Editorial

6 pages, 232 KiB

Open AccessEditorial

Advances in Molecular Exploration of Crop Plants under Environmental Stresses from Genetic and Genomic Perspectives

by Fengjie Sun and Gustavo Caetano-Anollés

Agronomy 2023, 13(10), 2653; https://doi.org/10.3390/agronomy13102653 - 22 Oct 2023

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It is well known and has been evidently indicated by numerous studies that the demand for food and energy supply has been rapidly increasing for many years worldwide [...] Full article

(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges)

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17 pages, 2847 KiB

Open AccessArticle

Expression of AtAAP Gene Family and Endosperm-Specific Expression of AtAAP1 Gene Promotes Amino Acid Absorption in Arabidopsis thaliana and Maize

by Zhanyu Chen, Yingying Zhang, Jiating Zhang, Bei Fan, Ying Zhou and Xiyan Cui

Agronomy 2021, 11(8), 1668; https://doi.org/10.3390/agronomy11081668 - 21 Aug 2021

Cited by 5 | Viewed by 2312

Abstract

The amino acid permease (AAP) is an important transmembrane protein that is involved in the absorption and transport of amino acids in plants. We investigated the expression patterns of AtAAP genes in Arabidopsis thaliana, based on quantitative real-time PCR. The results revealed [...] Read more.

The amino acid permease (AAP) is an important transmembrane protein that is involved in the absorption and transport of amino acids in plants. We investigated the expression patterns of AtAAP genes in Arabidopsis thaliana, based on quantitative real-time PCR. The results revealed differential expression patterns of eight AtAAP genes in different tissues, with five genes (AtAAP1, AtAAP2, AtAAP6, AtAAP7, and AtAAP8) expressed at relatively high levels in both flowers and siliques, suggesting their shared functions in the accumulation of amino acids. In transgenic plants, with endosperm-specific overexpression of AtAAP1, both AtAAP1 and AtAAP6 were up-regulated in both the roots and siliques, while AtAAP2, AtAAP3, AtAAP4, and AtAAP5 showed similar expression levels in the stems and siliques, whereas AtAAP7 and AtAAP8 were expressed at their highest levels in the stems and roots. The results of the amino acid affinity experiments revealed varied absorption capacities for different amino acids, by AtAAP1, and increased acid amino contents in the reproductive organs. These results were verified in transgenic maize plants, with the overexpression of AtAAP1, revealing higher amino acid contents in the reproductive organs than those of the vegetative organs. Our study clearly demonstrated that the endosperm-specific promoter increased the amino acid contents in the reproductive organs and improved the effective utilization of organic nitrogen in plants. Full article

(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges)

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20 pages, 4139 KiB

Open AccessArticle

Effects of Laser Mutagenesis on Microalgae Production and Lipid Accumulation in Two Economically Important Fresh Chlorella Strains under Heterotrophic Conditions

by Wei Xing, Ruihao Zhang, Qun Shao, Chunxiao Meng, Xiaodong Wang, Zuoxi Wei, Fengjie Sun, Chang Wang, Kai Cao, Bingkui Zhu and Zhengquan Gao

Agronomy 2021, 11(5), 961; https://doi.org/10.3390/agronomy11050961 - 12 May 2021

Cited by 9 | Viewed by 2556

Abstract

Microalgae produce a variety of high-value products. Enhancing product contents in microalgal cells is one of the efficient ways to decrease production costs. Improved germplasm and heterotrophic cultivation may enhance microalgae biomass and lipid content. In this study, we investigated the effect of [...] Read more.

