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A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Plant, Algae and Fungi Cell Biology".

Deadline for manuscript submissions: closed (15 June 2022) | Viewed by 43080

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Dr. Francesco Mercati

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Institute of Biosciences and BioResources, Division of Palermo, National Research Council, Corso Calatafimi, 414, I-90129 Palermo, Italy
Interests: plant genetics; plant nutrition; breeding; molecular markers; NGS (next-generation sequencing); PGPR
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Dr. Francesco Carimi

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Institute of Biosciences and BioResources, Division of Palermo, National Research Council, Via Ugo La Malfa, n° 153, I-90146 Palermo, Italy
Interests: plant cell biology; plant biotechnology; somatic embryogenesis; genetic diversity
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

In the past decades, conventional methods and molecular tools were successfully adopted in plant breeding to improve agronomic important traits in crop plants. However, climate changes and the growing human population have imposed rapid changes in the global food supply that the conventional breeding approaches are not guaranteed to accommodate.

At present, the development in omics technologies has made available high-throughput screening approaches, speeding up trait improvement in crops with a new evolution of plant breeding that is more able to clarify the relationship between genotype and phenotype. Genomics, transcriptomics, metabolomics, proteomics, and phenomics, supported by bioinformatics approaches, are helping to understand the molecular basis of complex traits and improving the knowledge about the key mechanisms behind crop features. The omics-assisted breeding has shown advantages and had a positive impact on genetic crop improvement, allowing plant geneticists to discover genes, regulatory sequences, and markers useful for the novel marker-assisted breeding (MAB). Omics technologies are giving plant breeders the possibility of “designing” new plant varieties with more resilience by improving tolerance/resistance to biotic and abiotic stresses and/or with increased yield of higher quality.

This Special Issue of Cells aims to publish original research articles, reviews, or shorter perspective articles on all aspects related to the omics approaches to advancing the knowledge and the genetic dissection of agronomic complex traits of interest. Especially, studies applying omics technologies and exploring their possible integration through bioinformatic approaches as tools to support future crop breeding programs are welcome.

Dr. Francesco Mercati
Dr. Francesco Carimi
Guest Editors

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Keywords

next-generation sequencing (NGS)
genomics
transcriptomics
proteomics
metabolomics
phenomics
QTLs mapping
genome-wide assisted selection (GWAS)
crop breeding

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Omics Approaches for A Sustainable and Low-impact Agriculture in Cells

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13 pages, 3493 KiB

Open AccessArticle

Genotype-by-Environment Interaction Analysis of Metabolites in Pearl Millet Genotypes with High Concentrations of Slowly Digestible and Resistant Starch in Their Grains

by Chandra Bhan Yadav, Prakash I. Gangashetty, Manfred Beckmann, Luis A. J. Mur and Rattan S. Yadav

Cells 2022, 11(19), 3109; https://doi.org/10.3390/cells11193109 - 2 Oct 2022

Cited by 2 | Viewed by 2114

Abstract

Genotype × environment interactions (GEIs) should play an important role in the selection of suitable germplasm in breeding programmes. We here assessed GEI effects on pearl millet (Pennisetum glaucum L.) genotypes, selected to possess a high concentration of slowly digestible starch (SDS) and resistant starch (RS) in their grains. Entries were grown in a randomized complete block design with three replications at locations in Bawku-Ghana, Sadore-Niger, Bamako-Mali, Konni-Nigeria, and Gampella-Burkina Faso across West Africa. Harvested grains from these locations were metabolomically profiled using flow injection ionization-high-resolution mass spectrometry (FIE-HRMS). A total of 3144 mass features (m/z) (1560 negative ion mode and 1584 positive ion mode) were detected, of which, 475 m/z were linked to metabolites be involved in starch, antioxidant and lipid biosynthesis, and vitamin metabolism. Combined ANOVA revealed that the GEI was significantly evident for 54 health-benefiting metabolites, many associated with sugar, especially galactose, metabolism. Additive main effects and multiplicative interaction (AMMI) analysis examined genotype variation and GEI effects, which, when combined with principal component analysis (PCA), found that m/z 171.14864 (positive ionisation, propenyl heptanoate) accounted for 89% of the GEI variation along PC1. The AMMI-based stability parameter (ASTAB), modified AMMI stability value (MASV), and modified AMMI stability index (MASI) were then applied to identify stable and high-performing genotypes for all the health-benefiting metabolites. Similarly, the best-linear-unbiased-prediction (BLUP)-based stability estimation was also performed using the harmonic mean of genotypic values (HMGV), relative performance of genotypic values (RPGV), and harmonic mean of relative performance of genotypic values (HMRPGV), to identify genotype rankings across multiple environments. The multi-trait stability index (MTSI) was calculated and found that the genotypes G1 (ICMH-177111) and G24 (ICMX-207137) were the most stable and were the best mean performers across 52 health-benefiting metabolic traits. These findings demonstrate the potential of G × E assessments on the delivery of health-benefiting metabolite-rich grains in future varieties and hybrids of pearl millet. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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21 pages, 3160 KiB

