Editorial

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4 pages, 188 KiB

Open AccessEditorial

Advances in Crop Molecular Breeding and Genetics

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Agronomy 2023, 13(9), 2311; https://doi.org/10.3390/agronomy13092311 - 01 Sep 2023

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Abstract

Selecting crop varieties with high and stable yields, as well as improving quality and economic benefits, has become a long-term topic while facing the continuous increasing population and the adverse effects of environmental changes [...] Full article

(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics)

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16 pages, 6020 KiB

Open AccessArticle

Agro-Morphological Variability of Wild Vigna Species Collected in Senegal

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Mouhamadou Moussa Diangar

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Joel Romaric Nguepjop

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Diarietou Sambakhe

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Mamadou Sidybe

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Diaga Diouf

Agronomy 2023, 13(11), 2761; https://doi.org/10.3390/agronomy13112761 - 02 Nov 2023

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Abstract

The domesticated Vigna species still need some of the beneficial characters that exist in the wild Vigna species, despite the improvements obtained so far. This study was carried out to enhance our understanding of the Senegalese wild Vigna diversity by exploring the agro-morphological [...] Read more.

The domesticated Vigna species still need some of the beneficial characters that exist in the wild Vigna species, despite the improvements obtained so far. This study was carried out to enhance our understanding of the Senegalese wild Vigna diversity by exploring the agro-morphological characteristics of some accessions using 22 traits. The phenotyping was carried out in a shaded house for two consecutive rainy seasons (2021 and 2022) using the alpha-lattice experimental design with 55 accessions. Multiple correspondence analysis was carried out based on the qualitative traits, which showed considerable variability for the wild species (Vigna unguiculata var. spontanea, Vigna racemosa, Vigna radiata and the unidentified accession). The quantitative traits were subjected to statistical analysis using descriptive statistics and ANOVA. Our results revealed that ninety-five percent (95%) pod maturity ranged from 74.2 to 125.8 days in accession 3 of V. unguiculata and in accession 92 (V. racemosa), respectively. In addition, accession 14 of V. radiata recorded the highest weight for 100 seeds with a value of 4.8 g, while accession 18 of V. unguiculata had the lowest (1.48 g). The ANOVA showed significant differences for the accessions during each season (p ≤ 0.05). Seasonal effects (accession × season) were observed for some quantitative traits, such as the terminal leaflet length and width, time to 50% flowering and 95% pod maturity, pod length and 100-seed weight. Principal component analysis showed that reproductive traits, such as the time to 50% flowering, number of locules per pod, pod length, pod width and 100-seed weight, were the major traits that accounted for the variations among the wild Vigna accessions. The genetic relationship based on qualitative and quantitative traits showed three clusters among the wild Vigna accessions. Indeed, the diversity observed in this study could be used to select parents for breeding to improve the cultivated species of Vigna. Full article

(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics)

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16 pages, 2312 KiB

Open AccessArticle

Mapping of the Waxy Gene in Brassica napus L. via Bulked Segregant Analysis (BSA) and Whole-Genome Resequencing

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Agronomy 2023, 13(10), 2611; https://doi.org/10.3390/agronomy13102611 - 13 Oct 2023

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Abstract

Plant cuticular wax is the covering of the outer layer of the plant. It forms a protective barrier on the epidermis of plants and plays a vital role like a safeguard from abiotic and biotic stresses. In the present study, Brassica napus L. [...] Read more.

