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Advances in Genetic Diversity and Population Structure of Plant Species,...
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Advances in Genetic Diversity and Population Structure of Plant Species, 2nd Edition

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (28 February 2025) | Viewed by 21097

Special Issue Editors

Dr. Muhammud Qasim Shahid

E-Mail Website
Guest Editor
College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Interests: molecular markers; plant breeding and genetics; agricultural biotechnology; plant genomics; polyploidy; rice; agronomy; plant reproduction
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Xiangdong Liu

E-Mail Website
Guest Editor
College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Interests: plant breeding and genetics; cytogenetics; plant reproduction biology; polyploidy; rice; plant germplasm enhancement
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Due to the success of the first volume of the Special Issue and the undiminished enthusiasm for this topic, we are launching its second volume.

The world is currently being confronted with an increasing population, food insecurity, and climate change. As of April 2019, the world population was estimated at 7.7 billion, and it is forecast to grow to more than 9 billion by 2050. Because the world’s population is growing at an unprecedented rate, feeding this population is becoming a big challenge, and there is a need to increase the world’s food production by 60–110%. Industrialization has brought economic prosperity; additionally, it has resulted in a larger population and urbanization. However, it has played a significant role in climate change as well. Climate change is causing a hazardous scenario for global food security by reducing food production by disturbing the cropping pattern and lowering the resistance of crops to biotic and biotic stress. Researchers have applied plant breeding as the most effective tool for dealing with these issues. However, the role of plant breeding in genetic erosion is also universally accepted. Therefore, our current food cultivars are not performing well under these unprecedented climatic conditions because of a genetic bottleneck. To mitigate all these problems, there is a need to harness plant diversity.

Exploring and managing genetic resources is a valuable approach, encompassing the collection, preservation, and characterization of genetic materials. This strategy proves instrumental in unraveling both genotypic and phenotypic variations, offering a rich resource for the breeding community. Addressing the limited genetic diversity of our food crops is achievable through the inclusion of landraces, crop wild relatives, and the often-overlooked plant species. Diversifying the genetic base lays the foundation for developing novel crop varieties resilient to diverse biotic and abiotic stress factors while concurrently enhancing yield and nutritional quality. The judicious combination of both traditional and cutting-edge breeding technologies expedites this process. By tapping into the vast reservoir of genetic resources, the creation of a new generation of crops emerges—ones characterized by heightened resistance, improved nutritional content, and an enhanced taste profile. Ultimately, the strategic utilization of plant diversity has the potential to revolutionize dietary patterns and contribute to improved public health. The exploration and incorporation of genetic resources open doors to the development of foods and ingredients that not only cater to enhanced nutritional needs but also elevate the overall sensory experience, thereby promoting the well-being of the population.

This Special Issue will focus on highlighting the importance of plant biodiversity and genetic resources for a sustainable agricultural production system. We welcome original research papers, reviews, perspectives, opinions, and modeling approaches regarding plant genetic diversity, breeding, omics, biotechnological technologies, and the biodiversity conservation of plant species.

Dr. Muhammud Qasim Shahid
Prof. Dr. Xiangdong Liu
Guest Editors

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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • germplasm characterization
  • phenotypic evaluation
  • molecular characterization
  • molecular breeding
  • germplasm conservation
  • phenotypic markers
  • molecular markers
  • functional markers
  • molecular breeding
  • next generation sequencing
  • genotyping by sequencing
  • marker-assisted selection
  • genetic mapping
  • QTL mapping
  • GWAS
  • plants
  • cereals
  • legumes
  • oilseeds
  • medicinal plants
  • endangered species
  • horticultural crops
  • genetic erosion
  • biodiversity conservation and enhancement
  • valuing plant genetic diversity
  • plant wild relatives
  • genetic improvement of crops
  • DNA banking for plant breeding
  • climate change resilience
  • cultivar development
  • agricultural productivity
  • omics and biotechnological technologies

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Related Special Issue

Published Papers (5 papers)

