Agronomy

Editorial

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6 pages, 204 KiB

Open AccessEditorial

New Insights into Crop Molecular Breeding and Genetics

by Yaqi Su, Zhen Cheng, Jiezheng Ying, Chaolei Liu and Zhiyong Li

Agronomy 2024, 14(12), 2999; https://doi.org/10.3390/agronomy14122999 - 17 Dec 2024

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Abstract

As the global population continues to grow, the need to increase agricultural productivity is becoming increasingly urgent [...] Full article

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

4 pages, 188 KiB

Open AccessEditorial

Advances in Crop Molecular Breeding and Genetics

by Wanning Liu, Guan Li, Jiezheng Ying and Zhiyong Li

Agronomy 2023, 13(9), 2311; https://doi.org/10.3390/agronomy13092311 - 1 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)

Research

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9 pages, 923 KiB

Open AccessArticle

Quantitative Trait Locus Analysis for Panicle and Flag Leaf Traits in Barley (Hordeum vulgare L.) Based on a High-Density Genetic Linkage Map

by Yichen Ye, Shuting Wen, Guo Zhang, Xingzhe Yang, Dawei Xue, Yunxia Fang and Xiaoqin Zhang

Agronomy 2024, 14(12), 2953; https://doi.org/10.3390/agronomy14122953 - 11 Dec 2024

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Abstract

The yield of barley (Hordeum vulgare L.) is determined by many factors, which have always been research hotspots for agronomists and molecular scientists. In this study, five important agronomic traits related to panicle and flag leaf, including awn length (AL), panicle length [...] Read more.

The yield of barley (Hordeum vulgare L.) is determined by many factors, which have always been research hotspots for agronomists and molecular scientists. In this study, five important agronomic traits related to panicle and flag leaf, including awn length (AL), panicle length (PL), panicle neck length (NL), flag leaf length (LL) and flag leaf width (LW), were investigated and quantitative trait locus (QTL) analyses were carried out. Using a high-density genetic map of 134 recombinant inbred lines based on specific-locus amplified fragment sequencing (SLAF-seq) technology, a total of 32 QTLs were identified, which explained 12.4% to 50% of the phenotypic variation. Among them, qAL5, qNL2, qNL3, qNL6, qPL2, and qLW2 were detected in 3 consecutive years and all of the contribution rates were more than 13.8%, revealing that these QTLs were stable major QTLs and were less affected by environmental factors. Furthermore, LL and LW exhibited significant positive correlations and the localization intervals of qLL2 and qLL3 were highly overlapped with those of qLW2 and qLW3, respectively, indicating that qLL2 and qLW2, qLL3 and qLW3 may be regulated by the same genes. Full article

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

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22 pages, 3465 KiB

Open AccessArticle

Expression Analysis of the Extensive Regulation of Mitogen-Activated Protein Kinase (MAPK) Family Genes in Buckwheat (Fagopyrum tataricum) During Organ Differentiation and Stress Response

by Guoqing Dong, Zihao Gui, Yi Yuan, Yun Li and Dengxiang Du

Agronomy 2024, 14(11), 2613; https://doi.org/10.3390/agronomy14112613 - 6 Nov 2024

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Abstract

The mitogen-activated protein kinase (MAPK) signaling cascade is a unique and relatively conserved signaling pathway in eukaryotes, transmitting extracellular signals into cells through successive phosphorylation and eliciting appropriate responses from the organism. While its mechanism in plant immune response has been partially elucidated [...] Read more.

