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Agronomy
Special Issues
Genetic Analysis in Crops
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Genetic Analysis in Crops

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

Deadline for manuscript submissions: closed (15 November 2023) | Viewed by 7910

Special Issue Editors

Dr. Fang Bai

E-Mail Website
Guest Editor
College of Agricultural and Life Sciences, University of Florida, P.O. Box 110690, Gainesville, FL 32611, USA
Interests: genetic and epigenetic regulation of seed development in maize; alternative splicing adaptations to the climate changes in cereals; the mechanism of cell division and proliferation in cereal endosperm
Dr. Kevin Begcy

E-Mail Website
Guest Editor
Environmental Horticulture Department, University of Florida, Gainesville, FL 32611, USA
Interests: plant reproduction; stress biology; epigenetics; bioinformatics; cereals
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Crops contribute to the global food, energy and environmental changes. Crop genetics studies gene function and regulation, genetic variation and modification, genetic heredity, and gene interaction and their network. Understanding crop genetics has major economic and environmental impacts in the world by providing new insights into improving crop nutrients, resistance to the disease, and resilience to environmental stresses. The traditional genetic analysis includes morphological characterization, mutant screening, gene identification, molecular testing, and biochemistry study, etc. With the aid of the next generation of sequencing and gene editing technique, crop genetics shows great potential in promoting agricultural breeding by improving the crop quality and quantity.

This Special Issue calls for contributions on Genetic Analysis in Crops. We welcome original research, reviews, mini-reviews, and methods related to, but not limited to, the following areas: gene identification and analysis during crop development; gene regulation and molecular mechanism in response to abiotic stress or biotic stress; genetics, genomics and evolutionary study of crop genes; novel approaches to investigate crop genes.

Dr. Fang Bai
Dr. Kevin Begcy
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 genes
  • genetics and genomics
  • crop gene identification and analysis
  • crop development
  • crop adapt to the climate changes
  • crop evolutionary study
  • crops in response to abiotic stress and biotic stress
  • gene editing, AI techniques and other novel methods in crop research

Published Papers (6 papers)