Microalgae produce a variety of high-value products. Enhancing product contents in microalgal cells is one of the efficient ways to decrease production costs. Improved germplasm and heterotrophic cultivation may enhance microalgae biomass and lipid content. In this study, we investigated the effect of three types of laser irradiation and heterotrophic cultivation on lipid productivity, lipid content, and biomass of two Chlorella strains (i.e., FACHB 9 and FACHB 31). Results showed that the highest biomasses of 4.81 g/L (15.03-fold) and 4.66 g/L (7.32-fold) were obtained in the third generation of FACHB 9 and FACHB 31 induced by a neodymium-doped yttrium aluminum garnet (Nd:YAG) laser for 8 min and 12 min, respectively. The highest lipid contents were 525.6 mg/g (1.67-fold) dry weight (DW) and 780.0 mg/g DW (2.20-fold) in the third and the first generations of FACHB 9 and FACHB 31 induced by Nd:YAG for 8 min and by a helium–neon (He–Ne) laser for 4 min, respectively. The highest lipid productivities of 69.82 ± 3.29 mg/L/d (19.7-fold) and 30.71 ± 3.77 mg/L/d (3.1-fold) were obtained in FACHB 9 and FACHB 31 treated by a semiconductor (SC) laser for 4 min and by a He–Ne laser for 12 min, respectively. Our study suggested that laser mutagenesis is a potential method for screening economically important oleaginous microalgae strains. Full article

(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges)

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17 pages, 3087 KiB

Open AccessArticle

Comparative Analyses Reveal Peroxidases Play Important Roles in Soybean Tolerance to Aluminum Toxicity

by Juge Liu, Xiangting Wang, Ning Wang, Yang Li, Ting Jin, Junyi Gai and Yan Li

Agronomy 2021, 11(4), 670; https://doi.org/10.3390/agronomy11040670 - 01 Apr 2021

Cited by 7 | Viewed by 1948

Abstract

Aluminum (Al) toxicity is an important barrier to soybean (Glycine max (L.) Merr.) production in acid soils. However, little is known about the genes underlying Al tolerance in soybean. We aim to find the key candidate genes and investigate their roles in [...] Read more.

Aluminum (Al) toxicity is an important barrier to soybean (Glycine max (L.) Merr.) production in acid soils. However, little is known about the genes underlying Al tolerance in soybean. We aim to find the key candidate genes and investigate their roles in soybean tolerance to Al toxicity in this study. Comparative transcriptome analyses of the Al-tolerant (KF) and Al-sensitive (GF) soybean varieties under control and Al stress at 6, 12, and 24 h were investigated. A total of 1411 genes showed specific up-regulation in KF or more up-regulation in KF than in GF by Al stress, which were significantly enriched in the GO terms of peroxidase (POD) activity, transporter activity (including the known Al tolerance-related ABC transporter, ALMT, and MATE), and four families of transcription factors (AP2, C3H4, MYB, WRKY). The expression levels of seven POD genes were up-regulated by Al stress for at least one time point in KF. The H₂O₂ pretreatment significantly improved Al tolerance of KF, which is likely due to increased POD activity induced by H₂O₂. Our results suggest that PODs play important roles in soybean tolerance to Al toxicity. We also propose a list of candidate genes for Al tolerance in KF, which would provide valuable insights into the Al tolerance mechanisms in soybean. Full article

(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges)

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28 pages, 2620 KiB

Open AccessArticle

RNAseq Reveals Differential Gene Expression Contributing to Phytophthora nicotianae Adaptation to Partial Resistance in Tobacco

by Jing Jin, Rui Shi, Ramsey Steven Lewis and Howard David Shew

Agronomy 2021, 11(4), 656; https://doi.org/10.3390/agronomy11040656 - 30 Mar 2021

Cited by 1 | Viewed by 2176

Abstract

Phytophthora nicotianae is a devastating oomycete plant pathogen with a wide host range. On tobacco, it causes black shank, a disease that can result in severe economic losses. Deployment of host resistance is one of the most effective means of controlling tobacco black [...] Read more.

