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Plant Breeding: Molecular Genetics, Challenges, Opportunities and Future Perspectives
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Plant Breeding: Molecular Genetics, Challenges, Opportunities and Future Perspectives

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (25 July 2023) | Viewed by 8440

Special Issue Editors

Dr. Muhammad Ashfaq

E-Mail Website
Guest Editor
Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, New Campus, Lahore, Pakistan
Interests: crop science; crop improvement; crop production; plant breeding; seed production; plant genetics
Dr. Xianting Wu

E-Mail Website
Guest Editor
State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
Interests: plant genetics; molecular biology

Special Issue Information

Dear Colleagues,

We are serving as the Guest Editors for the Special Issue “Plant Breeding: Molecular Genetics, Challenges, Opportunities and Future Perspectives” in the journal Genes (https://www.mdpi.com/journal/genes). The rapidly increasing global population has resulted in a reduction in the amount of productive agricultural lands and cultivated cropped area. Furthermore, rapid changes in the regional and global climates are causing multiple biotic and abiotic stresses, i.e., drought, heat, high temperatures and various types of diseases, etc., which are more challenging in the current scenario. To overcome such types of problems in a changing climatic environment there is a dire need for the adoption of new molecular plant breeding and plant genetics techniques for the improvement of various plant varieties with a broader genetic base. A larger and more prosperous human population will place unprecedented demands on our food system. Indeed, it is thought that food production will need to double worldwide to meet future needs. This increasing demand, coupled with the impacts of climate change, will require advanced crop development that takes full advantage of modern plant breeding and genetics techniques, genomics, bioinformatics, mutation breeding, plant biology and systems biology. Management systems must be devised to realize the potential of these new technologies. While increasing the yield of agriculture is essential, it is also critical to simultaneously reduce the environmental impacts of agriculture. Numerous strategies are being used to sustain agricultural production, including the development of climate-resilient genotypes, land races, wild species, and elite breeding lines, etc. These may include a combination of many different techniques, i.e., genetic resources, crop evolution, genetic diversity, utilization of wide-type germplasms, utilization of wild-type species and utilization of modern hybridization and mutation breeding techniques. These may be effective in improving the quality and yield under various types of stresses in a changing climatic environment.

This Special Issue will focus on the impacts of producing genetic variants, gene mapping populations, mutation mapping, breeding populations (RILs, NILs, F2, etc.), the genetic modification of plants, marker association with plant traits, the identification of new QTLs linked with distinct traits, the identification of genotypic and phenotypic associations, and the evolution of new crop varieties and new plant populations through breeding and genetics. Research, review articles, editorials and short communications focusing on any of the above-described aspects will be gladly considered for this Special Issue.

Dr. Muhammad Ashfaq
Dr. Xianting Wu
Guest Editors

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 submissions that pass pre-check are 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. Genes is an international peer-reviewed open access monthly 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 2600 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.

Keywords

  • breeding
  • genetics
  • gene identification
  • crop improvement
  • genetic mapping
  • breeding populations
  • marker-assisted selection
  • traits improvements
  • crop evolution under stress environments
  • mutation breeding
  • molecular characterization

Published Papers (5 papers)