The mitogen-activated protein kinase (MAPK) signaling cascade is a unique and relatively conserved signaling pathway in eukaryotes, transmitting extracellular signals into cells through successive phosphorylation and eliciting appropriate responses from the organism. While its mechanism in plant immune response has been partially elucidated in Arabidopsis, it has been rarely examined in Tartary buckwheat (Fagopyrum tataricum). Based on the conserved MAPK domain, we identified 16 MAPK family genes in Tartary buckwheat. The FtMAPKs have similar structures and motif compositions, indicating that this gene family is conserved yet functionally diverse. Using quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis, we observed significant expression variation in 15 genes across different organs, except for FtMAPK12. FtMAPK9 showed specific expression in vegetative organs, FtMAPK4 in reproductive organs, and FtMAPK1 and FtMAPK10 in leaves and flowers, respectively, indicating their regulatory roles in Tartary buckwheat development. Following drought and salt stress treatments, 12 and 14 FtMAPKs, respectively, showed significantly altered expression in leaves exhibiting notable biological oxidation. Among these, FtMAPK3, FtMAPK4, and FtMAPK8 demonstrated highly significant changes across both treatments. Transcriptome analysis confirmed these findings, suggesting that these three genes play pivotal roles in Tartary buckwheat’s response to abiotic stress and hold potential for molecular breeding improvements. Full article

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

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13 pages, 3936 KiB

Open AccessArticle

Natural Variability of Genomic Sequences of Mal d 1 Allergen in Apples as Revealed by Restriction Profiles and Homolog Polymorphism

by Lucia Urbanová, Jana Bilčíková, Dagmar Moravčíková and Jana Žiarovská

Agronomy 2024, 14(9), 2056; https://doi.org/10.3390/agronomy14092056 - 9 Sep 2024

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Abstract

Apples are a popular fruit worldwide, with many health and nutritional benefits. However, this fruit is also among those that, particularly in Central and Northern Europe, are allergenic due to the Mal d 1 allergen. Mal d 1 is a homologous allergen to [...] Read more.

Apples are a popular fruit worldwide, with many health and nutritional benefits. However, this fruit is also among those that, particularly in Central and Northern Europe, are allergenic due to the Mal d 1 allergen. Mal d 1 is a homologous allergen to Bet v 1—the main pollen allergen of birch. In this study, two different approaches were used to identify the natural length polymorphism of Bet v 1 homologs in apple varieties, with the aim of characterizing their effectiveness. BBAP (Bet v 1 based amplified polymorphism) and RFLP (restriction fragments length polymorphism) profiles were characterized and compared. RFLP analysis recognizes the genetic diversity of M. domestica Mal d 1 sequences at a relatively low level. In BBAP profiles, the genetic dissimilarity was up to 50%, which appears suitable for intraspecific fingerprinting and serves as an additional method for RFLP analysis. RFLP analysis was able to distinguish some varieties that BBAP could not, such as Sonet. Full article

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

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14 pages, 3386 KiB

Open AccessArticle

Genetic Basis and Exploration of Major Expressed QTL qLA2-3 Underlying Leaf Angle in Maize

by Yonghui He, Chenxi Wang, Xueyou Hu, Youle Han, Feng Lu, Huanhuan Liu, Xuecai Zhang and Zhitong Yin

Agronomy 2024, 14(9), 1978; https://doi.org/10.3390/agronomy14091978 - 1 Sep 2024

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Abstract

Leaf angle (LA) is closely related to plant architecture, photosynthesis and density tolerance in maize. In the current study, we used a recombinant inbred line population constructed by two maize-inbred lines to detect quantitative trait loci (QTLs) controlling LA. Based on the average [...] Read more.

Leaf angle (LA) is closely related to plant architecture, photosynthesis and density tolerance in maize. In the current study, we used a recombinant inbred line population constructed by two maize-inbred lines to detect quantitative trait loci (QTLs) controlling LA. Based on the average LA in three environments, 13 QTLs were detected, with the logarithm of odds ranging from 2.7 to 7.21, and the phenotypic variation explained by a single QTL ranged from 3.93% to 12.64%. A stable QTL, qLA2-3, on chromosome 2 was detected and was considered to be the major QTL controlling the LA. On the basis of verifying the genetic effect of qLA2-3, a fine map was used to narrow the candidate interval, and finally, the target segment was located at a physical distance of approximately 338.46 kb (B73 RefGen_v4 version), containing 16 genes. Re-sequencing and transcriptome results revealed that five candidate genes may be involved in the regulation of LA. The results enrich the information for molecular marker-assisted selection of maize LA and provide genetic resources for the breeding of dense planting varieties. Full article