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Research

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13 pages, 2217 KiB  
Article
Identification of Phenotypic Diversity and DArTseq Loci Associated with Vitamin A Contents in Turkish Common Bean Germplasm Through GWAS
by Yeter Çilesiz, Muhammad Tanveer Altaf, Muhammad Azhar Nadeem, Amjad Ali, Uğur Sesiz, Ahmad Alsaleh, Ahmet İlçim, Mehmet Sertaç Özer, Tunahan Erdem, Israr Aziz, Sheikh Mansoor, Tolga Karaköy and Faheem Shehzad Baloch
Plants 2025, 14(5), 776; https://doi.org/10.3390/plants14050776 - 3 Mar 2025
Viewed by 724
Abstract
Biofortification has emerged as an important approach for improving minerals and vitamin deficiencies through the application of agronomic and biotechnological methodologies. Vitamin A, one of the most deficient vitamins, disproportionately affects children in developing countries, highlighting the urgent need for vitamin A-enriched cultivars. [...] Read more.
Biofortification has emerged as an important approach for improving minerals and vitamin deficiencies through the application of agronomic and biotechnological methodologies. Vitamin A, one of the most deficient vitamins, disproportionately affects children in developing countries, highlighting the urgent need for vitamin A-enriched cultivars. The present study aimed to characterize common bean germplasm for vitamin A contents and to identify the genomic regions associated with this trait. A total of 177 common bean landraces and 6 commercial cultivars were evaluated under five environments and two locations. Analysis of variance revealed highly significant environmental effects and genotype × environment interactions. Across all years and all locations, Bilecik-6 exhibited the lowest vitamin A contents (1.67 µg/100 g dry seed), while Civril-Bolu had the highest (3.23 µg/100 g dry seed). Landraces from Balıkesir province were found to be rich in vitamin A content and should be considered as potential genetic resources for common bean biofortification. Additionally, a genomic region located on Pv06 was identified as being linked to vitamin A content. The genomic and genetic resources identified in this study will be valuable for the breeding community aiming to develop vitamin A-enriched common bean cultivars. Full article
(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species, 2nd Edition)
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20 pages, 6545 KiB  
Article
Genome Scan Analysis for Advancing Knowledge and Conservation Strategies of Primitivo Clones (Vitis vinifera L.)
by Silvia Procino, Monica Marilena Miazzi, Vito Nicola Savino, Pierfederico La Notte, Pasquale Venerito, Nunzio D’Agostino, Francesca Taranto and Cinzia Montemurro
Plants 2025, 14(3), 437; https://doi.org/10.3390/plants14030437 - 2 Feb 2025
Viewed by 895
Abstract
The success of the Primitivo variety underscores the critical need for the managing of clone genetic conservation, utilization, and improvement. By combining genomic and environmental data, breeders can better predict the performance of varieties, thereby improving breeding efficiency and enabling more targeted development [...] Read more.
The success of the Primitivo variety underscores the critical need for the managing of clone genetic conservation, utilization, and improvement. By combining genomic and environmental data, breeders can better predict the performance of varieties, thereby improving breeding efficiency and enabling more targeted development of high-quality grapevine cultivars. In this study, 35 Primitivo clones were analysed, including selected and certified clones that have been propagated over several years in Apulia. Genetic variability among the Primitivo clones was assessed through genotyping by sequencing. Using 38,387 filtered SNPs, pairwise identity-by-state (IBS) analysis demonstrated the uniqueness of the 35 clones (IBS < 0.75), indicating a high degree of variability among the samples. Genetic diversity analysis revealed three primary groups, which were differentiated based on geographic origin. The clones from Gioia del Colle were grouped into two distinct clusters, which aligns with the observed variation in grape-related traits. The fixation index (FST > 0.50) identified numerous loci putatively associated with stress responses and developmental traits, including genes involved in key plant biological processes, stress response regulation, and adaptation to environmental conditions such as glutamate receptors, auxin, and ethylene signalling. Full article
(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species, 2nd Edition)
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18 pages, 19648 KiB  
Article
The Phylogeography of Deciduous Tree Ulmus macrocarpa (Ulmaceae) in Northern China
by Hang Ye, Yiling Wang, Hengzhao Liu, Dingfan Lei, Haochen Li, Zhimei Gao, Xiaolong Feng, Mian Han, Qiyang Qie and Huijuan Zhou
Plants 2024, 13(10), 1334; https://doi.org/10.3390/plants13101334 - 12 May 2024
Cited by 2 | Viewed by 1702
Abstract
Disentangling how climate oscillations and geographical events significantly influence plants’ genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current [...] Read more.
Disentangling how climate oscillations and geographical events significantly influence plants’ genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of U. macrocarpa using chloroplast DNA with ecological niche modeling. The results indicated that the populations’ genetic differentiation coefficient (NST) value was significantly greater than the haplotype frequency (GST) (p < 0.05), suggesting that U. macrocarpa had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle–late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for U. macrocarpa during the glacial period in Northern China. Our results illuminated the demography pattern of U. macrocarpa and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China. Full article
(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species, 2nd Edition)
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Review

