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Agronomy
Special Issues
Recent Advances in Bioinformatics for Plant Genetic Traits
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Recent Advances in Bioinformatics for Plant Genetic Traits

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (1 March 2024) | Viewed by 6006

Special Issue Editor

Dr. Radosław Suchecki

E-Mail Website
Guest Editor
CSIRO Agriculture and Food, Urrbrae, Australia
Interests: bioinformatics workflows; bioinformatics algorithms; plant genomics; plant transcriptomics; candidate gene identification; sequence analysis; single-nucleotide polymorphisms (SNPs); functional markers; genotyping; pre-breeding

Special Issue Information

Dear Colleagues,

The application of bioinformatics to plant research is providing new and powerful ways to understand the genetics of plants and their associated traits. Bioinformatics approaches are being used to identify genes associated with specific traits, to understand the function of genes, and to predict the effect of mutations. These approaches are providing new insights into plant development and physiology and facilitate the development of new and improved plant varieties.

The aim of this Special Issue is to provide a broad overview of the latest advances in the field of bioinformatics as they relate to plant genetic traits. This Special Issue will cover a wide range of topics, including the development of new workflows, algorithms and software tools for the analysis of plant genomes, the use of bioinformatics to identify and characterize plant genes associated with important traits, and the application of bioinformatics to plant breeding and crop improvement. We aim to bring together experts in this field to share their latest research and insights on these topics. It will be of interest to plant scientists, breeders, and anyone involved in the use of bioinformatics to study or improve plant genetic traits. The Special Issue will be a valuable resource for anyone interested in keeping up with the latest advances in this rapidly evolving field.

Dr. Radosław Suchecki
Guest Editor

Manuscript Submission Information

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.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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 (5 papers)

