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12 pages, 1159 KiB

Open AccessArticle

Evaluation of Cross-Species Transferability of SSR Markers in Foeniculum vulgare

by Domenico Aiello, Nicoletta Ferradini, Lorenzo Torelli, Chiara Volpi, Joep Lambalk, Luigi Russi and Emidio Albertini

Plants 2020, 9(2), 175; https://doi.org/10.3390/plants9020175 - 01 Feb 2020

Cited by 16 | Viewed by 3600

Abstract

Fennel (Foeniculum vulgare) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites—also known as simple sequence repeats (SSRs)—are codominant markers [...] Read more.

Fennel (Foeniculum vulgare) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites—also known as simple sequence repeats (SSRs)—are codominant markers widely used to perform cross-amplification tests starting from markers developed in related species. SSRs represent a powerful tool, especially for those species lacking genomic information. In this study, a set of primers previously designed in Daucus carota for polymorphic SSR loci was tested in commercial varieties and breeding lines of fennel in order to: (i) test their cross-genera transferability, (ii) look at their efficiency in assessing genetic diversity, and (iii) identify their usefulness for marker-assisted selection (MAS) in breeding programs. Thirty-nine SSR markers from carrot were selected and tested for their transferability score, and only 23% of them resulted suitable for fennel. The low rate of SSR transferability between the two species evidences the difficulties of the use of genomic SSR in cross-genera transferability. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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10 pages, 2453 KiB

Open AccessArticle

Identification of Stem Rust Resistance Genes in the Winter Wheat Collection from Southern Russia

by Andrey V. Alabushev, Nataliya N. Vozhzhova, Natiya T. Kupreyshvili, Nikolay V. Shishkin, Dmitry M. Marchenko and Elena V. Ionova

Plants 2019, 8(12), 559; https://doi.org/10.3390/plants8120559 - 30 Nov 2019

Cited by 5 | Viewed by 2964

Abstract

The high yield potential of winter wheats cannot be realized due to disease pressure under field conditions. One of the most harmful of such diseases is stem rust, hence the constant search for sources of resistance and the development of new varieties resistant [...] Read more.

The high yield potential of winter wheats cannot be realized due to disease pressure under field conditions. One of the most harmful of such diseases is stem rust, hence the constant search for sources of resistance and the development of new varieties resistant to stem rust is of great relevance. This study deals with the identification of stem rust resistance genes in a collection of winter wheats grown in Southern Russia. This genepool has not been studied yet. A total of 620 samples of winter soft wheat from various ecological and geographical zones were tested under field conditions. To identify the specific genes or alleles responsible for resistance, all samples were genotyped using PCR. As a result, the groups of resistant samples, carrying the Sr2, Sr31, Sr38 and Sr44 genes in various combinations, were identified. Most of the stem rust resistance was provided by the presence of the effective Sr44 gene. This information can be used in the future breeding work for stem rust resistance. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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15 pages, 2045 KiB

Open AccessArticle

Comparative Analysis of the YABBY Gene Family of Bienertia sinuspersici, a Single-Cell C₄ Plant

by Prabhakaran Soundararajan, So Youn Won, Dong Suk Park, Yeon-Hee Lee and Jung Sun Kim

Plants 2019, 8(12), 536; https://doi.org/10.3390/plants8120536 - 22 Nov 2019

Cited by 12 | Viewed by 3753

Abstract

The emergence and expression of the YABBY gene family (YGF) coincided with the evolution of leaves in seed plants, and was integral to the early evidence of lamina followed by reproductive development. YGF contains six subclasses, i.e., CRC, INO, FIL, YAB2, YAB3, and [...] Read more.

