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Agronomy
Special Issues
Analysis of the Genetic Diversity of Crops and Associated Microbiota
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Analysis of the Genetic Diversity of Crops and Associated Microbiota

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

Deadline for manuscript submissions: closed (20 October 2022) | Viewed by 18450

Special Issue Editors

Prof. Dr. Antonio M. De Ron

E-Mail Website
Guest Editor
Misión Biológica de Galicia (MBG), CSIC, 36143 Pontevedra, Spain
Interests: agronomy; crop genetics and breeding; genetic resources; legumes; agrosystems; cropping systems
Special Issues, Collections and Topics in MDPI journals
Dr. A. Paula Rodiño

E-Mail Website
Guest Editor
Misión Biológica de Galicia (MBG), CSIC, 36143 Pontevedra, Spain
Interests: bean; breeding; genetic diversity; germplasm; rhizobia; stress
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue of Agronomy, dedicated to the analysis of the genetic diversity of crops and associated microbiota (Rhizobia, Mycorrhiza, and Plant Growth-Promoting Rhizobacteria) is aimed at publishing original research or review papers dedicated to the study of the diversity of crop genetic resources and genetics of cultivated plant species, and also, to the study of its associated microbiota, considering Nitrogen-fixing bacteria, mycorrhizae, and growth-promoting bacteria. Genetic resources are the basic element of the genetic study of crops and allow their genetic improvement. Soil rhizobia contributes to the sustainability of agriculture worldwide due to its role of increasing the amount of nitrogen available to plants by biological nitrogen fixation (BNF), reducing the demand for external nitrogen fertilizers, and the overall nitrous oxide emissions. Mycorrhizal fungi increase the surface absorbing area of roots, thereby greatly improving the ability of the plant to access soil resources. Plant growth-promoting rhizobacteria (PGPR) can enhance plant growth and protect plants from disease and abiotic stresses through a wide variety of mechanisms.

These aspects will be included in the Special Issue, although not exclusively, since other aspects related to the analysis of crop genetic and germplasm diversity will also be welcome in this volume.

Prof. Dr. Antonio M. De Ron
Dr. A. Paula Rodiño
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 genetics
  • biology of agrosystems
  • germplams diversity
  • genetic improvement of crops
  • adaptation of crops
  • cropping systems
  • rhizobia
  • mycorrizae
  • plant growth-promoting rhizobacteria
  • symbiosis

Published Papers (7 papers)

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Editorial

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4 pages, 200 KiB  
Editorial
Analysis of the Genetic Diversity of Crops and Associated Microbiota
by Antonio M. De Ron and Ana Paula Rodiño
Agronomy 2023, 13(8), 2132; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13082132 - 14 Aug 2023
Cited by 1 | Viewed by 770
Abstract
Plant genetic resources are the basis for genetic improvements in cultivated plants and in future food and feed security [...] Full article
(This article belongs to the Special Issue Analysis of the Genetic Diversity of Crops and Associated Microbiota)