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Research

13 pages, 4021 KiB  
Article
Genome-Wide Identification and Characterization of the OFP Gene Family in the Wild Strawberry Fragaria vesca
by Xiao Xu, Xinyu Wang, Sirui Zhou, Xumo Huang, Pengcheng Liu, Bojun Ma and Xifeng Chen
Agronomy 2024, 14(3), 569; https://doi.org/10.3390/agronomy14030569 - 12 Mar 2024
Viewed by 748
Abstract
OVATE family proteins (OFPs) are a kind of plant-specific transcription factor, which play important roles in the growth and development of plants. Here, we performed a genome-wide investigation of the OFP gene family members in the wild diploid strawberry (Fragaria vesca, [...] Read more.
OVATE family proteins (OFPs) are a kind of plant-specific transcription factor, which play important roles in the growth and development of plants. Here, we performed a genome-wide investigation of the OFP gene family members in the wild diploid strawberry (Fragaria vesca, 2n = 14), and analyzed their physical and chemical properties, gene structure, phylogeny, expression patterns, and the subcellular localizations of these genes. Fourteen OFP genes from F.vesca were identified. Collinearity analysis showed ten pairs of collinearity between F. vesca and Arabidopsis. Phylogenetic analysis divided FvOFP genes into five different clades. The expression patterns of the FvOFP genes assayed in different tissues of F. vesca by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) showed that FvOFP1, FvOFP11, FvOFP12, and FvOFP14 were highly expressed in achene and their expression was further verified in the fruits at different developmental stages. Additionally, the subcellular localizations of FvOFP1, FvOFP11, FvOFP12, and FvOFP14 were preliminarily analyzed in tobacco leaves. The results showed clear fluorescent signals in the nucleus. Our results provided a comprehensive understanding of the potential function of FvOFP genes in strawberries. Full article
(This article belongs to the Special Issue Recent Advances in Bioinformatics for Plant Genetic Traits)
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18 pages, 3323 KiB  
Article
Comparative Transcriptome Analysis and Expression of Genes Associated with Polysaccharide Biosynthesis in Dendrobium officinale Diploid and Tetraploid Plants
by Phu Long Pham, Thi Tuyet Cham Le, Thi Thuy Hang Vu, Thanh Tuan Nguyen, Zhi-Sheng Zhang, Rui-Zhen Zeng, Li Xie, Minh Ngoc Nguyen, Vuong Thi Huyen Trang, Tran Dang Xuan and Tran Dang Khanh
Agronomy 2024, 14(1), 69; https://doi.org/10.3390/agronomy14010069 - 27 Dec 2023
Cited by 1 | Viewed by 1028
Abstract
Dendrobium officinale Kimura et Migo is a kind of herb with high medicinal, ornamental, and commercial value, and is rich in polysaccharides. Polyploid breeding is an important breeding method for the genome doubling of medicinal species to increase biomass and polysaccharide production. Previous [...] Read more.
Dendrobium officinale Kimura et Migo is a kind of herb with high medicinal, ornamental, and commercial value, and is rich in polysaccharides. Polyploid breeding is an important breeding method for the genome doubling of medicinal species to increase biomass and polysaccharide production. Previous studies have revealed comparative transcriptome analysis and polysaccharide biosynthesis across the growth stages and plant parts, but there have been no studies dissecting such genes and pathways in tetraploid D. officinale. Therefore, this study aimed to unravel the molecular mechanisms of the increase in polysaccharide content in tetraploid D. officinale via the generation of four transcriptomic libraries for protocorm-like bodies and six-month-old seedlings of both diploid and tetraploid D. officinale plants. In this study, a total of 230,786,618 clean reads remained with a total of 34.62 Gb nucleotides generated; 274,403 unigenes were assembled, of which 73.99% were annotated to at least one of the protein databases; and of 17,451 unigenes, 6.35% were annotated to all seven protein databases (NR, NT, KO, Swiss-Prot, FAM, GO, and KOG). Putative genes encoding enzymes related to polysaccharide biosynthetic pathways were determined. RT-qPCR for 11 randomly selected genes involved in polysaccharides indicated consistency with RNA-Seq data and polysaccharide content. The expressions of nine genes were higher in tetraploid than in diploid plants, while the expressions of the other two genes encoding bifunctional enzymes were the opposite. This study has provided a foundation for subsequent works regarding the biosynthetic pathways of metabolites involved in the autoploidy of Dendrobium species in general, and D. officinale in particular. Full article
(This article belongs to the Special Issue Recent Advances in Bioinformatics for Plant Genetic Traits)
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18 pages, 7158 KiB  
Article
Genome-Wide Association Analysis of Rice Leaf Traits
by Nansheng Wang, Xingmeng Wang, Yingzhi Qian, Di Bai, Yaling Bao, Xueyu Zhao, Peng Xu, Keyang Li, Jianfeng Li, Kang Li, Dewen Zhang and Yingyao Shi
Agronomy 2023, 13(11), 2687; https://doi.org/10.3390/agronomy13112687 - 25 Oct 2023
Viewed by 1041
Abstract
Yield-related traits have always been a research hotspot in rice breeding, and functional leaves directly affect the photosynthetic efficiency and yield of rice. Therefore, it is of great significance to explore the genes related to rice leaf size and shape to improve rice [...] Read more.
Yield-related traits have always been a research hotspot in rice breeding, and functional leaves directly affect the photosynthetic efficiency and yield of rice. Therefore, it is of great significance to explore the genes related to rice leaf size and shape to improve rice leaf morphology, photosynthesis efficiency, and yield. This study detected the quantitative trait loci (QTLs) for the length, width, length–width ratio, and area of rice flag leaf and second leaf in 393 accessions from the 3000 Rice Genome Project (3KRGP) by high-density single-nucleotide polymorphism genotyping. As a result, 91 QTLs were detected, among which 5 candidate genes (LOC_Os03g29170, LOC_Os06g17285, LOC_Os04g35060, LOC_Os03g27450, and LOC_Os09g16280) were identified. In addition, the epistatic interactions affecting leaf-related traits were also investigated, resulting in the identification of 134 significant QQIs (QTL by QTL interactions) pairs. The results of this study provide an important genetic basis for mining genes associated with rice leaf shape and valuable genetic information for rice breeding. Full article
