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Agronomy
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Fruits Crops Improvements in View of Marker Development, Genetic Diversity,...
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Fruits Crops Improvements in View of Marker Development, Genetic Diversity, Population Structure Traits Tagging and GWAS

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 May 2024) | Viewed by 4219

Special Issue Editor

Dr. Manosh Biswas

E-Mail Website
Guest Editor
Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, UK
Interests: bio-informatics; genetics; genomics; cytogenetics; molecular biology; breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues，

The information on genetic diversity and population structure constitutes the key parameters for modern day’s plant breeders, conservationists, genome scientists and plant biologists. Advances in genomic technology, like NGS and bio-informatics platform, accelerate the genetic improvement of crop plant species. Fruit crops species contribute a significant amount of foods, fodders and essential human products. Consequently, the consumption demand increasing day by day, in order to meet the global demands of scientists, has initiated a huge number of research projects all over the world in the past several decades. A remarkable advancement is achieved in pomology research, including nationwide fruit germplasm (gene bank) center establishment, the characterization of wild and domesticated cultivars, digital genetic and genomic resources, application of marker technology, agronomic traits tagging, whole genome sequencing, etc. The recent advancements in fruit crop plants research creates opportunities and challenges for pomologists.

This Special Issue opens the door for the fruit crops research community to share their up-to-date progress, and inventions in the fields of genetic diversity, molecular breeding, population genetics, bio-informatics and conservation genetics. Original research articles and concepts for review articles to address major issues are welcome.

Dr. Manosh Biswas
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.

Keywords

  • Next generation sequencing
  • Molecular Markers
  • SSR
  • SNP
  • Agronomic traits
  • Bioinformatics
  • Population structure
  • Genetic diversity
  • Germplasm
  • Gene banks

Published Papers (3 papers)

