Genome projects and gene pools: new germplasm for plant breeding?

A Review of Transcriptomics and Metabolomics in Plant Quality and Environmental Response: From Bibliometric Analysis to Science Mapping and Future Trends

Transcriptomics and metabolomics offer distinct advantages in investigating the differentially expressed genes and cellular entities that have the greatest influence on end-phenotype, making them crucial techniques for studying plant quality and environmental responses. While numerous relevant articles have been published, a comprehensive summary is currently lacking. This review aimed to understand the global and longitudinal research trends of transcriptomics and metabolomics in plant quality and environmental response (TMPQE). Utilizing bibliometric methods, we presented a comprehensive science mapping of the social structure, conceptual framework, and intellectual foundation of TMPQE. We uncovered that TMPQE research has been categorized into three distinct stages since 2020. A citation analysis of the 29 most cited articles, coupled with a content analysis of recent works (2020-2023), highlight five potential research streams in plant quality and environmental responses: (1) biosynthetic pathways, (2) abiotic stress, (3) biotic stress, (4) development and ripening, and (5) methodologies and tools. Current trends and future directions are shaped by technological advancements, species diversity, evolving research themes, and an environmental ecology focus. Overall, this review provides a novel and comprehensive perspective to understand the longitudinal trend on TMPQE.

What plant breeding may (and may not) look like in 2050?

At the turn of 2000 many authors envisioned future plant breeding. Twenty years after, which of those authors' visions became reality or not, and which ones may become so in the years to come. After two decades of debates, climate change is a "certainty," food systems shifted from maximizing farm production to reducing environmental impact, and hopes placed into GMOs are mitigated by their low appreciation by consumers. We revise herein how plant breeding may raise or reduce genetic gains based on the breeder's equation. "Accuracy of Selection" has significantly improved by many experimental-scale field and laboratory implements, but also by vulgarizing statistical models, and integrating DNA markers into selection. Pre-breeding has really promoted the increase of useful "Genetic Variance." Shortening "Recycling Time" has seen great progression, to the point that achieving a denominator equal to "1" is becoming a possibility. Maintaining high "Selection Intensity" remains the biggest challenge, since adding any technology results in a higher cost per progeny, despite the steady reduction in cost per datapoint. Furthermore, the concepts of variety and seed enterprise might change with the advent of cheaper genomic tools to monitor their use and the promotion of participatory or citizen science. The technological and societal changes influence the new generation of plant breeders, moving them further away from field work, emphasizing instead the use of genomic-based selection methods relying on big data. We envisage what skills plant breeders of tomorrow might need to address challenges, and whether their time in the field may dwindle.

Insights on cisgenic plants with durable disease resistance under the European Green Deal

Significant shares of harvests are lost to pests and diseases, therefore, minimizing these losses could solve part of the supply constraints to feed the world. Cisgenesis is defined as the insertion of genetic material into a recipient organism from a donor that is sexually compatible. Here, we review (i) conventional plant breeding, (ii) cisgenesis, (iii) current pesticide-based disease management, (iv) potential economic implications of cultivating cisgenic crops with durable disease resistances, and (v) potential environmental implications of cultivating such crops; focusing mostly on potatoes, but also apples, with resistances to Phytophthora infestans and Venturia inaequalis, respectively. Adopting cisgenic varieties could provide benefits to farmers and to the environment through lower pesticide use, thus contributing to the European Green Deal target.

Development of source material for pea breeding through chemical mutagenesis and evaluation of its genetic diversity using SSR markers

Background. Pea (Pisum sativum L.) is a valuable leguminous crop of worldwide importance. The main problem of modern plant breeding is a decrease in the genetic diversity of crops, including pea. One of the ways to increase genetic polymorphism is the use of chemically induced mutagenesis. Sodium azide (NaN3) is a highly effective chemical mutagen successfully used in mutation breeding to increase the productivity of cultivated plants and enrich them with new useful traits. We used it to obtain new pea breeding material.

