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Functional Genomics for Plant Breeding 2.0

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 31791

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Special Issue Editors

Dr. Fatemeh Maghuly

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Institute of Molecular Biotechnology, Department of Biotechnology, VIBT, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
Interests: plant functional genomics; plant breeding; plant physiology; population genetics; omic strategies and molecular biology
Special Issues, Collections and Topics in MDPI journals

Dr. Eva M. Sehr

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Guest Editor

Austrian Institute of Technology (AIT), Tulln, Austria
Interests: genetic marker; genotyping; transcriptomics; genomics

Dr. Rachit Saxena

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The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India
Interests: plant genetics; genomics & molecular breeding

Dr. David J. Konkin

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Guest Editor

Aquatic and Crop Resource Development (ACRD), National Research Council Canada (NRC), Saskatoon, SK, Canada
Interests: agricultural genomics; genomic technologies; gene regulation; pea genomics; hemp genomics

Special Issue Information

Dear Colleagues,

Next-generation genome sequencing technology in plants has accelerated the generation of multiomic data at the DNA, RNA, protein, and metabolite levels, leading to a new era of "big data". This can provide us an integrative view, and opens up new possibilities to draw attention to the importance of recording and analyzing large-scale omics data obtained in different systems and their relationship to phenotypes, and also for understanding how the exploration of these relationships can be used for management intervention and agricultural innovation in breeding programs.

Large-scale sequence-based markers and precise phenotypic data provide a crucial basis for the application of GWAS and QTL-mapping analysis. Besides, genomic research has facilitated and accelerated the breeding process and offers applications for genetic improvement such as GS, MAS, and gene pyramiding.

On the other hand, it is not just the sequence of plant DNA that matters: how do some genes get activated, and why are others silenced? How can genomics facilitate the study of complex traits in plant breeding? These are questions of widespread interest, and genome editing has shown to be a crucial tool for functional genomic research that could be utilized as a precision-breeding approach for any programs seeking to improve traits of interest.

This Special Issue, “Functional Genomics for Plant Breeding”, will cover a selection of research topics and review articles regarding the recent development of genomics, epigenomics, and epitranscriptomics, that can enhance breeding strategies to shorten the time and efficiency of development of new crop cultivars.

Dr. Fatemeh Maghuly
Dr. Eva-Maria Sehr
Dr. Rachit Saxena
Dr. David Konkin
Guest Editors

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Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (11 papers)

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Editorial

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4 pages, 200 KiB

Open AccessEditorial

Editorial: Functional Genomics in Plant Breeding 2.0

by Fatemeh Maghuly, Eva M. Molin, Rachit Saxena and David J. Konkin

Int. J. Mol. Sci. 2022, 23(13), 6959; https://doi.org/10.3390/ijms23136959 - 23 Jun 2022

Cited by 2 | Viewed by 1143

Abstract

Scientists agree that the increased human impact on the environment since the 19th century has positioned our planet in a period of rapid and intense change, particularly to our natural ecosystems [...] Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

Research

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18 pages, 2289 KiB

Open AccessArticle

Comparative Analysis of Coding and Non-Coding Features within Insect Tolerance Loci in Wheat with Their Homologs in Cereal Genomes

by Tugdem Muslu, Bala Ani Akpinar, Sezgi Biyiklioglu-Kaya, Meral Yuce and Hikmet Budak

Int. J. Mol. Sci. 2021, 22(22), 12349; https://doi.org/10.3390/ijms222212349 - 16 Nov 2021

Cited by 6 | Viewed by 2038

Abstract

Food insecurity and malnutrition have reached critical levels with increased human population, climate fluctuations, water shortage; therefore, higher-yielding crops are in the spotlight of numerous studies. Abiotic factors affect the yield of staple food crops; among all, wheat stem sawfly (Cephus cinctus Norton) and orange wheat blossom midge (Sitodiplosis mosellana) are two of the most economically and agronomically harmful insect pests which cause yield loss in cereals, especially in wheat in North America. There is no effective strategy for suppressing this pest damage yet, and only the plants with intrinsic tolerance mechanisms such as solid stem phenotypes for WSS and antixenosis and/or antibiosis mechanisms for OWBM can limit damage. A major QTL and a causal gene for WSS resistance were previously identified in wheat, and 3 major QTLs and a causal gene for OWBM resistance. Here, we present a comparative analysis of coding and non-coding features of these loci of wheat across important cereal crops, barley, rye, oat, and rice. This research paves the way for our cloning and editing of additional WSS and OWBM tolerance gene(s), proteins, and metabolites. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