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

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15 pages, 641 KiB

Open AccessArticle

Yield Performance of RD6 Glutinous Rice near Isogenic Lines Evaluated under Field Disease Infection at Northeastern Thailand

by Jirapong Yangklang, Jirawat Sanitchon, Jonaliza L. Siangliw, Tidarat Monkham, Sompong Chankaew, Meechai Siangliw, Kanyanath Sirithunya and Theerayut Toojinda

Agronomy 2024, 14(8), 1871; https://doi.org/10.3390/agronomy14081871 - 22 Aug 2024

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Abstract

RD6, the most popular glutinous rice in Thailand, is high in quality but susceptible to blast and bacterial blight disease. It was thus improved for disease resistance through marker-assisted backcross selection (MAS). The objective of this study was to evaluate the performance of [...] Read more.

RD6, the most popular glutinous rice in Thailand, is high in quality but susceptible to blast and bacterial blight disease. It was thus improved for disease resistance through marker-assisted backcross selection (MAS). The objective of this study was to evaluate the performance of improved near isogenic lines. Eight RD6 rice near isogenic lines (NILs) derived from MAS were selected for evaluation with RD6, a standard susceptible check variety, as well as recurrent parent for a total of nine genotypes. The experiment was conducted during the wet season under six environments at three locations, Khon Kaen, Nong Khai, and Roi Et, which was repeated at two years from 2019 to 2020. Nine genotypes, including eight RD6 rice near isogenic lines (NILs) selected from two in-tandem breeding programs and the standard check variety RD6, were evaluated to select the high-performance new improved lines. The first group, including four NILs G1–G4, was gene pyramiding of blast and BB resistance genes, and the second group, including another four NILs G5–G8, was gene pyramiding of blast resistance and salt tolerance genes. Field disease screening was observed for all environments. Two disease occurrences, blast (leaf blast) and bacterial blight, were found during the rainy season of all environments. The NILs containing blast resistance genes were excellent in gene expression. On the other hand, the improved lines containing the xa5 gene were not highly resistant under the severe stress of bacterial blight (Nong Khai 2020). Notwithstanding, G2 was greater among the NILs for yield maintenance than the other genotypes. The agronomic traits of most NILs were the same as RD6. Interestingly, the traits of G2 were different in plant type from RD6, specifically photosensitivity and plant height. Promising rice RD6 NILs with high yield stability, good agronomic traits, and disease resistance were identified in the genotypes G1, G2, and G7. The high yield stability G1 and G7 are recommended for widespread use in rain-fed areas. The G2 is specifically recommended for use in the bacterial blight (BB) disease prone areas. Full article

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

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14 pages, 1797 KiB

Open AccessArticle

Transcriptome-Wide Genetic Variations in the Legume Genus Leucaena for Fingerprinting and Breeding

by Yong Han, Alexander Abair, Julian van der Zanden, Madhugiri Nageswara-Rao, Saipriyaa Purushotham Vasan, Roopali Bhoite, Marieclaire Castello, Donovan Bailey, Clinton Revell, Chengdao Li and Daniel Real

Agronomy 2024, 14(7), 1519; https://doi.org/10.3390/agronomy14071519 - 12 Jul 2024

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Abstract

Leucaena is a versatile legume shrub/tree used as tropical livestock forage and in timber industries, but it is considered a high environmental weed risk due to its prolific seed production and broad environmental adaptation. Interspecific crossings between Leucaena species have been used to [...] Read more.