Materials and methods. Experiments were carried out to obtain pea mutants using sodium azide at the concentrations of 1, 5 and 10 mM and the exposure time of 3 and 9 h. Molecular genetic polymorphism of the М2 plants and the original cultivar was assessed using 10 SSR markers from the microsatellite genomic library (Agrogene®, France).

Results. Optimal concentrations of sodium azide and the duration of seed treatment with it were identified: 1–5 mM for 3 h. Sixteen mutant populations were obtained; in ten of them a change in the leaf type was found. An analysis of the yield structure components revealed a significant superiority (p < 0.05) over the initial cultivar ‘Pamyati Khangildina’ in the mutant populations No. 1, No. 5, No. 9, No. 10, No. 15 and No. 16 in the number of seeds per pod, No. 9 and No. 16 in the weight of 1000 seeds, and No. 16 in the weight of seeds per plant. A dendrogram constructed on the basis of the SSR analysis data showed the degree of differences between the M2 populations of pea plants and the initial cultivar ‘Pamyati Khangildina’.

Conclusion. The obtained mutant populations are planned to be used in pea breeding as sources of high seed numbers in pods, seed yield, seed weight per plant, and large seed size. A microsatellite analysis with 10 SSR markers revealed differences among the M2 mutant populations at the genetic level and made it possible to identify them.

Genetic Identity, Diversity, and Population Structure of CIP's Sweetpotato (I. batatas) Germplasm Collection

The in trust sweetpotato collection housed by the International Center of Potato (CIP) is one of the largest assemblages of plant material representing the genetic resources of this important staple crop. The collection currently contains almost 6,000 accessions of Ipomoea batatas (cultivated sweetpotato) and over 1,000 accessions of sweetpotato crop wild relatives (CWRs). In this study, the entire cultivated collection (5,979 accessions) was genotyped with a panel of 20 simple sequence repeat (SSR) markers to assess genetic identity, diversity, and population structure. Genotyping and phenotyping of in vitro plantlets and mother plants were conducted simultaneously on 2,711 accessions (45% of the total collection) to identify and correct possible genetic identity errors which could have occurred at any time over the thirty plus years of maintenance in the in vitro collection. Within this group, 533 accessions (19.6%) had errors in identity. Field evaluations of morphological descriptors were carried out to confirm the marker data. A phylogenetic tree was constructed to reveal the intraspecific relationships in the population which uncovered high levels of redundancy in material from Peru and Latin America. These genotypic data were supported by morphological data. Population structure analysis demonstrated support for four ancestral populations with many of the accessions having lower levels of gene flow from the other populations. This was especially true of germplasm derived from Peru, Ecuador, and Africa. The set of 20 SSR markers was subsequently utilized to examine a subset of 189 accessions from the USDA sweetpotato germplasm collection and to identify and reconcile potential errors in the identification of clones shared between these collections. Marker analysis demonstrated that the USDA subset of material had 65 unique accessions that were not found in the larger CIP collection. As far as the authors are aware, this is the first report of genotyping an entire sweetpotato germplasm collection in its entirety.

Analysis of genetic differentiation and genomic variation to reveal potential regions of importance during maize improvement

BACKGROUND

Exploring genetic differentiation and genomic variation is important for both the utilization of heterosis and the dissection of the genetic bases of complex traits.

METHODS

We integrated 1857 diverse maize accessions from America, Africa, Europe and Asia to investigatetheir genetic differentiation, genomic variation using 43,252 high-quality single-nucleotide polymorphisms(SNPs),combing GWAS and linkage analysis strategy to exploring the function of relevant genetic segments.

RESULTS

We uncovered many more subpopulations that recently or historically formed during the breeding process. These patterns are represented by the following lines: Mo17, GB, E28, Ye8112, HZS, Shen137, PHG39, B73, 207, A634, Oh43, Reid Yellow Dent, and the Tropical/subtropical (TS) germplasm. A total of 85 highly differentiated regions with a DEST of more than 0.2 were identified between the TS and temperate subpopulations. These regions comprised 79% of the genetic variation, and most were significantly associated with adaptive traits. For example, the region containing the SNP tag PZE.108075114 was highly differentiated, and this region was significantly associated with flowering time (FT)-related traits, as supported by a genome-wide association study (GWAS) within the interval of FT-related quantitative trait loci (QTL). This region was also closely linked to zcn8 and vgt1, which were shown to be involved in maize adaptation. Most importantly, 197 highly differentiated regions between different subpopulation pairs were located within an FT- or plant architecture-related QTL.