Open AccessArticle

A Genomic BSAseq Approach for the Characterization of QTLs Underlying Resistance to Fusarium oxysporum in Eggplant

by Maria Rosaria Tassone, Paolo Bagnaresi, Francesca Desiderio, Laura Bassolino, Lorenzo Barchi, Francesco Elia Florio, Francesco Sunseri, Tiziana Maria Sirangelo, Giuseppe Leonardo Rotino and Laura Toppino

Cells 2022, 11(16), 2548; https://doi.org/10.3390/cells11162548 - 16 Aug 2022

Cited by 7 | Viewed by 2464

Abstract

Eggplant (Solanum melongena L.), similar to many other crops, suffers from soil-borne diseases, including Fusarium oxysporum f. sp. melongenae (Fom), causing wilting and heavy yield loss. To date, the genetic factors underlying plant responses to Fom are not well known. We previously developed a Recombinant Inbred Lines (RILs) population using as a female parent the fully resistant line ‘305E40’ and as a male parent the partially resistant line ‘67/3’. The fully resistant trait to Fom was introgressed from the allied species S. aethiopicum. In this work, the RIL population was assessed for the responses to Fom and by using a genomic mapping approach, two major QTLs on chromosomes CH02 and CH11 were identified, associated with the full and partial resistance trait to Fom, respectively. A targeted BSAseq procedure in which Illumina reads bulks of RILs grouped according to their resistance score was aligned to the appropriate reference genomes highlighted differentially enriched regions between resistant/susceptible progeny in the genomic regions underlying both QTLs. The characterization of such regions allowed us to identify the most reliable candidate genes for the two resistance traits. With the aim of revealing exclusive species-specific contigs and scaffolds inherited from the allied species and thus associated with the full resistance trait, a draft de-novo assembly of available Illumina sequences of the ‘305E40’ parent was developed to better resolve the non-recombining genomic region on its CH02 carrying the introgressed Fom resistance locus from S. aethiopicum. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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21 pages, 6012 KiB

Open AccessArticle

Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm

by Rajasekhar Srungarapu, Mahesh Damodhar Mahendrakar, Lal Ahamed Mohammad, Uttam Chand, Venkata Ramana Jagarlamudi, Kiran Prakash Kondamudi, Himabindu Kudapa and Srinivasan Samineni

Cells 2022, 11(15), 2457; https://doi.org/10.3390/cells11152457 - 8 Aug 2022

Cited by 11 | Viewed by 4326

Abstract

Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In the current study, a chickpea reference set of 280 accessions, including landraces, breeding lines, and advanced cultivars, was evaluated for grain protein, Fe, Zn content and agronomic traits over two seasons. Using a mid-density 5k SNP array, 4603 highly informative SNPs distributed across the chickpea genome were used for GWAS analysis. Population structure analysis revealed three subpopulations (K = 3). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 20 and 46 marker-trait associations (MTAs) were identified for grain nutrient and agronomic traits, respectively, using FarmCPU and BLINK models. Of which seven SNPs for grain protein, twelve for Fe, and one for Zn content were distributed on chromosomes 1, 4, 6, and 7. The marker S4_4477846 on chr4 was found to be co-associated with grain protein over seasons. The markers S1_11613376 and S1_2772537 co-associated with grain Fe content under NSII and pooled seasons and S7_9379786 marker under NSI and pooled seasons. The markers S4_31996956 co-associated with grain Fe and days to maturity. SNP annotation of associated markers were found to be related to gene functions of metal ion binding, transporters, protein kinases, transcription factors, and many more functions involved in plant metabolism along with Fe and protein homeostasis. The identified significant MTAs has potential use in marker-assisted selection for developing nutrient-rich chickpea cultivars after validation in the breeding populations. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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20 pages, 5660 KiB