Leucaena is a versatile legume shrub/tree used as tropical livestock forage and in timber industries, but it is considered a high environmental weed risk due to its prolific seed production and broad environmental adaptation. Interspecific crossings between Leucaena species have been used to create non-flowering or sterile triploids that can display reduced weediness and other desirable traits for broad use in forest and agricultural settings. However, assessing the success of the hybridisation process before evaluating the sterility of putative hybrids in the target environment is advisable. Here, RNA sequencing was used to develop breeding markers for hybrid parental identification in Leucaena. RNA-seq was carried out on 20 diploid and one tetraploid Leucaena taxa, and transcriptome-wide unique genetic variants were identified relative to a L. trichandra draft genome. Over 16 million single-nucleotide polymorphisms (SNPs) and 0.8 million insertions and deletions (indels) were mapped. These sequence variations can differentiate all species of Leucaena from one another, and a core set of about 75,000 variants can be genetically mapped and transformed into genotyping arrays/chips for the conduction of population genetics, diversity assessment, and genome-wide association studies in Leucaena. For genetic fingerprinting, more than 1500 variants with even allele frequencies (0.4–0.6) among all species were filtered out for marker development and testing in planta. Notably, SNPs were preferable for future testing as they were more accurate and displayed higher transferability within the genus than indels. Hybridity testing of ca. 3300 putative progenies using SNP markers was also more reliable and highly consistent with the field observations. The developed markers pave the way for rapid, accurate, and cost-effective diversity assessments, variety identification and breeding selection in Leucaena. Full article

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

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13 pages, 4343 KiB

Open AccessArticle

Authenticity Identification of F₁ Hybrid Offspring and Analysis of Genetic Diversity in Pineapple

by Panpan Jia, Shenghui Liu, Wenqiu Lin, Honglin Yu, Xiumei Zhang, Xiou Xiao, Weisheng Sun, Xinhua Lu and Qingsong Wu

Agronomy 2024, 14(7), 1490; https://doi.org/10.3390/agronomy14071490 - 9 Jul 2024

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Abstract

Breeding is an effective method for the varietal development of pineapple. However, due to open pollination, it is necessary to conduct authentic identification of the hybrid offspring. In this study, we identified the authenticity of offspring and analyzed the genetic diversity within the [...] Read more.

Breeding is an effective method for the varietal development of pineapple. However, due to open pollination, it is necessary to conduct authentic identification of the hybrid offspring. In this study, we identified the authenticity of offspring and analyzed the genetic diversity within the offspring F₁ hybrids resulting from crosses between ‘Josapine’ and ‘MD2’ by single nucleotide polymorphism (SNP) markers. From the resequencing data, 26 homozygous loci that differentiate between the parents have been identified. Then, genotyping was performed on both the parents and 36 offspring to select SNP markers that are suitable for authentic identification. The genotyping results revealed that 2 sets of SNP primers, namely SNP4010 and SNP22550, successfully identified 395 authentic hybrids out of 451 hybrid offspring. We randomly selected two true hybrids and four pseudohybrids for sequencing validation, and the results have shown that two true hybrids had double peaks with A/G, while pseudohybrids had single peaks with base A or G. Further study showed that the identification based on SNP molecular markers remained consistent with the morphological identification results in the field, with a true hybridization rate of 87.58%. K-means clustering and UPGMA tree analysis revealed that the hybrid offspring could be categorized into two groups. Among them, 68.5% of offspring aggregated with MD2, while 31.95% were grouped with Josapine. The successful application of SNP marker to identify pineapple F₁ hybrid populations provides a theoretical foundation and practical reference for the future development of rapid SNP marker-based methods for pineapple hybrid authenticity and purity testing. Full article

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

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14 pages, 253 KiB

Open AccessArticle

Combining Ability, Heritability, and Heterosis for Seed Weight and Oil Content Traits of Castor Bean (Ricinus communis L.)

by Mu Peng, Zhiyan Wang, Zhibiao He, Guorui Li, Jianjun Di, Rui Luo, Cheng Wang and Fenglan Huang

Agronomy 2024, 14(6), 1115; https://doi.org/10.3390/agronomy14061115 - 23 May 2024

Cited by 1 | Viewed by 1499

Abstract

Hybridization is an important evolutionary force, and heterosis describes the phenomenon where hybrids exhibit superior traits compared to their parents. This study aimed to evaluate the one-hundred-seed weight and fatty acid content in F₁ generations, investigating the effects of different parental crosses [...] Read more.