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Research

21 pages, 3482 KiB  
Article
Multi-Trait Selection Index for Simultaneous Selection of Water Yam (Dioscorea alata L.) Genotypes
by Fatoumata Ouattara, Paterne A. Agre, Idris I. Adejumobi, Malachy O. Akoroda, Fatogoma Sorho, Koutoua Ayolié and Ranjana Bhattacharjee
Agronomy 2024, 14(1), 128; https://doi.org/10.3390/agronomy14010128 - 03 Jan 2024
Viewed by 959
Abstract
Water yam (Dioscorea alata L.) is the most widely cultivated yam species with good agronomic attributes. However, several biotic and abiotic constraints and its lower food quality such as poor pound ability limit its production and use. Therefore, the identification of superior [...] Read more.
Water yam (Dioscorea alata L.) is the most widely cultivated yam species with good agronomic attributes. However, several biotic and abiotic constraints and its lower food quality such as poor pound ability limit its production and use. Therefore, the identification of superior genotypes with suitable characteristics is needed for water yam improvement. This study aims to assess a panel of half-sib (progenies with one parent in common) and full-sib (progenies with the same male and female parents) progenies as well as their parents for selection of desirable ideotypes based on their agronomic and quality characteristics. A total of 280 progenies from bi-parental populations as well as five parents were evaluated, and a significant variation was observed (p < 0.01) in their performances for the eight traits used in the study. A moderate to high broad-sense heritability (30% < H2–H2 ≥ 60%) was observed for all traits except for tuber pound ability (H2 < 30%). Positive correlations were displayed between the traits, while the hierarchical clustering grouped genotypes into three clusters indicating the potential for selection of diverse genotypes for multiple traits from the four families under study. Plant vigor and number of tubers per plant contributed (p < 0.01) positively to the yield per plant in the path coefficient analysis. Using the multi-trait genotype–ideotype distance index (MGIDI), a total of 39 most promising genotypes were identified. These promising genotypes could be further used as progenitors in D. alata improvement programs targeting good agronomic and quality traits targeted for farmers and end users. Full article
(This article belongs to the Special Issue Genetic Analysis in Crops)
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15 pages, 2517 KiB  
Article
The Purple leaf (Pl) Alleles, Plw and Pli, Regulate Leaf Color Development Independently from the Pb Gene of Purple pericarp (Prp) in Rice
by Sang Gu Kang, Kyung Eun Lee, Jegeun Cho, Jeong Wook Lee, Geum Sook Do and Mohammad Nurul Matin
Agronomy 2023, 13(11), 2845; https://doi.org/10.3390/agronomy13112845 - 19 Nov 2023
Viewed by 931
Abstract
Color development in various rice organs results from the complementary expression of genes involved in anthocyanin biosynthesis. The Purple pericarp (Prp) trait and the Purple leaf (Pl) trait both display epistasis, relying on the complement of the Pb and [...] Read more.
Color development in various rice organs results from the complementary expression of genes involved in anthocyanin biosynthesis. The Purple pericarp (Prp) trait and the Purple leaf (Pl) trait both display epistasis, relying on the complement of the Pb and Pp genes for pericarp coloration and the Pl and Pp genes for leaf coloration, respectively. However, there is still genetic uncertainty in identifying the genes responsible for the various color expressions and intensities of rice grain pericarp and leaves. In this study, we characterized the inheritance patterns of color development and the mode of anthocyanin pigments in rice by crossing two parental mutant lines. YUM051, exhibiting dark purple leaves (Plw) and purple pericarp (Prp), was crossed with YUM144, which displayed light purple leaves (Pli) and a white pericarp (prp). The F1 plants exhibited dark purple leaves with purple pericarps, indicating the dominant nature of the purple leaf (Pl) and purple pericarp (Prp) traits. The rice Prp traits display a complementary interaction, reflected in a 9:7 ratio of purple to white pericarp. However, the Prp trait followed Mendelian segregation with a 3:1 ratio of purple to white pericarp in this cross, indicating homozygous dominant Pp alleles in both parental plants. Meanwhile, the segregation of the purple leaf color in the F2 generation of this cross followed complementary inheritance, exhibiting a 9:7 segregation ratio between purple leaves and greenish leaves with purple leaf margins. Moreover, the co-segregation of Prp and Pl traits in the cross between YUM051 (Plw) and YUM144 (Pli) plants did not adhere to the Mendelian 9:3:3:1 independent assortment ratio, confirming that the Pl gene and Pb gene are linked on the same chromosome. Cyanidin-3-O-glucoside (C3G) was detected in the leaves of all progeny resulting from the Plw and Pli cross. However, C3G was exclusively identified in the seeds of offspring carrying the dominant Pb gene. Therefore, the Plw and Pli alleles are Pl genes responsible for purple leaf color, while the Pb gene is responsible for purple pericarp color in rice; these genes function independently of each other. Full article
(This article belongs to the Special Issue Genetic Analysis in Crops)
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12 pages, 1720 KiB  
Article
Determination of Genetic Diversity of Some Upland and Sea Island Cotton Genotypes Using High-Resolution Capillary Electrophoresis Gel
by Adnan Aydin
Agronomy 2023, 13(9), 2407; https://doi.org/10.3390/agronomy13092407 - 18 Sep 2023
Cited by 1 | Viewed by 769
Abstract
Cotton is a major source of natural fibre for the global textile industry and is also an important oilseed crop. Cotton fibre is the main source of textiles, the seeds are used for oil and the remaining bagasse is used as high-protein animal [...] Read more.
Cotton is a major source of natural fibre for the global textile industry and is also an important oilseed crop. Cotton fibre is the main source of textiles, the seeds are used for oil and the remaining bagasse is used as high-protein animal feed. In addition, cotton’s so-called short fibre is used in more than 50 industries. Cotton breeding is generally based on crossing the best yielding and fibre quality genotypes. However, cotton breeding programmes are negatively affected by the narrow genetic diversity of varieties. It is for this reason that the identification of genetic resources and the disclosure of genetic diversity are so important. Here, the genetic diversity of G. hirsutum and G. barbadense genotypes was determined using high-resolution capillary gel electrophoresis. Using 19 EST-SSR markers, a total of 47 genotypes were screened. The PIC values of the markers used ranged from 0.268 to 0.889. The mean PIC value was calculated to be 0.603. In terms of clustering, PCoA and population structure analyses gave similar results, and the genotypes could be divided into three main groups. Genetic admixture with G. hirsutum was found in some genotypes of the G. barbadense species. We can conclude that (i) the EST-SSR markers used in this study are effective in the determination of genetic diversity, (ii) the genetic diversity should be increased through the collection of genetic resources and (iii) the genetic EST-SSR markers in this study should be considered in breeding programmes by using them in QTL studies. Full article