CONCLUSIONS

Here we reported that 700-1000 SNPs were necessary needed to robustly estimate the genetic differentiation of a naturally diverse panel. In addition, 13 subpopulations were observed in maize germplasm, 85 genetic regions with higher differentiation between TS and temperate maize germplasm, 197 highly differentiated regions between different subpopulation pairs, which contained some FT- related QTNs/QTLs/genes supported by GWAS and linkage analysis, and these regions were expected to play important roles in maize adaptation.

Diversity in global gene expression and morphology across a watercress (Nasturtium officinale R. Br.) germplasm collection: first steps to breeding

Watercress (Nasturtium officinale R. Br.) is a nutrient intense, leafy crop that is consumed raw or in soups across the globe, but for which, currently no genomic resources or breeding programme exists. Promising morphological, biochemical and functional genomic variation was identified for the first time in a newly established watercress germplasm collection, consisting of 48 watercress accessions sourced from contrasting global locations. Stem length, stem diameter and anti-oxidant (AO) potential varied across the accessions. This variation was used to identify three extreme contrasting accessions for further analysis. Variation in global gene expression was investigated using an Affymetrix Arabidopsis ATH1 microarray gene chip, using the commercial control (C), an accession selected for dwarf phenotype with a high AO potential (dwarfAO, called 'Boldrewood') and one with high AO potential alone. A set of transcripts significantly differentially expressed between these three accessions, were identified, including transcripts involved in the regulation of growth and development and those involved in secondary metabolism. In particular, when differential gene expression was compared between C and dwarfAO, the dwarfAO was characterised by increased expression of genes encoding glucosinolates, which are known precursors of phenethyl isothiocyanate, linked to the anti-carcinogenic effects well-documented in watercress. This study provides the first analysis of natural variation across the watercress genome and has identified important underpinning information for future breeding for enhanced anti-carcinogenic properties and morphology traits in this nutrient-intense crop.

Aridity and grazing as convergent selective forces: an experiment with an Arid Chaco bunchgrass

It has been proposed that aridity and grazing are convergent selective forces: each one selects for traits conferring resistance to both. However, this conceptual model has not yet been experimentally validated. The aim of this work was to experimentally evaluate the effect of aridity and grazing, as selective forces, on drought and grazing resistance of populations of Trichloris crinita, a native perennial forage grass of the Argentinean Arid Chaco region. We collected seeds in sites with four different combinations of aridity and grazing history (semiarid/ subhumid x heavily grazed/lightly grazed), established them in pots in a common garden, and subjected the resulting plants to different combinations of drought and defoliation. Our results agreed with the convergence model. Aridity has selected T. crinita genotypes that respond better to drought and defoliation in terms of sexual reproduction and leaf growth, and that can evade grazing due to a lower shoot: root ratio and a higher resource allocation to reserves (starch) in stem bases. Similarly, grazing has selected genotypes that respond better to drought and defoliation in terms of sexual reproduction and that can evade grazing due to a lower digestibility of leaf blades. These results allow us to extend concepts of previous models in plant adaptation to herbivory to models on plant adaptation to drought. The only variable in which we obtained a result opposite to predictions was plant height, as plants from semiarid sites were taller (and with more erect tillers) than plants from subhumid sites; we hypothesize that this result might have been a consequence of the selection exerted by the high solar radiation and soil temperatures of semiarid sites. In addition, our work allows for the prediction of the effects of dry or wet growing seasons on the performance of T. crinita plants. Our results suggest that we can rely on dry environments for selecting grazing-resistant genotypes and on high grazing pressure history environments for selecting drought-resistant ones.