Hybridization is an important evolutionary force, and heterosis describes the phenomenon where hybrids exhibit superior traits compared to their parents. This study aimed to evaluate the one-hundred-seed weight and fatty acid content in F₁ generations, investigating the effects of different parental crosses using a 9 × 3 incomplete diallel design (NCII). One of the challenges faced in this study was the complexity of accurately determining the influence of both genetic and environmental factors on trait inheritance. A total of 36 F₁ crosses were analyzed for general combining ability (GCA), specific combining ability (SCA), and heritability. The results showed that the level of each index in F₁ is closely related to its parents. Significant differences in GCA and SCA were observed among parental traits in most crosses. The ratio of GCA to SCA ranged from 0 to 3, indicating the pivotal role of SCA over GCA in castor breeding efforts. High narrow-sense heritability was recorded in palmitic acid (30.98%), oleic acid (28.68%), and arachidonic acid (21.34%), suggesting that these traits are predominantly under the control of additive gene action, and hence these characters can be improved by selection. Additionally, heterosis exhibited diverse patterns across traits. Based on the evaluated combining ability, heritability, and heterosis, the inbred lines CSR181 and 20111149 were recommended for castor crossbreeding due to their potential to yield progeny with optimal oil-related traits. This research contributes valuable knowledge to the field of castor breeding, providing a foundation for developing superior castor cultivars. Full article

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

9 pages, 1378 KiB

Open AccessCommunication

Creation of Bacterial Blight Resistant Rice by Targeting Homologous Sequences of Xa13 and Xa25 Genes

by Yiwang Zhu, Xiaohuai Yang, Peirun Luo, Jingwan Yan, Xinglan Cao, Hongge Qian, Xiying Zhu, Yujin Fan, Fating Mei, Meiying Fan, Lianguang Shang, Feng Wang and Yu Zhang

Agronomy 2024, 14(4), 800; https://doi.org/10.3390/agronomy14040800 - 12 Apr 2024

Cited by 2 | Viewed by 1504

Abstract

Bacterial blight is a destructive disease in rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Single resistance genes often have limitations in providing broad-spectrum resistance, as pathogens continuously evolve and vary. Breeding rice varieties with multiple disease resistance genes has proven to be [...] Read more.

Bacterial blight is a destructive disease in rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Single resistance genes often have limitations in providing broad-spectrum resistance, as pathogens continuously evolve and vary. Breeding rice varieties with multiple disease resistance genes has proven to be an effective strategy for controlling bacterial blight. In this study, a single Cas9/gRNA construct was used to target the homologous sequences of Xa13 and Xa25 genes through destroying the target gene function, creating bacterial blight resistance in five rice varieties. These materials provide promising germplasm resources for the development of rice varieties with durable resistance to bacterial blight. Full article

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

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18 pages, 3537 KiB

Open AccessArticle

Characterization and Transcriptome Analysis Reveal Exogenous GA₃ Inhibited Rosette Branching via Altering Auxin Approach in Flowering Chinese Cabbage

by Xinghua Qi, Ying Zhao, Ningning Cai, Jian Guan, Zeji Liu, Zhiyong Liu, Hui Feng and Yun Zhang

Agronomy 2024, 14(4), 762; https://doi.org/10.3390/agronomy14040762 - 8 Apr 2024

Cited by 1 | Viewed by 1250

Abstract

Branching is an important agronomic trait that is conducive to plant architecture and yield in flowering Chinese cabbage. Plant branching is regulated by a complex network mediated by hormones; gibberellin (GA) is one of the important hormones which is involved in the formation [...] Read more.