(This article belongs to the Special Issue Genetic Analysis in Crops)
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13 pages, 4183 KiB  
Article
Identification and Analysis of the Catalase Gene Family Response to Abiotic Stress in Nicotiana tabacum L.
by Zhonghui Liu, Di Wang, Heng Tang, Haozhen Li, Xiaohua Zhang, Shaolin Dong, Li Zhang and Long Yang
Agronomy 2023, 13(3), 936; https://doi.org/10.3390/agronomy13030936 - 22 Mar 2023
Cited by 3 | Viewed by 1520
Abstract
Catalase (CAT) is an enzyme encoded by the catalase gene family that plays an important role in the removal of reactive oxygen species. In this study, seven CAT genes were identified in Nicotiana tabacum L. and were classified into three groups. Gene structure [...] Read more.
Catalase (CAT) is an enzyme encoded by the catalase gene family that plays an important role in the removal of reactive oxygen species. In this study, seven CAT genes were identified in Nicotiana tabacum L. and were classified into three groups. Gene structure analysis revealed that NtCAT1–6 has six or seven introns while NtCAT7 only contains one. The relative position of introns in NtCAT1 and NtCAT2 had high similarity. Tissue-specific analysis shows that NtCAT1–4 were expressed intensively in the shoot while NtCAT5 and NtCAT6 were in the root. NtCAT7 expression was influenced by circadian rhythms. NtCATs expression had the greatest change under drought stress. Additionally, expression of NtCAT5, NtCAT6 and NtCAT7 were upregulated under cold stress but downregulated under drought and salt stress. This study will help in understanding the behavior of CAT genes during environmental stress in tobacco. Full article
(This article belongs to the Special Issue Genetic Analysis in Crops)
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17 pages, 2525 KiB  
Communication
Long-Read cDNA Sequencing Revealed Novel Expressed Genes and Dynamic Transcriptome Landscape of Triticale (x Triticosecale Wittmack) Seed at Different Developing Stages
by Ekaterina Polkhovskaya, Anna Bolotina, Pavel Merkulov, Maxim Dudnikov, Alexander Soloviev and Ilya Kirov
Agronomy 2023, 13(2), 292; https://doi.org/10.3390/agronomy13020292 - 18 Jan 2023
Cited by 1 | Viewed by 1666
Abstract
Developing seed is a unique stage of plant development with highly dynamic changes in transcriptome. Here, we aimed to detect the novel previously unannotated, genes of the triticale (x Triticosecale Wittmack, AABBRR genome constitution) genome that are expressed during different stages and at [...] Read more.
Developing seed is a unique stage of plant development with highly dynamic changes in transcriptome. Here, we aimed to detect the novel previously unannotated, genes of the triticale (x Triticosecale Wittmack, AABBRR genome constitution) genome that are expressed during different stages and at different parts of the developing seed. For this, we carried out the Oxford Nanopore sequencing of cDNA obtained for middle (15 days post-anthesis, dpa) and late (20 dpa) stages of seed development. The obtained data together with our previous direct RNA sequencing of early stage (10 dpa) of seed development revealed 39,914 expressed genes including 7128 (17.6%) genes that were not previously annotated in A, B, and R genomes. The bioinformatic analysis showed that the identified genes belonged to long non-coding RNAs (lncRNAs), protein-coding RNAs, and TE-derived RNAs. The gene set analysis revealed the transcriptome dynamics during seed development with distinct patterns of over-represented gene functions in early and middle/late stages. We performed analysis of the lncRNA genes polymorphism and showed that the genes of some of the tested lncRNAs are indeed polymorphic in the triticale collection. Altogether, our results provide information on thousands of novel loci expressed during seed development that can be used as new targets for GWAS analysis, the marker-assisted breeding of triticale, and functional elucidation. Full article
(This article belongs to the Special Issue Genetic Analysis in Crops)
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12 pages, 1921 KiB  
Article
Morphological and Genetic Analysis of Wild Hop (Humulus lupulus L.) Germplasm from Calabria Region in South Italy
by Antonio Calvi, Meriem Miyassa Aci, Antonio Lupini and Giovanni Preiti
Agronomy 2023, 13(1), 252; https://doi.org/10.3390/agronomy13010252 - 14 Jan 2023
Cited by 1 | Viewed by 1401
Abstract
Hops (Humulus lupulus L.) constitute a species that grows spontaneously in the region of Calabria (South Italy), but the species’ morphological and genetic characterization have not yet been explored. Thus, we explored some morphological traits related to cones of wild hops from [...] Read more.
Hops (Humulus lupulus L.) constitute a species that grows spontaneously in the region of Calabria (South Italy), but the species’ morphological and genetic characterization have not yet been explored. Thus, we explored some morphological traits related to cones of wild hops from three Calabrian sites: Cosenza (CS), Catanzaro (CZ), and Vibo Valentia (VV). In addition, eight Simple Sequence Repeats (SSR) were adopted to investigate the genetic diversity and population structure of the local germplasm, which were also compared to commercial varieties. Cone length exhibited large variation among the different populations, whereas cone shape was the most discriminant trait according to principal coordinate analysis. Eighty-one alleles were detected with a high mean of alleles per locus (10.12). The SSRs used in the present study were highly informative with a genetic diversity of 0.829 and a PIC value > 0.62, thereby confirming the high genetic variability in Calabria. Finally, genetic structure analysis revealed the existence of two distinct groups regardless of the specimens’ sampling sites. Further studies including other wild hops populations from Calabria will be performed in order to detect specific alleles for new breeding programs. Full article
(This article belongs to the Special Issue Genetic Analysis in Crops)
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