Special Issue "Plant Genetics and Molecular Breeding"
Deadline for manuscript submissions: 20 February 2019
Dr. Pedro Martínez-Gómez
CEBAS- CSIC, Centro de Edafología y Biología Aplicada del Segura, Department of Plant Breeding, Murcia, Spain
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Interests: plant breeding approaches; marker assisted selection; evaluation of agronomical traits; integrating genetic, genomic, transcriptomic and proteomic approaches
The development of new plant varieties is a long and tedious process involving the generation of large seedling populations for the selection of the best individuals. While the ability of breeders to generate large populations is almost unlimited, the management, phenotyping (genetic studies) and selection of these seedlings are the main factors limiting the generation of new cultivars. Genomic (DNA) studies for the development of marker-assisted selection (MAS) strategies are particularly useful when the evaluation of the character is expensive, time-consuming or with long juvenile periods. More recently, proteomic (proteins and enzymes) and transcriptomic (RNA) studies have been used for the clarification of the mentioned genomic studies.
Papers submitted to this Special Issue must report high novelty results and/or plausible and testable new models for the integrative analysis of the different approaches applied to plant breeding including genetic (phenotyping and transmission of agronomic characters), genomic (DNA regions responsible for the different agronomic characters), proteomic (proteins and enzymes involved in the expression of the characters) and transcriptomic (gene expression analysis of the characters) approaches for the development of new MAS strategies. In addition, the application of massive sequencing methodologies ("deep-sequencing") of the genome (DNA-Seq) and transcriptome (RNA-Seq), based on lowering the costs of DNA sequencing, could be an additional interesting approach in this Special Issue.
Dr. Pedro Martínez-Gómez
Manuscript Submission Information
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.
- throughput analysis
- assisted selection
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Title: Annotation-based transcriptome SNP discovery in three polyploid blueberry crops using second-generation sequencing without a reference genome sequence
Authors: Wang Yunsheng, Muhammad Qasim Shahid, Faheem Shehzad Baloch, Fozia Ghouri, Nie Fei
Abstract: Blueberry is a kind of new popular fruit with high quality and nutritional value. Currently, the planting area and distribution are expanding rapidly to satisfy the huge demand of people in the world, which bring the utmost need for evolving new varieties to adapt global climate, soil and farming characters. As a perennial fruit crop, molecular marker assisted breeding is an ideal method with the merit of short breeding cycle compared to the conventional breeding methods. Here, we sequenced the leaves transcriptome of 19 rabbit-eye blueberry accessions, 13 southern high-bush blueberry accessions and 22 northern high-bush blueberry accessions by using next generation sequencing technologies. We obtained 80.825G data clean with an average of 1.50G data per accession. We detected 58968, 55973 and 53887 unigenes by using the clean data from rabbit-eye blueberry, southern high-bush blueberry and northern high-bush blueberry, respectively, and identified more than 5000 SSR loci and 50000 SNP from the unigenes annotation of each kind blueberry. We also detected more than 1000 unigenes that are candidate of varied resistance genes. The results would offer large amount of molecular markers for marker assisted breeding to produce blueberry cultivars with different adaptive characteristics, and will also be helpful for the molecular genetics and association analysis of blueberry and the basic molecular information of pest and disease resistance of blueberry.
Title: Identification of quantitative trait loci governing Nutrient Use Efficiency (NuUE) related traits using SNP markers in an early backcross population of rice (Oryza sativa L.)