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Research

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16 pages, 2989 KiB  
Article
Genetic Diversity and Population Structure of African Sorghum (Sorghum bicolor L. Moench) Accessions Assessed through Single Nucleotide Polymorphisms Markers
by Muhammad Ahmad Yahaya, Hussein Shimelis, Baloua Nebie, Chris Ochieng Ojiewo, Abhishek Rathore and Roma Das
Genes 2023, 14(7), 1480; https://doi.org/10.3390/genes14071480 - 20 Jul 2023
Viewed by 1467
Abstract
Assessing the genetic diversity and population structure of cultivated sorghum is important for heterotic grouping, breeding population development, marker-assisted cultivar development, and release. The objectives of the present study were to assess the genetic diversity and deduce the population structure of 200 sorghum [...] Read more.
Assessing the genetic diversity and population structure of cultivated sorghum is important for heterotic grouping, breeding population development, marker-assisted cultivar development, and release. The objectives of the present study were to assess the genetic diversity and deduce the population structure of 200 sorghum accessions using diversity arrays technology (DArT)-derived single nucleotide polymorphism (SNP) markers. The expected heterozygosity values ranged from 0.10 to 0.50 with an average of 0.32, while the average observed heterozygosity (0.15) was relatively low, which is a typical value for autogamous crops species like sorghum. Moderate polymorphic information content (PIC) values were identified with a mean of 0.26, which indicates the informativeness of the chosen SNP markers. The population structure and cluster analyses revealed four main clusters with a high level of genetic diversity among the accessions studied. The variation within populations (41.5%) was significantly higher than that among populations (30.8%) and between samples within the structure (27.7%). The study identified distantly related sorghum accessions such as SAMSORG 48, KAURA RED GLUME; Gadam, AS 152; CSRO1, ICNSL2014-062; and YALAI, KAFI MORI. The accessions exhibited wide genetic diversity that will be useful in developing new gene pools and novel genotypes for West Africa sorghum breeding programs. Full article
(This article belongs to the Special Issue Plant Breeding: Molecular Genetics, Challenges, Opportunities and Future Perspectives)
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18 pages, 3532 KiB  
Article
Genome-Wide Association Mapping for Yield and Yield-Related Traits in Rice (Oryza Sativa L.) Using SNPs Markers
by Muhammad Ashfaq, Abdul Rasheed, Renshan Zhu, Muhammad Ali, Muhammad Arshad Javed, Alia Anwar, Javaria Tabassum, Shabnum Shaheen and Xianting Wu
Genes 2023, 14(5), 1089; https://doi.org/10.3390/genes14051089 - 15 May 2023
Cited by 1 | Viewed by 1632
Abstract
Rice (Oryza sativa L.) is a staple food for more than 50% of the world’s population. Rice cultivar improvement is critical in order to feed the world’s growing population. Improving yield is one of the main aims of rice breeders. However, yield [...] Read more.
Rice (Oryza sativa L.) is a staple food for more than 50% of the world’s population. Rice cultivar improvement is critical in order to feed the world’s growing population. Improving yield is one of the main aims of rice breeders. However, yield is a complex quantitative trait controlled by many genes. The presence of genetic diversity is the key factor to improve the yield hence, the presence of diversity in any germplasm is important for yield improvement. In the current study, the rice germplasm was collected from Pakistan and the United States of America and a panel of 100 diverse genotypes was utilized to identify important yield and yield-related traits. For this, a genome-wide association study (GWAS) was performed to identify the genetic loci related to yield. The GWAS on the diverse germplasm will lead to the identification of new genes which can be utilized in the breeding program for improvement of yield. For this reason, firstly, the germplasm was phenotypically evaluated in two growing seasons for yield and yield-related traits. The analysis of variance results showed significant differences among traits which showed the presence of diversity in the current germplasm. Secondly, the germplasm was also genotypically evaluated using 10K SNP. Genetic structure analysis showed the presence of four groups which showed that enough genetic diversity was present in the rice germplasm to be used for association mapping analysis. The results of GWAS identified 201 significant marker trait associations (MTAs. 16 MTAs were identified for plant height, 49 for days to flowering, three for days to maturity, four for tillers per plant, four for panicle length, eight for grains per panicle, 20 unfilled grains per panicle, 81 for seed setting %, four for thousand-grain weight, five for yield per plot and seven for yield per hectare. Apart from this, some pleiotropic loci were also identified. The results showed that panicle length (PL) and thousand-grain weight (TGW) were controlled by a pleiotropic locus OsGRb23906 on chromosome 1 at 10,116,371 cM. The loci OsGRb25803 and OsGRb15974 on chromosomes 4 and 8 at the position of 14,321,111 cM and 6,205,816 cM respectively, showed pleiotropic effects for seed setting % (SS) and unfilled grain per panicle (UG/P). A locus OsGRb09180 on chromosome 4 at 19,850,601 cM was significantly linked with SS and yield/ha. Furthermore, gene annotation was performed, and results indicated that the 190 candidate genes or QTLs that closely linked with studied traits. These candidate genes and novel significant markers could be useful in marker-assisted gene selection and QTL pyramiding to improve rice yield and the selection of potential parents, recombinants and MTAs which could be used in rice breeding programs to develop high-yielding rice varieties for sustainable food security. Full article
(This article belongs to the Special Issue Plant Breeding: Molecular Genetics, Challenges, Opportunities and Future Perspectives)
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16 pages, 4452 KiB  
Article
TPD1-like Gene as a Suitable Marker for Early Sex Determination in Date Palm (Phoenix dactylifera L.)
by Plosha Khanum, Asif Ali Khan, Iqrar Ahmad Khan, Abdul Ghaffar and Zulqurnain Khan
Genes 2023, 14(4), 907; https://doi.org/10.3390/genes14040907 - 13 Apr 2023
Cited by 1 | Viewed by 1232
Abstract
Date palm (Phoenix dactylifera L.) is a considerably beneficial and economically profitable fruit crop. Female date palm plants produce fruit that is rich in fiber and sugar. Date palm is propagated by two means: suckers and seed. The propagation of date palm [...] Read more.
Date palm (Phoenix dactylifera L.) is a considerably beneficial and economically profitable fruit crop. Female date palm plants produce fruit that is rich in fiber and sugar. Date palm is propagated by two means: suckers and seed. The propagation of date palm through seeds is very necessary for germplasm conservation and breeding. The late reproductive age (4–5 years) and dioecious nature of date palm make genetic improvement and breeding difficult. Early sex determination is the only way to improve breeding by selecting experimental male and female plants at the seedling stage. The primers for Tapetum Determinant 1 (TPD1-like) were designed using Amplify software. The DNA amplification of selected date palm suckers of three genotypes (Ajwa, Amber, and Medjool) was observed through PCR. Expression profiling of selected genotypes was carried out through semi-q PCR and RT-PCR by using the cDNA of suckers and unknown seedlings. Different in silico analyses were performed for the gene and protein characterization and identification of cis-acting elements in the promoter region. The promoter was identified along with the protein’s properties and functionality. The expression of TPD1-like gene was found in the leaves of three selected genotypes of male sucker and in some plants of selected unknown seedlings that are considered male plants, and no expression was observed in female suckers and unknown seedlings that are considered female plants. The findings suggested that the TPD1-like gene has the potential for sex differentiation at the seedling stage, as the TPD1-like gene is essential to the specialization of tapetal cells and plays a critical role in plant reproduction. Full article
(This article belongs to the Special Issue Plant Breeding: Molecular Genetics, Challenges, Opportunities and Future Perspectives)
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14 pages, 2999 KiB  
Article
Genome-Wide Identification, and In-Silico Expression Analysis of YABBY Gene Family in Response to Biotic and Abiotic Stresses in Potato (Solanum tuberosum)
by Hafiz Sabah-Ud-Din Mazhar, Muhammad Shafiq, Haider Ali, Muhammad Ashfaq, Alia Anwar, Javaria Tabassum, Qurban Ali, Ghulam Jilani, Muhammad Awais, Ravi Sahu and Muhammad Arshad Javed
Genes 2023, 14(4), 824; https://doi.org/10.3390/genes14040824 - 29 Mar 2023
Cited by 5 | Viewed by 2114
Abstract
YABBY is among the specific transcription factor (TF) gene family in plants and plays an important role in the development of the leaves and floral organs. Its specific roles include lateral organ development, the establishment of dorsoventral polarity, and response to abiotic stress. [...] Read more.
YABBY is among the specific transcription factor (TF) gene family in plants and plays an important role in the development of the leaves and floral organs. Its specific roles include lateral organ development, the establishment of dorsoventral polarity, and response to abiotic stress. Potato is an important crop worldwide and YABBY genes are not still identified and characterized in potato. So, little has been known about YABBY genes in potato until now. This study was carried out to perform genome-wide analysis, which will provide an in-depth analysis about the role of YABBY genes in potato. There have been seven StYAB genes identified, which are found to be located on seven different chromosomes. Through multiple sequence analyses, it has been predicted that the YABBY domain was present in all seven genes while the C2-C2 domain was found to be absent only in StYAB2. With the help of cis-element analysis, the involvement of StYAB genes in light, stress developmental, and hormonal responsiveness has been found. Furthermore, expression analysis from RNA-seq data of different potato organs indicated that all StYAB genes have a role in the vegetative growth of the potato plant. In addition to this, RNA-seq data also identified StYAB3, StYAB5, and StYAB7 genes showing expression during cadmium, and drought stress, while StYAB6 was highly expressed during a viral attack. Moreover, during the attack of Phytophthora infestans on a potato plant StYAB3, StYAB5, StYAB6, and StYAB7 showed high expression. This study provides significant knowledge about the StYAB gene structures and functions, which can later be used for gene cloning, and functional analysis; this information may be utilized by molecular biologists and plant breeders for the development of new potato lines. Full article
(This article belongs to the Special Issue Plant Breeding: Molecular Genetics, Challenges, Opportunities and Future Perspectives)
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Review