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20 pages, 6251 KiB

Open AccessArticle

Genotype-Dependent Effect of Silencing of TaCKX1 and TaCKX2 on Phytohormone Crosstalk and Yield-Related Traits in Wheat

by Bartosz Jablonski, Andrzej Bajguz, Joanna Bocian, Waclaw Orczyk and Anna Nadolska-Orczyk

Int. J. Mol. Sci. 2021, 22(21), 11494; https://doi.org/10.3390/ijms222111494 - 25 Oct 2021

Cited by 8 | Viewed by 1550

Abstract

The influence of silenced TaCKX1 and TaCKX2 on coexpression of other TaCKX gene family members (GFMs), phytohormone regulation and yield-related traits was tested in awned-spike cultivar. We documented a strong feedback mechanism of regulation of TaCKX GFM expression in which silencing of TaCKX1 upregulated expression of TaCKX2 genes and vice versa. Additionally, downregulation of TaCKX2 highly upregulated the expression of TaCKX5 and TaNAC2-5A. In contrast, expression of these genes in silenced TaCKX1 was downregulated. Silenced TaCKX1 T₂ lines with expression decreased by 47% had significantly higher thousand grain weight (TGW) and seedling root mass. Silenced TaCKX2 T₂ lines with expression of TaCKX2.2.1 and TaCKX2.2.2 decreased by 33% and 30%, respectively, had significantly higher chlorophyll content in flag leaves. TaCKX GFM expression, phytohormone metabolism and phenotype were additionally modified by Agrobacterium-mediated transformation. Two novel phytohormones, phenylacetic acid (PAA) and topolins, lack of gibberellic acid (GA) and changed phytohormone contents in the 7 days after pollination (DAP) spikes of the awned-spike cultivar compared to a previously tested, awnless one, were detected. We documented that major mechanisms of coregulation of the expression of TaCKX GFMs were similar in different spring wheat cultivars, but, depending on content and composition of phytohormones, regulation of yield-related traits was variously impacted. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

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13 pages, 1326 KiB

Open AccessArticle

Discovery and Chromosomal Location a Highly Effective Oat Crown Rust Resistance Gene Pc50-5

by Joanna Toporowska, Sylwia Sowa, Andrzej Kilian, Aneta Koroluk and Edyta Paczos-Grzęda

Int. J. Mol. Sci. 2021, 22(20), 11183; https://doi.org/10.3390/ijms222011183 - 17 Oct 2021

Cited by 5 | Viewed by 1692

Abstract

Crown rust, caused by Puccinia coronata f. sp. avenae, is one of the most destructive fungal diseases of oat worldwide. Growing disease-resistant oat cultivars is the preferred method of preventing the spread of rust and potential epidemics. The object of the study was Pc50-5, a race-specific seedling crown rust resistant gene, highly effective at all growth stages, selected from the differential line Pc50 (Avena sterilis L. CW 486-1 × Pendek). A comparison of crown rust reaction as well as an allelism test showed the distinctiveness of Pc50-5, whereas the proportions of phenotypes in segregating populations derived from a cross with two crown rust-susceptible Polish oat cultivars, Kasztan × Pc50-5 and Bingo × Pc50-5, confirmed monogenic inheritance of the gene, indicating its usefulness in oat breeding programs. Effective gene introgression depends on reliable gene identification in the early stages of plant development; thus, the aim of the study was to develop molecular markers that are tightly linked to Pc50-5. Segregating populations of Kasztan × Pc50-5 were genotyped using DArTseq technology based on next-generation Illumina short-read sequencing. Markers associated with Pc50-5 were located on chromosome 6A of the current version of the oat reference genome (Avena sativa OT3098 v2, PepsiCo) in the region between 434,234,214 and 440,149,046 bp and subsequently converted to PCR-based SCAR (sequence-characterized amplified region) markers. Furthermore, 5426978_SCAR and 24031809_SCAR co-segregated with the Pc50-5 resistance allele and were mapped to the partial linkage group at 0.6 and 4.0 cM, respectively. The co-dominant 58163643_SCAR marker was the best diagnostic and it was located closest to Pc50-5 at 0.1 cM. The newly discovered, very strong monogenic crown rust resistance may be useful for oat improvement. DArTseq sequences converted into specific PCR markers will be a valuable tool for marker-assisted selection in breeding programs. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

