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13 pages, 2077 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of Cytosine DNA Methyltransferase Genes Related to Somaclonal Variation in Pineapple (Ananas comosus L.)

by Wenqiu Lin, Xi’ou Xiao, Weisheng Sun, Shenghui Liu, Qingsong Wu, Yanli Yao, Hongna Zhang and Xiumei Zhang

Agronomy 2022, 12(5), 1039; https://doi.org/10.3390/agronomy12051039 - 27 Apr 2022

Cited by 11 | Viewed by 2454

Abstract

DNA methylation plays an important role in somaclonal variation. Cytosine-5 DNA methyltransferases (C5-MTases) are crucial enzymes for maintaining the de novo genome DNA methylation status, and the gene family has been identified and characterized in several species. However, limited information is available about [...] Read more.

DNA methylation plays an important role in somaclonal variation. Cytosine-5 DNA methyltransferases (C5-MTases) are crucial enzymes for maintaining the de novo genome DNA methylation status, and the gene family has been identified and characterized in several species. However, limited information is available about the role of C5-MTases in the somaclonal variation of pineapple. Herein, the characteristic of DNA methylation in the leaf variants of pineapple showed that the methylation rate of variants decreased and the demethylation was mainly. Six AcC5-MTases were identified from pineapple genome. Phylogenetic analysis indicated that the six members could be classified into four subgroups, namely, AcMET, AcCMT, AcDRM, and AcDNMT, demonstrating evolutionary conservation in the C5-MTases across pineapple and other plant species. Cis-elements were presented in AcC5-MTase promoters, including light-responsive, phytohormone-responsive, and plant growth and development elements. Furthermore, we investigated the expression profiles of AcC5-MTases in different tissues and their transcript abundance in the leaves of somaclonal variation. Interestingly, most AcC5-MTase genes were highly expressed in leaf and carpopodium. AcMET, AcCMT2, and AcDRM2 were upregulated in pineapple somaclonal variants, indicating that AcC5-MTases might play an important role in the somaclonal variation of pineapple. Our results will aid in understanding the complex roles of methylation in plants and provide a basis for analyzing the role of methylation modification in the somaclonal variation of pineapple. Full article

(This article belongs to the Special Issue Horticultural Genetics and Biotechnology)

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13 pages, 532 KiB

Open AccessArticle

Near-Infrared Spectroscopy to Predict Provitamin A Carotenoids Content in Maize

by Aldo Rosales, José Crossa, Jaime Cuevas, Luisa Cabrera-Soto, Thanda Dhliwayo, Thokozile Ndhlela and Natalia Palacios-Rojas

Agronomy 2022, 12(5), 1027; https://doi.org/10.3390/agronomy12051027 - 25 Apr 2022

Cited by 5 | Viewed by 3166

Abstract

Vitamin A deficiency (VAD) is a public health issue worldwide. Provitamin A (PVA) biofortified maize serves as an alternative to help combat VAD. Breeding efforts to develop maize varieties with high PVA carotenoid content combine molecular and phenotypic selection strategies. The phenotypic assessment [...] Read more.

Vitamin A deficiency (VAD) is a public health issue worldwide. Provitamin A (PVA) biofortified maize serves as an alternative to help combat VAD. Breeding efforts to develop maize varieties with high PVA carotenoid content combine molecular and phenotypic selection strategies. The phenotypic assessment of carotenoids is currently done using liquid chromatography, a precise but time- and resource-consuming methodology. Using near-infrared spectroscopy (NIRS) could increase the breeding efficiency. This study used ultra-performance liquid chromatography (UPLC) data from 1857 tropical maize genotypes as a training set and NIRS data to do an independent test of a set of 650 genotypes to predict PVA carotenoids using Bayesian and modified partial least square (MPLS) regression models. Both regression methods produced similar prediction accuracies for the total carotenoids (r² = 0.75), lutein (r² = 0.55), zeaxanthin (r²= 0.61), β-carotene (r² = 0.22) and β-cryptoxanthin (BCX) (r² = 0.57). These results demonstrate that Bayesian and MPLS regression of BCX on NIRS data can be used to predict BCX content, the current focus on PVA enhancement, and thus offers opportunities for high-throughput phenotyping at a low cost, especially in the early stages of PVA maize breeding pipeline when many genotypes must be screened. Full article

(This article belongs to the Special Issue Horticultural Genetics and Biotechnology)

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17 pages, 3364 KiB

Open AccessArticle

Cloning and Functional Analysis of the Soybean GmRIQ2 Promoter

by Binbin Zhang, Huayi Yin, Zhihui Sun, Xiaohui Song, Jing Deng, Qian Zhang and Dongmei Li

Agronomy 2022, 12(1), 227; https://doi.org/10.3390/agronomy12010227 - 17 Jan 2022

Cited by 2 | Viewed by 2948

Abstract

The RIQ gene can optimize the structure of light-harvesting complex II by regulating the degree of granum stacking, and ultimately participates in plant light stress responses. The GmRIQ2 gene contributes to plant photoprotection and may be involved in negative regulation of yield. To [...] Read more.