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21 pages, 3266 KiB  
Review
Finally Freed—Cannabis in South Africa: A Review Contextualised within Global History, Diversity, and Chemical Profiles
by Valencia V. Ndlangamandla, Adeola Salawu-Rotimi, Vuyiswa S. Bushula-Njah, Nompilo L. Hlongwane, Gugu F. Sibandze, Fikisiwe C. Gebashe and Nokuthula P. Mchunu
Plants 2024, 13(19), 2695; https://doi.org/10.3390/plants13192695 - 26 Sep 2024
Cited by 1 | Viewed by 3540
Abstract
Cannabis sativa L. is a monotypic genus belonging to the family Cannabaceae. It is one of the oldest species cultivated by humans, believed to have originated in Central Asia. In pivotal judgements in 2016 and 2018, the South African Constitutional Court legalised the [...] Read more.
Cannabis sativa L. is a monotypic genus belonging to the family Cannabaceae. It is one of the oldest species cultivated by humans, believed to have originated in Central Asia. In pivotal judgements in 2016 and 2018, the South African Constitutional Court legalised the use of Cannabis within the country for medicinal and recreational purposes, respectively. These decrees opened opportunities for in-depth research where previously there had been varying sentiments for research to be conducted on the plant. This review seeks to examine the history, genetic diversity, and chemical profile of Cannabis. The cultivation of Cannabis by indigenous people of southern Africa dates back to the eighteenth century. Indigenous rural communities have been supporting their livelihoods through Cannabis farming even before its legalisation. However, there are limited studies on the plant’s diversity, both morphologically and genetically, and its chemical composition. Also, there is a lack of proper documentation of Cannabis varieties in southern Africa. Currently, the National Centre for Biotechnology Information (NCBI) has 15 genome assemblies of Cannabis obtained from hemp and drug cultivars; however, none of these are representatives of African samples. More studies are needed to explore the species’ knowledge gaps on genetic diversity and chemical profiles to develop the Cannabis sector in southern Africa. Full article
(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species, 2nd Edition)
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32 pages, 2161 KiB  
Review
Modern Plant Breeding Techniques in Crop Improvement and Genetic Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence—A Critical Review
by Lixia Sun, Mingyu Lai, Fozia Ghouri, Muhammad Amjad Nawaz, Fawad Ali, Faheem Shehzad Baloch, Muhammad Azhar Nadeem, Muhammad Aasim and Muhammad Qasim Shahid
Plants 2024, 13(19), 2676; https://doi.org/10.3390/plants13192676 - 24 Sep 2024
Cited by 13 | Viewed by 13150
Abstract
With the development of new technologies in recent years, researchers have made significant progress in crop breeding. Modern breeding differs from traditional breeding because of great changes in technical means and breeding concepts. Whereas traditional breeding initially focused on high yields, modern breeding [...] Read more.
With the development of new technologies in recent years, researchers have made significant progress in crop breeding. Modern breeding differs from traditional breeding because of great changes in technical means and breeding concepts. Whereas traditional breeding initially focused on high yields, modern breeding focuses on breeding orientations based on different crops’ audiences or by-products. The process of modern breeding starts from the creation of material populations, which can be constructed by natural mutagenesis, chemical mutagenesis, physical mutagenesis transfer DNA (T-DNA), Tos17 (endogenous retrotransposon), etc. Then, gene function can be mined through QTL mapping, Bulked-segregant analysis (BSA), Genome-wide association studies (GWASs), RNA interference (RNAi), and gene editing. Then, at the transcriptional, post-transcriptional, and translational levels, the functions of genes are described in terms of post-translational aspects. This article mainly discusses the application of the above modern scientific and technological methods of breeding and the advantages and limitations of crop breeding and diversity. In particular, the development of gene editing technology has contributed to modern breeding research. Full article
(This article belongs to the Special Issue Advances in Genetic Diversity and Population Structure of Plant Species, 2nd Edition)
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