Research

Jump to: Editorial

16 pages, 850 KiB  
Article
Exploring the Genetic Diversity of Carrot Genotypes through Phenotypically and Genetically Detailed Germplasm Collection
by Davinder Singh, Tarsem Singh Dhillon, Talha Javed, Rajinder Singh, Jalpa Dobaria, Surender Kumar Dhankhar, Farzad Kianersi, Baber Ali, Peter Poczai and Uttam Kumar
Agronomy 2022, 12(8), 1921; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12081921 - 15 Aug 2022
Cited by 10 | Viewed by 2227
Abstract
Germplasm evaluation, classification, characterization, and preservation are the initial requirements for any crop genetic improvement programs meant to promote economically important traits. Mean performance and range of different expressible traits through ANOVA showed highly significant differences within the various genotypes and helped to [...] Read more.
Germplasm evaluation, classification, characterization, and preservation are the initial requirements for any crop genetic improvement programs meant to promote economically important traits. Mean performance and range of different expressible traits through ANOVA showed highly significant differences within the various genotypes and helped to evaluate several promising carrot genotypes. The multivariate analysis method was used in this study, which was helpful in resolving different phenotypic and genotypic parameters/measurements of big collections into easy interpretable dimensions.The research work was carried out with eighty-one genotypes to evaluate genetic diversity in a germplasm collection through multivariate analysis.The divergence analysis grouped all eighty-one genotypes into ten clusters and cluster VI was found to be the biggest, comprised of 30 genotypes, followed by IV, which was comprised of 16 genotypes. Cluster X exhibited a high mean value for root weight and anthocyanin content; cluster III showed high value for days to 1st root harvest and root girth, and cluster V for dry matter content, total sugar content, and carotene content; respectively. The maximum distance between clusters was recorded among II and X cluster (43,678.5) follow by I and X (43,199.7), and it indicated that genotypes from these far away clusters could be used efficiently in breeding programs to obtain superior hybrids. Total sugar content (36.14%) contributed most to genetic divergence, followed by anthocyanin content (35.74%). Out of four principal components, PC1 largely contributed towards total variation, followed by PC2. The partial variances (%) from the first to fourth PC-axes were 36.77, 25.50, 12.67, and 10.17, respectively. Genotypes like PC-161, PC-173, PAU-J-15, PC-103, and PC-43 were considered superior with respect to marketable yield and its associated traits such as root length and root weight, and hence can be released directly as a variety. Full article
(This article belongs to the Special Issue Analysis of the Genetic Diversity of Crops and Associated Microbiota)
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14 pages, 3429 KiB  
Article
Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species
by Haizheng Xiong, Yilin Chen, San-Ji Gao, Yong-Bao Pan and Ainong Shi
Agronomy 2022, 12(2), 412; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12020412 - 06 Feb 2022
Cited by 5 | Viewed by 2731
Abstract
Sugarcane (Saccharum spp. hybrids) is one of the most important commercial crops for sugar, ethanol, and other byproducts production; therefore, it is of great significance to carry out genetic research. Assessing the genetic population structure and diversity plays a vital role in [...] Read more.
Sugarcane (Saccharum spp. hybrids) is one of the most important commercial crops for sugar, ethanol, and other byproducts production; therefore, it is of great significance to carry out genetic research. Assessing the genetic population structure and diversity plays a vital role in managing genetic resources and gene mapping. In this study, we assessed the genetic diversity and population structure among 196 Saccharum accessions, including 34 S. officinarum, 69 S. spontaneum, 17 S. robustum, 25 S. barberi, 13 S. sinense, 2 S. edule, and 36 Saccharum spp. hybrids. A total of 624 polymorphic SSR alleles were amplified by PCR with 22 pairs of fluorescence-labeled highly polymorphic SSR primers and identified on a capillary electrophoresis (CE) detection system including 109 new alleles. Three approaches (model-based clustering, principal component analysis, and phylogenetic analysis) were conducted for population structure and genetic diversity analyses. The results showed that the 196 accessions could be grouped into either three (Q) or eight (q) sub-populations. Phylogenetic analysis indicated that most accessions from each species merged. The species S. barberi and S. sinense formed one group. The species S. robustum, S. barberi, S. spontaneum, S. edule, and sugarcane hybrids merged into the second group. The S. officinarum accessions formed the third group located between the other two groups. Two-way chi-square tests derived a total of 24 species-specific or species-associated SSR alleles, including four alleles each for S. officinarum, S. spontaneum, S. barberi, and S. sinense, five alleles for S. robustum. and three alleles for Saccharum spp. hybrids. These species-specific or species-associated SSR alleles will have a wide application value in sugarcane breeding and species identification. The overall results provide useful information for future genetic study of the Saccharum genus and efficient utilization of sugarcane germplasm resources in sugarcane breeding. Full article