The RIQ gene can optimize the structure of light-harvesting complex II by regulating the degree of granum stacking, and ultimately participates in plant light stress responses. The GmRIQ2 gene contributes to plant photoprotection and may be involved in negative regulation of yield. To understand the regulatory mechanisms of GmRIQ2 expression, we isolated the GmRIQ2 promoter (PGmRIQ2) from the KenFeng 16 soybean genome. Sequence analysis showed that several cis-acting elements were involved in hormone responsiveness, seed-specific regulation, anaerobic induction and light responsiveness. PGmRIQ2 was expressed in soybean roots. GUS activity was detected in Arabidopsis thaliana rosette leaves, stems and roots, indicating that PGmRIQ2 tended to drive expression in rosette leaf vascular tissue and had spatiotemporal expression characteristics at the early growth stage. Three promoter deletion fragments of 450 bp, 284 bp and 194 bp were obtained by 5′ deletion. These three fragments all drove GUS gene expression in Arabidopsis thaliana rosette leaves, stems and roots. GUS gene expression decreased with deletion fragment truncation. In addition, the PGmRIQ2 auxin (IAA), abscisic acid (ABA) and methyl jasmonate (MeJA) response elements were located at base pairs −1661~−450, −450~−284 and −284~−194, respectively, and the promoter was induced by IAA, ABA, MeJA and light. Full article

(This article belongs to the Special Issue Horticultural Genetics and Biotechnology)

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21 pages, 3492 KiB

Open AccessArticle

Genotypic and Phenotypic Characterization of Lettuce Bacterial Pathogen Xanthomonas hortorum pv. vitians Populations Collected in Quebec, Canada

by Pierre-Olivier Hébert, Martin Laforest, Dong Xu, Marie Ciotola, Mélanie Cadieux, Carole Beaulieu and Vicky Toussaint

Agronomy 2021, 11(12), 2386; https://doi.org/10.3390/agronomy11122386 - 24 Nov 2021

Cited by 6 | Viewed by 2970

Abstract

Bacterial leaf spot of lettuce, caused by Xanthomonas hortorum pv. vitians, is an economically important disease worldwide. For instance, it caused around 4 million CAD in losses in only a few months during the winter of 1992 in Florida. Because only one [...] Read more.

Bacterial leaf spot of lettuce, caused by Xanthomonas hortorum pv. vitians, is an economically important disease worldwide. For instance, it caused around 4 million CAD in losses in only a few months during the winter of 1992 in Florida. Because only one pesticide is registered to control this disease in Canada, the development of lettuce cultivars tolerant to bacterial leaf spot remains the most promising approach to reduce the incidence and severity of the disease in lettuce fields. The lack of information about the genetic diversity of the pathogen, however, impairs breeding programs, especially when disease resistance is tested on newly developed lettuce germplasm lines. To evaluate the diversity of X. hortorum pv. vitians, a multilocus sequence analysis was performed on 694 isolates collected in Eastern Canada through the summers of 2014 to 2017 and two isolates in 1996 and 2007. All isolates tested were clustered into five phylogroups. Six pathotypes were identified following pathogenicity tests conducted in greenhouses, but when phylogroups were compared with pathotypes, no correlation could be drawn. However, in vitro production of xanthan and xanthomonadins was investigated, and isolates with higher production of xanthomonadins were generally causing less severe symptoms on the tolerant cultivar Little Gem. Whole-genome sequencing was undertaken for 95 isolates belonging to the pathotypes identified, and de novo assembly made with reads unmapped to the reference strain’s genome sequence resulted in 694 contigs ranging from 128 to 120,795 bp. Variant calling was performed prior to genome-wide association studies computed with single-nucleotide polymorphisms (SNPs), copy-number variants and gaps. Polymorphisms with significant p-values were only found on the cultivar Little Gem. Our results allowed molecular identification of isolates likely to cause bacterial leaf spot of lettuce, using two SNPs identified through genome-wide association study. Full article

(This article belongs to the Special Issue Horticultural Genetics and Biotechnology)

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14 pages, 2336 KiB

Open AccessArticle

Evaluation of Complete Fertilizer in the Aspect of the Antioxidant Enzyme System of Maize Hybrids

by Árpád Illés, Csaba Bojtor, Seyed Mohammad Nasir Mousavi, Adrienn Széles, Brigitta Tóth, Atala Szabó and János Nagy

Agronomy 2021, 11(11), 2129; https://doi.org/10.3390/agronomy11112129 - 24 Oct 2021

Cited by 5 | Viewed by 2181

Abstract

Studies on physiological and biochemical processes in crops are highly relevant for breeders to produce hybrids with high yield. Two different maturity groups of maize hybrids were tested in this study. The research site was located at the Látókép Experimental Station of the [...] Read more.