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15 pages, 1384 KiB  
Review
Role of Actin Dynamics and GhACTIN1 Gene in Cotton Fiber Development: A Prototypical Cell for Study
by Adnan Iqbal, Sibgha Aslam, Mukhtar Ahmed, Fahad Khan, Qurban Ali and Shiming Han
Genes 2023, 14(8), 1642; https://doi.org/10.3390/genes14081642 - 18 Aug 2023
Cited by 1 | Viewed by 1429
Abstract
Cotton crop is considered valuable for its fiber and seed oil. Cotton fiber is a single-celled outgrowth from the ovule epidermis, and it is a very dynamic cell for study. It has four distinct but overlapping developmental stages: initiation, elongation, secondary cell wall [...] Read more.
Cotton crop is considered valuable for its fiber and seed oil. Cotton fiber is a single-celled outgrowth from the ovule epidermis, and it is a very dynamic cell for study. It has four distinct but overlapping developmental stages: initiation, elongation, secondary cell wall synthesis, and maturation. Among the various qualitative characteristics of cotton fiber, the important ones are the cotton fiber staple length, tensile strength, micronaire values, and fiber maturity. Actin dynamics are known to play an important role in fiber elongation and maturation. The current review gives an insight into the cotton fiber developmental stages, the qualitative traits associated with cotton fiber, and the set of genes involved in regulating these developmental stages and fiber traits. This review also highlights some prospects for how biotechnological approaches can improve cotton fiber quality. Full article
(This article belongs to the Special Issue Plant Breeding: Molecular Genetics, Challenges, Opportunities and Future Perspectives)
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