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25 pages, 5357 KiB

Open AccessArticle

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses

by Mirosław Tyrka, Beata Bakera, Magdalena Szeliga, Magdalena Święcicka, Paweł Krajewski, Monika Mokrzycka and Monika Rakoczy-Trojanowska

Int. J. Mol. Sci. 2021, 22(17), 9146; https://doi.org/10.3390/ijms22179146 - 24 Aug 2021

Cited by 6 | Viewed by 2536

Abstract

Among the natural mechanisms used for wheat hybrid breeding, the most desirable is the system combining the cytoplasmic male sterility (cms) of the female parent with the fertility-restoring genes (Rf) of the male parent. The objective of this study was to identify Rf candidate genes in the wheat genome on the basis of transcriptome sequencing (RNA-seq) and paralog analysis data. Total RNA was isolated from the anthers of two fertility-restorer (Primépi and Patras) and two non-restorer (Astoria and Grana) varieties at the tetrad and late uninucleate microspore stages. Of 36,912 differentially expressed genes (DEGs), 21 encoding domains in known fertility-restoring proteins were selected. To enrich the pool of Rf candidates, 52 paralogs (PAGs) of the 21 selected DEGs were included in the analyses. The expression profiles of most of the DEGs and PAGs determined bioinformatically were as expected (i.e., they were overexpressed in at least one fertility-restorer variety). However, these results were only partially consistent with the quantitative real-time PCR data. The DEG and PAG promoters included cis-regulatory elements common among PPR-encoding genes. On the basis of the obtained results, we designated seven genes as Rf candidate genes, six of which were identified for the first time in this study. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

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20 pages, 5284 KiB

Open AccessArticle

Transcriptomic and Metabolic Profiling of High-Temperature Treated Storage Roots Reveals the Mechanism of Saccharification in Sweetpotato (Ipomoea batatas (L.) Lam.)

by Chen Li, Meng Kou, Mohamed Hamed Arisha, Wei Tang, Meng Ma, Hui Yan, Xin Wang, Xiaoxiao Wang, Yungang Zhang, Yaju Liu, Runfei Gao and Qiang Li

Int. J. Mol. Sci. 2021, 22(13), 6641; https://doi.org/10.3390/ijms22136641 - 22 Jun 2021

Cited by 7 | Viewed by 2560

Abstract

The saccharification of sweetpotato storage roots is a common phenomenon in the cooking process, which determines the edible quality of table use sweetpotato. In the present study, two high saccharified sweetpotato cultivars (Y25, Z13) and one low saccharified cultivar (X27) in two growth periods (S1, S2) were selected as materials to reveal the molecular mechanism of sweetpotato saccharification treated at high temperature by transcriptome sequencing and non-targeted metabolome determination. The results showed that the comprehensive taste score, sweetness, maltose content and starch change of X27 after steaming were significantly lower than those of Y25 and Z13. Through transcriptome sequencing analysis, 1918 and 1520 differentially expressed genes were obtained in the two periods of S1 and S2, respectively. Some saccharification-related transcription factors including MYB families, WRKY families, bHLH families and inhibitors were screened. Metabolic analysis showed that 162 differentially abundant metabolites related to carbohydrate metabolism were significantly enriched in starch and sucrose capitalization pathways. The correlation analysis between transcriptome and metabolome confirmed that the starch and sucrose metabolic pathways were significantly co-annotated, indicating that it is a vitally important metabolic pathway in the process of sweetpotato saccharification. The data obtained in this study can provide valuable resources for follow-up research on sweetpotato saccharification and will provide new insights and theoretical basis for table use sweetpotato breeding in the future. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

