to promote collaborations between stakeholders and breeders for development of new cassava varieties with desired traits including high dry matter content, high root yield, high starch content and other desired key quality traits.

The potential of metabolomics in assessing global compositional changes resulting from the application of CRISPR/Cas9 technologies.

Exhaustive analysis of genetically modified crops over multiple decades has increased societal confidence in the technology. New Plant Breeding Techniques are now emerging with improved precision and the ability to generate products containing no foreign DNA and mimic/replicate conventionally bred varieties. In the present study, metabolomic analysis was used to compare (i) tobacco genotypes with and without the CRISPR associated protein 9 (Cas9), (ii) tobacco lines with the edited and non-edited DE-ETIOLATED-1 gene without phenotype and (iii) leaf and fruit tissue from stable non-edited tomato progeny with and without the Cas9. In all cases, multivariate analysis based on the difference test using LC-HRMS/MS and GC-MS data indicated no significant difference in their metabolomes. The variations in metabolome composition that were evident could be associated with the processes of tissue culture regeneration and/or transformation (e.g. interaction with Agrobacterium). Metabolites responsible for the variance included quantitative changes of abundant, well characterised metabolites such as phenolics (e.g. chlorogenic acid) and several common sugars such as fructose. This study provides fundamental data on the characterisation of gene edited crops, that are important for the evaluation of the technology and its assessment. The approach also suggests that metabolomics could contribute to routine product-based analysis of crops/foods generated from New Plant Breeding approaches.

Breeding by intervening: Exploring the role of associations and deliberation in consumer acceptance of different breeding techniques.

New plant breeding techniques may play an important role in improving food quality, global food security and sustainability. Previous breeding techniques have, however, met with substantial resistance from society. This study examined the role of associations and deliberation in the evaluation of breeding techniques. Breeding techniques studied included conventional breeding, gene-editing, genetic modification (cisgenesis and transgenesis), marker-assisted breeding and synthetic biology. By using focus group discussions that included individual tasks, we found that when participants relied on their spontaneous associations, gene-editing was evaluated similarly as genetic modification. However, after information provision and group discussion, gene-editing was preferred over genetic modification. Perceived naturalness was found to be the main reason for obtaining different levels of acceptance, not only between gene-editing and genetic modification but across all breeding techniques examined. These findings highlight the importance of associations and show that beliefs about naturalness remain crucial in understanding how consumers evaluate breeding techniques.