Sorghum bicolor's transcriptome response to dehydration, high salinity and ABA

Genome wide changes in gene expression were monitored in the drought tolerant C4 cereal Sorghum bicolor, following exposure of seedlings to high salinity (150 mM NaCl), osmotic stress (20% polyethylene glycol) or abscisic acid (125 microM ABA). A sorghum cDNA microarray providing data on 12,982 unique gene clusters was used to examine gene expression in roots and shoots at 3- and 27-h post-treatment. Expression of approximately 2200 genes, including 174 genes with currently unknown functions, of which a subset appear unique to monocots and/or sorghum, was altered in response to dehydration, high salinity or ABA. The modulated sorghum genes had homology to proteins involved in regulation, growth, transport, membrane/protein turnover/repair, metabolism, dehydration protection, reactive oxygen scavenging, and plant defense. Real-time PCR was used to quantify changes in relative mRNA abundance for 333 genes that responded to ABA, NaCl or osmotic stress. Osmotic stress inducible sorghum genes identified for the first time included a beta-expansin expressed in shoots, actin depolymerization factor, inositol-3-phosphate synthase, a non-C4 NADP-malic enzyme, oleosin, and three genes homologous to 9-cis-epoxycarotenoid dioxygenase that may be involved in ABA biosynthesis. Analysis of response profiles demonstrated the existence of a complex gene regulatory network that differentially modulates gene expression in a tissue- and kinetic-specific manner in response to ABA, high salinity and water deficit. Modulation of genes involved in signal transduction, chromatin structure, transcription, translation and RNA metabolism contributes to sorghum's overlapping but nonetheless distinct responses to ABA, high salinity, and osmotic stress. Overall, this study provides a foundation of information on sorghum's osmotic stress responsive gene complement that will accelerate follow up biochemical, QTL and comparative studies.

Unused natural variation can lift yield barriers in plant breeding

Natural biodiversity is an underexploited sustainable resource that can enrich the genetic basis of cultivated plants with novel alleles that improve productivity and adaptation. We evaluated the progress in breeding for increased tomato (Solanum lycopersicum) yield using genotypes carrying a pyramid of three independent yield-promoting genomic regions introduced from the drought-tolerant green-fruited wild species Solanum pennellii. Yield of hybrids parented by the pyramided genotypes was more than 50% higher than that of a control market leader variety under both wet and dry field conditions that received 10% of the irrigation water. This demonstration of the breaking of agricultural yield barriers provides the rationale for implementing similar strategies for other agricultural organisms that are important for global food security.

Dramatic improvements in crop yield (in tomatoes, in this case) can be achieved by breeding selected genetic regions from wild species into domesticated varieties

DNA markers in plant improvement: an overview

The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection has the potential to deploy favorable gene combinations for disease control. Comparative studies between incompatible species using these markers has resulted in synteny maps which are useful not only in predicting genome organization and evolution but also have practical application in plant breeding. DNA marker technology has found application in fingerprinting genotypes, in determining seed purity, in systematic sampling of germplasm, and in phylogenetic analysis. This review discusses the use of this technology for the genetic improvement of plants.

The impact zone: genomics and breeding for durable disease resistance

Durable disease resistance is a major but elusive goal of many crop improvement programs. Genomic approaches will have a significant impact on efforts to ameliorate plant diseases by increasing the definition of and access to genepools available for crop improvement. This approach will involve the detailed characterization of the many genes that confer resistance, as well as technologies for the precise manipulation and deployment of resistance genes. Genomic studies on pathogens are providing an understanding of the molecular basis of specificity and the opportunity to select targets for more durable resistance. There are, however, several biological and societal issues that will have to be resolved before the full impact of genomics on breeding for disease resistance is realized.

Improving plant breeding with exotic genetic libraries

Naturally occurring variation among wild relatives of cultivated crops is an under-exploited resource in plant breeding. Here, I argue that exotic libraries, which consist of marker-defined genomic regions taken from wild species and introgressed onto the background of elite crop lines, provide plant breeders with an important opportunity to improve the agricultural performance of modern crop varieties. These libraries can also act as reagents for the discovery and characterization of genes that underlie traits of agricultural value.