Plant cuticular wax is the covering of the outer layer of the plant. It forms a protective barrier on the epidermis of plants and plays a vital role like a safeguard from abiotic and biotic stresses. In the present study, Brassica napus L. materials with and without wax powder were observed. Genetic analysis showed that the separation ratio of waxy plants to waxless plants was 15:1 in the F₂ population, which indicated that the wax powder formation was controlled by two pairs of genes. In order to identify the candidate genes associated with the wax powder trait of B. napus L., bulked segregant analysis (BSA) was performed. The homozygous waxy plants, the homozygous waxless plants, and plants from three parents were selected for establishing five DNA pools for genome-wide resequencing. The results of the resequencing showed that the site associated with wax powder trait was located in the region of 590,663–1,657,546 bp on chromosome A08. And 48 single nucleotide polymorphisms (SNPs) were found between the DNA sequences of waxy plants and waxless plants in this region. These SNPs were distributed across 16 gene loci. qRT-PCR analysis was conducted for the 16 candidate genes and three genes (BnaA08g01070D, BnaA08g02130D, and BnaA08g00890D) showed significantly differential expression between waxy and waxless parents. BnaA08g01070D and BnaA08g02130D were significantly down-regulated in the waxless parent, while BnaA08g00890D was significantly up-regulated in the waxless parent. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the BnaA08g02130D gene was enriched in lipid biosynthetic or metabolic processes. All the results in our study would provide valuable clues for exploring the genes involved in wax powder development. Full article

(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics)

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13 pages, 4831 KiB

Open AccessArticle

Overexpression of the Peanut AhDGAT3 Gene Increases the Oil Content in Soybean

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Agronomy 2023, 13(9), 2333; https://doi.org/10.3390/agronomy13092333 - 07 Sep 2023

Viewed by 632

Abstract

Soybean (Glycine max) is the main oilseed crop that provides vegetable oil for human nutrition. The main objective of its breeding research is to increase the total oil content. In the Kennedy pathway, Diacylglycerol acyltransferase (DGAT) is a rate-limiting enzyme that [...] Read more.

Soybean (Glycine max) is the main oilseed crop that provides vegetable oil for human nutrition. The main objective of its breeding research is to increase the total oil content. In the Kennedy pathway, Diacylglycerol acyltransferase (DGAT) is a rate-limiting enzyme that converts diacylglycerol (DAG) to triacylglycerol (TAG). Here, the AhDGAT3 gene was cloned from peanut and overexpressed in the wild-type (WT) Arabidopsis. The total fatty acid content in T₃AhDGAT3 transgenic Arabidopsis seeds was 1.1 times higher on average than that of the WT. Therefore, AhDGAT3 was transferred into the WT (JACK), and four T₃ transgenic soybean lines were obtained, which proved to be positive using molecular biological detection. Specific T-DNA insertion region location information was also obtained via genome re-sequencing. The results of high-performance gas chromatography showed that the contents of oleic acid (18:1) composition and total fatty acids in transgenic soybean plants were significantly higher than that of the WT. However, linoleic acid (18:2) was much lower compared to the WT. The agronomic trait survey showed that the quantitative and yield traits of AhDGAT3 transgenic soybean were better than those of the WT. These results suggest that fatty acids in transgenic soybeans, especially oleic acid and total fatty acid, are enhanced by the over-expression of AhDGAT3. Full article

(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics)

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13 pages, 2121 KiB

Open AccessArticle

Multi-Omics Revealed the Molecular Mechanism of Maize (Zea mays L.) Seed Germination Regulated by GA3

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Agronomy 2023, 13(7), 1929; https://doi.org/10.3390/agronomy13071929 - 21 Jul 2023

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Abstract

Maize is a valuable raw material for feed and food production. Healthy seed germination is important for improving the yield and quality of maize. However, the molecular mechanisms that regulate maize seed germination remain unclear. In this study, multi-omics was used to reveal [...] Read more.

