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Agronomy
Special Issues
Genetic Diversity and Population Structure in Crop and Woody Plants
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Genetic Diversity and Population Structure in Crop and Woody Plants

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

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 17930

Special Issue Editors

Dr. Evangelia V. Avramidou

E-Mail Website
Guest Editor
Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, ELGO DEMETER, Athens, Greece
Interests: genetic and epigenetic diversity; genetic structure; population genetics; QTLs; genetic mapping
Special Issues, Collections and Topics in MDPI journals
Dr. Aliki Kapazoglou

E-Mail Website
Guest Editor
Department Of Vitis, Hellenic Agricultural Organization-Demeter (Hao-Demeter), Institute Of Olive Tree Subtropical Crops And Viticulture (Iosv), Athens, Greece
Interests: genetics; epigenetics; epigenomics; transcriptomics; functional genomics; grafting
Dr. Ermioni Malliarou

E-Mail Website
Guest Editor
Institute of Plant Breeding and Genetic Resources，ELGO DIMITRA, Athens, Greece
Interests: genetic and epigenetic diversity; population genetics; molecular and conservation genetics; quantitative genetics

Special Issue Information

Dear Colleagues,

In recent decades, climate change has strongly and directly affected plants and their crops. The rise in temperature in combination with prolonged periods of drought significantly affects crop yields in many parts of the world. This has necessitated the search for more resilient plant varieties that will be able to withstand adverse environmental conditions without compromising the maximum yield. Useful tools for this purpose are the extensive investigations of genetic and epigenetic diversity across a wide range of crop plants and wild relatives, which can provide us with a wealth of important information regarding the future viability of plant species in a changing environment. A combination of genetic and epigenetic inheritance of critical traits may be key to the generation of tolerant/resistant varieties to a series of newly emerging abiotic or biotic stressors in an era of ongoing climate change.

The aim of this topic is to publish new cutting-edge articles that combine the genetic structure (based on different molecular methods) and the epigenetic profile of cultivated and woody plants.

Dr. Evangelia V. Avramidou
Dr. Aliki Kapazoglou
Dr. Ermioni Malliarou
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. 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

  • crop plants
  • genetic structure
  • molecular methods
  • epigenetic diversity
  • crop varieties

Published Papers (7 papers)