Studies on physiological and biochemical processes in crops are highly relevant for breeders to produce hybrids with high yield. Two different maturity groups of maize hybrids were tested in this study. The research site was located at the Látókép Experimental Station of the University of Debrecen and the experiment lasted for 2 years. The examined nitrogen ranges were separated into two parts. Firstly, the effects of nitrogen fertilizer ranging from 120–300 kg ha⁻¹ were examined, supplemented with a constant, high-level P₂O₅ and K₂O. Secondly, the optimal ratio of N:P:K was measured. In order to monitor the health status of maize hybrids, stress indicators including the activity of ascorbate peroxidase (APX), and superoxide dismutase (SOD), the rate of lipid peroxidation (LP), and grain yield were measured. The samples were taken in five phenological stages. Variance analysis based on nitrogen fertilizer showed variation in sampling times and fertilizers on APX, LP, and SOD. Variance analysis based on NPK indicated variation in sampling times, years, and fertilizer levels on APX, LP, and SOD. Correlation analysis showed that yield correlated negatively with SOD during the use of NPK fertilizer, as the use of nitrogen fertilizer cannot make corrections to yield with SOD but phosphorus and potassium can correlate with yield, and SOD. Principal component analysis showed that NPK5 and N5 had maximum stability and effect on yield. The activity of APX had the highest value during silking, and LP was in the V14 leaf stage. The correlation and principal component analysis showed that silking and the V14 leaf stage are the most important stages for yield, thus, higher attention must be paid to these stages in the LP and the activation of APX to achieve maximum yield. Full article

(This article belongs to the Special Issue Horticultural Genetics and Biotechnology)

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16 pages, 5070 KiB

Open AccessArticle

Using Principal Component Analysis and RNA-Seq to Identify Candidate Genes That Control Salt Tolerance in Garlic (Allium sativum L.)

by Xiangjun Zhou, Yanxia Dou, Xiaoxia Huang, Gang Li, Hongrui Zhang, Dagang Jiang, Jinping Fan, Jorge Alberto Condori-Apfata, Xiaoqin Liu, Sandro Jhonatan Condori-Pacsi, Roxana M. Bardales, Mayela Elizabeth Mayta Anco, Helbert O. Lazo, Herbert Angel Delgado Salazar, Maria Valderrama Valencia and Cankui Zhang

Agronomy 2021, 11(4), 691; https://doi.org/10.3390/agronomy11040691 - 5 Apr 2021

Cited by 5 | Viewed by 4486

Abstract

To examine physiological responses of garlic to salinity, 17-day-old seedlings of eight soft-neck accessions were treated with 200 mM NaCl for seven days in a hydroponic system. Several morphological and physiological traits were measured at the end of the treatment, including shoot height, [...] Read more.

To examine physiological responses of garlic to salinity, 17-day-old seedlings of eight soft-neck accessions were treated with 200 mM NaCl for seven days in a hydroponic system. Several morphological and physiological traits were measured at the end of the treatment, including shoot height, shoot fresh weight, shoot dry weight, root length, root fresh weight, root dry weight, photosynthesis rate, and concentrations of Na⁺ and K⁺ in leaves. The principal component analysis showed that shoot dry weight and K⁺/Na⁺ ratio contribute the most to salt tolerance among the garlic accessions. As a result, salt-tolerant and sensitive accessions were grouped based on these two parameters. Furthermore, to investigate the molecular mechanisms in garlic in response to salinity, the transcriptomes of leaves and roots between salt-tolerant and salt-sensitive garlic accessions were compared. Approximately 1.5 billion read pairs were obtained from 24 libraries generated from the leaves and roots of the salt-tolerant and salt-sensitive garlic accessions. A total of 47,509 genes were identified by mapping the cleaned reads to the garlic reference genome. Statistical analysis indicated that 1282 and 1068 genes were upregulated solely in the tolerant leaves and roots, whereas 1505 and 1203 genes were downregulated exclusively in the tolerant leaves and roots after NaCl treatment, respectively. Functional categorization of these genes revealed their involvement in a variety of biological processes. Several genes important for carotenoid biosynthesis, auxin signaling, and K⁺ transport were strongly altered in roots by NaCl treatment and could be candidate genes for garlic salt tolerance improvement. Full article