The emergence and expression of the YABBY gene family (YGF) coincided with the evolution of leaves in seed plants, and was integral to the early evidence of lamina followed by reproductive development. YGF contains six subclasses, i.e., CRC, INO, FIL, YAB2, YAB3, and YAB5. This study aims to extract the genome sequences of the YGF in Bienertia sinuspersici, an important model plant for single-cell C₄ (SCC₄), non-Kranz photosynthesis. A comparative genomic analysis was undertaken with Vitis vinefera, Arabidopsis thaliana, Brassica rapa, and Chenopodium quinoa. Six copies of YGF were present in B. sinuspersici and A. thaliana with a single copy of each YGF subgroup. V. vinefera possessed seven copies of YGF with duplicates in FIL and YAB2 subgroups, but no YAB3. B. rapa and C. quinoa after whole genome duplication contained additional copies of YGF. The gene structure and conserved motifs were analyzed among the YGF. In addition, the relative quantification of YGF was analyzed in the leaves, reproductive developmental stages such as the bud, and the pre-anthesis and anthesis stages in B. sinuspersici, A. thaliana, and B. rapa. CRC and INO possessed conserved floral-specific expression. Temporal and perpetual changes in the expression of YGF orthologs were observed in the leaves and reproductive developmental stages. The results of this study provide an overview of YGF evolution, copy number, and its differential expression in B. sinuspersici. Further studies are required to shed light on the roles of YABBY genes in the evolution of SCC₄ plants and their distinct physiologies. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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14 pages, 1257 KiB

Open AccessArticle

Genetic Diversity, Population Structure, and Marker-Trait Association for Drought Tolerance in US Rice Germplasm

by Uttam Bhattarai and Prasanta K. Subudhi

Plants 2019, 8(12), 530; https://doi.org/10.3390/plants8120530 - 21 Nov 2019

Cited by 13 | Viewed by 4434

Abstract

Drought is a major constraint in some rice-growing areas of the United States. Its impact is most severe at the reproductive stage resulting in low grain yield. Therefore, assessment of genetic and phenotypic variation for drought tolerance in US rice germplasm is necessary [...] Read more.

Drought is a major constraint in some rice-growing areas of the United States. Its impact is most severe at the reproductive stage resulting in low grain yield. Therefore, assessment of genetic and phenotypic variation for drought tolerance in US rice germplasm is necessary to accelerate the breeding effort. Evaluation of 205 US rice genotypes for drought tolerance at the reproductive stage revealed tolerant response in rice genotypes Bengal, Jupiter, Cypress, Jazzman, Caffey, and Trenasse. Harvest index and fresh shoot weight were identified as important traits to explain the majority of variability among the genotypes under drought tolerance. Genotyping with 80 SSR markers indicated a low level of genetic diversity in US germplasm. Population structure analysis grouped the genotypes into eight clusters. The genotypes from California, Louisiana, and Arkansas formed distinct subgroups. Texas genotypes were similar to those from Louisiana and Arkansas. Marker-trait association analysis showed significant association of RM570 and RM351 with grain yield, spikelet fertility, and harvest index whereas shoot dry weight showed association with RM302 and RM461. The drought-tolerant genotypes identified in this study and the SSR markers associated with drought tolerance attributes will be helpful for development of improved drought-tolerant rice varieties through marker assisted selection. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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23 pages, 1961 KiB

Open AccessArticle

Identification of Superior Alleles for Seedling Stage Salt Tolerance in the USDA Rice Mini-Core Collection

by Jai S. Rohila, Jeremy D. Edwards, Gioi D. Tran, Aaron K. Jackson and Anna M. McClung

Plants 2019, 8(11), 472; https://doi.org/10.3390/plants8110472 - 05 Nov 2019

Cited by 22 | Viewed by 3981

Abstract

Salt stress is a major constraint to rice acreage and production worldwide. The purpose of this study was to evaluate the natural genetic variation available in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) for early vigor traits under salt [...] Read more.

Salt stress is a major constraint to rice acreage and production worldwide. The purpose of this study was to evaluate the natural genetic variation available in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) for early vigor traits under salt stress and identify quantitative trait loci (QTLs) for seedling-stage salt tolerance via a genome-wide association study (GWAS). Using a hydroponic system, the seedlings of 162 accessions were subjected to electrical conductivity (EC) 6.0 dS m⁻¹ salt stress at the three-to-four leaf stage. After completion of the study, 59.4% of the accessions were identified as sensitive, 23.9% were identified as moderately tolerant, and 16.7% were identified as highly tolerant. Pokkali was the most tolerant variety, while Nerica-6 was the most sensitive. Adapting standard International Rice Research Institute (IRRI) protocols, eight variables associated with salt tolerance were determined. The GWAS of the URMC, using over three million single-nucleotide polymorphisms (SNPs), identified nine genomic regions associated with salt tolerance that were mapped to five different chromosomes. Of these, none were in the known Saltol QTL region, suggesting different probable genes and mechanisms responsible for salt tolerance in the URMC. The study uncovered genetic loci that explained a large portion of the variation in salt tolerance at the seedling stage. Fourteen highly salt-tolerant accessions, six novel loci, and 16 candidate genes in their vicinity were identified that may be useful in breeding for salt stress tolerance. Identified QTLs can be targeted for fine mapping, candidate gene verification, and marker-assisted breeding in future studies. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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12 pages, 1702 KiB