Open AccessArticle

Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice

by Nitika Rana, Surbhi Kumawat, Virender Kumar, Ruchi Bansal, Rushil Mandlik, Pallavi Dhiman, Gunvant B. Patil, Rupesh Deshmukh, Tilak Raj Sharma and Humira Sonah

Cells 2022, 11(7), 1144; https://doi.org/10.3390/cells11071144 - 28 Mar 2022

Cited by 2 | Viewed by 2779

Abstract

Nutritional quality improvement of rice is the key to ensure global food security. Consequently, enormous efforts have been made to develop genomics and transcriptomics resources for rice. The available omics resources along with the molecular understanding of trait development can be utilized for efficient exploration of genetic resources for breeding programs. In the present study, 80 genes known to regulate the nutritional and cooking quality of rice were extensively studied to understand the haplotypic variability and gene expression dynamics. The haplotypic variability of selected genes were defined using whole-genome re-sequencing data of ~4700 diverse genotypes. The analytical workflow identified 133 deleterious single-nucleotide polymorphisms, which are predicted to affect the gene function. Furthermore, 788 haplotype groups were defined for 80 genes, and the distribution and evolution of these haplotype groups in rice were described. The nucleotide diversity for the selected genes was significantly reduced in cultivated rice as compared with that in wild rice. The utility of the approach was successfully demonstrated by revealing the haplotypic association of chalk5 gene with the varying degree of grain chalkiness. The gene expression atlas was developed for these genes by analyzing RNA-Seq transcriptome profiling data from 102 independent sequence libraries. Subsequently, weighted gene co-expression meta-analyses of 11,726 publicly available RNAseq libraries identified 19 genes as the hub of interactions. The comprehensive analyses of genetic polymorphisms, allelic distribution, and gene expression profiling of key quality traits will help in exploring the most desired haplotype for grain quality improvement. Similarly, the information provided here will be helpful to understand the molecular mechanism involved in the development of nutritional and cooking quality traits in rice. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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20 pages, 4500 KiB

Open AccessArticle

WRKY Gene Family Drives Dormancy Release in Onion Bulbs

by Guglielmo Puccio, Antonino Crucitti, Antonio Tiberini, Antonio Mauceri, Anna Taglienti, Antonio Palumbo Piccionello, Francesco Carimi, Martijn van Kaauwen, Olga Scholten, Francesco Sunseri, Ben Vosman and Francesco Mercati

Cells 2022, 11(7), 1100; https://doi.org/10.3390/cells11071100 - 24 Mar 2022

Cited by 11 | Viewed by 3503

Abstract

Onion (Allium cepa L.) is an important bulb crop grown worldwide. Dormancy in bulbous plants is an important physiological state mainly regulated by a complex gene network that determines a stop of vegetative growth during unfavorable seasons. Limited knowledge on the molecular mechanisms that regulate dormancy in onion were available until now. Here, a comparison between uninfected and onion yellow dwarf virus (OYDV)-infected onion bulbs highlighted an altered dormancy in the virus-infected plants, causing several symptoms, such as leaf striping, growth reduction, early bulb sprouting and rooting, as well as a lower abscisic acid (ABA) level at the start of dormancy. Furthermore, by comparing three dormancy stages, almost five thousand four hundred (5390) differentially expressed genes (DEGs) were found in uninfected bulbs, while the number of DEGs was significantly reduced (1322) in OYDV-infected bulbs. Genes involved in cell wall modification, proteolysis, and hormone signaling, such as ABA, gibberellins (GAs), indole-3-acetic acid (IAA), and brassinosteroids (BRs), that have already been reported as key dormancy-related pathways, were the most enriched ones in the healthy plants. Interestingly, several transcription factors (TFs) were up-regulated in the uninfected bulbs, among them three genes belonging to the WRKY family, for the first time characterized in onion, were identified during dormancy release. The involvement of specific WRKY genes in breaking dormancy in onion was confirmed by GO enrichment and network analysis, highlighting a correlation between AcWRKY32 and genes driving plant development, cell wall modification, and division via gibberellin and auxin homeostasis, two key processes in dormancy release. Overall, we present, for the first time, a detailed molecular analysis of the dormancy process, a description of the WRKY-TF family in onion, providing a better understanding of the role played by AcWRKY32 in the bulb dormancy release. The TF co-expressed genes may represent targets for controlling the early sprouting in onion, laying the foundations for novel breeding programs to improve shelf life and reduce postharvest. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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34 pages, 5745 KiB