(This article belongs to the Special Issue Horticultural Genetics and Biotechnology)

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20 pages, 2647 KiB

Open AccessArticle

Single Nucleotide Polymorphism (SNP) Discovery and Association Study of Flowering Times, Crude Fat and Fatty Acid Composition in Rapeseed (Brassica napus L.) Mutant Lines Using Genotyping-by-Sequencing (GBS)

by Jaihyunk Ryu, Jae Il Lyu, Dong-Gun Kim, Kwang Min Koo, Baul Yang, Yeong Deuk Jo, Sang Hoon Kim, Soon-Jae Kwon, Bo-Keun Ha, Si-Yong Kang, Jin-Baek Kim and Joon-Woo Ahn

Agronomy 2021, 11(3), 508; https://doi.org/10.3390/agronomy11030508 - 9 Mar 2021

Cited by 10 | Viewed by 3660

Abstract

Rapeseed is the most important oil crop used in the food and biodiesel industries. In this study, based on single nucleotide polymorphism (SNP) identified from genotyping-by-sequencing (GBS), and an association study of flowering time, crude fat and fatty acid contents were investigated in [...] Read more.

Rapeseed is the most important oil crop used in the food and biodiesel industries. In this study, based on single nucleotide polymorphism (SNP) identified from genotyping-by-sequencing (GBS), and an association study of flowering time, crude fat and fatty acid contents were investigated in 46 rapeseed mutant lines derived from gamma rays. A total of 623,026,394 clean data reads were generated with 6.6 million reads on average. A set of 37,721 filtered SNPs was used to perform gene ontology and phylogenetic analysis. Hierarchical cluster analysis of the rapeseed mutant lines gave eight groups based on flowering time and fatty acid compositions. Gene ontological analysis of the mutant lines showed that many genes displaying SNPs are involved in cellular processes, cellular anatomy, and binding. A total of 40 SNPs were significantly associated with flowering time (1 SNP), crude fat content (2 SNPs), and fatty acid content (37 SNPs). A total of 21 genes were annotated from fatty acid content SNPs; among them, nine genes were significantly enriched in reproductive processes, such as embryonic development, fruit development, and seed development. This study demonstrated that SNPs are efficient tools for mutant screening and it provides a basis that the improving the oil qualities of rapeseed. Full article

(This article belongs to the Special Issue Horticultural Genetics and Biotechnology)

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14 pages, 3285 KiB

Open AccessArticle

Transcriptomic Changes Induced by Drought Stress in Hardneck Garlic during the Bolting/Bulbing Stage

by Xiangjun Zhou, Jorge Alberto Condori-Apfata, Xiaoqin Liu, Sandro Jhonatan Condori-Pacsi, Maria Valderrama Valencia and Cankui Zhang

Agronomy 2021, 11(2), 246; https://doi.org/10.3390/agronomy11020246 - 29 Jan 2021

Cited by 15 | Viewed by 4964

Abstract

Garlic (Allium sativum L.) is an economically important, monocotyledonous plant with a strong taste and odor. Drought stress adversely affects its growth, development, and yield, particularly during the bolting/bulbing stage. Herein we performed RNA-seq to assess transcriptomic changes induced by drought stress [...] Read more.

Garlic (Allium sativum L.) is an economically important, monocotyledonous plant with a strong taste and odor. Drought stress adversely affects its growth, development, and yield, particularly during the bolting/bulbing stage. Herein we performed RNA-seq to assess transcriptomic changes induced by drought stress in bolting/bulbing hardneck garlic plants (Purple Glazer). We observed that drought stress significantly reduced photosynthesis rate, fresh weight, and leaf water content. Transcriptomic analysis of garlic leaves under normal conditions and drought stress led to the identification of 5215 differentially expressed genes (2748 up- and 2467 downregulated). The upregulated DEGs were primarily involved in “biological process”, “metabolic process”, “oxidation-reduction process”, carbohydrate and lipid metabolism, and “proteolysis”, whereas the downregulated DEGs were mainly involved in “biological process” and metabolism of various molecules. In addition, genes encoding abscisic acid biosynthetic and catabolic enzymes, heat shock proteins, and E3 ubiquitin ligases were significantly altered by drought stress, indicating involvement in drought tolerance. A further comparison with the DEGs related to salinity stress-treated garlic revealed 867 and 305 DEGs with a similar and reverse expression alteration tendency, respectively. Full article

(This article belongs to the Special Issue Horticultural Genetics and Biotechnology)

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