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23 pages, 6728 KiB

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Comparative Transcriptome Analysis Identified Candidate Genes for Late Leaf Spot Resistance and Cause of Defoliation in Groundnut

by Sunil S. Gangurde, Spurthi N. Nayak, Pushpesh Joshi, Shilp Purohit, Hari K. Sudini, Annapurna Chitikineni, Yanbin Hong, Baozhu Guo, Xiaoping Chen, Manish K. Pandey and Rajeev K. Varshney

Int. J. Mol. Sci. 2021, 22(9), 4491; https://doi.org/10.3390/ijms22094491 - 26 Apr 2021

Cited by 15 | Viewed by 4369

Abstract

Late leaf spot (LLS) caused by fungus Nothopassalora personata in groundnut is responsible for up to 50% yield loss. To dissect the complex nature of LLS resistance, comparative transcriptome analysis was performed using resistant (GPBD 4), susceptible (TAG 24) and a resistant introgression line (ICGV 13208) and identified a total of 12,164 and 9954 DEGs (differentially expressed genes) respectively in A- and B-subgenomes of tetraploid groundnut. There were 135 and 136 unique pathways triggered in A- and B-subgenomes, respectively, upon N. personata infection. Highly upregulated putative disease resistance genes, an RPP-13 like (Aradu.P20JR) and a NBS-LRR (Aradu.Z87JB) were identified on chromosome A02 and A03, respectively, for LLS resistance. Mildew resistance Locus (MLOs)-like proteins, heavy metal transport proteins, and ubiquitin protein ligase showed trend of upregulation in susceptible genotypes, while tetratricopeptide repeats (TPR), pentatricopeptide repeat (PPR), chitinases, glutathione S-transferases, purple acid phosphatases showed upregulation in resistant genotypes. However, the highly expressed ethylene responsive factor (ERF) and ethylene responsive nuclear protein (ERF2), and early responsive dehydration gene (ERD) might be related to the possible causes of defoliation in susceptible genotypes. The identified disease resistance genes can be deployed in genomics-assisted breeding for development of LLS resistant cultivars to reduce the yield loss in groundnut. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

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14 pages, 2087 KiB

Open AccessArticle

Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly

by Parwinder Kaur, Christopher Lui, Olga Dudchenko, Raja Sekhar Nandety, Bhavna Hurgobin, Melanie Pham, Erez Lieberman Aiden, Jiangqi Wen and Kirankumar S Mysore

Int. J. Mol. Sci. 2021, 22(9), 4326; https://doi.org/10.3390/ijms22094326 - 21 Apr 2021

Cited by 10 | Viewed by 3880

Abstract

Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. Medicago truncatula is a well-established model legume, and extensive studies in fundamental molecular, physiological, and developmental biology have been undertaken to translate into trait improvements in economically important legume crops worldwide. However, M. truncatula reference genome was generated in the accession Jemalong A17, which is highly recalcitrant to transformation. M. truncatula R108 is more attractive for genetic studies due to its high transformation efficiency and Tnt1-insertion population resource for functional genomics. The need to perform accurate synteny analysis and comprehensive genome-scale comparisons necessitates a chromosome-length genome assembly for M. truncatula cv. R108. Here, we performed in situ Hi-C (48×) to anchor, order, orient scaffolds, and correct misjoins of contigs in a previously published genome assembly (R108 v1.0), resulting in an improved genome assembly containing eight chromosome-length scaffolds that span 97.62% of the sequenced bases in the input assembly. The long-range physical information data generated using Hi-C allowed us to obtain a chromosome-length ordering of the genome assembly, better validate previous draft misjoins, and provide further insights accurately predicting synteny between A17 and R108 regions corresponding to the known chromosome 4/8 translocation. Furthermore, mapping the Tnt1 insertion landscape on this reference assembly presents an important resource for M. truncatula functional genomics by supporting efficient mutant gene identification in Tnt1 insertion lines. Our data provide a much-needed foundational resource that supports functional and molecular research into the Leguminosae for sustainable agriculture and feeding the future. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