Open AccessArticle

Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

by Jae-Ryoung Park, Won-Tae Yang, Yong-Sham Kwon, Hyeon-Nam Kim, Kyung-Min Kim and Doh-Hoon Kim

Plants 2019, 8(11), 471; https://doi.org/10.3390/plants8110471 - 04 Nov 2019

Cited by 18 | Viewed by 3198

Abstract

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples [...] Read more.

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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13 pages, 5177 KiB

Open AccessArticle

Characterization and Mapping of a Novel Premature Leaf Senescence Mutant in Common Tobacco (Nicotiana tabacum L.)

by Xiaoming Gao, Xinru Wu, Guanshan Liu, Zenglin Zhang, Jiangtao Chao, Zhiyuan Li, Yongfeng Guo and Yuhe Sun

Plants 2019, 8(10), 415; https://doi.org/10.3390/plants8100415 - 15 Oct 2019

Cited by 6 | Viewed by 3942

Abstract

As the last stage of plant development, leaf senescence has a great impact on plant’s life cycle. Genetic manipulation of leaf senescence has been used as an efficient approach in improving the yield and quality of crop plants. Here we describe an ethyl [...] Read more.

As the last stage of plant development, leaf senescence has a great impact on plant’s life cycle. Genetic manipulation of leaf senescence has been used as an efficient approach in improving the yield and quality of crop plants. Here we describe an ethyl methane sulfonate (EMS) mutagenesis induced premature leaf senescence mutant yellow leaf 1 (yl1) in common tobacco (Nicotiana tabacum L.). The yl1 plants displayed early leaf yellowing. Physiological parameters and marker genes expression indicated that the yl1 phenotype was caused by premature leaf senescence. Genetic analyses indicated that the yl1 phenotype was controlled by a single recessive gene that was subsequently mapped to a specific interval of tobacco linkage group 11 using simple sequence repeat (SSR) markers. Exogenous plant hormone treatments of leaves showed that the yl1 mutant was more sensitive to ethylene and jasmonic acid than the wild type. No similar tobacco premature leaf senescence mutants have been reported. This study laid a foundation for finding the gene controlling the mutation phenotype and revealing the molecular regulation mechanism of tobacco leaf senescence in the next stage. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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22 pages, 2011 KiB

Open AccessArticle

Deciphering the Genetic Architecture of Plant Height in Soybean Using Two RIL Populations Sharing a Common M8206 Parent

by Yongce Cao, Shuguang Li, Guoliang Chen, Yanfeng Wang, Javaid Akhter Bhat, Benjamin Karikari, Jiejie Kong, Junyi Gai and Tuanjie Zhao

Plants 2019, 8(10), 373; https://doi.org/10.3390/plants8100373 - 26 Sep 2019

Cited by 14 | Viewed by 4037

Abstract

Plant height (PH) is an important agronomic trait that is closely related to soybean yield and quality. However, it is a complex quantitative trait governed by multiple genes and is influenced by environment. Unraveling the genetic mechanism involved in PH, and developing soybean [...] Read more.