Open AccessArticle

Proteomic Studies of Roots in Hypoxia-Sensitive and -Tolerant Tomato Accessions Reveal Candidate Proteins Associated with Stress Priming

by Małgorzata Czernicka, Kinga Kęska, Sébastien Planchon, Małgorzata Kapusta, Marzena Popielarska-Konieczna, Wojciech Wesołowski, Marek Szklarczyk and Jenny Renaut

Cells 2022, 11(3), 500; https://doi.org/10.3390/cells11030500 - 31 Jan 2022

Cited by 6 | Viewed by 3407

Abstract

Tomato (Solanum lycopersicum L.) is a vegetable frequently exposed to hypoxia stress induced either by being submerged, flooded or provided with limited oxygen in hydroponic cultivation systems. The purpose of the study was to establish the metabolic mechanisms responsible for overcoming hypoxia in two tomato accessions with different tolerance to this stress, selected based on morphological and physiological parameters. For this purpose, 3-week-old plants (plants at the juvenile stage) of waterlogging-tolerant (WL-T), i.e., POL 7/15, and waterlogging-sensitive (WL-S), i.e., PZ 215, accessions were exposed to hypoxia stress (waterlogging) for 7 days, then the plants were allowed to recover for 14 days, after which another 7 days of hypoxia treatment was applied. Root samples were collected at the end of each time-point and 2D-DIGE with MALDI TOF/TOF, and expression analyses of gene and protein-encoded alcohol dehydrogenase (ADH2) and immunolabelling of ADH were conducted. After collating the obtained results, the different responses to hypoxia stress in the selected tomato accessions were observed. Both the WL-S and WL-T tomato accessions revealed a high amount of ADH2, which indicates an intensive alcohol fermentation pathway during the first exposure to hypoxia. In comparison to the tolerant one, the expression of the adh2 gene was about two times higher for the sensitive tomato. Immunohistochemical analysis confirmed the presence of ADH in the parenchyma cells of the cortex and vascular tissue. During the second hypoxia stress, the sensitive accession showed a decreased accumulation of ADH protein and similar expression of the adh2 gene in comparison to the tolerant accession. Additionally, the proteome showed a greater protein abundance of glyceraldehyde-3-phosphate dehydrogenase in primed WL-S tomato. This could suggest that the sensitive tomato overcomes the oxygen limitation and adapts by reducing alcohol fermentation, which is toxic to plants because of the production of ethanol, and by enhancing glycolysis. Proteins detected in abundance in the sensitive accession are proposed as crucial factors for hypoxia stress priming and their function in hypoxia tolerance is discussed. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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12 pages, 5191 KiB

Open AccessArticle

Could Causal Discovery in Proteogenomics Assist in Understanding Gene–Protein Relations? A Perennial Fruit Tree Case Study Using Sweet Cherry as a Model

by Maria Ganopoulou, Michail Michailidis, Lefteris Angelis, Ioannis Ganopoulos, Athanassios Molassiotis, Aliki Xanthopoulou and Theodoros Moysiadis

Cells 2022, 11(1), 92; https://doi.org/10.3390/cells11010092 - 29 Dec 2021

Cited by 9 | Viewed by 2658

Abstract

Genome-wide transcriptome analysis is a method that produces important data on plant biology at a systemic level. The lack of understanding of the relationships between proteins and genes in plants necessitates a further thorough analysis at the proteogenomic level. Recently, our group generated a quantitative proteogenomic atlas of 15 sweet cherry (Prunus avium L.) cv. ‘Tragana Edessis’ tissues represented by 29,247 genes and 7584 proteins. The aim of the current study was to perform a targeted analysis at the gene/protein level to assess the structure of their relation, and the biological implications. Weighted correlation network analysis and causal modeling were employed to, respectively, cluster the gene/protein pairs, and reveal their cause–effect relations, aiming to assess the associated biological functions. To the best of our knowledge, this is the first time that causal modeling has been employed within the proteogenomics concept in plants. The analysis revealed the complex nature of causal relations among genes/proteins that are important for traits of interest in perennial fruit trees, particularly regarding the fruit softening and ripening process in sweet cherry. Causal discovery could be used to highlight persistent relations at the gene/protein level, stimulating biological interpretation and facilitating further study of the proteogenomic atlas in plants. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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19 pages, 2700 KiB