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Research

24 pages, 6198 KiB  
Article
Core Collection Formation in Guatemalan Wild Avocado Germplasm with Phenotypic and SSR Data
by José Alejandro Ruiz-Chután, Marie Kalousová, Anna Maňourová, Hewan Demissie Degu, Julio Ernesto Berdúo-Sandoval, Carlos Enrique Villanueva-González and Bohdan Lojka
Agronomy 2023, 13(9), 2385; https://doi.org/10.3390/agronomy13092385 - 14 Sep 2023
Cited by 1 | Viewed by 1409
Abstract
Guatemala’s wild avocado germplasm holds vital genetic value, but lacking conservation strategies imperils it. Studying its diversity is pivotal for conservation and breeding. The study aimed to comprehensively assess the wild avocado germplasm in Guatemala by combining phenotypic and genotypic data and to [...] Read more.
Guatemala’s wild avocado germplasm holds vital genetic value, but lacking conservation strategies imperils it. Studying its diversity is pivotal for conservation and breeding. The study aimed to comprehensively assess the wild avocado germplasm in Guatemala by combining phenotypic and genotypic data and to create a core collection for conservation and future breeding programs. A total of 189 mature avocado trees were sampled across Guatemala’s northern, southern, and western regions. Morphological characteristics were documented, and genetic diversity was assessed using 12 SSR loci. The investigated germplasm revealed three distinct genetic clusters, exhibiting an average gene diversity of 0.796 and a 7.74% molecular variation among them. The samples showed various morphological characteristics that indicate the presence of three avocado races in Guatemala. The weak correlation between phenotypic and genotypic distances highlighted their independence and complementary nature. The joint matrix effectively integrated and captured genotypic and phenotypic data for comprehensive genetic diversity analysis. A core collection comprising 20% of total accessions that captured maximum genetic diversity was formed. This study exposed wild Guatemalan avocados’ genetic diversity, morphological traits, and conservation significance. Integrated data capture via clustering validates holistic genetic insight for conservation and breeding strategies. Full article
(This article belongs to the Special Issue Genetic Diversity and Population Structure in Crop and Woody Plants)
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17 pages, 2513 KiB  
Article
Population Structure and Genetic Diversity of Rice (Oryza sativa L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP)
by Paul Kitenge Kimwemwe, Chance Bahati Bukomarhe, Edward George Mamati, Stephen Mwangi Githiri, René Mushizi Civava, Jacob Mignouna, Wilson Kimani and Mamadou Fofana
Agronomy 2023, 13(7), 1906; https://doi.org/10.3390/agronomy13071906 - 19 Jul 2023
Cited by 5 | Viewed by 2898
Abstract
Understanding the genetic diversity and population structure of rice is crucial for breeding programs, conservation efforts, and the development of sustainable agricultural practices. This study aimed to assess the genetic diversity and population structure of 94 rice (Oryza sativa L.) genotypes from [...] Read more.
Understanding the genetic diversity and population structure of rice is crucial for breeding programs, conservation efforts, and the development of sustainable agricultural practices. This study aimed to assess the genetic diversity and population structure of 94 rice (Oryza sativa L.) genotypes from the Democratic Republic of Congo using a set of 8389 high-quality DArTseq-based single nucleotide polymorphism (SNP) markers. The average polymorphic information content (PIC) of the markers was 0.25. About 42.4% of the SNPs had a PIC value between 0.25 and 0.5, which were moderately informative. The ADMIXTURE program was used for structure analysis, which revealed five sub-populations (K = 5), with admixtures. In principal component analysis (PCA), the first three principal components accounted for 36.3% of the total variation. Analysis of molecular variance revealed significant variation between sub-populations (36.09%) and within genotypes (34.04%). The low overall number of migrants (Nm = 0.23) and high fixation index (Fst = 0.52) indicated limited gene flow and significant differentiation between the sub-populations. Observed heterozygosity (Ho = 0.08) was lower than expected heterozygosity (He = 0.14) because of the high inbreeding (Fis = 0.52) nature of rice. A high average Euclidean genetic distance (0.87) revealed the existence of genetic diversity among the 94 genotypes. The significant genetic diversity among the evaluated rice genotypes can be further explored to obtain potentially desirable genes for rice improvement. Full article
(This article belongs to the Special Issue Genetic Diversity and Population Structure in Crop and Woody Plants)
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22 pages, 11509 KiB  
Article
Comparative Evaluation of Pyrus Species to Identify Possible Resources of Interest in Pear Breeding
by Leontina I. Simionca Mărcășan, Rodica Pop, Peter A. Somsai, Ion Oltean, Sergiu Popa, Adriana F. Sestras, Mădălina Militaru, Mihai Botu and Radu E. Sestras
Agronomy 2023, 13(5), 1264; https://doi.org/10.3390/agronomy13051264 - 28 Apr 2023
Cited by 2 | Viewed by 1697
Abstract
Pear is one of the most important fruit species grown in the temperate zones of the globe. Besides fruit production, pear species are highly valued in forestry and agroforestry systems; in landscaping, as ornamental features; as fruits of ecological value, and in other [...] Read more.