(This article belongs to the Special Issue Recent Advances in Bioinformatics for Plant Genetic Traits)
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14 pages, 2862 KiB  
Article
Full-Length Transcriptome and the Identification of lncRNAs Involved in Salicylic Acid-Induced Flowering in Duckweed (Lemna gibba)
by Lili Fu, Deguan Tan, Xuepiao Sun, Zehong Ding and Jiaming Zhang
Agronomy 2023, 13(10), 2631; https://doi.org/10.3390/agronomy13102631 - 17 Oct 2023
Viewed by 836
Abstract
Long noncoding RNAs (lncRNAs) are crucial components in regulating the flowering of plants. However, the regulatory mechanism of lncRNAs underlying salicylic acid (SA)-induced flowering remains unknown in duckweed (e.g., Lemna gibba L.), an aquatic model species with significant potential applications in agriculture and [...] Read more.
Long noncoding RNAs (lncRNAs) are crucial components in regulating the flowering of plants. However, the regulatory mechanism of lncRNAs underlying salicylic acid (SA)-induced flowering remains unknown in duckweed (e.g., Lemna gibba L.), an aquatic model species with significant potential applications in agriculture and industry. In this work, L. gibba plants were collected at four crucial time points during SA-induced flowering and subjected to PacBio full-length sequencing and strand-specific RNA sequencing. A total of 474 lncRNAs were identified, of which 31 were differentially expressed and involved in SA-induced flowering. A trans-regulatory analysis found that these lncRNAs displayed temporal-specific expression trends and mainly participated in stress metabolism, photosynthesis, jasmonate metabolism, and transport under SA treatment. Five lncRNAs were determined to act as targets of miRNAs that played critical roles in regulating flowering. In addition, fifteen lncRNAs showed co-expression with flowering-related genes, and lncRNA03 and lncRNA25 were identified as key players involved in flowering via lncRNA-miRNA-mRNA interactions. Finally, twelve lncRNAs related to trans-regulation, miRNA targets, or co-expression with flowering-related genes were verified by qRT-PCR. These findings deepen our understanding of lncRNAs in SA-induced flowering in duckweed and provide valuable resources for in-depth functional analysis in the future. Full article
(This article belongs to the Special Issue Recent Advances in Bioinformatics for Plant Genetic Traits)
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24 pages, 3355 KiB  
Article
Detection of High-Performance Wheat Genotypes and Genetic Stability to Determine Complex Interplay between Genotypes and Environments
by Ibrahim Al-Ashkar, Mohammed Sallam, Khalid F. Almutairi, Mohamed Shady, Abdullah Ibrahim and Salem S. Alghamdi
Agronomy 2023, 13(2), 585; https://doi.org/10.3390/agronomy13020585 - 18 Feb 2023
Cited by 7 | Viewed by 1727
Abstract
Abiotic stress decreases crop production worldwide. In order to recommend suitable genotypes for cultivation under water deficit and heat stress conditions, an overall understanding of the genetic basis and plant responses to these stresses and their interactions with the environment is required. To [...] Read more.
Abiotic stress decreases crop production worldwide. In order to recommend suitable genotypes for cultivation under water deficit and heat stress conditions, an overall understanding of the genetic basis and plant responses to these stresses and their interactions with the environment is required. To achieve these goals, the multitrait genotype-ideotype distance index (MGIDI) was utilized to recognize abiotic-stress-tolerant wheat genotypes, and the weighted average of absolute scores (WAASB) index as well as the superiority index, which enables weighting between the mean performance and stability (WAASBY), were utilized to recognize high-yielding and stable genotypes. Twenty wheat genotypes were examined to determine the abiotic stress tolerance capacity of the investigated genotypes under nine test environments (three seasons × three treatments). Abiotic stress significantly decreased most morpho-physiological and all agronomic traits; however, some abiotic-stress-tolerant genotypes expressed a slight reduction in the measured traits as compared with the control group. G04, G12, G13, and G17 were identified as convenient and stable genotypes using the MGIDI index under all environments. Based on the scores of the genotype index (WAASB), G01, G05, G12, and G17 were selected as superior genotypes with considerable stability in terms of the grain yield (GY). G04, G06, G12, and G18 were classified as cluster (I), the productive and stable genotypes, using the WAASBY superiority index. The combined indices (MGIDI and WAASB) and (MGIDI and WAASBY) revealed genotypes G12 and G17 and genotypes G04 and G12, respectively, as the most stable candidates. Therefore, these are considered novel genetic resources for improving productivity and stabilizing GY in wheat programs under optimal conditions, water deficit, and heat stress. The genotype G12 was jointly expressed in all three indices. Stability measures using WAASB may help breeders with decision-making when selecting genotypes and conducting multi-environment trials. Hence, these methods, if jointly conducted, can serve as a powerful tool to assist breeders in multi-environment trials. Full article
(This article belongs to the Special Issue Recent Advances in Bioinformatics for Plant Genetic Traits)
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