Authors: Zilhas A. Jewel, Jauhar Ali, Mahender Anumalla, Yulong Pang, and Zhikang Li
Abstract: Development of nutrient use efficient (NuUE) rice cultivars is highly crucial for sustaining the global rice production in Asia and Africa. However, it requires a better understanding of the genetics of NuUE related traits and their relationship to grain yield. In this study, simultaneous efforts were made to develop NuUE rice cultivars and to map quantitative trait loci (QTLs) governing NUE related traits in rice. 230 BC1F5 introgression lines (ILs) developed from a single early backcross population involving Weed Tolerant Rice 1 as recipient parent and Haoannong as donor parent for constructing of high density linkage map through genotyping by a single nucleotide polymorphism (SNP) array. The ILs were cultivated in field conditions with a different combination of fertilizer schedule under six nutrient conditions, i.e., N, -P, -NP, -NPK, 75N and NPK conditions. A total of 261 QTLs mapped for seven promising vital NuUE traits in all 12 chromosomes, of which forty nine QTLs showed high (20.25–34.68%) contribution to phenotypic variation and LOD score ranged from 9.44 to 17.76 respectively. Also, discovered 14 hotspot QTL regions, which had ≥ (more than) five QTLs located on the same region of chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 11. Further analysis of these 14 QTLs, refined to four topmost hotspot QTLs (QTL harbor-I to IV) located on chromosomes 3 (SNP_3_853802), 5 (SNP_5_5588965), 9 (SNP_9_12154616) and 11 (SNP_11_1706087). Majority of the QTLs identified for NuUE allied traits were clustered together in the QTL harbors (q1000Gwt, qPFP, qBY, qFGN, qGY and qPSPF1) under all six nutrient conditions. We identified four novel putative QTLs for agronomic efficiency and 22 QTLs for partial factor productivity (PFP) under –P, and 75N conditions with a LOD score ranged from 2.55-4.52, 3.39-12.15 and together explained their phenotypic variation ranges from 5.92 -10.27% and 7.81-25.28% respectively. The identified potential QTLs were novel and of remarkable value for marker-aided selection and pyramiding of multiple QTLs, which would provide supportive evidence for the enhancement of grain yield and cloning of NuUE tolerance-responsive genes in rice.
Title: GmBRC1 is a Candidate Gene for Branching in Soybean
Author: Suk-Ha Lee
Abstract: The number of branches in soybean is one of the most important factors directly affects the yield. However, only a few QTLs have been reported and the genes controlling the number of branches have not been characterized because it is affected immensely by various environmental factors. In this study, we identified six DNA markers associated with branch numbers in the genomic region of qBR6-1, a major QTL for branching previously reported, from a set of 430 soybean germplasms with three geographical replications through single marker ANOVA and regression analysis. Out of six markers, four were located in the genic regions including BRANCHED 1 (BRC1) and a gene encoding transcription factor TFIIE alpha subunit, and two were in intergenic regions. No significant association with branch numbers was identified by the genome-wide association study. We constructed a set of near isogenic lines (NILs) derived from a F6 residual heterozygous line of Jiyu69 x SS0404-T5-76, which have 99.9% of homozygous genetic background and significant differences in the number of branches. The gene BRC1, reported as a negative regulator of branching in Arabidopsis, was up-regulated in shoot apical meristem of the less-branching NIL while the more-branching NIL showed down-regulated expression of BRC1. No significant difference in the level of gene expression was observed in the other gene. In BRC1 two nucleotide variations were identified between NILs, one in the genic and the other in upstream region. Genetic association of these markers was observed in another set of soybean germplasms comprised by 59 accessions provided by USDA. In conclusion, we suggest the BRC1 gene is a strong candidate gene controlling branch development in soybean.
Title: Date Palm Salinity Tolerance in the Omic Area
Authors: Khaled Hazzouri, Khaled Amiri and Khaled Masmoudi
Abstract: Date palm is a major crop in arid regions of the world contributing to food security. However, its cultivation is facing shortage in water demand. Although date palms are known for their drought and salinity tolerance to a certain extent, the growing salinity of water in the region requires improving the tolerance of date palm to salt in order to ensure the sustainability of this crop. In this review paper, we outline a strategy to address the salinity problem using omics available data. Accomplishing the objective of developing date palm varieties that can tolerate increased saline ground water and soil, we emphasis on breeding and marker assisted selection, as well as discovering and using the microbiome in the arid regions.
Title: A New Theory of Mutation which May Help to Occur the Gene Linkage and Pave a Way to Breed Super Crop in Future
Author: Xuan Tran Dang
Title: DNA Methylation Analysis of Dormancy Breaking in Almond Flower Buds using Cre-epiGBS (cost reduced epi-Genotyping by Sequencing)
Author: Pedro Martínez-Gómez