Plant height (PH) is an important agronomic trait that is closely related to soybean yield and quality. However, it is a complex quantitative trait governed by multiple genes and is influenced by environment. Unraveling the genetic mechanism involved in PH, and developing soybean cultivars with desirable PH is an imperative goal for soybean breeding. In this regard, the present study used high-density linkage maps of two related recombinant inbred line (RIL) populations viz., MT and ZM evaluated in three different environments to detect additive and epistatic effect quantitative trait loci (QTLs) as well as their interaction with environments for PH in Chinese summer planting soybean. A total of eight and 12 QTLs were detected by combining the composite interval mapping (CIM) and mixed-model based composite interval mapping (MCIM) methods in MT and ZM populations, respectively. Among these QTLs, nine QTLs viz., QPH-2, qPH-6-2_MT, QPH-6, qPH-9-1_ZM, qPH-10-1_ZM, qPH-13-1_ZM, qPH-16-1_MT, QPH-17 and QPH-19 were consistently identified in multiple environments or populations, hence were regarded as stable QTLs. Furthermore, Out of these QTLs, three QTLs viz., qPH-4-2_ZM, qPH-15-1_MT and QPH-17 were novel. In particular, QPH-17 could detect in both populations, which was also considered as a stable and major QTL in Chinese summer planting soybean. Moreover, eleven QTLs revealed significant additive effects in both populations, and out of them only six showed additive by environment interaction effects, and the environment-independent QTLs showed higher additive effects. Finally, six digenic epistatic QTLs pairs were identified and only four additive effect QTLs viz., qPH-6-2_MT, qPH-19-1_MT/QPH-19, qPH-5-1_ZM and qPH-17-1_ZM showed epistatic effects. These results indicate that environment and epistatic interaction effects have significant influence in determining genetic basis of PH in soybean. These results would not only increase our understanding of the genetic control of plant height in summer planting soybean but also provide support for implementing marker assisted selection (MAS) in developing cultivars with ideal plant height as well as gene cloning to elucidate the mechanisms of plant height. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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18 pages, 622 KiB

Open AccessEditor’s ChoiceArticle

SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus

by Paulina Ballesta, Carlos Maldonado, Paulino Pérez-Rodríguez and Freddy Mora

Plants 2019, 8(9), 331; https://doi.org/10.3390/plants8090331 - 05 Sep 2019

Cited by 31 | Viewed by 5463

Abstract

Eucalyptus globulus (Labill.) is one of the most important cultivated eucalypts in temperate and subtropical regions and has been successfully subjected to intensive breeding. In this study, Bayesian genomic models that include the effects of haplotype and single nucleotide polymorphisms (SNP) were assessed [...] Read more.

Eucalyptus globulus (Labill.) is one of the most important cultivated eucalypts in temperate and subtropical regions and has been successfully subjected to intensive breeding. In this study, Bayesian genomic models that include the effects of haplotype and single nucleotide polymorphisms (SNP) were assessed to predict quantitative traits related to wood quality and tree growth in a 6-year-old breeding population. To this end, the following markers were considered: (a) ~14 K SNP markers (SNP), (b) ~3 K haplotypes (HAP), and (c) haplotypes and SNPs that were not assigned to a haplotype (HAP-SNP). Predictive ability values (PA) were dependent on the genomic prediction models and markers. On average, Bayesian ridge regression (BRR) and Bayes C had the highest PA for the majority of traits. Notably, genomic models that included the haplotype effect (either HAP or HAP-SNP) significantly increased the PA of low-heritability traits. For instance, BRR based on HAP had the highest PA (0.58) for stem straightness. Consistently, the heritability estimates from genomic models were higher than the pedigree-based estimates for these traits. The results provide additional perspectives for the implementation of genomic selection in Eucalyptus breeding programs, which could be especially beneficial for improving traits with low heritability. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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17 pages, 4355 KiB

Open AccessArticle

Genome-Wide Identification, Expression Pattern Analysis and Evolution of the Ces/Csl Gene Superfamily in Pineapple (Ananas comosus)

by Shijiang Cao, Han Cheng, Jiashuo Zhang, Mohammad Aslam, Maokai Yan, Anqi Hu, Lili Lin, Simon Peter Ojolo, Heming Zhao, S.V.G.N. Priyadarshani, Yuan Yu, Guangqiu Cao and Yuan Qin

Plants 2019, 8(8), 275; https://doi.org/10.3390/plants8080275 - 08 Aug 2019

Cited by 11 | Viewed by 4375

Abstract

The cellulose synthase (Ces) and cellulose synthase-like (Csl) gene families belonging to the cellulose synthase gene superfamily, are responsible for the biosynthesis of cellulose and hemicellulose of the plant cell wall, and play critical roles in plant development, growth and evolution. However, the [...] Read more.