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Research

13 pages, 3327 KiB  
Article
The Musa Marker Database: A Comprehensive Genomic Resource for the Improvement of the Musaceae Family
by Manosh Kumar Biswas, Dhiman Biswas, Ganjun Yi and Guiming Deng
Agronomy 2024, 14(4), 838; https://doi.org/10.3390/agronomy14040838 - 17 Apr 2024
Viewed by 320
Abstract
Molecular markers, including Simple Sequence Repeat (SSR), Single Nucleotide Polymorphism (SNP), and Intron Length Polymorphism (ILP), are widely utilized in crop improvement and population genetics studies. However, these marker resources remain insufficient for Musa species. In this study, we developed genome-wide SSR, SNP, [...] Read more.
Molecular markers, including Simple Sequence Repeat (SSR), Single Nucleotide Polymorphism (SNP), and Intron Length Polymorphism (ILP), are widely utilized in crop improvement and population genetics studies. However, these marker resources remain insufficient for Musa species. In this study, we developed genome-wide SSR, SNP, and ILP markers from Musa and its sister species, creating a comprehensive molecular marker repository for the improvement of Musa species. This database contains 2,115,474 SSR, 63,588 SNP, and 91,547 ILP markers developed from thirteen Musa species and two of its relative species. We found that 77% of the SSR loci are suitable for marker development; 38% of SNP markers originated from the genic region, and transition mutations (C↔T; A↔G) were more frequent than transversion. The database is freely accessible and follows a ‘three-tier architecture,’ organizing marker information in MySQL tables. It has a user-friendly interface, written in JavaScript, PHP, and HTML code. Users can employ flexible search parameters, including marker location in the chromosome, transferability, polymorphism, and functional annotation, among others. These distinctive features distinguish the Musa Marker Database (MMdb) from existing marker databases by offering a novel approach that is tailored to the precise needs of the Musa research community. Despite being an in silico method, searching for markers based on various attributes holds promise for Musa research. These markers serve various purposes, including germplasm characterization, gene discovery, population structure analysis, and QTL mapping. Full article
(This article belongs to the Special Issue Fruits Crops Improvements in View of Marker Development, Genetic Diversity, Population Structure Traits Tagging and GWAS)
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17 pages, 3146 KiB  
Article
Characterization and Analysis of the Full-Length Transcriptome Provide Insights into Fruit Quality Formation in Kiwifruit Cultivar Actinidia arguta cv. Qinziyu
by Yun Jia, Ying Zhang, Lei Zhang, Fengwei Wang, Gang Yu, Yaling Wang, Xiaoyan Kang and Yongpeng Wu
Agronomy 2023, 13(1), 143; https://doi.org/10.3390/agronomy13010143 - 01 Jan 2023
Viewed by 1488
Abstract
Kiwifruit is an economically important horticultural crop with extremely high values in nutrition and health care. However, the molecular mechanisms underlying fruit quality formation remain largely limited for most kiwifruit varieties. Recently, a new kiwifruit cultivar with a high level of soluble solids, [...] Read more.
Kiwifruit is an economically important horticultural crop with extremely high values in nutrition and health care. However, the molecular mechanisms underlying fruit quality formation remain largely limited for most kiwifruit varieties. Recently, a new kiwifruit cultivar with a high level of soluble solids, Actinidia arguta cv. Qinziyu (full-red flesh) was discovered through the introduction and propagation test. To provide new insights into fruit quality formation in a typical kiwifruit cultivar, we integrated full-length transcriptome surveys based on PacBio single-molecule real-time (SMRT) sequencing, key enzyme genes expression involved in carbohydrate and amino acids metabolism pathways, and bHLH gene family analysis to enhance the understanding of soluble sugar, organic acid, and anthocyanin biosynthesis in A. arguta cv. Qinziyu. A total of 175,913 CCSs were generated, of which 124,789 were identified as FLNC transcripts. In total, 45,923 (86.99%) transcripts were successfully annotated, and more than 76.05% of the transcripts were longer than 1 Kb. KEGG pathway analysis showed that 630 candidate genes encoding 55 enzymes were mainly involved in carbohydrate and amino acid biosynthesis pathways. Further analysis verified the expression of 12 key enzyme genes (e.g., pyruvate kinase (PK), enolase (ENO), hexokinase (HK), and phosphoglycerate kinase (PGK)) in flowers using quantitative real-time PCR. Furthermore, we also screened 10 AabHLH proteins’ function in anthocyanin biosynthesis and characterized the AabHLH gene family in A. arguta cv. Qinziyu. Overall, our research data generated by SMRT technology provide the first set of gene isoforms from a full-length transcriptome in A. arguta cv. Qinziyu and more comprehensive insights into the molecular mechanism of fruit quality formation. Full article
(This article belongs to the Special Issue Fruits Crops Improvements in View of Marker Development, Genetic Diversity, Population Structure Traits Tagging and GWAS)
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15 pages, 1776 KiB  
Article
Inter Simple Sequence Repeat-Based Genetic Divergence and Varietal Identification of Banana in Pakistan
by Saima Noor, Aish Muhammad, Armghan Shahzad, Iqbal Hussain, Muhammad Zeshan, Kazim Ali, Sania Begum, Muhammad Aqeel, Mian Numan, Raja Mohib Muazzam Naz, Shehla Shoukat, Hina Hafeez, Imdad Ullah Zaid and Ghulam Muhammad Ali
Agronomy 2022, 12(12), 2932; https://doi.org/10.3390/agronomy12122932 - 23 Nov 2022
Cited by 3 | Viewed by 1293
Abstract
Banana is one of the major cash and fruit crops of Pakistan. The lack of information concerning genetic diversity and purity within locally cultivated banana varieties is a major bottleneck in improving its genetics. Due to the existence of a narrow genetic background, [...] Read more.
Banana is one of the major cash and fruit crops of Pakistan. The lack of information concerning genetic diversity and purity within locally cultivated banana varieties is a major bottleneck in improving its genetics. Due to the existence of a narrow genetic background, it’s quite important to find genomic variations in banana varieties. DNA marker-based techniques have been used to effectively characterize banana varieties. In the current study, Inter Simple Sequence Repeat (ISSR) markers were used to characterize banana cultivars and to assess the genetic diversity of 14 local banana varieties grown in Pakistan. Out of the 45 primers used, 40 primers revealed reproducible results and produced 121 polymorphic bands, which contributed a ratio of 47.87 polymorphism. The ISSR UBC-835 and UBC-834 possessed the highest PIC ranged between (86–88%) in banana varieties, while the lowest PIC (46%) was detected in the case of UBC−857 marker with (100–1500 bp) PCR product size. Pairwise Jaccard’s similarity coefficient values were also calculated, and these were ranged from 0.56–0.88. Multivariate analysis divided 14 banana varieties into two distinct groups—A and B respectively—and furthermore into subgroups, clusters, and sub−clusters. Our results indicated that at the molecular level, the banana varieties in group—A were found to be 66% similar whereas in group B were 88% similar. Nei’s genetic diversity, PCA analysis, and a minimum spanning tree depicted Fenjiao, Dajiao, and NIGAB-2 as the most diverse members as compared to all other varieties of the three populations. Out of 14 varieties used, 11 varieties were uniquely identified by 54 polymorphic ISSR bands of different sizes. Some varieties like NIGAB-2 and NIGAB-3 were uniquely identified only with one band while others were tagged by multiple unique bands. In future, this study will be utilized to establish a molecular-based protocol for the identification of banana varieties. Full article
(This article belongs to the Special Issue Fruits Crops Improvements in View of Marker Development, Genetic Diversity, Population Structure Traits Tagging and GWAS)
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