Maize is a valuable raw material for feed and food production. Healthy seed germination is important for improving the yield and quality of maize. However, the molecular mechanisms that regulate maize seed germination remain unclear. In this study, multi-omics was used to reveal the molecular mechanism of seed germination induced by gibberellin (GA) in maize. The results indicated that 25,603 genes were differentially expressed (DEGs) and annotated in the GO database, of which 2515 genes were annotated in the KEGG database. In addition, 791 mature miRNAs with different expression levels were identified, of which 437 were known in the miRbase database and 354 were novel miRNAs. Integrative analysis of DEGs and miRNAs suggested that carbohydrate, lipid, amino acid, and energy metabolisms are the primary metabolic pathways in maize seed germination. Interestingly, a lipid metabolism-related gene named ZmSLP was found to negatively regulate maize germination. We transformed this gene into Arabidopsis thaliana to verify its function. The results showed that the germination rate of transgenic Arabidopsis seeds was obviously decreased, and the growth of seedlings was weaker and slower than that of WT plants, suggesting that this gene plays an important role in promoting seed germination. These findings provide a valuable reference for further research on the mechanisms of maize seed germination. Full article

(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics)

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18 pages, 4877 KiB

Open AccessArticle

Genome-Wide Analysis of the HD-Zip Gene Family in Chinese Cabbage (Brassica rapa subsp. pekinensis) and the Expression Pattern at High Temperatures and in Carotenoids Regulation

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Agronomy 2023, 13(5), 1324; https://doi.org/10.3390/agronomy13051324 - 09 May 2023

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Abstract

HD-Zip, a special class of transcription factors in high plants, has a role in plant development and responding to external environmental stress. Heat stress has always been an important factor affecting plant growth, quality, and yield. Carotenoid content is also an important factor [...] Read more.

HD-Zip, a special class of transcription factors in high plants, has a role in plant development and responding to external environmental stress. Heat stress has always been an important factor affecting plant growth, quality, and yield. Carotenoid content is also an important factor affecting the color of the inner leaf blades of Chinese cabbage. In this study, the genomes of three Brassicaceae plants were selected: Chinese cabbage (Brassica rapa subsp. pekinensis), Brassica oleracea, and Brassica napus. We identified 93, 96, and 184 HD-Zip genes in the B. rapa, B. oleracea, and B. napus, respectively. The HD-Zip gene family was classified into four subfamilies based on phylogeny: I, II, III, and IV;. The results of cis-acting element analysis suggested that HD-Zip family genes may participate in various biological processes, such as pigment synthesis, cell cycle regulation, defense stress response, etc. Conserved motifs prediction revealed that three motifs exist among the four HD-Zip gene families and that different motifs exhibit significant effects on the structural differences in HD-Zips. Synteny, Ks, and 4DTv results displayed that genome-wide triplication events act in HD-Zip gene family expansion. Transcriptome data showed that 18 genes responded (>1.5-fold change) to heat stress in Chinese cabbage, and 14 of 18 genes were from the HD-Zip I subfamily. Three genes had up-regulation, and eight genes had down-regulation in high-carotenoid-content Chinese cabbage. The BraA09g011460.3C expression level was up-regulated after heat stress treatment and significantly reduced in varieties with high carotenoid content, indicating its potential for heat stress tolerance and carotenoid content regulation. This study provided important gene resources for the subsequent breeding of Chinese cabbage. Full article

(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics)

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18 pages, 6983 KiB

Open AccessArticle

Phylogenetic Analyses and Transcriptional Survey Reveal the Characteristics, Evolution, and Expression Profile of NBS-Type Resistance Genes in Papaya

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Agronomy 2023, 13(4), 970; https://doi.org/10.3390/agronomy13040970 - 25 Mar 2023

Viewed by 1241

Abstract

Carica papaya maintains an abnormally small but complete NLR family while showing weak disease resistance. To better understand their origin, evolution, and biological function, we identified 59 NLR genes via a customized RGAugury and investigated their characteristics, evolutionary history, and expression profiles based [...] Read more.