The cellulose synthase (Ces) and cellulose synthase-like (Csl) gene families belonging to the cellulose synthase gene superfamily, are responsible for the biosynthesis of cellulose and hemicellulose of the plant cell wall, and play critical roles in plant development, growth and evolution. However, the Ces/Csl gene family remains to be characterized in pineapple, a highly valued and delicious tropical fruit. Here, we carried out genome-wide study and identified a total of seven Ces genes and 25 Csl genes in pineapple. Genomic features and phylogeny analysis of Ces/Csl genes were carried out, including phylogenetic tree, chromosomal locations, gene structures, and conserved motifs identification. In addition, we identified 32 pineapple AcoCes/Csl genes with 31 Arabidopsis AtCes/Csl genes as orthologs by the syntenic and phylogenetic approaches. Furthermore, a RNA-seq investigation exhibited the expression profile of several AcoCes/Csl genes in various tissues and multiple developmental stages. Collectively, we provided comprehensive information of the evolution and function of pineapple Ces/Csl gene superfamily, which would be useful for screening out and characterization of the putative genes responsible for tissue development in pineapple. The present study laid the foundation for future functional characterization of Ces/Csl genes in pineapple. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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16 pages, 4566 KiB

Open AccessArticle

Genetic Structure of Cultivated Varieties of Radicchio (Cichorium intybus L.): A Comparison between F1 Hybrids and Synthetics

by Alice Patella, Francesco Scariolo, Fabio Palumbo and Gianni Barcaccia

Plants 2019, 8(7), 213; https://doi.org/10.3390/plants8070213 - 10 Jul 2019

Cited by 13 | Viewed by 3652

Abstract

Cichorium intybus L., well known in Italy with the common name “Radicchio”, is an important leafy vegetable that is prevalently reproduced by allogamy due to very efficient barriers of self-incompatibility. Marker-assisted breeding is widely used by seed firms to develop new hybrid varieties [...] Read more.

Cichorium intybus L., well known in Italy with the common name “Radicchio”, is an important leafy vegetable that is prevalently reproduced by allogamy due to very efficient barriers of self-incompatibility. Marker-assisted breeding is widely used by seed firms to develop new hybrid varieties that manifest genetic distinctiveness, uniformity and stability. A total of 29 mapped microsatellite markers were used for genotyping 504 samples of the Red of Chioggia biotype: First, two synthetics, four F1 hybrids and two derived F2 populations were compared to assess the distinctiveness of their gene pool and structure; then, the uniformity and stability of 3 years of production of a commercial F1 variety were also investigated. Genetic similarity and diversity statistics as well as the genetic structure of populations were analysed, including allele and genotype frequencies. The mean estimates and ranges of genetic similarity enabled the molecular discrimination of OP synthetics from F1 varieties and their F2 progenies and the determination of individual plant memberships. Moreover, the genetic structure of F1 hybrids produced in 3 years unexpectedly revealed two main clusters that discriminate the first 2 years from the 3rd, mainly because of the presence of uncommon specific alleles and different allele frequencies. Overall, this molecular information will enable breeders to determine the genetic distinctness, uniformity and stability of commercial and experimental varieties, as well as their genetic relationships and relatedness. Hence, this work provides a useful tool for achieving the molecular characterisation and genetic identification of different radicchio populations. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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16 pages, 3542 KiB

Open AccessArticle

Karyological Analysis and DNA Barcoding of Pompia Citron: A First Step toward the Identification of Its Relatives

by Grazia Viglietti, Giulio Galla, Andrea Porceddu, Gianni Barcaccia, Franck Curk, Francois Luro and Grazia Maria Scarpa

Plants 2019, 8(4), 83; https://doi.org/10.3390/plants8040083 - 31 Mar 2019

Cited by 9 | Viewed by 3975

Abstract

Pompia is a citrus fruit endemic of Sardinia, Italy, with an essential oil profile showing outstanding anti-inflammatory and anti-microbic properties. Despite its remarkable pharmaceutical potential, little taxonomic and genetic information is available for this species. We applied flow cytometry and classical cytogenetic techniques [...] Read more.

Pompia is a citrus fruit endemic of Sardinia, Italy, with an essential oil profile showing outstanding anti-inflammatory and anti-microbic properties. Despite its remarkable pharmaceutical potential, little taxonomic and genetic information is available for this species. We applied flow cytometry and classical cytogenetic techniques to assess the DNA content and to reconstruct the karyotype of several Pompia accessions. Molecular data from plastid DNA barcoding and nuclear DNA sequencing were used to study the genetic distance between Pompia and other citrus species. Flow cytometric estimates of DNA content and somatic chromosome counts suggest that Pompia is a regular diploid Citrus species. DNA polymorphisms of nuclear and chloroplast markers allowed us to investigate the genetic relationships between Pompia accessions and other Citrus species. Based on DNA polymorphism data we propose that Pompia is a very recent interspecific hybrid generated by a cross between C. aurantium (as seed bearer) and C. medica (as pollen donor). Our findings pave the way for further and more specific investigations of local Pompia germplasm resources that may help the preservation and valorisation of this valuable citrus fruit tree. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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Review