Phytophthora nicotianae is a devastating oomycete plant pathogen with a wide host range. On tobacco, it causes black shank, a disease that can result in severe economic losses. Deployment of host resistance is one of the most effective means of controlling tobacco black shank, but adaptation to complete and partial resistance by P. nicotianae can limit the long-term effectiveness of the resistance. The molecular basis of adaptation to partial resistance is largely unknown. RNAseq was performed on two isolates of P. nicotianae (adapted to either the susceptible tobacco genotype Hicks or the partially resistant genotype K 326 Wz/Wz) to identify differentially expressed genes (DEGs) during their pathogenic interactions with K 326 Wz/Wz and Hicks. Approximately 69% of the up-regulated DEGs were associated with pathogenicity in the K 326 Wz/Wz-adapted isolate when sampled following infection of its adapted host K 326 Wz/Wz. Thirty-one percent of the up-regulated DEGs were associated with pathogenicity in the Hicks-adapted isolate on K 326 Wz/Wz. A broad spectrum of over-represented gene ontology (GO) terms were assigned to down-regulated genes in the Hicks-adapted isolate. In the host, a series of GO terms involved in nuclear biosynthesis processes were assigned to the down-regulated genes in K 326 Wz/Wz inoculated with K 326 Wz/Wz-adapted isolate. This study enhances our understanding of the molecular mechanisms of P. nicotianae adaptation to partial resistance in tobacco by elucidating how the pathogen recruits pathogenicity-associated genes that impact host biological activities. Full article

(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges)

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13 pages, 1894 KiB

Open AccessArticle

The Evaluation of Agronomic Traits of Wild Soybean Accessions (Glycine soja Sieb. and Zucc.) in Heilongjiang Province, China

by Wei Li, Mu Peng, Zhen Wang, Yingdong Bi, Miao Liu, Ling Wang, Shufeng Di, Jianxin Liu, Chao Fan, Guang Yang and Deyue Yu

Agronomy 2021, 11(3), 586; https://doi.org/10.3390/agronomy11030586 - 19 Mar 2021

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Abstract

Wild soybean germplasm is distributed widely in China, particularly in Heilongjiang Province. In this study, 242 wild soybean accessions from four agricultural divisions in Heilongjiang Province were evaluated based on six qualitative and eight quantitative traits. Results showed that a large amount of [...] Read more.

Wild soybean germplasm is distributed widely in China, particularly in Heilongjiang Province. In this study, 242 wild soybean accessions from four agricultural divisions in Heilongjiang Province were evaluated based on six qualitative and eight quantitative traits. Results showed that a large amount of variation occurred in these evaluated traits. Abundant qualitative traits included the wild type (78.51%), purple flowers (90.50%), needle leaf (39.26%), black seed (83.88%), brown hilum (52.07%), and mud film (87.60). Results of multivariate analysis based on quantitative traits showed that 100-seed weight, seeds weight per plant, number of seeds per plant, number of effective pods, and number of invalid pods were significantly different among samples (p < 0.05). A total of 27 germplasms were screened. Cluster analysis identified the 242 accessions into two groups, not following the geographical distribution pattern, with rich wild soybean resources revealed in the northern site. The present study indicated that wild soybean in Heilongjiang Province should be conserved in situ. The rich genetic diversity revealed in soybeans of different sites in Heilongjiang Province suggested its significant potential utilization in genetic improvement and breakthrough for soybean breeding. This information will help to exploit and conserve wild soybean accessions in Heilongjiang Province. Full article

(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges)

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14 pages, 3527 KiB

Open AccessArticle

Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers

by HyokChol Kim, Pei Lei, Aizhi Wang, Shuo Liu, Yong Zhao, Fenglan Huang, Zhenliang Yu, Guoli Zhu, Zhibiao He, Deyun Tan, Hongwei Wang and Fanjuan Meng

Agronomy 2021, 11(3), 457; https://doi.org/10.3390/agronomy11030457 - 01 Mar 2021

Cited by 14 | Viewed by 3073

Abstract

Castor (Ricinus communis L.), known as castor oil plant or castor bean, is a non-edible oilseed crop. In the present study, the genetic diversity among 54 samples (3 wild and 51 cultivated) collected worldwide was evaluated using inter-simple sequence repeats (ISSRs) and [...] Read more.