Branching is an important agronomic trait that is conducive to plant architecture and yield in flowering Chinese cabbage. Plant branching is regulated by a complex network mediated by hormones; gibberellin (GA) is one of the important hormones which is involved in the formation of shoot branching. Research on the regulatory mechanism of GA influencing rosette branch numbers is limited for flowering Chinese cabbage. In this study, the exogenous application of 600 mg/L GA₃ effectively inhibited rosette branching and promoted internode elongation in flowering Chinese cabbage. RNA-Seq analysis further found that these DEGs were significantly enriched in ‘the plant hormone signal transduction’ pathways, and auxin-related genes were significantly differentially expressed between MB and MB_GA. The upregulation of auxin (AUX) and the upregulation of auxin/indole-3-acetic acid (AUX/IAA), as well as the downregulation of SMALL AUXIN-UPREGULATED RNA (SAUR), were found in the negative regulation of the rosette branching. The qRT-PCR results showed that the expression of AUX/IAA and SAUR from IAA gene family members were consistent with the results of transcriptome data. Phytohormone profiling by targeted metabolism revealed that endogenous auxin contents were significantly increased in MB_GA. Transcriptome and metabolome analysis clarified the main plant hormones and genes underlying the rosette branching in flowering Chinese cabbage, confirming that auxin could inhibit rosette branching. In this regard, the results present a novel angle for revealing the mechanism of gibberellin acting on the branching architecture in flowering Chinese cabbage. Full article

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

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16 pages, 3020 KiB

Open AccessArticle

The Role of the ADF Gene Family in Maize Response to Abiotic Stresses

by Ruisi Yang, Fei Wang, Ping Luo, Zhennan Xu, Houwen Wang, Runze Zhang, Wenzhe Li, Ke Yang, Zhuanfang Hao and Wenwei Gao

Agronomy 2024, 14(4), 717; https://doi.org/10.3390/agronomy14040717 - 29 Mar 2024

Cited by 1 | Viewed by 1152

Abstract

The highly conserved actin depolymerizing factor (ADF) plays an important role in plant growth, development and responses to biotic and abiotic stresses. A total of 72 ADF genes in Arabidopsis, wheat, rice and sorghum can be divided into four groups. The multicollinearity analysis [...] Read more.

The highly conserved actin depolymerizing factor (ADF) plays an important role in plant growth, development and responses to biotic and abiotic stresses. A total of 72 ADF genes in Arabidopsis, wheat, rice and sorghum can be divided into four groups. The multicollinearity analysis revealed that the maize ADF gene family exhibited more collinearity events with closely related gramineous plants. Fifteen ADF genes in maize were screened from the latest database, and bioinformatics analysis showed that these ADF genes were distributed across seven chromosomes in maize. The gene structure of the ADF gene family in maize exhibits significant conservation and cluster consistency. The promoter region contains rich regulatory elements that are involved in various regulations related to growth, development and adverse stresses. The drought-tolerant ZmADF5 gene in maize was further studied, and it was found that the allelic variations in ZmADF5 were mainly concentrated in its promoter region. A superior haplotype, with drought tolerance, was identified by candidate-gene association analysis of 115 inbred lines. By comparing the phenotypes of anthesis silking interval, grain yield and ear height, it was found that Hap2 performed better than Hap1 under drought stress. This study provides a theoretical reference for understanding the function of the ADF gene family and proposes further investigation into the role of ZmADF5 in abiotic-stress tolerance. Full article

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

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15 pages, 4125 KiB

Open AccessArticle

Fine Mapping and Functional Verification of the Brdt1 Gene Controlling Determinate Inflorescence in Brassica rapa L.

by Cuiping Chen, Xuebing Zhu, Zhi Zhao, Dezhi Du and Kaixiang Li

Agronomy 2024, 14(2), 281; https://doi.org/10.3390/agronomy14020281 - 27 Jan 2024

Cited by 1 | Viewed by 1473

Abstract

Brassica rapa, a major oilseed crop in high-altitude areas, is well known for its indeterminate inflorescences. However, this experiment revealed an intriguing anomaly within the plot: a variant displaying a determinate growth habit (520). Determinate inflorescences have been recognized for their role [...] Read more.