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27 pages, 598 KiB

Open AccessReview

The Role of Major Transcription Factors in Solanaceous Food Crops under Different Stress Conditions: Current and Future Perspectives

by Lemessa Negasa Tolosa and Zhengbin Zhang

Plants 2020, 9(1), 56; https://doi.org/10.3390/plants9010056 - 02 Jan 2020

Cited by 48 | Viewed by 7178

Abstract

Plant growth, development, and productivity are adversely affected by environmental stresses such as drought (osmotic stress), soil salinity, cold, oxidative stress, irradiation, and diverse diseases. These impacts are of increasing concern in light of climate change. Noticeably, plants have developed their adaptive mechanism [...] Read more.

Plant growth, development, and productivity are adversely affected by environmental stresses such as drought (osmotic stress), soil salinity, cold, oxidative stress, irradiation, and diverse diseases. These impacts are of increasing concern in light of climate change. Noticeably, plants have developed their adaptive mechanism to respond to environmental stresses by transcriptional activation of stress-responsive genes. Among the known transcription factors, DoF, WRKY, MYB, NAC, bZIP, ERF, ARF and HSF are those widely associated with abiotic and biotic stress response in plants. Genome-wide identification and characterization analyses of these transcription factors have been almost completed in major solanaceous food crops, emphasizing these transcription factor families which have much potential for the improvement of yield, stress tolerance, reducing marginal land and increase the water use efficiency of solanaceous crops in arid and semi-arid areas where plant demand more water. Most importantly, transcription factors are proteins that play a key role in improving crop yield under water-deficient areas and a place where the severity of pathogen is very high to withstand the ongoing climate change. Therefore, this review highlights the role of major transcription factors in solanaceous crops, current and future perspectives in improving the crop traits towards abiotic and biotic stress tolerance and beyond. We have tried to accentuate the importance of using genome editing molecular technologies like CRISPR/Cas9, Virus-induced gene silencing and some other methods to improve the plant potential in giving yield under unfavorable environmental conditions. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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24 pages, 2530 KiB

Open AccessReview

Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement

by Ahmad Ali, Mehran Khan, Rahat Sharif, Muhammad Mujtaba and San-Ji Gao

Plants 2019, 8(9), 344; https://doi.org/10.3390/plants8090344 - 12 Sep 2019

Cited by 50 | Viewed by 8626

Abstract

Sugarcane is an important crop from Poaceae family, contributing about 80% of the total world’s sucrose with an annual value of around US$150 billion. In addition, sugarcane is utilized as a raw material for the production of bioethanol, which is an alternate source [...] Read more.

Sugarcane is an important crop from Poaceae family, contributing about 80% of the total world’s sucrose with an annual value of around US$150 billion. In addition, sugarcane is utilized as a raw material for the production of bioethanol, which is an alternate source of renewable energy. Moving towards sugarcane omics, a remarkable success has been achieved in gene transfer from a wide variety of plant and non-plant sources to sugarcane, with the accessibility of efficient transformation systems, selectable marker genes, and genetic engineering gears. Genetic engineering techniques make possible to clone and characterize useful genes and also to improve commercially important traits in elite sugarcane clones that subsequently lead to the development of an ideal cultivar. Sugarcane is a complex polyploidy crop, and hence no single technique has been found to be the best for the confirmation of polygenic and phenotypic characteristics. To better understand the application of basic omics in sugarcane regarding agronomic characters and industrial quality traits as well as responses to diverse biotic and abiotic stresses, it is important to explore the physiology, genome structure, functional integrity, and collinearity of sugarcane with other more or less similar crops/plants. Genetic improvements in this crop are hampered by its complex genome, low fertility ratio, longer production cycle, and susceptibility to several biotic and abiotic stresses. Biotechnology interventions are expected to pave the way for addressing these obstacles and improving sugarcane crop. Thus, this review article highlights up to date information with respect to how advanced data of omics (genomics, transcriptomic, proteomics and metabolomics) can be employed to improve sugarcane crops. Full article

(This article belongs to the Special Issue Genomics for Plant Breeding)

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