(This article belongs to the Special Issue Analysis of the Genetic Diversity of Crops and Associated Microbiota)
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18 pages, 3669 KiB  
Article
Genetic Diversity and Primary Core Collection Construction of Turnip (Brassica rapa L. ssp. rapifera Matzg) Landraces in Tibet Revealed via Morphological and SSR Markers
by Rongrong Li, Fangyuan Zhou, Yingying Gao, Chenlu Liu, Shubo Yu, Kun Zhao, Wenfeng Gong, Jie Lang, Haijuan Zhang and Xiaolin Yu
Agronomy 2021, 11(10), 1901; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11101901 - 22 Sep 2021
Cited by 3 | Viewed by 1884
Abstract
Turnip, one of the oldest groups of cultivated Brassica rapa species, is a traditional crop as well as a form of animal fodder, a vegetable, and a herbal medicine that is widely cultivated in farming and farming-pastoral regions in Tibet. Different regions of [...] Read more.
Turnip, one of the oldest groups of cultivated Brassica rapa species, is a traditional crop as well as a form of animal fodder, a vegetable, and a herbal medicine that is widely cultivated in farming and farming-pastoral regions in Tibet. Different regions of the Qinghai–Tibet Plateau (QTP) are home to a rich diversity of turnip owing to their high altitudes and variable climate types. However, information on the morphology and genetic diversity of Tibetan turnip remains limited. Therefore, the genetic diversity of 171 turnip varieties from China and elsewhere (Japan, Korea, and Europe) was analyzed using 58 morphological characteristics and 31 simple sequence repeat (SSR) markers in this study. The varieties showed that the genetic distance ranged from 0.12 to 1.00, and the genetic similarity coefficient ranged between 0.73 and 0.95. Cluster tree showed two distinct clusters. Both morphotype and geography contributed to the group classification. A combination of morphological traits and molecular markers could refine the precision of accurate identification compared to the separate morphological and molecular data analyses. The sampling ratio of 15% to utmost precisely represent the initial population was compared to ratios of 10% and 20%, and the sampling ratio of 15% is recommended for future works when a primary core collection of turnip resources is constructed. These results could furnish a foundation for germplasm conservation and effective turnip breeding in future studies. Full article
(This article belongs to the Special Issue Analysis of the Genetic Diversity of Crops and Associated Microbiota)
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14 pages, 3980 KiB  
Article
Semi-Quantification of Lectins in Rice (Oryza sativa L.) Genotypes via Hemagglutination
by Haseena Gulzar, Muhammad Asif Nawaz, Asad Jan, Farhat Ali Khan, Sumaira Naz, Muhammad Zahoor, Dil Naz, Riaz Ullah, Essam A. Ali and Hidayat Hussain
Agronomy 2021, 11(10), 1899; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11101899 - 22 Sep 2021
Cited by 2 | Viewed by 2145
Abstract
Lectins are unique glycoproteins that react with specific sugar residues on cell surfaces resulting in agglutination. They offer enormous applications in therapeutics, diagnostics, medicine, and agriculture. Rice lectins are naturally expressed during biotic and abiotic stresses suggesting their importance in stress resistance physiology. [...] Read more.
Lectins are unique glycoproteins that react with specific sugar residues on cell surfaces resulting in agglutination. They offer enormous applications in therapeutics, diagnostics, medicine, and agriculture. Rice lectins are naturally expressed during biotic and abiotic stresses suggesting their importance in stress resistance physiology. The objective of this study was to determine the presence and relative concentration of lectins in different accessions of rice obtained from IABGR/NARC Islamabad mainly originated from Pakistan. About 210 rice accessions including 02 local varieties and 05 transgenic seeds were screened for seed lectins using a hemagglutination (HA) assay with 5% Californian bred rabbits’ erythrocytes. A protein concentration of 3–8 mg/100 mg of seed flour was measured for all the rice accessions; the highest was 8.03 mg for accession 7600, while the lowest noted was 3.05 mg for accession 7753. Out of 210 accessions, 106 showed the highest HA activity. These 106 genotypes were further screened for titer analysis and specific activity. The highest titer and specific activity were observed for accession 7271 as 1024 and 236 hemagglutination unit (HAU), respectively. The selected accessions’ relative affinity and HA capability were evaluated using blood from four different sources: human, broiler chicken, local rabbit, and Californian-breed rabbit. The highest HA activity was observed with Californian-breed rabbit RBCs. The lectin assay was stable for about 1–2 h. After the required investigations, the accessions with higher lectin concentration and HA capability could be used as a readily available source of lectins for further characterization and utilization in crop improvement programs. Full article