Pear is one of the most important fruit species grown in the temperate zones of the globe. Besides fruit production, pear species are highly valued in forestry and agroforestry systems; in landscaping, as ornamental features; as fruits of ecological value, and in other areas. The Pyrus species, obtained from a gene bank, were evaluated for the different morphological traits of the trees, leaves, flowers, and fruits, as well as their responses to attacks from principal diseases and pests. Phenotypic data were examined using correlation and multivariate analyses, and a dendrogram of morphological traits was completed via molecular investigations at the DNA level using the RAPD markers. The findings revealed the complexities of the phenotypic and genetic connections among Pyrus species, as well as the difficulty in establishing phylogenetic relationships among pear species. The findings also demonstrated that the wide variability between species with different geographical origins, and their multiple peculiarities of interest, represents a cornerstone as the source of genes of great utility for pear breeding or for utilizing trees for different edible crops and for silvocultural, landscape, or ecological purposes. Full article
(This article belongs to the Special Issue Genetic Diversity and Population Structure in Crop and Woody Plants)
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16 pages, 2562 KiB  
Article
Deciphering Early Movements and Domestication of Coffea arabica through a Comprehensive Genetic Diversity Study Covering Ethiopia and Yemen
by Christophe Montagnon, Faris Sheibani, Tadesse Benti, Darrin Daniel and Adugna Debela Bote
Agronomy 2022, 12(12), 3203; https://doi.org/10.3390/agronomy12123203 - 16 Dec 2022
Cited by 5 | Viewed by 5158
Abstract
The coffee species Coffea arabica is facing numerous challenges regarding climate change, pests and disease pressure. Improved varieties will be part of the solution. Making optimal use of the scarce genetic diversity of the species is hence essential. In this paper, we present [...] Read more.
The coffee species Coffea arabica is facing numerous challenges regarding climate change, pests and disease pressure. Improved varieties will be part of the solution. Making optimal use of the scarce genetic diversity of the species is hence essential. In this paper, we present the first study of C. arabica genetic diversity covering its complete native habitat in Ethiopia together with its main domestication centers: Yemen and Hararghe region in Ethiopia. All in all, 555 samples were analyzed with a set of Single Sequence Repeat markers. Through admixture genetic analysis, six clusters were identified. A total of two “Core Ethiopian” clusters did not participate in the domestication of the species. There were four clusters that were part of the “Domestication Pathway” of C. arabica. The first one was named “Ethiopian Legacy” as it represents the genetic link between “Core Ethiopia” and the “Domestication Pathway” in Yemen and Hararghe. The geographic origin of this cluster in Ethiopia was the south of Ethiopia, namely Gedio, Guji and Sidama, which hence appears as the source of coffee seeds that led to the domestication of C. arabica. In Yemen, in addition to the “Ethiopian Legacy” cluster, we confirmed the “Typica/Bourbon” and “New-Yemen” clusters. In Hararghe, the “Harrar” cluster, never described before, likely originates from a re-introduction of domesticated coffee from Yemen into this region of Ethiopia. Cultivated varieties around the world today originate from the “Ethiopian Legacy” and “Typica/Bourbon” clusters and but none are related to the “new-Yemen” and “Harrar” clusters. Implications for breeding strategies are discussed. Full article
(This article belongs to the Special Issue Genetic Diversity and Population Structure in Crop and Woody Plants)
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11 pages, 1593 KiB  
Article
Genetic Diversity Assessment of Sweetpotato Germplasm in China Using InDel Markers
by Lukuan Zhao, Zhanghua Qi, Shizhuo Xiao, Fen Tang, Yang Liu, Yitong Deng, Xibin Dai, Zhilin Zhou, Wenjun Ou and Qinghe Cao
Agronomy 2022, 12(12), 3074; https://doi.org/10.3390/agronomy12123074 - 05 Dec 2022
Cited by 3 | Viewed by 1387
Abstract
Sweetpotato (Ipomoea batatas (L.) Lam.), whose roots are rich in starch, is widely grown around the world and plays a prominent role in ensuring food security. At present, there are no reports on the genetic diversity of sweetpotato germplasm revealed by InDel [...] Read more.
Sweetpotato (Ipomoea batatas (L.) Lam.), whose roots are rich in starch, is widely grown around the world and plays a prominent role in ensuring food security. At present, there are no reports on the genetic diversity of sweetpotato germplasm revealed by InDel markers. In this study, we developed a set of 30 InDel markers to evaluate the genetic diversity and relationships of 240 accessions, comprising 77 landraces, 80 introduced accessions, 82 improved varieties released in China, and a diploid wild relative Ipomoea trifida. A total of 94 reliable loci were obtained, with a mean of 3.13 loci per primer, and the PIC value ranged from 0.143 to 0.821. The whole population could be divided into three sub-populations according to a structure analysis based on the Bayesian model, which was consistent with the results of principal component analysis (PCA). A neighbor-joining tree was constructed based on Nei’s genetic distance ranging from 0 to 0.556 and discriminated the panel of the population into three main groups (Ⅰ, Ⅱ, Ⅲ). Group Ⅲ was further split into seven subgroups (ⅢA–ⅢG). The clustering pattern of the 240 accessions was unrelated to their geographic origins. Most of the accessions, whether landraces, improved varieties released in China or introduced germplasm, were mixed, which revealed the high level of genetic similarity among accessions from different regions. There was little difference in the level of genetic diversity between landraces and improved varieties, which was probably due to the exchange and utilization of accessions from different regions. More efforts should be made to collect and utilize sweetpotato germplasm resources and further broaden the genetic basis of sweetpotato cultivars. Full article
