Agronomy

Editorial

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5 pages, 181 KiB

Open AccessEditorial

Genetic Analysis in Crops

by Fang Bai and Kevin Begcy

Agronomy 2024, 14(6), 1293; https://doi.org/10.3390/agronomy14061293 - 14 Jun 2024

Viewed by 948

Abstract

Crops contribute to global food production, energy, and medicine [...] Full article

(This article belongs to the Special Issue Genetic Analysis in Crops)

Research

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21 pages, 3482 KiB

Open AccessArticle

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 - 3 Jan 2024

Cited by 3 | Viewed by 1951

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

Open AccessArticle

The Purple leaf (Pl) Alleles, Pl^w 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

Cited by 1 | Viewed by 1757

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 (Pl^w) 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 (Pl^w) 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 Pl^w and Plⁱ cross. However, C3G was exclusively identified in the seeds of offspring carrying the dominant Pb gene. Therefore, the Pl^w 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

Open AccessArticle

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 3 | Viewed by 1109

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

Open AccessArticle

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 6 | Viewed by 2093

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

Open AccessCommunication

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 4 | Viewed by 2172

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

Open AccessArticle

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 5 | Viewed by 1809

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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Review

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24 pages, 1780 KiB

Open AccessReview

Genetic and Molecular Regulation of Cotton Fiber Initiation and Elongation

by Fang Bai and Jodi Scheffler

Agronomy 2024, 14(6), 1208; https://doi.org/10.3390/agronomy14061208 - 3 Jun 2024

Cited by 1 | Viewed by 1161

Abstract

Cotton fiber, a crucial and sustainable resource for global textile production, undergoes a complex five-stage developmental process, encompassing initiation, elongation, transition, secondary cell wall biosynthesis, and maturation. These elongated single-cell fibers originate from the outer ovule epidermis. The development of cotton fibers involves [...] Read more.

Cotton fiber, a crucial and sustainable resource for global textile production, undergoes a complex five-stage developmental process, encompassing initiation, elongation, transition, secondary cell wall biosynthesis, and maturation. These elongated single-cell fibers originate from the outer ovule epidermis. The development of cotton fibers involves intricate changes in gene expression and physiological processes, resulting in a nearly pure cellulose product that is vital for the global cotton industry. Decoding the genes associated with fiber development enhances our understanding of cotton fiber mechanisms and facilitates the cultivation of varieties with enhanced quality. In recent decades, advanced omics approaches, including genomics, transcriptomics, and proteomics, have played a pivotal role in identifying the genes and gene products linked to cotton fiber development, including the MYB transcription factor family, which coordinates cotton fiber development. Molecular studies have revealed the transcription factors, like MYB, WRKY, Homeodomain Leucine Zipper (HD-ZIP), and basic helix–loop–helix (bHLH), influencing fiber initiation and elongation. The intricate interplay of phytohormones, like auxin, gibberellic acid (GA), brassinosteroids (BRs), jasmonic acid (JA), ethylene, abscisic acid (ABA), and cytokinin, is explored, providing a comprehensive perspective on the shaping of cotton fibers. Numerous candidate genes and cellular processes affecting various aspects of fiber development hold promise for genetic engineering or marker-assisted breeding to improve fiber quality. This review presents a comprehensive overview of key achievements in cotton molecular biology, with a specific emphasis on recent advancements in understanding the transcription factors and phytohormones involved in cotton fiber initiation and elongation. Full article

(This article belongs to the Special Issue Genetic Analysis in Crops)

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