(This article belongs to the Special Issue Analysis of the Genetic Diversity of Crops and Associated Microbiota)
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14 pages, 2798 KiB  
Article
GGE Biplot Analysis of Genotype × Environment Interaction and Yield Stability in Bambara Groundnut
by Oluwaseyi Samuel Olanrewaju, Olaniyi Oyatomi, Olubukola Oluranti Babalola and Michael Abberton
Agronomy 2021, 11(9), 1839; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11091839 - 14 Sep 2021
Cited by 23 | Viewed by 4939
Abstract
In plant breeding and agricultural research, biplot analysis has become an important statistical technique. The goal of this study was to find the winning genotype(s) for the test settings in a part of the Southwest region of Nigeria, as well as to investigate [...] Read more.
In plant breeding and agricultural research, biplot analysis has become an important statistical technique. The goal of this study was to find the winning genotype(s) for the test settings in a part of the Southwest region of Nigeria, as well as to investigate the nature and extent of genotype × environment interaction (GEI) effects on Bambara groundnut (BGN) production. The experiment was carried out in four environments (two separate sites, Ibadan and Ikenne, for two consecutive years, 2018 and 2019) with ninety-five BGN accessions. According to the combined analysis of variance over environments, genotypes and GEI both had a substantial (p < 0.001) impact on BGN yield. The results revealed that BGN accessions performed differently in different test conditions, indicating that the interaction was crossover in nature. The results revealed that BGN accessions performed differently in different test conditions, indicating that the interaction was crossover in nature. To examine and show the pattern of the interaction components, biplots with the genotype main effect and genotype × environment interaction (GEI) were used. The first two PCs explained 80% of the total variation of the GGE model (i.e., G + GE) (PC1 = 48.59%, PC2 = 31.41%). The accessions that performed best in each environment based on the “which-won-where” polygon were TVSu-2031, TVSu-1724, TVSu-1742, TVSu-2022, TVSu-1943, TVSu-1892, TVSu-1557, TVSu-2060, and TVSu-2017. Among these accessions, TVSu-2017, TVSu-1557, TVSu-2060, TVSu-1892, and TVSu-1943 were among the highest-yielding accessions on the field. The adaptable accessions were TVSu-1763, TVSu-1899, TVSu-2019, TVSu-1898, TVSu-1957, TVSu-2021, and TVSu-1850, and the stable accessions were TVSu-1589, TVSu-1905, and TVSu-2048. In terms of discriminating and representativeness for the environments, Ibadan 2019 is deemed to be a superior environment. The selected accessions are recommended as parental lines in breeding programs for grain yield improvement in Ibadan or Ikenne or similar agro-ecological zones. Full article
(This article belongs to the Special Issue Analysis of the Genetic Diversity of Crops and Associated Microbiota)
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17 pages, 2248 KiB  
Article
Phylogenetic Analyses of Rhizobia Isolated from Nodules of Lupinus angustifolius in Northern Tunisia Reveal Devosia sp. as a New Microsymbiont of Lupin Species
by Abdelhakim Msaddak, Luis Rey, Juan Imperial, José Manuel Palacios, Mohamed Mars and José J. Pueyo
Agronomy 2021, 11(8), 1510; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11081510 - 29 Jul 2021
Cited by 9 | Viewed by 2405
Abstract
Thirty-two bacterial isolates were obtained from root nodules of Lupinus angustifolius growing in Northern Tunisia. Phylogenetic analyses based on recA and gyrB partial gene sequences grouped the strains into six clusters: four clusters belonged to the genus Bradyrhizobium (22 isolates), one to Microvirga [...] Read more.
Thirty-two bacterial isolates were obtained from root nodules of Lupinus angustifolius growing in Northern Tunisia. Phylogenetic analyses based on recA and gyrB partial gene sequences grouped the strains into six clusters: four clusters belonged to the genus Bradyrhizobium (22 isolates), one to Microvirga (8 isolates) and one to Devosia (2 isolates), a genus that has not been previously reported to nodulate lupin. Representative strains of each group were further characterized. Multi-Locus Sequence Analysis (MLSA) based on recA and glnII gene sequences separated the strains within the genus Bradyrhizobium into four divergent clusters related to B. canariense, B. liaoningense, B. lupini, and B. algeriense, respectively. The latter might constitute a new Bradyrhizobium species. The strains in the Microvirga cluster showed high identity with M. tunisiensis. The Devosia isolates might also represent a new species within this genus. An additional phylogenetic analysis based on the symbiotic gene nodC affiliated the strains to symbiovars genistearum, mediterranense, and to a possibly new symbiovar. These results altogether contributed to the existing knowledge on the genetic diversity of lupin-nodulating microsymbionts and revealed a likely new, fast-growing, salt-tolerant rhizobial species within the genus Devosia as a potentially useful inoculant in agricultural practices or landscape restoration. Full article
(This article belongs to the Special Issue Analysis of the Genetic Diversity of Crops and Associated Microbiota)
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