Brassica rapa, a major oilseed crop in high-altitude areas, is well known for its indeterminate inflorescences. However, this experiment revealed an intriguing anomaly within the plot: a variant displaying a determinate growth habit (520). Determinate inflorescences have been recognized for their role in the genetic enhancement of crops. In this study, a genetic analysis in a determinate genotype (520) and an indeterminate genotype (515) revealed that two independently inherited recessive genes (Brdt1 and Brdt2) are responsible for the determinate trait. BSA-seq and SSR markers were employed to successfully locate the Brdt1 gene, which is localized within an approximate region 72.7 kb between 15,712.9 kb and 15,785.6 kb on A10. A BLAST analysis of these candidate intervals revealed that Bra009508 (BraA10.TFL1) shares homology with the A. thaliana TFL1 gene. Then, BraA10.TFL1 (gene from the indeterminate phenotype) and BraA10.tfl1 (gene from the determinate phenotype) were cloned and sequenced, and the results indicated that the open reading frame of the alleles comprises 537 bp. Using qRT-PCR, it was determined that BraA10.TFL1 expression levels in shoot apexes were significantly higher in NIL-520 compared to 520. To verify the function of BraA10.TFL1, the gene was introduced into the determinate A. thaliana tfl1 mutant, resulting in the restoration of indeterminate traits. These findings demonstrate that BraA10.tfl1 is a gene that controls the determinate inflorescence trait. Overall, the results of this study provide a theoretical foundation for the further investigation of determinate inflorescence. 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

by Demba Dramé, Amy Bodian, Daniel Fonceka, Hodo-Abalo Tossim, Mouhamadou Moussa Diangar, Joel Romaric Nguepjop, Diarietou Sambakhe, Mamadou Sidybe and Diaga Diouf

Agronomy 2023, 13(11), 2761; https://doi.org/10.3390/agronomy13112761 - 2 Nov 2023

Viewed by 1724

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

by Junying Zhang, Jifeng Zhu, Liyong Yang, Yanli Li, Weirong Wang, Xirong Zhou and Jianxia Jiang

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

Cited by 1 | Viewed by 1380

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

by Yang Xu, Fan Yan, Zhengwei Liang, Ying Wang, Jingwen Li, Lei Zhao, Xuguang Yang, Qingyu Wang and Jingya Liu

Agronomy 2023, 13(9), 2333; https://doi.org/10.3390/agronomy13092333 - 7 Sep 2023

Viewed by 1416

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

by Zanping Han, Yunqian Jin, Bin Wang and Yiyang Guo

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

Cited by 4 | Viewed by 1833

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

by Lian Yin, Yudong Sun, Xuehao Chen, Jiexia Liu, Kai Feng, Dexu Luo, Manyi Sun, Linchuang Wang, Wenzhao Xu, Lu Liu and Jianfeng Zhao

Agronomy 2023, 13(5), 1324; https://doi.org/10.3390/agronomy13051324 - 9 May 2023

Cited by 4 | Viewed by 2179

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

by Qian Jiang, Yu Wang, Aisheng Xiong, Hui Zhao, Ruizong Jia, Mengyao Li, Huaming An, Changmian Ji and Anping Guo

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

Viewed by 2136

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

by So-Myeong Lee, Nkulu Rolly Kabange, Ju-Won Kang, Youngho Kwon, Jin-Kyung Cha, Hyeonjin Park, Ki-Won Oh, Jeonghwan Seo, Hee-Jong Koh and Jong-Hee Lee

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

Viewed by 1923

Abstract

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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Review

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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

by Diankai Gong, Xue Zhang, Fei He, Ying Chen, Rui Li, Jipan Yao, Manli Zhang, Wenjing Zheng and Guangxing Yu

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

Cited by 13 | Viewed by 4741

Abstract

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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