Open AccessArticle

Discovery of a Novel Leaf Rust (Puccinia recondita) Resistance Gene in Rye (Secale cereale L.) Using Association Genomics

by Nikolaj Meisner Vendelbo, Khalid Mahmood, Pernille Sarup, Mogens S. Hovmøller, Annemarie Fejer Justesen, Peter Skov Kristensen, Jihad Orabi and Ahmed Jahoor

Cells 2022, 11(1), 64; https://doi.org/10.3390/cells11010064 - 27 Dec 2021

Cited by 10 | Viewed by 3362

Abstract

Leaf rust constitutes one of the most important foliar diseases in rye (Secale cereale L.). To discover new sources of resistance, we phenotyped 180 lines belonging to a less well-characterized Gülzow germplasm at three field trial locations in Denmark and Northern Germany in 2018 and 2019. We observed lines with high leaf rust resistance efficacy at all locations in both years. A genome-wide association study using 261,406 informative single-nucleotide polymorphisms revealed two genomic regions associated with resistance on chromosome arms 1RS and 7RS, respectively. The most resistance-associated marker on chromosome arm 1RS physically co-localized with molecular markers delimiting Pr3. In the reference genomes Lo7 and Weining, the genomic region associated with resistance on chromosome arm 7RS contained a large number of nucleotide-binding leucine-rich repeat (NLR) genes. Residing in close proximity to the most resistance-associated marker, we identified a cluster of NLRs exhibiting close protein sequence similarity with the wheat leaf rust Lr1 gene situated on chromosome arm 5DL in wheat, which is syntenic to chromosome arm 7RS in rye. Due to the close proximity to the most resistance-associated marker, our findings suggest that the considered leaf rust R gene, provisionally denoted Pr6, could be a Lr1 ortholog in rye. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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24 pages, 4346 KiB

Open AccessArticle

Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study

by Amin Abedi, Zahra Hajiahmadi, Mojtaba Kordrostami, Qassim Esmaeel and Cédric Jacquard

Cells 2022, 11(1), 37; https://doi.org/10.3390/cells11010037 - 23 Dec 2021

Cited by 9 | Viewed by 4260

Abstract

The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the BrassicaLysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes’ function had not changed over time. The BrassicaLysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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13 pages, 1994 KiB

Open AccessArticle

Metabolite Diversity and Metabolic Genome-Wide Marker Association Studies (Mgwas) for Health Benefiting Nutritional Traits in Pearl Millet Grains

by Chandra Bhan Yadav, Rakesh K. Srivastava, Prakash I. Gangashetty, Rama Yadav, Luis A. J. Mur and Rattan S. Yadav