Carica papaya maintains an abnormally small but complete NLR family while showing weak disease resistance. To better understand their origin, evolution, and biological function, we identified 59 NLR genes via a customized RGAugury and investigated their characteristics, evolutionary history, and expression profiles based on the improved papaya genome and large-scale RNA-seq data. The results indicated that duplication is a major evolutionary force driving the formation of the papaya NLR family. Synteny analyses of papaya and other angiosperms showed that both insertion and inheritance-derived NLRs are present in papaya. Transcriptome-based expression and network analyses revealed that NLRs are actively involved in biotic stress responses. For example, a papaya-specific inserted TNL was up-regulated strongly by the fungal infection. Both transcriptome and qRT-PCR analyses confirmed the expression divergence of an RNL and an RCNL, a pair of tandem duplication genes involved in different co-expression modules. Furthermore, we observed an inserted gene cluster composed of five duplicated CNLs, showing dosage effects and functional differentiation of disease-resistance genes during evolution. This research will enhance our knowledge of the special NLR family in papaya, which may serve as a model plant for disease-resistance genetic studies. Full article

(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics)

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16 pages, 1607 KiB

Open AccessArticle

Identifying QTLs Related to Grain Filling Using a Doubled Haploid Rice (Oryza sativa L.) Population

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Agronomy 2023, 13(3), 912; https://doi.org/10.3390/agronomy13030912 - 19 Mar 2023

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Grain filling is an important trait of rice that affects the yield of grain-oriented crop species with sink capacity-related traits. Here, we used a doubled haploid (DH) population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica) to [...] Read more.

Grain filling is an important trait of rice that affects the yield of grain-oriented crop species with sink capacity-related traits. Here, we used a doubled haploid (DH) population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica) to investigate quantitative traits loci (QTLs) controlling grain filling in rice employing the Kompetitive allele-specific PCR (KASP) markers. The mapping population was grown under early-, normal-, and late-cultivation periods. The phenotypic evaluation revealed that spikelet number per panicle positively correlated with the grain-filling ratio under early cultivation conditions. Notably, three significant QTLs associated with the control of grain filling, qFG3, qFG5-1, and qFG5-2, were identified. Genes harbored by these QTLs are linked with diverse biological processes and molecular functions. Likewise, genes associated with abiotic stress response and transcription factor activity and redox homeostasis were detected. Genes such as MYB, WRKY60, and OsSh1 encoding transcription factor, β-catenin, and the tubulin FtsZ, as well as those encoding cytochrome P450, would play a forefront role in controlling grain filling under early cultivation conditions. Our results suggest that qFG3-related genes could mediate the transition between grain filling and abiotic stress response mechanisms. Fine-mapping these QTLs would help identify putative candidate genes for downstream functional characterization. Full article

(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics)

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26 pages, 1336 KiB

Open AccessReview

Genetic Improvements in Rice Grain Quality: A Review of Elite Genes and Their Applications in Molecular Breeding

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Agronomy 2023, 13(5), 1375; https://doi.org/10.3390/agronomy13051375 - 15 May 2023

Cited by 4 | Viewed by 1720

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High yield and superior quality are the main objectives of rice breeding and research. While innovations in rice breeding have increased production to meet growing demand, the universal issue of balancing high yield and susperior quality has led to a lack of focus [...] Read more.

High yield and superior quality are the main objectives of rice breeding and research. While innovations in rice breeding have increased production to meet growing demand, the universal issue of balancing high yield and susperior quality has led to a lack of focus on improving rice quality. With rising living standards, improving rice quality has become increasingly important. Rice grain quality is a complex trait influenced by both genetic and environmental factors, with four primary aspects: milling quality, appearance quality, eating and cooking quality, and nutritional quality. While different populations have varying demands for rice quality, the core traits that contribute to rice quality include grain shape and chalkiness in terms of appearance, as well as endosperm composition that influences cooking and sensory evaluation. Researchers have made substantial advancements in discovering genes/QTLs associated with critical traits including appearance, aroma, texture, and nutritional properties. Markers derived from these genetic discoveries have provided an efficient tool for marker-assisted selection to improve rice quality. Thus, this review focuses on elite genes and their applications in breeding practices to quickly develop superior quality rice varieties that meet various market demands. Full article

(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics)

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