(This article belongs to the Special Issue Genetic Diversity and Population Structure in Crop and Woody Plants)
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27 pages, 5104 KiB  
Article
Revealing the Genetic Architecture of Yield-Related and Quality Traits in Indian Mustard [Brassica juncea (L.) Czern. and Coss.] Using Meta-QTL Analysis
by Rahul Kumar, Dinesh Kumar Saini, Mukesh Kumar, Veerala Priyanka, Javed Akhatar, Deepak Kaushik, Amit Sharma, Parmdeep Singh Dhanda and Prashant Kaushik
Agronomy 2022, 12(10), 2442; https://doi.org/10.3390/agronomy12102442 - 09 Oct 2022
Cited by 7 | Viewed by 2028
Abstract
A meta-QTL analysis was conducted in Indian mustard to identify robust and stable meta-QTLs (MQTLs) by utilizing 1504 available QTLs, which included 891 QTLs for yield-related traits and 613 QTLs for quality traits. For yield-related traits, a total of 57 MQTLs (YRTs_MQTLs) were [...] Read more.
A meta-QTL analysis was conducted in Indian mustard to identify robust and stable meta-QTLs (MQTLs) by utilizing 1504 available QTLs, which included 891 QTLs for yield-related traits and 613 QTLs for quality traits. For yield-related traits, a total of 57 MQTLs (YRTs_MQTLs) were uncovered from the clustering of 560 projected QTLs, which had a 4.18-fold smaller confidence interval (CI) than that of the initial QTLs, whereas, for quality traits, as many as 51 MQTLs (Quality_MQTLs) were derived from 324 projected QTLs, which had a 2.65-fold smaller CI than that of the initial QTLs. Sixteen YRTs_MQTLs were observed to share chromosomal positions with 16 Quality_MQTLs. Moreover, four most promising YRTs_MQTLs and eight Quality-MQTLs were also selected and recommended for use in breeding programs. Four of these selected MQTLs were also validated with significant SNPs that were identified in previously published genome-wide association studies. Further, in silico functional analysis of some promising MQTLs allowed the detection of as many as 1435 genes, which also involved 15 high-confidence candidate genes (CGs) for yield-related traits and 46 high-confidence CGs for quality traits. After validation, the identified CGs can also be exploited to model the plant architecture and to improve quality traits through marker-assisted breeding, genetic engineering, and genome editing approaches. Full article
(This article belongs to the Special Issue Genetic Diversity and Population Structure in Crop and Woody Plants)
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14 pages, 3102 KiB  
Article
Pollen: A Potential Explant for Genetic Transformation in Wheat (Triticum aestivum L.)
by Mehwish Kanwal, Neelam Gogoi, Brian Jones, Harbans Bariana, Urmil Bansal and Nabil Ahmad
Agronomy 2022, 12(9), 2009; https://doi.org/10.3390/agronomy12092009 - 25 Aug 2022
Cited by 3 | Viewed by 2283
Abstract
The use of biotechnology for the genetic improvement of wheat (Triticum aestivum L.) has been hampered by its recalcitrance to standard transformation and regeneration protocols. Male gametes present a potentially useful option for introducing gene edits via clustered regularly interspaced short palindromic [...] Read more.
The use of biotechnology for the genetic improvement of wheat (Triticum aestivum L.) has been hampered by its recalcitrance to standard transformation and regeneration protocols. Male gametes present a potentially useful option for introducing gene edits via clustered regularly interspaced short palindromic repeats (CRISPR). However, the utility of male gametes for introducing genetic improvements would be dependent on the retention of viability after treatment to introduce the CRISPR components. We have studied wheat pollen morphology and its viability in a range of germination media to identify conditions that optimize the viability of in vitro hydrated pollen. The size, shape, and aperture from seven different wheat genotypes were compared using scanning electron microscope (SEM). The SEM results revealed that the pollen of all of the wheat genotypes examined in this study were monoporate; however, a significant variation in the size of the mature pollen grains was observed. The hydrated pollen of the wheat genotypes remained viable for up to five hours at 20 ± 2 °C. Of all of the germination media tested, the medium containing 5% sucrose, 10% PEG4000, 100 mg/L boric acid, 200 mg/L calcium nitrate, 100 mg/L potassium nitrate, and 100 mg/L magnesium sulphate at pH 6.5 achieved the highest percentage of pollen germination after 5 h of hydration. Impedance Flow Cytometry (IFC) provided similar results to the in vitro germination study. This work elucidates important factors that can form the basis for a pollen-based non-genetically modified system for gene editing in wheat. Full article
(This article belongs to the Special Issue Genetic Diversity and Population Structure in Crop and Woody Plants)
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