Cells 2021, 10(11), 3076; https://doi.org/10.3390/cells10113076 - 8 Nov 2021

Cited by 19 | Viewed by 4009

Abstract

As efforts are made to increase food security, millets are gaining increasing importance due to their excellent nutritional credentials. Among the millets, pearl millet is the predominant species possessing several health benefiting nutritional traits in its grain that are helpful in mitigating chronic illnesses such as type−2 diabetes and obesity. In this paper, we conducted metabolomic fingerprinting of 197 pearl millet inbred lines drawn randomly from within the world collection of pearl millet germplasm and report the extent of genetic variation for health benefitting metabolites in these genotypes. Metabolites were extracted from seeds and assessed using flow infusion high-resolution mass spectrometry (FIE-HRMS). Metabolite features (m/z), whose levels significantly differed among the germplasm inbred lines, were identified by ANOVA corrected for FDR and subjected to functional pathway analysis. A number of health-benefiting metabolites linked to dietary starch, antioxidants, vitamins, and lipid metabolism-related compounds were identified. Metabolic genome-wide association analysis (mGWAS) performed using the 396 m/z as phenotypic traits and the 76 K SNP as genotypic variants identified a total of 897 SNPs associated with health benefiting nutritional metabolite at the -log p-value ≤ 4.0. From these associations, 738 probable candidate genes were predicted to have an important role in starch, antioxidants, vitamins, and lipid metabolism. The mGWAS analysis focused on genes involved in starch branching (α-amylase, β-amylase), vitamin-K reductase, UDP-glucuronosyl, and UDP-glucosyl transferase (UGTs), L-ascorbate oxidase, and isoflavone 2′-monooxygenase genes, which are known to be linked to increases in human health benefiting metabolites. We demonstrate how metabolomic, genomic, and statistical approaches can be utilized to pinpoint genetic variations and their functions linked to key nutritional properties in pearl millet, which in turn can be bred into millets and other cereals crops using plant breeding methods. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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16 pages, 1311 KiB

Open AccessReview

Proteomic Analysis Dissects Molecular Mechanisms Underlying Plant Responses to Phosphorus Deficiency

by Ming Zhou, Shengnan Zhu, Xiaohui Mo, Qi Guo, Yaxue Li, Jiang Tian and Cuiyue Liang

Cells 2022, 11(4), 651; https://doi.org/10.3390/cells11040651 - 14 Feb 2022

Cited by 13 | Viewed by 3778

Abstract

Phosphorus (P) is an essential nutrient for plant growth. In recent decades, the application of phosphate (Pi) fertilizers has contributed to significant increases in crop yields all over the world. However, low efficiency of P utilization in crops leads to intensive application of Pi fertilizers, which consequently stimulates environmental pollution and exhaustion of P mineral resources. Therefore, in order to strengthen the sustainable development of agriculture, understandings of molecular mechanisms underlying P efficiency in plants are required to develop cultivars with high P utilization efficiency. Recently, a plant Pi-signaling network was established through forward and reverse genetic analysis, with the aid of the application of genomics, transcriptomics, proteomics, metabolomics, and ionomics. Among these, proteomics provides a powerful tool to investigate mechanisms underlying plant responses to Pi availability at the protein level. In this review, we summarize the recent progress of proteomic analysis in the identification of differential proteins that play roles in Pi acquisition, translocation, assimilation, and reutilization in plants. These findings could provide insights into molecular mechanisms underlying Pi acquisition and utilization efficiency, and offer new strategies in genetically engineering cultivars with high P utilization efficiency. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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18 pages, 1085 KiB

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Strategies to Increase Prediction Accuracy in Genomic Selection of Complex Traits in Alfalfa (Medicago sativa L.)

by Cesar A. Medina, Harpreet Kaur, Ian Ray and Long-Xi Yu

Cells 2021, 10(12), 3372; https://doi.org/10.3390/cells10123372 - 30 Nov 2021

Cited by 12 | Viewed by 3897

Abstract

Agronomic traits such as biomass yield and abiotic stress tolerance are genetically complex and challenging to improve through conventional breeding approaches. Genomic selection (GS) is an alternative approach in which genome-wide markers are used to determine the genomic estimated breeding value (GEBV) of individuals in a population. In alfalfa (Medicago sativa L.), previous results indicated that low to moderate prediction accuracy values (<70%) were obtained in complex traits, such as yield and abiotic stress resistance. There is a need to increase the prediction value in order to employ GS in breeding programs. In this paper we reviewed different statistic models and their applications in polyploid crops, such as alfalfa and potato. Specifically, we used empirical data affiliated with alfalfa yield under salt stress to investigate approaches that use DNA marker importance values derived from machine learning models, and genome-wide association studies (GWAS) of marker-trait association scores based on different GWASpoly models, in weighted GBLUP analyses. This approach increased prediction accuracies from 50% to more than 80% for alfalfa yield under salt stress. Finally, we expended the weighted GBLUP approach to potato and analyzed 13 phenotypic traits and obtained similar results. This is the first report on alfalfa to use variable importance and GWAS-assisted approaches to increase the prediction accuracy of GS, thus helping to select superior alfalfa lines based on their GEBVs. Full article

(This article belongs to the Special Issue Omics in Plant Genetics and Breeding)

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