Castor (Ricinus communis L.), known as castor oil plant or castor bean, is a non-edible oilseed crop. In the present study, the genetic diversity among 54 samples (3 wild and 51 cultivated) collected worldwide was evaluated using inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPD) markers. A total of 9 ISSR primers produced 83 high-resolution bands with 61 (74.53%) as polymorphic. The percentage of polymorphic bands per primer and the genetic similarity coefficient ranged from 54.55% (UBC-836) to 100% (UBC-808) and from 0.74 to 0.96, respectively. A total of 11 out of 20 RAPD primers amplified unique polymorphic products with an average percentage of polymorphic bands of 60.98% (56 polymorphic bands out of a total of 90 bands obtained). The percentage of polymorphic bands per primer ranged from 25% (OPA-02 and B7) to 90.91% (B21) with the genetic similarity coefficient ranging from 0.73 to 0.98. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram using two molecular markers divided 54 castor genotypes into three groups. Furthermore, based on morphological data, all 54 castor varieties were grouped into three main clusters. The genetic diversity analysis based on two molecular makers showed that most varieties from China were closely related to each other with three varieties (GUANGDONGwild, ZHEJIANGWild, and HANNANWild) belonging to a wild group separated from most of the cultivated castor samples from China, India, France, and Jordan. These results suggested that the cultivated castor contains a narrow genetic base. Accordingly, we recommend that wild castor genetic resources be introduced for breeding novel castor varieties. Furthermore, the Vietnam, Malaysia, Indonesia, and Nigeria accessions were clustered into the same group. The results of principal coordinate analysis (PCoA) and UPGMA cluster analysis were consistent with each other. The findings of this study are important for future breeding studies of castor. Full article

(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges)

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13 pages, 1775 KiB

Open AccessEditor’s ChoiceArticle

Overexpression of Transcription Factor GmTGA15 Enhances Drought Tolerance in Transgenic Soybean Hairy Roots and Arabidopsis Plants

by Zhanyu Chen, Xiaokun Fang, Xueshun Yuan, Yingying Zhang, Huiying Li, Ying Zhou and Xiyan Cui

Agronomy 2021, 11(1), 170; https://doi.org/10.3390/agronomy11010170 - 18 Jan 2021

Cited by 21 | Viewed by 3326

Abstract

Soybean (Glycine max) is one of the important oil crops worldwide. In recent years, environmental stresses such as drought and soil salinization have severely deteriorated soybean yield and quality. We investigated the overexpression of the transcription factor GmTGA15 in response to [...] Read more.

Soybean (Glycine max) is one of the important oil crops worldwide. In recent years, environmental stresses such as drought and soil salinization have severely deteriorated soybean yield and quality. We investigated the overexpression of the transcription factor GmTGA15 in response to drought stress in transgenic soybean hairy roots and Arabidopsis plants. The results of quantitative real time polymerase chain reaction (qRT-PCR) analyses showed that GmTGA15 was greatly induced by salt, PEG6000, salicylic acid (SA), gibberellic acid (GA), abscisic acid (ABA), and methyl jasmonate (MeJA) in soybean. In response to drought stress, the contents of both chlorophyll and proline were significantly increased, while the content of malondialdehyde (MDA) was significantly decreased in the soybean hairy roots with the overexpression of GmTGA15 in comparison to wild type (WT). Under the simulated drought conditions, the transgenic Arabidopsis plants showed significantly longer roots and lower mortality than that of the wild type. These results suggest that GmTGA15 promotes tolerance to drought stress in both soybean and Arabidopsis plants. This study provides the scientific evidence for further functional analysis of soybean TGA transcription factors in drought stress and the breeding of drought-resistance crops. Full article

(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges)

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