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Review

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21 pages, 1876 KiB

Open AccessReview

Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

by Cassandria Geraldine Tay Fernandez, Benjamin John Nestor, Monica Furaste Danilevicz, Mitchell Gill, Jakob Petereit, Philipp Emanuel Bayer, Patrick Michael Finnegan, Jacqueline Batley and David Edwards

Int. J. Mol. Sci. 2022, 23(5), 2671; https://doi.org/10.3390/ijms23052671 - 28 Feb 2022

Cited by 13 | Viewed by 3476

Abstract

Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

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17 pages, 3196 KiB

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Molecular Network for Regulation of Ovule Number in Plants

by Muslim Qadir, Xinfa Wang, Syed Rehmat Ullah Shah, Xue-Rong Zhou, Jiaqin Shi and Hanzhong Wang

Int. J. Mol. Sci. 2021, 22(23), 12965; https://doi.org/10.3390/ijms222312965 - 30 Nov 2021

Cited by 11 | Viewed by 3010

Abstract

In seed-bearing plants, the ovule (“small egg”) is the organ within the gynoecium that develops into a seed after fertilization. The gynoecium located in the inner compartment of the flower turns into a fruit. The number of ovules in the ovary determines the upper limit or the potential of seed number per fruit in plants, greatly affecting the final seed yield. Ovule number is an important adaptive characteristic for plant evolution and an agronomic trait for crop improvement. Therefore, understanding the mechanism and pathways of ovule number regulation becomes a significant research aspect in plant science. This review summarizes the ovule number regulators and their regulatory mechanisms and pathways. Specially, an integrated molecular network for ovule number regulation is constructed, in which phytohormones played a central role, followed by transcription factors, enzymes, other protein and micro-RNA. Of them, AUX, BR and CK are positive regulator of ovule number, whereas GA acts negatively on it. Interestingly, many ovule number regulators have conserved functions across several plant taxa, which should be the targets of genetic improvement via breeding or gene editing. Many ovule number regulators identified to date are involved in the diverse biological process, such as ovule primordia formation, ovule initiation, patterning, and morphogenesis. The relations between ovule number and related characteristics/traits especially of gynoecium/fruit size, ovule fertility, and final seed number, as well as upcoming research questions, are also discussed. In summary, this review provides a general overview of the present finding in ovule number regulation, which represents a more comprehensive and in-depth cognition on it. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

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27 pages, 2217 KiB

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Understanding Starch Metabolism in Pea Seeds towards Tailoring Functionality for Value-Added Utilization

by Bianyun Yu, Daoquan Xiang, Humaira Mahfuz, Nii Patterson and Dengjin Bing

Int. J. Mol. Sci. 2021, 22(16), 8972; https://doi.org/10.3390/ijms22168972 - 20 Aug 2021

Cited by 10 | Viewed by 3434

Abstract

Starch is the most abundant storage carbohydrate and a major component in pea seeds, accounting for about 50% of dry seed weight. As a by-product of pea protein processing, current uses for pea starch are limited to low-value, commodity markets. The globally growing demand for pea protein poses a great challenge for the pea fractionation industry to develop new markets for starch valorization. However, there exist gaps in our understanding of the genetic mechanism underlying starch metabolism, and its relationship with physicochemical and functional properties, which is a prerequisite for targeted tailoring functionality and innovative applications of starch. This review outlines the understanding of starch metabolism with a particular focus on peas and highlights the knowledge of pea starch granule structure and its relationship with functional properties, and industrial applications. Using the currently available pea genetics and genomics knowledge and breakthroughs in omics technologies, we discuss the perspectives and possible avenues to advance our understanding of starch metabolism in peas at an unprecedented level, to ultimately enable the molecular design of multi-functional native pea starch and to create value-added utilization. Full article

(This article belongs to the Special Issue Functional Genomics for Plant Breeding 2.0)

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